From hlapp at gmx.net Sun Aug 1 06:04:43 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun Aug 1 06:06:07 2004 Subject: [Bioperl-l] SwissProt/UniProt GN line format changed In-Reply-To: Message-ID: <35C14CAA-E3A2-11D8-813A-000A959EB4C4@gmx.net> On Saturday, July 31, 2004, at 07:05 PM, Ewan Birney wrote: >> The problem with writing the new format is that that would require >> some >> additions to the object model, because it would require context for >> the >> individual annotation values ('Name', 'Synonym', 'OrderedLocusName', >> or >> ORFName). Presently, annotation values do not have context in Bioperl. >> > > Or rather I think we would have to make a new Annotation type, being > something like 'MultiTaggedValue' which would have tags 'Name', > 'Synonym' > etc and then the 'gene_name' annotation key would give a list of > 'MultiTaggedValues' --- presumably with some magic to detect "old > style" > simplevalue tags as well. The thing is that SimpleValue is not the only one that could use context. There are dbxrefs with context too. If you made annotation objects generally context aware (while it would be left to the implementing class to define what to do with the context - much as with as_text()), you'd kill all those cases simultaneously. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From sdavis2 at mail.nih.gov Mon Aug 2 07:05:42 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon Aug 2 07:05:35 2004 Subject: [Bioperl-l] biosql and relationships Message-ID: I have loaded a few databases for local use into a biosql database. I am interested in including bioentry_relationships between these databases. The information is typically included in the file (eg., the locuslink id in the refseq record). Is there a way to do this? I know this information is also stored in various dbxref tables, as well, but wondered how the bioentry_relationship table is used, if it is not for creating relationships between bioentries, even if they are in separate namespaces. Thanks, Sean From jason at cgt.duhs.duke.edu Mon Aug 2 08:22:37 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Mon Aug 2 08:24:02 2004 Subject: [Bioperl-l] xml converter In-Reply-To: <200407301706.i6UH6xgN017334@calisto.cib.csic.es> References: <200407301706.i6UH6xgN017334@calisto.cib.csic.es> Message-ID: What schema do you want it to be in? "XML" is not a format. Currently there is limited support to convert BLAST reports to BSML. I expect the HMMER reports will generally make it into the same report format. See scripts/utilities/search2BSML.PLS which uses the Bio::SearchIO::Writer::BSMLResultWriter module. -jason On Fri, 30 Jul 2004 rmaps005@cib.csic.es wrote: > hello, > i am newbie at bioperl and was trying to convert a hmmer result to XML > format. > I found that there is a package to convert genbank to XML(gb2xml) , is > there any for hmmer results? > > IlohaCIB > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From hlapp at gmx.net Mon Aug 2 08:28:53 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon Aug 2 08:29:57 2004 Subject: [Bioperl-l] biosql and relationships In-Reply-To: Message-ID: <8424BA78-E47F-11D8-BF77-000A959EB4C4@gmx.net> The bioentry_relationship table is meant for exactly this purpose indeed. Since bioperl doesn't have a straightforward corresponding class, however, it is not supported through the bioperl object layer except for Bio::ClusterI objects (e.g., Bio::Cluster::Unigene). There's different courses you could pursue. What I'm doing in my instance is making heavy use of SQL scripts that I run against the database on a regular basis, and which would synthesize those relationships based off of, for instance, dbxref-to-bioentry matches. Instead of running sql directly, you run also wrap a perl script around it for processing input files or things like iterative/recursive queries. Or you could amend bioperl (and then bioperl-db) to support this in a better fashion. -hilmar On Monday, August 2, 2004, at 12:05 PM, Sean Davis wrote: > I have loaded a few databases for local use into a biosql database. I > am interested in including bioentry_relationships between these > databases. The information is typically included in the file (eg., > the locuslink id in the refseq record). Is there a way to do this? I > know this information is also stored in various dbxref tables, as > well, but wondered how the bioentry_relationship table is used, if it > is not for creating relationships between bioentries, even if they are > in separate namespaces. > > Thanks, > Sean > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From peter at cordes.ca Sun Aug 1 22:29:36 2004 From: peter at cordes.ca (Peter Cordes) Date: Mon Aug 2 11:12:08 2004 Subject: [Bioperl-l] RNA fold In-Reply-To: <324F907B-E308-11D8-8A39-000A9568B714@uiuc.edu> References: <20040730204802.GH21869@GFC1.chem.ucla.edu> <324F907B-E308-11D8-8A39-000A9568B714@uiuc.edu> Message-ID: <20040802022936.GA18230@cordes.ca> On Sat, Jul 31, 2004 at 10:42:15AM -0500, Chris Fields wrote: > >The licensing for mfold is restrictive in that it cannot be > >re-distributed freely. > > Somewhat true. Basically, you need to agree to a license when using > the software (like most software, even freeware). AFAIK, you actually don't need to agree to a license to use Free software (e.g. GPL or BSD license). I think the way it works is this: If you don't accept the license, then you have your default rights under copyright law. Free software, doesn't make you agree to a license to download or install it, just like other copyrighted works, like web pages. You can read the web page, or run the program, without having to agree to anything. If you want to do something that you can't do by default under copyright law, such as modify or redistribute the work, you need a license. You get to do what the license says you can, as long as you agree to its terms. Sorry I don't have anything to add to the discussion, but I'm more of a sysadmin than a biologist or bioperl hacker, and I just subscribed to make a bugreport... (stay tuned :) -- #define X(x,y) x##y Peter Cordes ; e-mail: X(peter@cor , des.ca) "The gods confound the man who first found out how to distinguish the hours! Confound him, too, who in this place set up a sundial, to cut and hack my day so wretchedly into small pieces!" -- Plautus, 200 BC -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 351 bytes Desc: Digital signature Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040801/5de245bc/attachment.bin From cjfields at uiuc.edu Mon Aug 2 11:38:12 2004 From: cjfields at uiuc.edu (Chris Fields) Date: Mon Aug 2 11:39:39 2004 Subject: [Bioperl-l] RNA fold In-Reply-To: <20040802022936.GA18230@cordes.ca> References: <20040730204802.GH21869@GFC1.chem.ucla.edu> <324F907B-E308-11D8-8A39-000A9568B714@uiuc.edu> <20040802022936.GA18230@cordes.ca> Message-ID: <6.1.1.1.2.20040802102630.01d00ba0@express.cites.uiuc.edu> At 09:29 PM 8/1/2004, you wrote: >On Sat, Jul 31, 2004 at 10:42:15AM -0500, Chris Fields wrote: > > >The licensing for mfold is restrictive in that it cannot be > > >re-distributed freely. > > > > Somewhat true. Basically, you need to agree to a license when using > > the software (like most software, even freeware). > > AFAIK, you actually don't need to agree to a license to use Free software >(e.g. GPL or BSD license). I think the way it works is this: If you don't >accept the license, then you have your default rights under copyright law. >Free software, doesn't make you agree to a license to download or install >it, just like other copyrighted works, like web pages. You can read the web >page, or run the program, without having to agree to anything. > > If you want to do something that you can't do by default under copyright >law, such as modify or redistribute the work, you need a license. You get >to do what the license says you can, as long as you agree to its terms. Ah, now I see. Below is the wording from the web page I mentioned previously (http://www.bioinfo.rpi.edu/~zukerm/rna/mfold-3.1.html): Versions 3.xxx of mfold for Unix and Linux operating systems are available via a free license for academic and nonprofit use only; commercial use is available for a fee. Copyright ? is held by Washington University. Washington University seeks additional licensees for commercial development and marketing and invites all interested parties to submit proposals. Please direct all requests for licensing, information, and limited evaluation copies to Washington University's Office of Technology Management by E-mail ... I suppose the license is there to allow academics and non-profits to use the software, but the copyright is present to prevent dissemination and have commercial users pay a fee, especially if the code is included in proprietary software. Oh well, a bit off-topic now. Anyone else want to chip in on the original question? >#define X(x,y) x##y >Peter Cordes ; e-mail: X(peter@cor , des.ca) > __________________________________ Chris Fields - Postdoctoral Researcher Lab of Dr. Robert Switzer Address: University of Illinois at Urbana-Champaign Dept. of Biochemistry - 323 RAL 600 S. Mathews Ave. Urbana, IL 61801 Phone : (217) 333-7098 Fax : (217) 244-5858 From Csaba.Ortutay at uta.fi Tue Aug 3 02:17:13 2004 From: Csaba.Ortutay at uta.fi (Csaba Ortutay) Date: Tue Aug 3 02:18:15 2004 Subject: [Bioperl-l] TreeIO problem with nexus format Message-ID: <200408030917.13465.Csaba.Ortutay@uta.fi> Hello, I am working with phylogenetic trees, and I have the following problem. I want to build a tree from scratch, and according to some posts on the list I made this code: >>>>>>>>>>>>>>>>>>>>>> #!/usr/bin/perl -w use strict; use Bio::TreeIO; my $nodeL = new Bio::Tree::Node(); my $nodeR = new Bio::Tree::Node(); $nodeL->id("Left"); $nodeR->id("Right"); my $node = new Bio::Tree::Node(); $node->add_Descendent($nodeL); $node->add_Descendent($nodeR); my $tree = new Bio::Tree::Tree(-root => $node); my $treeio = new Bio::TreeIO(-format => 'newick', -file => '>try.tre'); $treeio->write_tree($tree); exit; <<<<<<<<<<<<<<<<<<<<<< This is working nicely, but when I try to save the tree in nexus format, I got this message: ------------- EXCEPTION ------------- MSG: Cannot call method write_tree on Bio::TreeIO object must use a subclass STACK Bio::TreeIO::nexus::write_tree /usr/lib/perl5/site_perl/5.8.0/Bio/TreeIO/nexus.pm:170 STACK toplevel ./makemaintree.pl:25 -------------------------------------- I am using bioperl 1.4. Do you have any idea, what is wrong? -- Csaba Ortutay PhD University of Tampere Institute of Medical Technology Bioinformatics Group Finland Csaba.Ortutay@uta.fi From jason at cgt.duhs.duke.edu Tue Aug 3 07:37:48 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Aug 3 07:39:12 2004 Subject: [Bioperl-l] TreeIO problem with nexus format In-Reply-To: <200408030917.13465.Csaba.Ortutay@uta.fi> References: <200408030917.13465.Csaba.Ortutay@uta.fi> Message-ID: write_tree is not supported for the nexus format for the 1.4 version of bioperl. You can use newick or you can get the latest version of the nexus.pm module from CVS which now has the ability to call write_tree. -jason On Tue, 3 Aug 2004, Csaba Ortutay wrote: > Hello, > > I am working with phylogenetic trees, and I have the following problem. > > I want to build a tree from scratch, and according to some posts on the list I > made this code: > > >>>>>>>>>>>>>>>>>>>>>> > #!/usr/bin/perl -w > use strict; > > use Bio::TreeIO; > > my $nodeL = new Bio::Tree::Node(); > my $nodeR = new Bio::Tree::Node(); > > $nodeL->id("Left"); > $nodeR->id("Right"); > my $node = new Bio::Tree::Node(); > $node->add_Descendent($nodeL); > $node->add_Descendent($nodeR); > > my $tree = new Bio::Tree::Tree(-root => $node); > my $treeio = new Bio::TreeIO(-format => 'newick', -file => '>try.tre'); > $treeio->write_tree($tree); > > exit; > <<<<<<<<<<<<<<<<<<<<<< > > > This is working nicely, but when I try to save the tree in nexus format, I got > this message: > > ------------- EXCEPTION ------------- > MSG: Cannot call method write_tree on Bio::TreeIO object must use a subclass > STACK Bio::TreeIO::nexus::write_tree > /usr/lib/perl5/site_perl/5.8.0/Bio/TreeIO/nexus.pm:170 > STACK toplevel ./makemaintree.pl:25 > -------------------------------------- > > I am using bioperl 1.4. > > Do you have any idea, what is wrong? > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From mayagao at hotmail.com Mon Aug 2 23:26:11 2004 From: mayagao at hotmail.com (Alex Zhang) Date: Tue Aug 3 07:46:18 2004 Subject: [Bioperl-l] SOS----for BioPerl Installing Message-ID: Dear friends, Hi! I faced some problems when installing BioPerl on Macintosh. I am using James D. Tisdall's Masterhing Perl for Bioinformatics and following the installation instructions. When running a test program, which is ************************ use Bio::Perl; $seq_object = get_sequence('swissprot',"R0A1_HUMAN"); write_sequence(">roa1.fasta",'fasta',$seq_object); ************************ it displayed that "Your systems does not have one of LWP, HTTP::Request::Common,IO::String installed so the DB retrieval method is not available. Full error message is: No such file or directory Bio::Perl::get_sequence('swissprot','ROA1-HUMAN') called at Bo11.pl line 3". Then I downloaded libwww-perl-5.64 and installed it. But two errors appeared. One was: "Checking for URI...........failed" and the other one was "Checking for HTML::Parser..failed". Then I downloaded the URI and HTML::Parser modules from CPAN and run the test program again. But the program still bothered me. So I wish I could get suggestions from you! Thanks, Alex _________________________________________________________________ Ãâ·ÑÏÂÔØ MSN Explorer: http://explorer.msn.com/lccn From jason at cgt.duhs.duke.edu Tue Aug 3 07:54:36 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Aug 3 07:55:54 2004 Subject: [Bioperl-l] SOS----for BioPerl Installing In-Reply-To: References: Message-ID: So.... are you using OS X or OS 9? You need to install IO::String, URI, HTML::Parser, and LWP if you want to use the remote access capabilities. You can also use the cpan interface which will automatically install dependancies for you. Try: perl -MCPAN -e shell On OS X you can also use fink to install Bioperl which will also install the necessary dependancies. -jason On Tue, 3 Aug 2004, Alex Zhang wrote: > Dear friends, > > Hi! I faced some problems when installing BioPerl on Macintosh. > > I am using James D. Tisdall's Masterhing Perl for Bioinformatics and > following the installation instructions. > > When running a test program, which is > > ************************ > > use Bio::Perl; > $seq_object = get_sequence('swissprot',"R0A1_HUMAN"); > write_sequence(">roa1.fasta",'fasta',$seq_object); > > ************************ > > it displayed that "Your systems does not have one of LWP, > HTTP::Request::Common,IO::String installed so the DB retrieval method is > not available. > > Full error message is: > No such file or directory > Bio::Perl::get_sequence('swissprot','ROA1-HUMAN') called at Bo11.pl > line 3". > > Then I downloaded libwww-perl-5.64 and installed it. But two errors > appeared. One was: "Checking for URI...........failed" and the other one > was "Checking for HTML::Parser..failed". Then I downloaded the URI and > HTML::Parser modules from CPAN and run the test program again. But the > program still bothered me. > > So I wish I could get suggestions from you! > > Thanks, > > Alex > > _________________________________________________________________ > Ãâ·ÑÏÂÔØ MSN Explorer: http://explorer.msn.com/lccn > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From brian_osborne at cognia.com Tue Aug 3 07:57:07 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Tue Aug 3 07:58:26 2004 Subject: [Bioperl-l] SOS----for BioPerl Installing In-Reply-To: Message-ID: Alex, >Then I downloaded the URI and >HTML::Parser modules from CPAN and run the test program again. But the >program still bothered me. What's the error message? Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Alex Zhang Sent: Monday, August 02, 2004 11:26 PM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] SOS----for BioPerl Installing Dear friends, Hi! I faced some problems when installing BioPerl on Macintosh. I am using James D. Tisdall's Masterhing Perl for Bioinformatics and following the installation instructions. When running a test program, which is ************************ use Bio::Perl; $seq_object = get_sequence('swissprot',"R0A1_HUMAN"); write_sequence(">roa1.fasta",'fasta',$seq_object); ************************ it displayed that "Your systems does not have one of LWP, HTTP::Request::Common,IO::String installed so the DB retrieval method is not available. Full error message is: No such file or directory Bio::Perl::get_sequence('swissprot','ROA1-HUMAN') called at Bo11.pl line 3". Then I downloaded libwww-perl-5.64 and installed it. But two errors appeared. One was: "Checking for URI...........failed" and the other one was "Checking for HTML::Parser..failed". Then I downloaded the URI and HTML::Parser modules from CPAN and run the test program again. But the program still bothered me. So I wish I could get suggestions from you! Thanks, Alex _________________________________________________________________ Ãâ·ÑÏÂÔØ MSN Explorer: http://explorer.msn.com/lccn _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From amackey at pcbi.upenn.edu Tue Aug 3 09:01:50 2004 From: amackey at pcbi.upenn.edu (Aaron J Mackey) Date: Tue Aug 3 09:03:10 2004 Subject: [Bioperl-l] Re: [Bioperl-guts-l] [Bug 1670] PrimarySeq.pm - _guess_alphabet incorrect In-Reply-To: <200408031142.i73Bg525009189@portal.open-bio.org> References: <200408031142.i73Bg525009189@portal.open-bio.org> Message-ID: On Tue, 3 Aug 2004 bugzilla-daemon@portal.open-bio.org wrote: > Patch applied. By the way, there is no need to escape anything but a bracket > within the brackets: > >> perl -e '$str = "?-.A"; $str =~ s/[-.?]//g; print $str,"\n";' Not since you (happened to?) put the '-' first; but if anyone were to add a character before it, an escaped '\-' would be necessary. And since anywhere else in a regexp, escaping is required, it's not entirely bad form to include them for clarity's sake. Your friendly Perl coding style police, -Aaron From rwcitek at alum.calberkeley.org Tue Aug 3 11:28:00 2004 From: rwcitek at alum.calberkeley.org (Robert Citek) Date: Tue Aug 3 11:29:46 2004 Subject: [Bioperl-l] on-line collaboration Message-ID: Just browsing through the archives: > Ewan Birney birney@ebi.ac.uk > Wed, 6 Sep 2000 11:10:03 +0100 (GMT) > > On Wed, 6 Sep 2000, Johann Visagie wrote: >> I feel that structured documents of some sort are one of the prime >> deliverables of any collaboration. >> ... >> Links again: >> Udell article: >> http://software-carpentry.codesourcery.com/Groupware/report.html >> WikiNG: http://dev.zope.org/Wikis/DevSite/Proposals/WikiNG >> STX NG: >> http://www.zope.org/Members/jim/StructuredTextWiki/StructuredTextNG >> >> Sorry for the long aside, but I'm becoming more and more interested >> in the >> whole online collaboration problem, and more convinced I should be >> doing >> something about it. Now, if only I had the time... :-) > > Indeed. - I'd like to work on something like that > as > well (close integration with irc and possibly IP-phones as well, for > that > crucial "quick-fix" contact). > > Hmmm. I guess in my copious free time.... ;) and browsing the bioperl.org site ( http://bioperl.org/ ). Is there a wiki page? Are there BBS like forums? Is there an IRC channel? Will keep googling, but thanks in advance if someone could point me in the right direction. Regards, - Robert From jason at cgt.duhs.duke.edu Tue Aug 3 11:57:23 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Aug 3 11:58:42 2004 Subject: [Bioperl-l] on-line collaboration In-Reply-To: References: Message-ID: On Tue, 3 Aug 2004, Robert Citek wrote: > > Just browsing through the archives: > > > Ewan Birney birney@ebi.ac.uk > > Wed, 6 Sep 2000 11:10:03 +0100 (GMT) > > > > On Wed, 6 Sep 2000, Johann Visagie wrote: > >> I feel that structured documents of some sort are one of the prime > >> deliverables of any collaboration. > >> ... > >> Links again: > >> Udell article: > >> http://software-carpentry.codesourcery.com/Groupware/report.html > >> WikiNG: http://dev.zope.org/Wikis/DevSite/Proposals/WikiNG > >> STX NG: > >> http://www.zope.org/Members/jim/StructuredTextWiki/StructuredTextNG > >> > >> Sorry for the long aside, but I'm becoming more and more interested > >> in the > >> whole online collaboration problem, and more convinced I should be > >> doing > >> something about it. Now, if only I had the time... :-) > > > > Indeed. - I'd like to work on something like that > > as > > well (close integration with irc and possibly IP-phones as well, for > > that > > crucial "quick-fix" contact). > > > > Hmmm. I guess in my copious free time.... ;) > > and browsing the bioperl.org site ( http://bioperl.org/ ). > > Is there a wiki page? There was, but nobody used it so we gave it up. We are pushing for people to write HOWTOs instead for structured documentation. For mailing list searching: http://search.open-bio.org/cgi-bin/mail-search.cgi (which doesn't seem to be linked anywhere yet) And site searching: http://search.open-bio.org/ general site searching. > Are there BBS like forums? > Is there an IRC channel? > nope - if someone wants to set it up that's great but I think most of the devs prefer to do the question answering via email. > Will keep googling, but thanks in advance if someone could point me in > the right direction. > > Regards, > - Robert > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From csardas at gmail.com Tue Aug 3 14:23:48 2004 From: csardas at gmail.com (Richie Gan) Date: Tue Aug 3 14:25:10 2004 Subject: [Bioperl-l] on-line collaboration In-Reply-To: References: Message-ID: > On Tue, 3 Aug 2004, Robert Citek wrote: > > > Is there a wiki page? > There was, but nobody used it so we gave it up. We are pushing for people > to write HOWTOs instead for structured documentation. > How about put the bptutorial on the wiki? I think it is suitable to edit structured documentation like bptutorial From cariaso at yahoo.com Tue Aug 3 17:24:26 2004 From: cariaso at yahoo.com (Mike Cariaso) Date: Tue Aug 3 17:25:41 2004 Subject: [Bioperl-l] bioperl is not playing nice with DProf on aix Message-ID: <20040803212426.51730.qmail@web52705.mail.yahoo.com> Don't you hate it when someone asks a question and then includes pages of code? What you really need is a small, tight example which can easily reproduce the problem. Ok, I've trimmed this down as much as I could. Here is the problem: > cat f2.pl use Bio::SeqIO; print "hello world\n"; > /usr/local/bin/perl -d:DProf f2.pl Illegal instruction (core dumped) To put that in some context... > cat f1.pl print "hello world\n"; > /usr/local/bin/perl -d:DProf f1.pl hello world > cat f2.pl use Bio::SeqIO; print "hello world\n"; > /usr/local/bin/perl -d:DProf f2.pl Illegal instruction (core dumped) > cat f3.pl use Data::Dumper; use POSIX; print "hello world\n"; > /usr/local/bin/perl -d:DProf f3.pl hello world > /usr/local/bin/perl f2.pl hello world This is perl, v5.6.1 built for aix-64all So... DProf alone works. DProf + 'use' works. bioperl alone works. But... DProf + bioperl doesn't work The error may be with DProf. But I don't think there is much of a DProf community to speak of. Can anyone else replicate, this? Or better yet shed light on a solution? ===== Mike Cariaso From amackey at pcbi.upenn.edu Tue Aug 3 17:48:53 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Tue Aug 3 17:50:09 2004 Subject: [Bioperl-l] bioperl is not playing nice with DProf on aix In-Reply-To: <20040803212426.51730.qmail@web52705.mail.yahoo.com> References: <20040803212426.51730.qmail@web52705.mail.yahoo.com> Message-ID: If you fire up gdb like so: % gdb /usr/local/bin/perl core % bt What do you get? -Aaron On Aug 3, 2004, at 5:24 PM, Mike Cariaso wrote: > Don't you hate it when someone asks a question and > then includes pages of code? What you really need is a > small, tight example which can easily reproduce the > problem. Ok, I've trimmed this down as much as I > could. > > Here is the problem: > >> cat f2.pl > use Bio::SeqIO; > print "hello world\n"; > >> /usr/local/bin/perl -d:DProf f2.pl > Illegal instruction (core dumped) > > > > To put that in some context... > > >> cat f1.pl > print "hello world\n"; > >> /usr/local/bin/perl -d:DProf f1.pl > hello world > >> cat f2.pl > use Bio::SeqIO; > print "hello world\n"; > >> /usr/local/bin/perl -d:DProf f2.pl > Illegal instruction (core dumped) > >> cat f3.pl > use Data::Dumper; > use POSIX; > print "hello world\n"; > >> /usr/local/bin/perl -d:DProf f3.pl > hello world > >> /usr/local/bin/perl f2.pl > hello world > > This is perl, v5.6.1 built for aix-64all > > So... > DProf alone works. > DProf + 'use' works. > bioperl alone works. > But... > DProf + bioperl doesn't work > > The error may be with DProf. But I don't think there > is much of a DProf community to speak of. > > Can anyone else replicate, this? > Or better yet shed light on a solution? > > > > > > > ===== > Mike Cariaso > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Aaron J. Mackey, Ph.D. Dept. of Biology, Goddard 212 University of Pennsylvania email: amackey@pcbi.upenn.edu 415 S. University Avenue office: 215-898-1205 Philadelphia, PA 19104-6017 fax: 215-746-6697 From cariaso at yahoo.com Tue Aug 3 18:13:34 2004 From: cariaso at yahoo.com (Mike Cariaso) Date: Tue Aug 3 18:15:15 2004 Subject: [Bioperl-l] bioperl is not playing nice with DProf on aix In-Reply-To: Message-ID: <20040803221334.59712.qmail@web52704.mail.yahoo.com> Many thanks for the quick reply. You were only slightly beaten by someone's 'Out of office' nice. > cat f2.pl use Bio::SeqIO; print "hello world\n"; > /usr/local/bin/perl -d:DProf f2.pl Illegal instruction (core dumped) > gdb /usr/local/bin/perl core GNU gdb 5.0-aix51-020209 Copyright 2000 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "powerpc-ibm-aix5.1.0.0"...(no debugging symbols found)... warning: core file may not match specified executable file. Program terminated with signal 4, Illegal instruction. (no debugging symbols found)...(no debugging symbols found)...(no debugging symbols found)...(no debugging symbols found)... (no debugging symbols found)...#0 0x110220a30 in ?? () from (unknown load module) (gdb) --- "Aaron J. Mackey" wrote: > > If you fire up gdb like so: > > % gdb /usr/local/bin/perl core > % bt > > What do you get? > > -Aaron > > On Aug 3, 2004, at 5:24 PM, Mike Cariaso wrote: > > > Don't you hate it when someone asks a question and > > then includes pages of code? What you really need > is a > > small, tight example which can easily reproduce > the > > problem. Ok, I've trimmed this down as much as I > > could. > > > > Here is the problem: > > > >> cat f2.pl > > use Bio::SeqIO; > > print "hello world\n"; > > > >> /usr/local/bin/perl -d:DProf f2.pl > > Illegal instruction (core dumped) > > > > > > > > To put that in some context... > > > > > >> cat f1.pl > > print "hello world\n"; > > > >> /usr/local/bin/perl -d:DProf f1.pl > > hello world > > > >> cat f2.pl > > use Bio::SeqIO; > > print "hello world\n"; > > > >> /usr/local/bin/perl -d:DProf f2.pl > > Illegal instruction (core dumped) > > > >> cat f3.pl > > use Data::Dumper; > > use POSIX; > > print "hello world\n"; > > > >> /usr/local/bin/perl -d:DProf f3.pl > > hello world > > > >> /usr/local/bin/perl f2.pl > > hello world > > > > This is perl, v5.6.1 built for aix-64all > > > > So... > > DProf alone works. > > DProf + 'use' works. > > bioperl alone works. > > But... > > DProf + bioperl doesn't work > > > > The error may be with DProf. But I don't think > there > > is much of a DProf community to speak of. > > > > Can anyone else replicate, this? > > Or better yet shed light on a solution? > > > > > > > > > > > > > > ===== > > Mike Cariaso > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > Aaron J. Mackey, Ph.D. > Dept. of Biology, Goddard 212 > University of Pennsylvania email: > amackey@pcbi.upenn.edu > 415 S. University Avenue office: > 215-898-1205 > Philadelphia, PA 19104-6017 fax: > 215-746-6697 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > ===== Mike Cariaso From cariaso at yahoo.com Tue Aug 3 18:15:14 2004 From: cariaso at yahoo.com (Mike Cariaso) Date: Tue Aug 3 18:16:30 2004 Subject: [Bioperl-l] bioperl is not playing nice with DProf on aix In-Reply-To: Message-ID: <20040803221514.12253.qmail@web52702.mail.yahoo.com> sorry I missed the bt on first read. (gdb) bt #0 0x110220a30 in ?? () from (unknown load module) Cannot access memory at address 0x1102208f0 --- "Aaron J. Mackey" wrote: > > If you fire up gdb like so: > > % gdb /usr/local/bin/perl core > % bt > > What do you get? > > -Aaron > > On Aug 3, 2004, at 5:24 PM, Mike Cariaso wrote: > > > Don't you hate it when someone asks a question and > > then includes pages of code? What you really need > is a > > small, tight example which can easily reproduce > the > > problem. Ok, I've trimmed this down as much as I > > could. > > > > Here is the problem: > > > >> cat f2.pl > > use Bio::SeqIO; > > print "hello world\n"; > > > >> /usr/local/bin/perl -d:DProf f2.pl > > Illegal instruction (core dumped) > > > > > > > > To put that in some context... > > > > > >> cat f1.pl > > print "hello world\n"; > > > >> /usr/local/bin/perl -d:DProf f1.pl > > hello world > > > >> cat f2.pl > > use Bio::SeqIO; > > print "hello world\n"; > > > >> /usr/local/bin/perl -d:DProf f2.pl > > Illegal instruction (core dumped) > > > >> cat f3.pl > > use Data::Dumper; > > use POSIX; > > print "hello world\n"; > > > >> /usr/local/bin/perl -d:DProf f3.pl > > hello world > > > >> /usr/local/bin/perl f2.pl > > hello world > > > > This is perl, v5.6.1 built for aix-64all > > > > So... > > DProf alone works. > > DProf + 'use' works. > > bioperl alone works. > > But... > > DProf + bioperl doesn't work > > > > The error may be with DProf. But I don't think > there > > is much of a DProf community to speak of. > > > > Can anyone else replicate, this? > > Or better yet shed light on a solution? > > > > > > > > > > > > > > ===== > > Mike Cariaso > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > Aaron J. Mackey, Ph.D. > Dept. of Biology, Goddard 212 > University of Pennsylvania email: > amackey@pcbi.upenn.edu > 415 S. University Avenue office: > 215-898-1205 > Philadelphia, PA 19104-6017 fax: > 215-746-6697 > > ===== Mike Cariaso From amackey at pcbi.upenn.edu Tue Aug 3 18:33:12 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Tue Aug 3 18:34:29 2004 Subject: [Bioperl-l] bioperl is not playing nice with DProf on aix In-Reply-To: <20040803221514.12253.qmail@web52702.mail.yahoo.com> References: <20040803221514.12253.qmail@web52702.mail.yahoo.com> Message-ID: <1A5A0CC1-E59D-11D8-AC1A-000A9577009E@pcbi.upenn.edu> Not very informative, unfortunately. What happens when you "use Bio::Root" or "use Bio::Root::IO" instead of Bio::SeqIO? Do you also get coredumps with these? I'm sorry to be debugging remotely (no AIX access anymore), perhaps we should take this off the list; we'll post back when (if?) we get to the bottom of this. -Aaron On Aug 3, 2004, at 6:15 PM, Mike Cariaso wrote: > sorry I missed the bt on first read. > > (gdb) bt > #0 0x110220a30 in ?? () from (unknown load module) > Cannot access memory at address 0x1102208f0 > > > > > > > > --- "Aaron J. Mackey" wrote: > >> >> If you fire up gdb like so: >> >> % gdb /usr/local/bin/perl core >> % bt >> >> What do you get? >> >> -Aaron >> >> On Aug 3, 2004, at 5:24 PM, Mike Cariaso wrote: >> >>> Don't you hate it when someone asks a question and >>> then includes pages of code? What you really need >> is a >>> small, tight example which can easily reproduce >> the >>> problem. Ok, I've trimmed this down as much as I >>> could. >>> >>> Here is the problem: >>> >>>> cat f2.pl >>> use Bio::SeqIO; >>> print "hello world\n"; >>> >>>> /usr/local/bin/perl -d:DProf f2.pl >>> Illegal instruction (core dumped) >>> >>> >>> >>> To put that in some context... >>> >>> >>>> cat f1.pl >>> print "hello world\n"; >>> >>>> /usr/local/bin/perl -d:DProf f1.pl >>> hello world >>> >>>> cat f2.pl >>> use Bio::SeqIO; >>> print "hello world\n"; >>> >>>> /usr/local/bin/perl -d:DProf f2.pl >>> Illegal instruction (core dumped) >>> >>>> cat f3.pl >>> use Data::Dumper; >>> use POSIX; >>> print "hello world\n"; >>> >>>> /usr/local/bin/perl -d:DProf f3.pl >>> hello world >>> >>>> /usr/local/bin/perl f2.pl >>> hello world >>> >>> This is perl, v5.6.1 built for aix-64all >>> >>> So... >>> DProf alone works. >>> DProf + 'use' works. >>> bioperl alone works. >>> But... >>> DProf + bioperl doesn't work >>> >>> The error may be with DProf. But I don't think >> there >>> is much of a DProf community to speak of. >>> >>> Can anyone else replicate, this? >>> Or better yet shed light on a solution? >>> >>> >>> >>> >>> >>> >>> ===== >>> Mike Cariaso >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> >> > http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> -- >> Aaron J. Mackey, Ph.D. >> Dept. of Biology, Goddard 212 >> University of Pennsylvania email: >> amackey@pcbi.upenn.edu >> 415 S. University Avenue office: >> 215-898-1205 >> Philadelphia, PA 19104-6017 fax: >> 215-746-6697 >> >> > > > ===== > Mike Cariaso > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Aaron J. Mackey, Ph.D. Dept. of Biology, Goddard 212 University of Pennsylvania email: amackey@pcbi.upenn.edu 415 S. University Avenue office: 215-898-1205 Philadelphia, PA 19104-6017 fax: 215-746-6697 From cariaso at yahoo.com Tue Aug 3 19:05:18 2004 From: cariaso at yahoo.com (Mike Cariaso) Date: Tue Aug 3 19:06:34 2004 Subject: [Bioperl-l] bioperl is not playing nice with DProf on aix In-Reply-To: <1A5A0CC1-E59D-11D8-AC1A-000A9577009E@pcbi.upenn.edu> Message-ID: <20040803230518.70249.qmail@web52701.mail.yahoo.com> Now looking at Bio/Root/IO.pm:328 bells and whistles go off. # we need to dup() the original filehandle because # doing fdopen() calls on an already open handle causes # the handle to go stale. is this going to work for non-unix # filehandles? -allen Raising the question. Is this a non unix system where it doesn't work. Oh how I loathe you aix. If its any easier I'm instant messenger as cariaso@yahoo or cariaso001@aim at the moment. --- "Aaron J. Mackey" wrote: > > Not very informative, unfortunately. What happens > when you "use > Bio::Root" or "use Bio::Root::IO" instead of > Bio::SeqIO? Do you also > get coredumps with these? > > I'm sorry to be debugging remotely (no AIX access > anymore), perhaps we > should take this off the list; we'll post back when > (if?) we get to the > bottom of this. > > -Aaron > > On Aug 3, 2004, at 6:15 PM, Mike Cariaso wrote: > > > sorry I missed the bt on first read. > > > > (gdb) bt > > #0 0x110220a30 in ?? () from (unknown load > module) > > Cannot access memory at address 0x1102208f0 > > > > > > > > > > > > > > > > --- "Aaron J. Mackey" > wrote: > > > >> > >> If you fire up gdb like so: > >> > >> % gdb /usr/local/bin/perl core > >> % bt > >> > >> What do you get? > >> > >> -Aaron > >> > >> On Aug 3, 2004, at 5:24 PM, Mike Cariaso wrote: > >> > >>> Don't you hate it when someone asks a question > and > >>> then includes pages of code? What you really > need > >> is a > >>> small, tight example which can easily reproduce > >> the > >>> problem. Ok, I've trimmed this down as much as I > >>> could. > >>> > >>> Here is the problem: > >>> > >>>> cat f2.pl > >>> use Bio::SeqIO; > >>> print "hello world\n"; > >>> > >>>> /usr/local/bin/perl -d:DProf f2.pl > >>> Illegal instruction (core dumped) > >>> > >>> > >>> > >>> To put that in some context... > >>> > >>> > >>>> cat f1.pl > >>> print "hello world\n"; > >>> > >>>> /usr/local/bin/perl -d:DProf f1.pl > >>> hello world > >>> > >>>> cat f2.pl > >>> use Bio::SeqIO; > >>> print "hello world\n"; > >>> > >>>> /usr/local/bin/perl -d:DProf f2.pl > >>> Illegal instruction (core dumped) > >>> > >>>> cat f3.pl > >>> use Data::Dumper; > >>> use POSIX; > >>> print "hello world\n"; > >>> > >>>> /usr/local/bin/perl -d:DProf f3.pl > >>> hello world > >>> > >>>> /usr/local/bin/perl f2.pl > >>> hello world > >>> > >>> This is perl, v5.6.1 built for aix-64all > >>> > >>> So... > >>> DProf alone works. > >>> DProf + 'use' works. > >>> bioperl alone works. > >>> But... > >>> DProf + bioperl doesn't work > >>> > >>> The error may be with DProf. But I don't think > >> there > >>> is much of a DProf community to speak of. > >>> > >>> Can anyone else replicate, this? > >>> Or better yet shed light on a solution? > >>> > >>> > >>> > >>> > >>> > >>> > >>> ===== > >>> Mike Cariaso > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l@portal.open-bio.org > >>> > >> > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > >>> > >>> > >> -- > >> Aaron J. Mackey, Ph.D. > >> Dept. of Biology, Goddard 212 > >> University of Pennsylvania email: > >> amackey@pcbi.upenn.edu > >> 415 S. University Avenue office: > >> 215-898-1205 > >> Philadelphia, PA 19104-6017 fax: > >> 215-746-6697 > >> > >> > > > > > > ===== > > Mike Cariaso > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > Aaron J. Mackey, Ph.D. > Dept. of Biology, Goddard 212 > University of Pennsylvania email: > amackey@pcbi.upenn.edu > 415 S. University Avenue office: > 215-898-1205 > Philadelphia, PA 19104-6017 fax: > 215-746-6697 > > ===== Mike Cariaso From smxie at sibs.ac.cn Wed Aug 4 01:08:47 2004 From: smxie at sibs.ac.cn (Songmin Xie) Date: Wed Aug 4 01:10:22 2004 Subject: [Bioperl-l] orthologous genes extracting Message-ID: <1356.10.10.120.61.1091596127.squirrel@webmail.sibs.ac.cn> > Is there a way of extracting orthologous genes from homologene database?> > Is there a perl module to do it? Thanks. Songmin Xie From mgaldzic at gmail.com Wed Aug 4 01:58:30 2004 From: mgaldzic at gmail.com (Michal Galdzicki) Date: Wed Aug 4 01:59:51 2004 Subject: [Bioperl-l] Trouble install Bioperl-Ext-1.4 & dpAlign Message-ID: I'm having the same problem discussed in June by jany (janynannan at yahoo.co.uk) and Aaron J Mackey. (http://bioperl.org/pipermail/bioperl-l/2004-June/016154.html, http://bioperl.org/pipermail/bioperl-l/2004-June/016153.html) Could anyone point me to the solution. During an install bioperl-ext-1.4 in Redhat9 with dpAlign. The following error comes up on 'make test' (and later when skipped in use dpAlign): ######################################################### PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl 1..9 # Running under perl version 5.008 for linux # Current time local: Wed Aug 4 01:15:51 2004 # Current time GMT: Wed Aug 4 05:15:51 2004 # Using Test.pm version 1.23 Not enough arguments for Bio::Ext::Align::Align_Protein_Sequences at /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/dpAlign.pm line 300, near "'blosum62')" Not enough arguments for Bio::Ext::Align::Align_Protein_Sequences at /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/dpAlign.pm line 355, near "'blosum62')" Compilation failed in require at test.pl line 15. BEGIN failed--compilation aborted at test.pl line 15. make: *** [test_dynamic] Error 255 ########################################################### Thank you, Michal Galdzicki ps. sorry if you received this twice From hlapp at gmx.net Wed Aug 4 05:19:17 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed Aug 4 05:20:17 2004 Subject: [Bioperl-l] biosql and relationships In-Reply-To: <20040804024007.GA7798@cecm.usp.br> Message-ID: <5C03157E-E5F7-11D8-B581-000A959EB4C4@gmx.net> On Wednesday, August 4, 2004, at 03:40 AM, Robson Francisco de Souza {S} wrote: > So, is it reasonable to use bioentry_relationship to store different > identifiers for the same bioentries, but from different or even the > same > database? I'm asking that because for many genes you will find several > names/identifiers like GI numbers, gene names or locus tags and > accession > numbers from different databases like KEGG, SWISSPROT, etc. You can represent that using bioentry_relationships but I wouldn't do so when it's artificial. I.e., I wouldn't dissect a Genbank entry into GI#, locus tag, gene name etc and make them all different bioentries that you would then need to link back together. If, however, you want to represent that two entries from different databases are, for instance, synonymous to each other, then loading both followed by establishing an entry in the bioentry_relationship table is how I would do that, using SQL or some hand-crafted script. > > Is it possible to load such identifiers for the sequences into > bioentry_relationship without actually loading the sequence data? Having a row in biosequence for a bioentry is optional, and this being optional is supported by bioperl-db. So, yes, the schema is aware that certain bioentries may not even have the concept of a sequence (like, e.g., a LL entry), and if you pass a SeqI object to bioperl-db that lacks a sequence you won't get a row in biosequence. > How could I do so if my sequence relationships are a set of > alternative identifiers for proteins in a tab separeted file > (non-redundant > sequences identifiers from PIR-NREF)? If it's just a list of identifiers for a certain entry then I'd add those identifiers as annotation (e.g., using Bio::Annotation::SimpleValue) to the existing entry. E.g., to process your tab-delimited file, look up the sequence object from the database using a unique key query by e.g. accession#, instantiate a Bio::Annotation::SimpleValue object for each additional identifier, and add it to the annotation bundle ($seq->annotation->add_Annotation()). When you're done re-serialize through $seq->store(). If the file rather is a cross-referencing table then I'd create bare-bones sequence objects for each and serialize them. > > Also, what I need is a database of sequence aliases, that would make > it easy to find identifiers for sequences in different resources > (UniProt, > Kegg/COG/KOG orthologous classifications, etc.). > Do you have any suggestion on how to implement such a database using > BioSQL/bioperl-db? See above. You can see those in action at symatlas.gnf.org (but there's no KEGG yet; also, InterPro is the only protein domain annotation at present). -hilmar > > Robson > >> Since bioperl doesn't have a straightforward corresponding class, >> however, it is not supported through the bioperl object layer except >> for Bio::ClusterI objects (e.g., Bio::Cluster::Unigene). >> >> There's different courses you could pursue. What I'm doing in my >> instance is making heavy use of SQL scripts that I run against the >> database on a regular basis, and which would synthesize those >> relationships based off of, for instance, dbxref-to-bioentry matches. >> Instead of running sql directly, you run also wrap a perl script >> around >> it for processing input files or things like iterative/recursive >> queries. Or you could amend bioperl (and then bioperl-db) to support >> this in a better fashion. >> >> -hilmar >> >> -- >> ------------------------------------------------------------- >> Hilmar Lapp email: lapp at gnf.org >> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 >> ------------------------------------------------------------- >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From rich at thevillas.eclipse.co.uk Wed Aug 4 07:12:07 2004 From: rich at thevillas.eclipse.co.uk (rich) Date: Wed Aug 4 07:17:40 2004 Subject: [Bioperl-l] bl2seq, Bio::AlignIO and looping through matches Message-ID: <4110C487.5000200@thevillas.eclipse.co.uk> Hi, i'm using bl2seq to align 2 sequences and parsing the results with Bio::AlignIO As i understand it in the instance where the two sequences match in more than one position I should be able to loop through each alignment using $aln = $report_align->next_aln() docs seem to back this up ...... " The only current exception is format "bl2seq" which parses results of the Blast bl2seq program and which may produce several alignment pairs. This set of alignment pairs can be read using multiple calls to next_aln." I can't get it to loop, it just pulls out one alignment i.e the first. Code and example bl2seq file below. Any help appreciated, thanks Rich use Bio::AlignIO; use Bio::Align::AlignI; my $report_align = Bio::AlignIO->new(-file => '/tmp/align' , '-format' => 'bl2seq'); my $loop_num=1; while(my $aln = $report_align->next_aln()){ print $loop_num++,"\n"; } Query= (523 letters) >, 1498 aa. Length = 1498 Score = 117 bits (292), Expect = 4e-30 Identities = 68/217 (31%), Positives = 120/217 (55%), Gaps = 3/217 (1%) Query: 299 GEVDVKDVTFTYQGKEKPALSHVSFSIPQGKTVALVGRSGSGKSTIANLFTRFYDVDSGS 358 G++ VKD+T Y L ++SFSI G+ V L+GR+GSGKST+ + F R + + G Sbjct: 1226 GQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRLLNTE-GE 1284 Query: 359 ICLDGHDVRDYKLTNLRRHFALVSQNVHLFNDTIANNIAYAAEGEYTREQIEQAARQAHA 418 I +DG L R+ F ++ Q V +F+ T N+ +++ ++I + A + Sbjct: 1285 IQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLD--PYEQWSDQEIWKVADEVGL 1342 Query: 419 MEFIENMPQGLDTVIGENGTSLSGGQRQRVAIARALLRDAPVLILDEATSALDTESERAI 478 IE P LD V+ + G LS G +Q + +AR++L A +L+LDE ++ LD + + I Sbjct: 1343 RSVIEQFPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPVTYQII 1402 Query: 479 QAALDELQKNKTVLVIAHRLSTIEQADEILVVDEGEI 515 + L + + TV++ HR+ + + + LV++E ++ Sbjct: 1403 RRTLKQAFADCTVILCEHRIEAMLECQQFLVIEENKV 1439 Score = 87.0 bits (214), Expect = 4e-21 Identities = 61/237 (25%), Positives = 116/237 (48%), Gaps = 20/237 (8%) Query: 278 FGLMDLETERDNGKYEAERVNGEVDVKDVTFTYQGKEKPALSHVSFSIPQGKTVALVGRS 337 FG + + +++N + NG+ + F+ G P L ++F I +G+ +A+ G + Sbjct: 423 FGELFEKAKQNNNNRKTS--NGDDSLFFSNFSLLGT--PVLKDINFKIERGQLLAVAGST 478 Query: 338 GSGKSTIANLFTRFYDVDSGSICLDGHDVRDYKLTNLRRHFALVSQNVHLFNDTIANNIA 397 G+GK+++ + + G I G + SQ + TI NI Sbjct: 479 GAGKTSLLMVIMGELEPSEGKIKHSGR-------------ISFCSQFSWIMPGTIKENII 525 Query: 398 YAAEGEYTREQIEQAARQAHAMEFIENMPQGLDTVIGENGTSLSGGQRQRVAIARALLRD 457 + Y + + E I + + V+GE G +LSGGQR R+++ARA+ +D Sbjct: 526 FGVS--YDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLSGGQRARISLARAVYKD 583 Query: 458 APVLILDEATSALDTESERAI-QAALDELQKNKTVLVIAHRLSTIEQADEILVVDEG 513 A + +LD LD +E+ I ++ + +L NKT +++ ++ +++AD+IL++ EG Sbjct: 584 ADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKMEHLKKADKILILHEG 640 Lambda K H 0.322 0.136 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 1908 Number of Sequences: 0 Number of extensions: 52 Number of successful extensions: 6 Number of sequences better than 10.0: 1 Number of HSP's better than 10.0 without gapping: 1 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2 length of query: 523 length of database: 1498 effective HSP length: 43 effective length of query: 480 effective length of database: 1455 effective search space: 698400 effective search space used: 698400 T: 11 A: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 30 (16.8 bits) S2: 30 (16.2 bits) From bmb9jrm at bmb.leeds.ac.uk Wed Aug 4 05:59:34 2004 From: bmb9jrm at bmb.leeds.ac.uk (Jon Manning) Date: Wed Aug 4 10:13:32 2004 Subject: [Bioperl-l] Secondary structure prediction Message-ID: <002d01c47a09$bfa1c1c0$7b84ff3e@g1b1r8> Hi all, I'm nearing the end of my Bioinformatics Masters thesis- I'm actually writing up! But I'd like to be able to (quickly!) incoporate some simple secondary structure prediction into my program. Could anyone point me in the direction of the best Bioperl way to plug this in? I've been looking at the Predator wrapper, but would appreciate any suggestions. Thanks, Jon From itubert at users.sourceforge.net Tue Aug 3 16:46:02 2004 From: itubert at users.sourceforge.net (Ivan Tubert-Brohman) Date: Wed Aug 4 10:13:36 2004 Subject: [Bioperl-l] PerlMol Message-ID: <410FF98A.1020100@users.sourceforge.net> Dear bioperl-l subscribers, The recent PerlMol project is a collection of Perl modules for chemoinformatics and computational chemistry. As such, I think it might be of interest to people using Perl for bioinformatics, considering the overlap between the (bio|chem)informatics fields. Homepage: http://www.perlmol.org/ . Features: * an object model for molecules * geometric functions * read and write common file formats: MDL Mol, SDF, XYZ, Mopac, SMILES, PDB. * ring perception * canonicalization * substructure pattern matching (SMARTS supported) * automatic bond and bond order assignment from 3D coordinates * Z-matrix builder * atom selection in macromolecules using Midas/Chimera atom specifiers * Mok: a concise AWK-like command-line language for "molecular munging". See http://www.perlmol.org/features.html for more details. Please note that this project has nothing to do (I hope) with an April fool's email sent to the CCP4 email list this year, and in fact it predates it. Regards, Ivan Tubert-Brohman From rfsouza at citri.iq.usp.br Tue Aug 3 22:40:07 2004 From: rfsouza at citri.iq.usp.br (Robson Francisco de Souza {S}) Date: Wed Aug 4 10:13:40 2004 Subject: [Bioperl-l] biosql and relationships In-Reply-To: <8424BA78-E47F-11D8-BF77-000A959EB4C4@gmx.net> References: <8424BA78-E47F-11D8-BF77-000A959EB4C4@gmx.net> Message-ID: <20040804024007.GA7798@cecm.usp.br> > On Monday, August 2, 2004, at 12:05 PM, Sean Davis wrote: > >I know this information is also stored in various dbxref tables, as > >well, but wondered how the bioentry_relationship table is used, if it > >is not for creating relationships between bioentries, even if they > >are in separate namespaces. On Mon, Aug 02, 2004 at 01:28:53PM +0100, Hilmar Lapp wrote: > The bioentry_relationship table is meant for exactly this purpose > indeed. So, is it reasonable to use bioentry_relationship to store different identifiers for the same bioentries, but from different or even the same database? I'm asking that because for many genes you will find several names/identifiers like GI numbers, gene names or locus tags and accession numbers from different databases like KEGG, SWISSPROT, etc. Is it possible to load such identifiers for the sequences into bioentry_relationship without actually loading the sequence data? How could I do so if my sequence relationships are a set of alternative identifiers for proteins in a tab separeted file (non-redundant sequences identifiers from PIR-NREF)? Also, what I need is a database of sequence aliases, that would make it easy to find identifiers for sequences in different resources (UniProt, Kegg/COG/KOG orthologous classifications, etc.). Do you have any suggestion on how to implement such a database using BioSQL/bioperl-db? Robson > Since bioperl doesn't have a straightforward corresponding class, > however, it is not supported through the bioperl object layer except > for Bio::ClusterI objects (e.g., Bio::Cluster::Unigene). > > There's different courses you could pursue. What I'm doing in my > instance is making heavy use of SQL scripts that I run against the > database on a regular basis, and which would synthesize those > relationships based off of, for instance, dbxref-to-bioentry matches. > Instead of running sql directly, you run also wrap a perl script around > it for processing input files or things like iterative/recursive > queries. Or you could amend bioperl (and then bioperl-db) to support > this in a better fashion. > > -hilmar > > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From trang at hcmc.netnam.vn Tue Aug 3 16:57:45 2004 From: trang at hcmc.netnam.vn (My Trang) Date: Wed Aug 4 10:13:44 2004 Subject: [Bioperl-l] Help with testing of parallel Smith-Waterman code on Message-ID: <002e01c4799c$8774bbd0$606319ac@trang> Hello Nemo Physche, I am searching parallel version of the Smith-Waterman (local alignment). Then I will try to run on Grid computing, using Globus flatform. (I use Linux) If you can, you send that program to me. Thank you very much for any your help. Trang Huynh. From amackey at pcbi.upenn.edu Wed Aug 4 10:58:32 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Wed Aug 4 11:01:07 2004 Subject: [Bioperl-l] Trouble install Bioperl-Ext-1.4 & dpAlign In-Reply-To: References: Message-ID: The resolution was that Yee had altered the API in Bio::Tools::dpAlign without regard to the expected arguments in bioperl-ext-1.4 You'll need to grab a CVS version of Bio/Tools/dpAlign.pm, to replace the one from bioperl 1.4 -Aaron On Aug 4, 2004, at 1:58 AM, Michal Galdzicki wrote: > I'm having the same problem discussed in June by jany (janynannan at > yahoo.co.uk) and Aaron J Mackey. > (http://bioperl.org/pipermail/bioperl-l/2004-June/016154.html, > http://bioperl.org/pipermail/bioperl-l/2004-June/016153.html) > > Could anyone point me to the solution. > > During an install bioperl-ext-1.4 in Redhat9 with dpAlign. > The following error comes up on 'make test' (and later when skipped in > use dpAlign): > > ######################################################### > PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl > 1..9 > # Running under perl version 5.008 for linux > # Current time local: Wed Aug 4 01:15:51 2004 > # Current time GMT: Wed Aug 4 05:15:51 2004 > # Using Test.pm version 1.23 > Not enough arguments for Bio::Ext::Align::Align_Protein_Sequences at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/dpAlign.pm line 300, near > "'blosum62')" > Not enough arguments for Bio::Ext::Align::Align_Protein_Sequences at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/dpAlign.pm line 355, near > "'blosum62')" > Compilation failed in require at test.pl line 15. > BEGIN failed--compilation aborted at test.pl line 15. > make: *** [test_dynamic] Error 255 > > ########################################################### > > Thank you, > Michal Galdzicki > > ps. sorry if you received this twice > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Aaron J. Mackey, Ph.D. Dept. of Biology, Goddard 212 University of Pennsylvania email: amackey@pcbi.upenn.edu 415 S. University Avenue office: 215-898-1205 Philadelphia, PA 19104-6017 fax: 215-746-6697 From Annie.Law at nrc-cnrc.gc.ca Wed Aug 4 11:17:56 2004 From: Annie.Law at nrc-cnrc.gc.ca (Law, Annie) Date: Wed Aug 4 11:19:13 2004 Subject: [Bioperl-l] GO path and GO relationships Message-ID: <10C94843061E094A98C02EB77CFC328722FE6E@nrcmrdex1d.imsb.nrc.ca> Hi, I would like to know if there are modules in bioperl that will help me find the go path, hierarchy corresponding to An input GO id. Also, I would like to know if there is something in bioperl if given as input a group of GO identifiers will indicate the Relationship between the GO identifiers ie. Parent or child of or is a. I am open to using resources available in bioperl db or separate modules. Thanks very much, Annie. From jason at cgt.duhs.duke.edu Wed Aug 4 11:25:15 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Aug 4 11:26:36 2004 Subject: [Bioperl-l] GO path and GO relationships In-Reply-To: <10C94843061E094A98C02EB77CFC328722FE6E@nrcmrdex1d.imsb.nrc.ca> References: <10C94843061E094A98C02EB77CFC328722FE6E@nrcmrdex1d.imsb.nrc.ca> Message-ID: The GO API is pretty powerful developed by Chris Mungall and others. http://www.godatabase.org/dev/ Click on go-perl and go-db-perl to see SYNOPSIS information. -jason On Wed, 4 Aug 2004, Law, Annie wrote: > Hi, > > I would like to know if there are modules in bioperl that will help me find > the go path, hierarchy corresponding to An input GO id. Also, I would like > to know if there is something in bioperl if given as input a group of GO > identifiers will indicate the > Relationship between the GO identifiers ie. Parent or child of or is a. > > I am open to using resources available in bioperl db or separate modules. > > Thanks very much, > Annie. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Wed Aug 4 12:38:18 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Aug 4 12:39:38 2004 Subject: [Bioperl-l] Bio::SearchIO In-Reply-To: <1091636602.3194.21.camel@tryps> References: <1091636602.3194.21.camel@tryps> Message-ID: I don't have time to play with your code right now, but the reason for your error is you are not getting an hsp for a hit - you need to either protect your hsp calls like this: if( $hsp = $hit->next_hsp ) { } and/or make sure B=V when you run blastall blastall -b 500 -v 500 -jason On Wed, 4 Aug 2004, Alberto Davila wrote: > Hi Jason, > > I am listing my code below... I tried it with the blast results (blastx) > annexed to this msg... the error msg I get is: > > Query= 366 > 2 > 0 > 28 > 46 > 201 > 437 > 174 > 247 > > Query= 366 > Can't call method "query" on an undefined value at parser.pl line 22, > line 8164. > > Curiously the script worked well (without any warning/error) parsing > another file resulting from a tblastx search. > > Thanks in advance, Alberto > > ***** > > CODE: > > #!/usr/bin/perl > > use lib "/usr/local/bioperl14"; > use Bio::SearchIO; > > $searchio = new Bio::SearchIO ('-format' => 'blast', > '-file' => 'clusters.blast'); > > while ($result = $searchio->next_result) { > $query_name = $result->query_name(); > $cluster_id = $query_name; > > while ($hit = $result->next_hit) { > ($gi) = $hit->name =~ /gi\|(\d+)\|/; > $hsp = $hit->next_hsp; > $accession = $hit->accession; > $description = $hit->description(); > $expect = $hit->significance(); > $score = $hit->raw_score(); > $length = $hit->length(); > print "Query= $cluster_id\n"; > $query_frame = $hsp->query->frame; > print "$query_frame\n"; > $hit_frame = $hsp->hit->frame; > print "$hit_frame\n"; > $identical=$hsp->num_identical; > print "$identical\n"; > $conserved=$hsp->num_conserved; > print "$conserved\n"; > $query_start=$hsp->start('query'); > print "$query_start\n"; > $query_end=$hsp->end('query'); > print "$query_end\n"; > $hit_start=$hsp->start('hit'); > print "$hit_start\n"; > $hit_end=$hsp->end('hit'); > print "$hit_end\n\n"; > > > > } > > } > > > > > On Wed, 2004-07-28 at 10:10, Jason Stajich wrote: > > good - so Alberto - we need some way to replicate your problem. What > > version of bioperl are you using, etc.... > > > > -jason > > > > On Wed, 28 Jul 2004, Brian Osborne wrote: > > > > > Jason, > > > > > > Yes, $hsp->end('query') works using the latest bioperl-live code. > > > > > > Brian O. > > > > > > -----Original Message----- > > > From: bioperl-l-bounces@portal.open-bio.org > > > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich > > > Sent: Tuesday, July 27, 2004 10:04 AM > > > To: davila > > > Cc: bioperl-l@bioperl.org > > > Subject: Re: [Bioperl-l] Bio::SearchIO > > > > > > It should still work. > > > > > > You may try: > > > $hsp->query->start > > > $hsp->query->end > > > > > > $hsp->hit->start > > > $hsp->hit->end > > > > > > This should be equivalent with > > > $hsp->start('hit'), $hsp->end('hit'), ... etc > > > > > > But it is possible that something has been changed in the object layer > > > that broke this. I'm not really sure since it should be in the tests... > > > > > > if you can post code + an example BLAST file as a bug report at > > > http://bugzilla.bioperl.org which demonstrates the problem we'll have a > > > look. > > > > > > -jason > > > > > > On Tue, 27 Jul 2004, davila wrote: > > > > > > > I was using the last year a Blast parser with the following lines: > > > > > > > > $query_start=$hsp->start('query'); > > > > $query_end=$hsp->end('query'); > > > > $hit_start=$hsp->start('hit'); > > > > $hit_end=$hsp->end('hit'); > > > > > > > > however it is no longer working and I had to comment them in order to have > > > the parser working. If there were any changes, how I could now catch the > > > "query_start", "query_end", "hit_start" and "hit_end" from the Blast results > > > ? > > > > > > > > Thanks in advance, Alberto > > > > > > > > > > > > _______________________________________________ > > > > Bioperl-l mailing list > > > > Bioperl-l@portal.open-bio.org > > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > > Jason Stajich > > > Duke University > > > jason at cgt.mc.duke.edu > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > Jason Stajich > > Duke University > > jason at cgt.mc.duke.edu > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From davila at ioc.fiocruz.br Wed Aug 4 12:23:23 2004 From: davila at ioc.fiocruz.br (Alberto Davila) Date: Wed Aug 4 13:16:14 2004 Subject: [Bioperl-l] Bio::SearchIO In-Reply-To: References: Message-ID: <1091636602.3194.21.camel@tryps> Hi Jason, I am listing my code below... I tried it with the blast results (blastx) annexed to this msg... the error msg I get is: Query= 366 2 0 28 46 201 437 174 247 Query= 366 Can't call method "query" on an undefined value at parser.pl line 22, line 8164. Curiously the script worked well (without any warning/error) parsing another file resulting from a tblastx search. Thanks in advance, Alberto ***** CODE: #!/usr/bin/perl use lib "/usr/local/bioperl14"; use Bio::SearchIO; $searchio = new Bio::SearchIO ('-format' => 'blast', '-file' => 'clusters.blast'); while ($result = $searchio->next_result) { $query_name = $result->query_name(); $cluster_id = $query_name; while ($hit = $result->next_hit) { ($gi) = $hit->name =~ /gi\|(\d+)\|/; $hsp = $hit->next_hsp; $accession = $hit->accession; $description = $hit->description(); $expect = $hit->significance(); $score = $hit->raw_score(); $length = $hit->length(); print "Query= $cluster_id\n"; $query_frame = $hsp->query->frame; print "$query_frame\n"; $hit_frame = $hsp->hit->frame; print "$hit_frame\n"; $identical=$hsp->num_identical; print "$identical\n"; $conserved=$hsp->num_conserved; print "$conserved\n"; $query_start=$hsp->start('query'); print "$query_start\n"; $query_end=$hsp->end('query'); print "$query_end\n"; $hit_start=$hsp->start('hit'); print "$hit_start\n"; $hit_end=$hsp->end('hit'); print "$hit_end\n\n"; } } On Wed, 2004-07-28 at 10:10, Jason Stajich wrote: > good - so Alberto - we need some way to replicate your problem. What > version of bioperl are you using, etc.... > > -jason > > On Wed, 28 Jul 2004, Brian Osborne wrote: > > > Jason, > > > > Yes, $hsp->end('query') works using the latest bioperl-live code. > > > > Brian O. > > > > -----Original Message----- > > From: bioperl-l-bounces@portal.open-bio.org > > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich > > Sent: Tuesday, July 27, 2004 10:04 AM > > To: davila > > Cc: bioperl-l@bioperl.org > > Subject: Re: [Bioperl-l] Bio::SearchIO > > > > It should still work. > > > > You may try: > > $hsp->query->start > > $hsp->query->end > > > > $hsp->hit->start > > $hsp->hit->end > > > > This should be equivalent with > > $hsp->start('hit'), $hsp->end('hit'), ... etc > > > > But it is possible that something has been changed in the object layer > > that broke this. I'm not really sure since it should be in the tests... > > > > if you can post code + an example BLAST file as a bug report at > > http://bugzilla.bioperl.org which demonstrates the problem we'll have a > > look. > > > > -jason > > > > On Tue, 27 Jul 2004, davila wrote: > > > > > I was using the last year a Blast parser with the following lines: > > > > > > $query_start=$hsp->start('query'); > > > $query_end=$hsp->end('query'); > > > $hit_start=$hsp->start('hit'); > > > $hit_end=$hsp->end('hit'); > > > > > > however it is no longer working and I had to comment them in order to have > > the parser working. If there were any changes, how I could now catch the > > "query_start", "query_end", "hit_start" and "hit_end" from the Blast results > > ? > > > > > > Thanks in advance, Alberto > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -- > > Jason Stajich > > Duke University > > jason at cgt.mc.duke.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu -------------- next part -------------- BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 333 (171 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 18,978,045 Number of Sequences: 153871 Number of extensions: 286529 Number of successful extensions: 900 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 894 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 900 length of database: 56,608,159 effective HSP length: 29 effective length of database: 52,145,900 effective search space used: 1407939300 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 334 (570 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 48,453,852 Number of Sequences: 153871 Number of extensions: 819428 Number of successful extensions: 1987 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1971 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1987 length of database: 56,608,159 effective HSP length: 103 effective length of database: 40,759,446 effective search space used: 3505312356 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 335 (368 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value VIME_ONCMY (P48674) Vimentin 35 0.058 >VIME_ONCMY (P48674) Vimentin Length = 461 Score = 34.7 bits (78), Expect = 0.058 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 2/99 (2%) Frame = -2 Query: 292 DDFKKYFYRDVDNRFSEMFDTCREYVSEADHLSRASEELAENHQNLRGWGNEQEKTLVSI 113 +D+ K + D+ + D R+ EA+ R + L +L+G E+ + + Sbjct: 284 EDWYKSKFADLSEAANRNTDAIRQAKQEANEYRRQVQALTCEVDSLKGTNESMERQMREL 343 Query: 112 KDEVIPKLLSSEQHNYE--FSQLSTDFGNFIDDMNKHLR 2 ++ E +N++ S+L D N D+M +HLR Sbjct: 344 EES-----FGCEANNFQDTISRLEDDIRNMKDEMARHLR 377 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 35,813,483 Number of Sequences: 153871 Number of extensions: 682381 Number of successful extensions: 2144 Number of sequences better than 1.0e-01: 1 Number of HSP's better than 0.1 without gapping: 2101 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2144 length of database: 56,608,159 effective HSP length: 89 effective length of database: 42,913,640 effective search space used: 1416150120 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 336 (182 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 17,891,745 Number of Sequences: 153871 Number of extensions: 250887 Number of successful extensions: 514 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 510 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 514 length of database: 56,608,159 effective HSP length: 33 effective length of database: 51,530,416 effective search space used: 1391321232 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 337 (540 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 52,237,302 Number of Sequences: 153871 Number of extensions: 956399 Number of successful extensions: 2456 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2252 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2421 length of database: 56,608,159 effective HSP length: 102 effective length of database: 40,913,317 effective search space used: 3150325409 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 338 (315 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 36,859,232 Number of Sequences: 153871 Number of extensions: 723393 Number of successful extensions: 2108 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2037 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2107 length of database: 56,608,159 effective HSP length: 73 effective length of database: 45,375,576 effective search space used: 1406642856 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 339 (432 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 42,475,041 Number of Sequences: 153871 Number of extensions: 791759 Number of successful extensions: 2365 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2309 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2364 length of database: 56,608,159 effective HSP length: 99 effective length of database: 41,374,930 effective search space used: 1820496920 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 340 (454 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 54,243,654 Number of Sequences: 153871 Number of extensions: 1231250 Number of successful extensions: 3140 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2929 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 3136 length of database: 56,608,159 effective HSP length: 99 effective length of database: 41,374,930 effective search space used: 2110121430 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 341 (354 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 27,199,086 Number of Sequences: 153871 Number of extensions: 392489 Number of successful extensions: 1044 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1025 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1043 length of database: 56,608,159 effective HSP length: 85 effective length of database: 43,529,124 effective search space used: 1392931968 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 342 (402 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 31,250,601 Number of Sequences: 153871 Number of extensions: 450318 Number of successful extensions: 851 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 841 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 851 length of database: 56,608,159 effective HSP length: 97 effective length of database: 41,682,672 effective search space used: 1500576192 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 343 (427 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 50,405,894 Number of Sequences: 153871 Number of extensions: 1158510 Number of successful extensions: 4343 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 4080 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 4328 length of database: 56,608,159 effective HSP length: 98 effective length of database: 41,528,801 effective search space used: 1785738443 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 344 (397 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 41,650,086 Number of Sequences: 153871 Number of extensions: 783460 Number of successful extensions: 2044 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1991 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2044 length of database: 56,608,159 effective HSP length: 97 effective length of database: 41,682,672 effective search space used: 1417210848 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 345 (410 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 34,486,246 Number of Sequences: 153871 Number of extensions: 569246 Number of successful extensions: 1369 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1343 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1369 length of database: 56,608,159 effective HSP length: 97 effective length of database: 41,682,672 effective search space used: 1625624208 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 346 (363 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 39,219,324 Number of Sequences: 153871 Number of extensions: 770169 Number of successful extensions: 2675 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2552 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2672 length of database: 56,608,159 effective HSP length: 87 effective length of database: 43,221,382 effective search space used: 1426305606 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 347 (422 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 39,780,061 Number of Sequences: 153871 Number of extensions: 735955 Number of successful extensions: 2027 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1990 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2027 length of database: 56,608,159 effective HSP length: 98 effective length of database: 41,528,801 effective search space used: 1744209642 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 348 (134 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value UBIQ_TRYBB (P15174) Ubiquitin 69 4e-12 UBIQ_TRYCR (P08565) Ubiquitin 67 8e-12 UBIQ_SOYBN (P03993) Ubiquitin 67 8e-12 UBIQ_LEIMA (Q05550) Ubiquitin 67 8e-12 UBIQ_EUPEU (P23324) Ubiquitin 67 8e-12 UBIQ_CHLRE (P14624) Ubiquitin 67 8e-12 UBIQ_ARATH (P59263) Ubiquitin 67 8e-12 UBIQ_ACECL (P42739) Ubiquitin 67 8e-12 UBIQ_ACACA (P49634) Ubiquitin 67 8e-12 UBIQ_YEAST (P61864) Ubiquitin 66 2e-11 UBIQ_TETPY (P20685) Ubiquitin 66 2e-11 UBIQ_STRPU (P23398) Ubiquitin 66 2e-11 UBIQ_PHYIN (P22589) Ubiquitin 66 2e-11 UBIQ_NEUCR (P13117) Ubiquitin 66 2e-11 UBIQ_HUMAN (P02248) Ubiquitin 66 2e-11 UBIQ_GEOCY (P59669) Ubiquitin 66 2e-11 UBIQ_EIMBO (P46574) Ubiquitin 66 2e-11 UBIQ_DROME (Q9VZL4) Ubiquitin 66 2e-11 UBIQ_DICDI (P08618) Ubiquitin 66 2e-11 UBIQ_CRYNE (P61863) Ubiquitin 66 2e-11 UBIQ_COPCO (P19848) Ubiquitin 66 2e-11 UBIQ_CANAL (P61862) Ubiquitin 66 2e-11 UBIQ_CAEEL (P14792) Ubiquitin 66 2e-11 UBIQ_AGLNE (P42740) Ubiquitin 66 2e-11 UBIQ_LEITA (P49635) Ubiquitin 65 5e-11 UBIL_NPVAC (P16709) Ubiquitin-like protein 62 3e-10 UBIL_NPVOP (Q05120) Ubiquitin-like protein 62 4e-10 RUB1_ARATH (Q9SHE7) Ubiquitin-related protein 1 precursor (AtRUB1) 45 3e-05 RUB2_ARATH (Q8RUC6) Ubiquitin-related protein 2 precursor (AtRUB2) 43 2e-04 NED8_MOUSE (P29595) Ubiquitin-like protein NEDD8 42 5e-04 NED8_HUMAN (Q15843) Ubiquitin-like protein NEDD8 42 5e-04 NED8_BOVIN (P61282) Ubiquitin-like protein NEDD8 42 5e-04 RUB3_ARATH (O65381) Ubiquitin-related protein 3 precursor (AtRUB3) 41 8e-04 UBL1_SCHPO (O14399) Ubiquitin-like protein 1 38 0.007 RUB1_YEAST (Q03919) Ubiquitin-like protein RUB1 precursor 35 0.034 A1UP_MOUSE (Q99NB8) Ataxin-1 ubiquitin-like interacting protein A1U 34 0.098 >UBIQ_TRYBB (P15174) Ubiquitin Length = 76 Score = 68.6 bits (166), Expect = 4e-12 Identities = 33/34 (97%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 76 >UBIQ_TRYCR (P08565) Ubiquitin Length = 76 Score = 67.4 bits (163), Expect = 8e-12 Identities = 32/34 (94%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTLADYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 >UBIQ_SOYBN (P03993) Ubiquitin Length = 76 Score = 67.4 bits (163), Expect = 8e-12 Identities = 32/34 (94%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTLADYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 >UBIQ_LEIMA (Q05550) Ubiquitin Length = 76 Score = 67.4 bits (163), Expect = 8e-12 Identities = 32/34 (94%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLEEGRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEEGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_EUPEU (P23324) Ubiquitin Length = 76 Score = 67.4 bits (163), Expect = 8e-12 Identities = 32/34 (94%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTLADYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 >UBIQ_CHLRE (P14624) Ubiquitin Length = 76 Score = 67.4 bits (163), Expect = 8e-12 Identities = 32/34 (94%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTLADYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 >UBIQ_ARATH (P59263) Ubiquitin Length = 76 Score = 67.4 bits (163), Expect = 8e-12 Identities = 32/34 (94%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTLADYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 >UBIQ_ACECL (P42739) Ubiquitin Length = 76 Score = 67.4 bits (163), Expect = 8e-12 Identities = 32/34 (94%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTLADYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 >UBIQ_ACACA (P49634) Ubiquitin Length = 76 Score = 67.4 bits (163), Expect = 8e-12 Identities = 32/34 (94%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTLADYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 >UBIQ_YEAST (P61864) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_TETPY (P20685) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_STRPU (P23398) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_PHYIN (P22589) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_NEUCR (P13117) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_HUMAN (P02248) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_GEOCY (P59669) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_EIMBO (P46574) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_DROME (Q9VZL4) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_DICDI (P08618) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_CRYNE (P61863) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_COPCO (P19848) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_CANAL (P61862) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_CAEEL (P14792) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_AGLNE (P42740) Ubiquitin Length = 76 Score = 66.2 bits (160), Expect = 2e-11 Identities = 31/34 (91%), Positives = 34/34 (100%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+GRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIQ_LEITA (P49635) Ubiquitin Length = 76 Score = 64.7 bits (156), Expect = 5e-11 Identities = 31/34 (91%), Positives = 33/34 (97%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFA KQLEEGRTL+DYNIQKESTLHLVLRLRGG Sbjct: 43 LIFADKQLEEGRTLSDYNIQKESTLHLVLRLRGG 76 >UBIL_NPVAC (P16709) Ubiquitin-like protein Length = 77 Score = 62.4 bits (150), Expect = 3e-10 Identities = 28/34 (82%), Positives = 33/34 (97%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IFAGKQLE+ +T+ADYNIQKESTLH+VLRLRGG Sbjct: 43 LIFAGKQLEDSKTMADYNIQKESTLHMVLRLRGG 76 >UBIL_NPVOP (Q05120) Ubiquitin-like protein Length = 93 Score = 61.6 bits (148), Expect = 4e-10 Identities = 28/34 (82%), Positives = 33/34 (97%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +I+AGKQLE+ +TLADYNIQKESTLH+VLRLRGG Sbjct: 43 LIYAGKQLEDAQTLADYNIQKESTLHMVLRLRGG 76 >RUB1_ARATH (Q9SHE7) Ubiquitin-related protein 1 precursor (AtRUB1) Length = 80 Score = 45.4 bits (106), Expect = 3e-05 Identities = 21/34 (61%), Positives = 26/34 (76%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +I+AGKQL + +T DYNI+ S LHLVL LRGG Sbjct: 43 LIYAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 76 >RUB2_ARATH (Q8RUC6) Ubiquitin-related protein 2 precursor (AtRUB2) Length = 78 Score = 43.1 bits (100), Expect = 2e-04 Identities = 20/35 (57%), Positives = 26/35 (74%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGGM 108 +I+AGKQL + +T DY I+ S LHLVL LRGG+ Sbjct: 43 LIYAGKQLADDKTAKDYAIEGGSVLHLVLALRGGL 77 >NED8_MOUSE (P29595) Ubiquitin-like protein NEDD8 Length = 81 Score = 41.6 bits (96), Expect = 5e-04 Identities = 19/34 (55%), Positives = 25/34 (73%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +I++GKQ+ + +T ADY I S LHLVL LRGG Sbjct: 43 LIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 76 >NED8_HUMAN (Q15843) Ubiquitin-like protein NEDD8 Length = 81 Score = 41.6 bits (96), Expect = 5e-04 Identities = 19/34 (55%), Positives = 25/34 (73%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +I++GKQ+ + +T ADY I S LHLVL LRGG Sbjct: 43 LIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 76 >NED8_BOVIN (P61282) Ubiquitin-like protein NEDD8 Length = 81 Score = 41.6 bits (96), Expect = 5e-04 Identities = 19/34 (55%), Positives = 25/34 (73%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +I++GKQ+ + +T ADY I S LHLVL LRGG Sbjct: 43 LIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 76 >RUB3_ARATH (O65381) Ubiquitin-related protein 3 precursor (AtRUB3) Length = 78 Score = 40.8 bits (94), Expect = 8e-04 Identities = 17/34 (50%), Positives = 24/34 (70%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +++ GKQL + T YN+++ S LHLVL LRGG Sbjct: 43 IVYTGKQLADDLTAKHYNLERGSVLHLVLALRGG 76 >UBL1_SCHPO (O14399) Ubiquitin-like protein 1 Length = 78 Score = 37.7 bits (86), Expect = 0.007 Identities = 16/34 (47%), Positives = 24/34 (70%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +I+AGKQ+ + + Y+++ S LHLVL LRGG Sbjct: 43 LIYAGKQMADDKNAESYHLEGGSVLHLVLALRGG 76 >RUB1_YEAST (Q03919) Ubiquitin-like protein RUB1 precursor Length = 77 Score = 35.4 bits (80), Expect = 0.034 Identities = 16/34 (47%), Positives = 24/34 (70%) Frame = +1 Query: 4 VIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGG 105 +IF GKQ+++ T+ D ++ + LHLVL LRGG Sbjct: 43 LIFQGKQIDDKLTVTDAHLVEGMQLHLVLTLRGG 76 >A1UP_MOUSE (Q99NB8) Ataxin-1 ubiquitin-like interacting protein A1U Length = 596 Score = 33.9 bits (76), Expect = 0.098 Identities = 15/31 (48%), Positives = 24/31 (77%) Frame = +1 Query: 1 VVIFAGKQLEEGRTLADYNIQKESTLHLVLR 93 V+IFAGK L++G TL+ + I+ T+HLV++ Sbjct: 53 VLIFAGKILKDGDTLSQHGIKDGLTVHLVIK 83 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 6,912,149 Number of Sequences: 153871 Number of extensions: 69061 Number of successful extensions: 234 Number of sequences better than 1.0e-01: 36 Number of HSP's better than 0.1 without gapping: 232 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 234 length of database: 56,608,159 effective HSP length: 18 effective length of database: 53,838,481 effective search space used: 1399800506 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 349 (148 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 16,044,075 Number of Sequences: 153871 Number of extensions: 226274 Number of successful extensions: 690 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 675 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 689 length of database: 56,608,159 effective HSP length: 22 effective length of database: 53,222,997 effective search space used: 1383797922 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 350 (127 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 14,458,014 Number of Sequences: 153871 Number of extensions: 174343 Number of successful extensions: 477 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 469 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 477 length of database: 56,608,159 effective HSP length: 15 effective length of database: 54,300,094 effective search space used: 1411802444 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 351 (256 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 28,881,512 Number of Sequences: 153871 Number of extensions: 512585 Number of successful extensions: 1642 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1592 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1642 length of database: 56,608,159 effective HSP length: 55 effective length of database: 48,145,254 effective search space used: 1396212366 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 352 (213 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 21,933,304 Number of Sequences: 153871 Number of extensions: 378979 Number of successful extensions: 970 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 967 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 970 length of database: 56,608,159 effective HSP length: 42 effective length of database: 50,145,577 effective search space used: 1404076156 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 353 (102 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.308 0.114 0.282 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 10,288,617 Number of Sequences: 153871 Number of extensions: 88373 Number of successful extensions: 244 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 244 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 244 length of database: 56,608,159 effective HSP length: 8 effective length of database: 55,377,191 effective search space used: 1384429775 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 354 (605 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 66,934,662 Number of Sequences: 153871 Number of extensions: 1482752 Number of successful extensions: 4455 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 4295 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 4454 length of database: 56,608,159 effective HSP length: 104 effective length of database: 40,605,575 effective search space used: 3938740775 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 355 (151 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 15,818,617 Number of Sequences: 153871 Number of extensions: 218198 Number of successful extensions: 646 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 642 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 646 length of database: 56,608,159 effective HSP length: 22 effective length of database: 53,222,997 effective search space used: 1437020919 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 356 (236 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 22,642,361 Number of Sequences: 153871 Number of extensions: 355049 Number of successful extensions: 1175 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1139 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1175 length of database: 56,608,159 effective HSP length: 49 effective length of database: 49,068,480 effective search space used: 1422985920 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 357 (1234 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 111,036,455 Number of Sequences: 153871 Number of extensions: 2439094 Number of successful extensions: 8718 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 7729 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 8687 length of database: 56,608,159 effective HSP length: 112 effective length of database: 39,374,607 effective search space used: 11733632886 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 358 (263 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value H3_LEIIN (P40285) Histone H3 49 3e-06 H3_MORAP (Q9HDN1) Histone H3 40 0.001 H34_STYLE (P81198) Histone H3-4 (Fragment) 39 0.002 H3_ZYGBA (P61836) Histone H3 39 0.003 H3_YEAST (P61830) Histone H3 39 0.003 H3_KLULA (P61831) Histone H3 39 0.003 H32_CANGA (Q8NJS5) Histone H3.2 39 0.003 H31_CANGA (P61833) Histone H3.1 39 0.003 H3_TRIRE (P61835) Histone H3 39 0.004 H3_NEUCR (P07041) Histone H3 39 0.004 H39_STYLE (P81196) Histone H3-2 (Fragment) 39 0.004 H37_STYLE (P81201) Histone H3-7 (Fragment) 39 0.004 H3_EUPCR (P90543) Histone H3 38 0.005 H33_SCHPO (P10651) Histone H3.3 38 0.005 H31_SCHPO (P09988) Histone H3.1/H3.2 38 0.005 H3_PENFN (P61834) Histone H3 37 0.009 H3_EMENI (P23753) Histone H3 37 0.009 H3_ASPFU (P61832) Histone H3 37 0.009 H3_AJECA (Q9P427) Histone H3 37 0.009 H32_XENLA (P02302) Histone H3.2 37 0.009 H3_PSAMI (P02298) Histone H3, embryonic 37 0.011 H3_DROME (P02299) Histone H3 37 0.011 H3_ACRFO (P22843) Histone H3 37 0.011 H3T_HUMAN (Q16695) Histone H3.4 (H3t) (H3/t) (H3/g) 37 0.011 H33_STYLE (P81197) Histone H3-3 (Fragment) 37 0.011 H33_HUMAN (P06351) Histone H3.3 (H3.A) (H3.B) (H3.3Q) 37 0.011 H33_CAEEL (Q10453) Histone H3.3 37 0.011 H32_BOVIN (P16105) Histone H3 (H3.2) 37 0.011 H3_VOLCA (P08437) Histone H3 37 0.015 H3_STRPU (P06352) Histone H3, embryonic 37 0.015 H3_PEA (P02300) Histone H3 37 0.015 H3_MASBA (Q9U7D1) Histone H3 37 0.015 H3_MAIZE (P05203) Histone H3 37 0.015 H3_HORVU (P06353) Histone H3 (Fragment) 37 0.015 H3_ENCAL (P08903) Histone H3 37 0.015 H3_ARATH (P59226) Histone H3 37 0.015 H35_STYLE (P81199) Histone H3-5 (Fragment) 37 0.015 H33_TRIPS (Q8WSF1) Histone H3.3 37 0.015 H33_TETTH (P41353) Histone H3.3 (HV2) 37 0.015 H33_ARATH (P59169) Histone H3.3 37 0.015 H32_TETPY (P15512) Histone H3.2 37 0.015 H32_MEDSA (P11105) Histone H3.2, minor 37 0.015 H31_TETPY (P15511) Histone H3.1 37 0.015 H3_ENTHI (Q06196) Histone H3 36 0.020 H3_CAEEL (P08898) Histone H3 36 0.020 H36_STYLE (P81200) Histone H3-6 (Fragment) 36 0.020 H31_STYLE (P81195) Histone H3-1 (Fragment) 36 0.020 H31_HUMAN (P16106) Histone H3.1 (H3/a) (H3/c) (H3/d) (H3/f) (H3/... 36 0.020 H32_ORYSA (P08860) Histone H3 36 0.026 H34_CAIMO (P06902) Histone H3.4 35 0.033 H38_STYLE (P81202) Histone H3-8 (Fragment) 35 0.033 CSE4_YEAST (P36012) Chromatin associated protein CSE4 34 0.074 >H3_LEIIN (P40285) Histone H3 Length = 129 Score = 48.9 bits (115), Expect = 3e-06 Identities = 23/30 (76%), Positives = 27/30 (90%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QEATE+YIVSL+ADTN ACIH+ RVTI+ Sbjct: 85 ALQEATEAYIVSLMADTNLACIHAKRVTIQ 114 >H3_MORAP (Q9HDN1) Histone H3 Length = 135 Score = 40.4 bits (93), Expect = 0.001 Identities = 19/30 (63%), Positives = 24/30 (80%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QEA+E+Y+VSL DTN A IH+ RVTI+ Sbjct: 91 ALQEASEAYLVSLFEDTNLAAIHAKRVTIQ 120 >H34_STYLE (P81198) Histone H3-4 (Fragment) Length = 112 Score = 39.3 bits (90), Expect = 0.002 Identities = 18/29 (62%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+GRVTI Sbjct: 82 AIQEAAEAYMVGLFEDTNLCAIHAGRVTI 110 >H3_ZYGBA (P61836) Histone H3 Length = 135 Score = 38.9 bits (89), Expect = 0.003 Identities = 18/30 (60%), Positives = 23/30 (76%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ E+Y+VSL DTN A IH+ RVTI+ Sbjct: 91 ALQESVEAYLVSLFEDTNLAAIHAKRVTIQ 120 >H3_YEAST (P61830) Histone H3 Length = 135 Score = 38.9 bits (89), Expect = 0.003 Identities = 18/30 (60%), Positives = 23/30 (76%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ E+Y+VSL DTN A IH+ RVTI+ Sbjct: 91 ALQESVEAYLVSLFEDTNLAAIHAKRVTIQ 120 >H3_KLULA (P61831) Histone H3 Length = 135 Score = 38.9 bits (89), Expect = 0.003 Identities = 18/30 (60%), Positives = 23/30 (76%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ E+Y+VSL DTN A IH+ RVTI+ Sbjct: 91 ALQESVEAYLVSLFEDTNLAAIHAKRVTIQ 120 >H32_CANGA (Q8NJS5) Histone H3.2 Length = 135 Score = 38.9 bits (89), Expect = 0.003 Identities = 18/30 (60%), Positives = 23/30 (76%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ E+Y+VSL DTN A IH+ RVTI+ Sbjct: 91 ALQESVEAYLVSLFEDTNLAAIHAKRVTIQ 120 >H31_CANGA (P61833) Histone H3.1 Length = 135 Score = 38.9 bits (89), Expect = 0.003 Identities = 18/30 (60%), Positives = 23/30 (76%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ E+Y+VSL DTN A IH+ RVTI+ Sbjct: 91 ALQESVEAYLVSLFEDTNLAAIHAKRVTIQ 120 >H3_TRIRE (P61835) Histone H3 Length = 135 Score = 38.5 bits (88), Expect = 0.004 Identities = 18/30 (60%), Positives = 22/30 (73%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ ESY+VSL DTN IH+ RVTI+ Sbjct: 91 ALQESVESYLVSLFEDTNLCAIHAKRVTIQ 120 >H3_NEUCR (P07041) Histone H3 Length = 135 Score = 38.5 bits (88), Expect = 0.004 Identities = 18/30 (60%), Positives = 22/30 (73%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ ESY+VSL DTN IH+ RVTI+ Sbjct: 91 ALQESVESYLVSLFEDTNLCAIHAKRVTIQ 120 >H39_STYLE (P81196) Histone H3-2 (Fragment) Length = 114 Score = 38.5 bits (88), Expect = 0.004 Identities = 18/29 (62%), Positives = 22/29 (75%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN A IH+ RVTI Sbjct: 84 ALQEASEAYLVGLFEDTNLAAIHAKRVTI 112 >H37_STYLE (P81201) Histone H3-7 (Fragment) Length = 114 Score = 38.5 bits (88), Expect = 0.004 Identities = 18/29 (62%), Positives = 22/29 (75%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN A IH+ RVTI Sbjct: 84 ALQEASEAYLVGLFEDTNLAAIHAKRVTI 112 >H3_EUPCR (P90543) Histone H3 Length = 135 Score = 38.1 bits (87), Expect = 0.005 Identities = 18/29 (62%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+VSL DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVSLFEDTNLCAIHAKRVTI 119 >H33_SCHPO (P10651) Histone H3.3 Length = 135 Score = 38.1 bits (87), Expect = 0.005 Identities = 18/30 (60%), Positives = 21/30 (70%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QEA E+Y+VSL DTN IH RVTI+ Sbjct: 91 ALQEAVEAYLVSLFEDTNLCAIHGKRVTIQ 120 >H31_SCHPO (P09988) Histone H3.1/H3.2 Length = 135 Score = 38.1 bits (87), Expect = 0.005 Identities = 18/30 (60%), Positives = 21/30 (70%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QEA E+Y+VSL DTN IH RVTI+ Sbjct: 91 ALQEAVEAYLVSLFEDTNLCAIHGKRVTIQ 120 >H3_PENFN (P61834) Histone H3 Length = 135 Score = 37.4 bits (85), Expect = 0.009 Identities = 17/30 (56%), Positives = 22/30 (73%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ E+Y+VSL DTN IH+ RVTI+ Sbjct: 91 ALQESVEAYLVSLFEDTNLCAIHAKRVTIQ 120 >H3_EMENI (P23753) Histone H3 Length = 135 Score = 37.4 bits (85), Expect = 0.009 Identities = 17/30 (56%), Positives = 22/30 (73%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ E+Y+VSL DTN IH+ RVTI+ Sbjct: 91 ALQESVEAYLVSLFEDTNLCAIHAKRVTIQ 120 >H3_ASPFU (P61832) Histone H3 Length = 135 Score = 37.4 bits (85), Expect = 0.009 Identities = 17/30 (56%), Positives = 22/30 (73%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ E+Y+VSL DTN IH+ RVTI+ Sbjct: 91 ALQESVEAYLVSLFEDTNLCAIHAKRVTIQ 120 >H3_AJECA (Q9P427) Histone H3 Length = 135 Score = 37.4 bits (85), Expect = 0.009 Identities = 17/30 (56%), Positives = 22/30 (73%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTIR 92 A QE+ E+Y+VSL DTN IH+ RVTI+ Sbjct: 91 ALQESVEAYLVSLFEDTNLCAIHAKRVTIQ 120 >H32_XENLA (P02302) Histone H3.2 Length = 135 Score = 37.4 bits (85), Expect = 0.009 Identities = 17/29 (58%), Positives = 22/29 (75%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V+L DTN IH+ RVTI Sbjct: 91 ALQEASEAYLVALFEDTNLCAIHAKRVTI 119 >H3_PSAMI (P02298) Histone H3, embryonic Length = 135 Score = 37.0 bits (84), Expect = 0.011 Identities = 17/29 (58%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEASEAYLVGLFEDTNLCAIHAKRVTI 119 >H3_DROME (P02299) Histone H3 Length = 135 Score = 37.0 bits (84), Expect = 0.011 Identities = 17/29 (58%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEASEAYLVGLFEDTNLCAIHAKRVTI 119 >H3_ACRFO (P22843) Histone H3 Length = 135 Score = 37.0 bits (84), Expect = 0.011 Identities = 17/29 (58%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEASEAYLVGLFEDTNLCAIHAKRVTI 119 >H3T_HUMAN (Q16695) Histone H3.4 (H3t) (H3/t) (H3/g) Length = 135 Score = 37.0 bits (84), Expect = 0.011 Identities = 18/29 (62%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA ESY+V L DTN IH+ RVTI Sbjct: 91 ALQEACESYLVGLFEDTNLCVIHAKRVTI 119 >H33_STYLE (P81197) Histone H3-3 (Fragment) Length = 114 Score = 37.0 bits (84), Expect = 0.011 Identities = 17/29 (58%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN IH+ RVTI Sbjct: 84 ALQEASEAYLVGLFEDTNLCAIHAKRVTI 112 >H33_HUMAN (P06351) Histone H3.3 (H3.A) (H3.B) (H3.3Q) Length = 135 Score = 37.0 bits (84), Expect = 0.011 Identities = 17/29 (58%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEASEAYLVGLFEDTNLCAIHAKRVTI 119 >H33_CAEEL (Q10453) Histone H3.3 Length = 135 Score = 37.0 bits (84), Expect = 0.011 Identities = 17/29 (58%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEASEAYLVGLFEDTNLCAIHAKRVTI 119 >H32_BOVIN (P16105) Histone H3 (H3.2) Length = 135 Score = 37.0 bits (84), Expect = 0.011 Identities = 17/29 (58%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEASEAYLVGLFEDTNLCAIHAKRVTI 119 >H3_VOLCA (P08437) Histone H3 Length = 134 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 90 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 118 >H3_STRPU (P06352) Histone H3, embryonic Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEASEAYLVRLFEDTNLCAIHAKRVTI 119 >H3_PEA (P02300) Histone H3 Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 119 >H3_MASBA (Q9U7D1) Histone H3 Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 119 >H3_MAIZE (P05203) Histone H3 Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 119 >H3_HORVU (P06353) Histone H3 (Fragment) Length = 80 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 36 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 64 >H3_ENCAL (P08903) Histone H3 Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 119 >H3_ARATH (P59226) Histone H3 Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 119 >H35_STYLE (P81199) Histone H3-5 (Fragment) Length = 114 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 84 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 112 >H33_TRIPS (Q8WSF1) Histone H3.3 Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 119 >H33_TETTH (P41353) Histone H3.3 (HV2) Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHARRVTI 119 >H33_ARATH (P59169) Histone H3.3 Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 119 >H32_TETPY (P15512) Histone H3.2 Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHARRVTI 119 >H32_MEDSA (P11105) Histone H3.2, minor Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHAKRVTI 119 >H31_TETPY (P15511) Histone H3.1 Length = 135 Score = 36.6 bits (83), Expect = 0.015 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAEAYLVGLFEDTNLCAIHARRVTI 119 >H3_ENTHI (Q06196) Histone H3 Length = 134 Score = 36.2 bits (82), Expect = 0.020 Identities = 16/29 (55%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ R+TI Sbjct: 90 ALQEAAEAYLVGLFEDTNLCAIHAKRITI 118 >H3_CAEEL (P08898) Histone H3 Length = 135 Score = 36.2 bits (82), Expect = 0.020 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEACEAYLVGLFEDTNLCAIHAKRVTI 119 >H36_STYLE (P81200) Histone H3-6 (Fragment) Length = 114 Score = 36.2 bits (82), Expect = 0.020 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 84 ALQEAAEAYMVGLFEDTNLCAIHAKRVTI 112 >H31_STYLE (P81195) Histone H3-1 (Fragment) Length = 114 Score = 36.2 bits (82), Expect = 0.020 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 84 ALQEAAEAYMVGLFEDTNLCAIHAKRVTI 112 >H31_HUMAN (P16106) Histone H3.1 (H3/a) (H3/c) (H3/d) (H3/f) (H3/h) (H3/i) (H3/j) (H3/k) (H3/l) Length = 135 Score = 36.2 bits (82), Expect = 0.020 Identities = 17/29 (58%), Positives = 20/29 (68%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y+V L DTN IH+ RVTI Sbjct: 91 ALQEACEAYLVGLFEDTNLCAIHAKRVTI 119 >H32_ORYSA (P08860) Histone H3 Length = 135 Score = 35.8 bits (81), Expect = 0.026 Identities = 17/29 (58%), Positives = 19/29 (65%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E Y+V L DTN IH+ RVTI Sbjct: 91 ALQEAAERYLVGLFEDTNLCAIHAKRVTI 119 >H34_CAIMO (P06902) Histone H3.4 Length = 135 Score = 35.4 bits (80), Expect = 0.033 Identities = 16/29 (55%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V L DTN IH+ RV+I Sbjct: 91 ALQEASEAYLVGLFEDTNLCAIHAKRVSI 119 >H38_STYLE (P81202) Histone H3-8 (Fragment) Length = 113 Score = 35.4 bits (80), Expect = 0.033 Identities = 16/29 (55%), Positives = 19/29 (65%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA E+Y++ L DTN IH RVTI Sbjct: 83 ALQEAAEAYMIGLFEDTNLCAIHGKRVTI 111 >CSE4_YEAST (P36012) Chromatin associated protein CSE4 Length = 229 Score = 34.3 bits (77), Expect = 0.074 Identities = 15/29 (51%), Positives = 21/29 (72%) Frame = +3 Query: 3 AAQEATESYIVSLLADTNRACIHSGRVTI 89 A QEA+E+Y+V LL TN +H+ R+TI Sbjct: 185 ALQEASEAYLVGLLEHTNLLALHAKRITI 213 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 24,147,113 Number of Sequences: 153871 Number of extensions: 369287 Number of successful extensions: 1085 Number of sequences better than 1.0e-01: 52 Number of HSP's better than 0.1 without gapping: 1074 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1085 length of database: 56,608,159 effective HSP length: 58 effective length of database: 47,683,641 effective search space used: 1382825589 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 359 (655 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 75,532,952 Number of Sequences: 153871 Number of extensions: 1880802 Number of successful extensions: 8047 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 7056 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 8002 length of database: 56,608,159 effective HSP length: 105 effective length of database: 40,451,704 effective search space used: 4530590848 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 360 (849 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 84,237,694 Number of Sequences: 153871 Number of extensions: 1733875 Number of successful extensions: 4379 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 4232 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 4379 length of database: 56,608,159 effective HSP length: 108 effective length of database: 39,990,091 effective search space used: 6958275834 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 361 (681 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value H4_PHYPO (P04915) Histone H4 71 2e-12 H4_WHEAT (P59258) Histone H4 70 4e-12 H4_OLILU (P82888) Histone H4 70 4e-12 H4_NEUCR (P04914) Histone H4 70 4e-12 H4_ARATH (P59259) Histone H4 70 4e-12 H41_EMENI (P23750) Histone H4.1 70 4e-12 H42_TETPY (P02311) Histone H4, minor 69 7e-12 H41_TETPY (P02310) Histone H4, major 69 7e-12 H4_LYCES (P35057) Histone H4 69 1e-11 H4_HUMAN (P02304) Histone H4 69 1e-11 H4_DROME (P02307) Histone H4 69 1e-11 H4_ACRFO (P35059) Histone H4 69 1e-11 H42_EMENI (P23751) Histone H4.2 69 1e-11 H4_MASBA (Q9U7D0) Histone H4 69 1e-11 H4_ENTHI (P40287) Histone H4 68 2e-11 H4_YEAST (P02309) Histone H4 67 4e-11 H4_VOLCA (P08436) Histone H4 67 4e-11 H4_CHLRE (P50566) Histone H4 67 4e-11 H4_CAEEL (P02306) Histone H4 67 5e-11 H4_EUPCR (P80739) Histone H4 66 6e-11 H4_PHACH (P35058) Histone H4 66 8e-11 H4_SOLST (P27996) Histone H4 65 1e-10 H4_OXYNO (P18836) Histone H4 65 1e-10 H4_ASCSU (Q27443) Histone H4 63 5e-10 H4_SCHPO (P09322) Histone H4 62 9e-10 H41_BLEJA (P80737) Histone H4-1 (Fragment) 60 3e-09 H42_BLEJA (P90516) Histone H4 (Fragment) 58 2e-08 >H4_PHYPO (P04915) Histone H4 Length = 102 Score = 71.2 bits (173), Expect = 2e-12 Identities = 31/49 (63%), Positives = 43/49 (87%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK+F+E V+RDA YTE++R+KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKTFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 100 >H4_WHEAT (P59258) Histone H4 Length = 102 Score = 70.1 bits (170), Expect = 4e-12 Identities = 31/49 (63%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RDA YTE++R+KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 100 >H4_OLILU (P82888) Histone H4 Length = 102 Score = 70.1 bits (170), Expect = 4e-12 Identities = 31/49 (63%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RDA YTE++R+KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKVFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 100 >H4_NEUCR (P04914) Histone H4 Length = 102 Score = 70.1 bits (170), Expect = 4e-12 Identities = 29/49 (59%), Positives = 44/49 (89%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK+F+EGV+RDA YTE++++KTVT++DVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKTFLEGVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTLYGF 100 >H4_ARATH (P59259) Histone H4 Length = 102 Score = 70.1 bits (170), Expect = 4e-12 Identities = 31/49 (63%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RDA YTE++R+KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 100 >H41_EMENI (P23750) Histone H4.1 Length = 102 Score = 70.1 bits (170), Expect = 4e-12 Identities = 29/49 (59%), Positives = 44/49 (89%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK+F+EGV+RDA YTE++++KTVT++DVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKTFLEGVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTLYGF 100 >H42_TETPY (P02311) Histone H4, minor Length = 102 Score = 69.3 bits (168), Expect = 7e-12 Identities = 32/49 (65%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 D+ R VLKSF+E VVRDA YTE++R+KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 DDSRQVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 100 >H41_TETPY (P02310) Histone H4, major Length = 102 Score = 69.3 bits (168), Expect = 7e-12 Identities = 32/49 (65%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 D+ R VLKSF+E VVRDA YTE++R+KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 DDSRQVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 100 >H4_LYCES (P35057) Histone H4 Length = 102 Score = 68.9 bits (167), Expect = 1e-11 Identities = 30/49 (61%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RD+ YTE++R+KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKIFLENVIRDSVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 100 >H4_HUMAN (P02304) Histone H4 Length = 102 Score = 68.9 bits (167), Expect = 1e-11 Identities = 30/49 (61%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RDA YTE++++KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF 100 >H4_DROME (P02307) Histone H4 Length = 102 Score = 68.9 bits (167), Expect = 1e-11 Identities = 30/49 (61%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RDA YTE++++KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF 100 >H4_ACRFO (P35059) Histone H4 Length = 102 Score = 68.9 bits (167), Expect = 1e-11 Identities = 30/49 (61%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RDA YTE++++KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF 100 >H42_EMENI (P23751) Histone H4.2 Length = 102 Score = 68.9 bits (167), Expect = 1e-11 Identities = 29/49 (59%), Positives = 43/49 (87%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLKSF+E V+RDA YTE++++KTVT++DVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKSFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTLYGF 100 >H4_MASBA (Q9U7D0) Histone H4 Length = 107 Score = 68.9 bits (167), Expect = 1e-11 Identities = 30/49 (61%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RD+ YTE++R+KTVTAMDVV AL+++G+ LYG+ Sbjct: 57 EETRGVLKVFLENVIRDSVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 105 >H4_ENTHI (P40287) Histone H4 Length = 118 Score = 67.8 bits (164), Expect = 2e-11 Identities = 29/50 (58%), Positives = 42/50 (84%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGYA 150 DE R VLK F+E V+RD+ YTE+++++TVTAMDVV AL+++G+ LYGY+ Sbjct: 69 DETRNVLKQFLEQVIRDSVTYTEHAKRRTVTAMDVVYALKRQGRTLYGYS 118 >H4_YEAST (P02309) Histone H4 Length = 102 Score = 67.0 bits (162), Expect = 4e-11 Identities = 28/49 (57%), Positives = 43/49 (87%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +EVR VLKSF+E V+RD+ YTE++++KTVT++DVV AL+++G+ LYG+ Sbjct: 52 EEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGF 100 >H4_VOLCA (P08436) Histone H4 Length = 102 Score = 67.0 bits (162), Expect = 4e-11 Identities = 29/49 (59%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E R VLK+F+E V+RD+ YTE++R+KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRTVLKNFLENVIRDSVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 100 >H4_CHLRE (P50566) Histone H4 Length = 102 Score = 67.0 bits (162), Expect = 4e-11 Identities = 29/49 (59%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E R VLK+F+E V+RD+ YTE++R+KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRTVLKTFLENVIRDSVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 100 >H4_CAEEL (P02306) Histone H4 Length = 102 Score = 66.6 bits (161), Expect = 5e-11 Identities = 29/49 (59%), Positives = 41/49 (83%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RDA Y E++++KTVTAMDVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKVFLENVIRDAVTYCEHAKRKTVTAMDVVYALKRQGRTLYGF 100 >H4_EUPCR (P80739) Histone H4 Length = 106 Score = 66.2 bits (160), Expect = 6e-11 Identities = 28/49 (57%), Positives = 41/49 (83%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E R VLK F+E V+RD+ YTE++++KTVTA+DVV AL+++GK LYG+ Sbjct: 56 EETRAVLKGFLESVIRDSVTYTEHAKRKTVTALDVVYALKRQGKTLYGF 104 >H4_PHACH (P35058) Histone H4 Length = 102 Score = 65.9 bits (159), Expect = 8e-11 Identities = 28/49 (57%), Positives = 41/49 (83%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RD+ YTE++++KTVTA+DVV AL++ G+ LYG+ Sbjct: 52 EETRGVLKIFLENVIRDSVTYTEHAKRKTVTALDVVYALKRSGRTLYGF 100 >H4_SOLST (P27996) Histone H4 Length = 102 Score = 65.5 bits (158), Expect = 1e-10 Identities = 28/49 (57%), Positives = 41/49 (83%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E RGVLK F+E V+RDA Y E++++KTVT+MDVV AL+++G+ LYG+ Sbjct: 52 EETRGVLKVFLENVIRDAVTYCEHAKRKTVTSMDVVYALKRQGRTLYGF 100 >H4_OXYNO (P18836) Histone H4 Length = 103 Score = 65.5 bits (158), Expect = 1e-10 Identities = 27/49 (55%), Positives = 42/49 (85%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E R VL+SF+E V+RD+ YTE++++KTVTA+DVV AL+++G+ LYG+ Sbjct: 53 EETRNVLRSFLENVIRDSVTYTEHAKRKTVTALDVVYALKRQGRTLYGF 101 >H4_ASCSU (Q27443) Histone H4 Length = 102 Score = 63.2 bits (152), Expect = 5e-10 Identities = 28/49 (57%), Positives = 39/49 (79%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E R VLK F+E V+RDA Y E++++KTVTAMDVV AL+ +G+ LYG+ Sbjct: 52 EETRSVLKVFLENVIRDAVTYCEHAKRKTVTAMDVVYALKHQGRTLYGF 100 >H4_SCHPO (P09322) Histone H4 Length = 102 Score = 62.4 bits (150), Expect = 9e-10 Identities = 25/49 (51%), Positives = 41/49 (83%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRGKILYGY 147 +E R VLK F+E V+RDA YTE++++KTVT++DVV +L+++G+ +YG+ Sbjct: 52 EETRAVLKLFLENVIRDAVTYTEHAKRKTVTSLDVVYSLKRQGRTIYGF 100 >H41_BLEJA (P80737) Histone H4-1 (Fragment) Length = 97 Score = 60.5 bits (145), Expect = 3e-09 Identities = 28/43 (65%), Positives = 36/43 (83%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRG 129 DE R VLK F+E VVRDA YTE++R+KTVTA+DVV AL+++G Sbjct: 55 DETRNVLKVFLENVVRDAVTYTEHARRKTVTALDVVYALKRQG 97 >H42_BLEJA (P90516) Histone H4 (Fragment) Length = 89 Score = 57.8 bits (138), Expect = 2e-08 Identities = 26/43 (60%), Positives = 36/43 (83%) Frame = +1 Query: 1 DEVRGVLKSFVEGVVRDATAYTEYSRKKTVTAMDVVNALRKRG 129 DE R VLK F+E VVRDA YTE+++++TVTA+DVV AL+++G Sbjct: 47 DETRNVLKVFLESVVRDAVTYTEHAKRETVTALDVVYALKRQG 89 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 50,751,947 Number of Sequences: 153871 Number of extensions: 832357 Number of successful extensions: 2958 Number of sequences better than 1.0e-01: 27 Number of HSP's better than 0.1 without gapping: 2832 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2953 length of database: 56,608,159 effective HSP length: 105 effective length of database: 40,451,704 effective search space used: 4894656184 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 362 (457 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value POLR_ELV (P35928) RNA replicase polyprotein (EC 2.7.7.48) 36 0.039 >POLR_ELV (P35928) RNA replicase polyprotein (EC 2.7.7.48) Length = 1748 Score = 35.8 bits (81), Expect = 0.039 Identities = 22/71 (30%), Positives = 35/71 (49%) Frame = +3 Query: 18 ILIQCRSTRLPNTYLINPSTHPTINTSSHPTHLNHAPPHYLKSTPTPGRLYYTNPSRTPT 197 +L+ S+ LP++ L P P+I + HP PP + PTP L +PS+T Sbjct: 552 LLLDSHSSFLPSSCL-QPPASPSIAAAPHPLPPAQKPPRPPTTVPTPKPL--ASPSQTQA 608 Query: 198 SLPKPQKPRNL 230 + P Q P ++ Sbjct: 609 AQPATQSPPSI 619 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 49,093,013 Number of Sequences: 153871 Number of extensions: 1095043 Number of successful extensions: 3761 Number of sequences better than 1.0e-01: 1 Number of HSP's better than 0.1 without gapping: 3302 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 3627 length of database: 56,608,159 effective HSP length: 100 effective length of database: 41,221,059 effective search space used: 2102274009 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 363 (142 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 11,802,194 Number of Sequences: 153871 Number of extensions: 127135 Number of successful extensions: 238 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 238 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 238 length of database: 56,608,159 effective HSP length: 20 effective length of database: 53,530,739 effective search space used: 1391799214 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 364 (488 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 52,771,233 Number of Sequences: 153871 Number of extensions: 1095257 Number of successful extensions: 3235 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 3171 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 3234 length of database: 56,608,159 effective HSP length: 101 effective length of database: 41,067,188 effective search space used: 2505098468 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 365 (1079 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value CYAA_YEAST (P08678) Adenylate cyclase (EC 4.6.1.1) (ATP pyrophos... 37 0.082 >CYAA_YEAST (P08678) Adenylate cyclase (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase) Length = 2026 Score = 37.0 bits (84), Expect = 0.082 Identities = 23/115 (20%), Positives = 53/115 (46%) Frame = -2 Query: 874 GELAFLYCKASGLNTISKLVSDDMFTEVCGSYNCVVQETVLANNGFIAKTDSHSAYIIVF 695 G LA ++ + +L + M T + ++N +++ + G+ KT+ A+++ F Sbjct: 1665 GNLAMVFTDIKSSTFLWELFPNAMRTAI-KTHNDIMRRQLRIYGGYEVKTEG-DAFMVAF 1722 Query: 694 NDIYQAVNTARKIQLGLMAVDWPSKILTLEASLRVKSIKTGMLLFNGIRAMTAIH 530 + +QL L+ WP +I +++ +V + G +++ G+ IH Sbjct: 1723 PTPTSGLTWCLSVQLKLLDAQWPEEITSVQDGCQVTD-RNGNIIYQGLSVRMGIH 1776 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 110,002,023 Number of Sequences: 153871 Number of extensions: 2351998 Number of successful extensions: 6659 Number of sequences better than 1.0e-01: 1 Number of HSP's better than 0.1 without gapping: 5930 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 6591 length of database: 56,608,159 effective HSP length: 110 effective length of database: 39,682,349 effective search space used: 9880904901 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 366 (444 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ORB6_SCHPO (O13310) Serine/threonine-protein kinase orb6 (EC 2.7... 91 1e-18 CBK1_YEAST (P53894) Serine/threonine-protein kinase CBK1 (EC 2.7... 86 2e-17 GAD8_SCHPO (Q9P7J8) Serine/threonine-protein kinase gad8 (EC 2.7... 85 7e-17 COT1_NEUCR (P38679) Serine/threonine-protein kinase cot-1 (EC 2.... 83 3e-16 ROC1_RABIT (O77819) Rho-associated protein kinase 1 (EC 2.7.1.37... 79 3e-15 ROC1_MOUSE (P70335) Rho-associated protein kinase 1 (EC 2.7.1.37... 79 3e-15 ROC1_HUMAN (Q13464) Rho-associated protein kinase 1 (EC 2.7.1.37... 79 3e-15 ROC1_RAT (Q63644) Rho-associated protein kinase 1 (EC 2.7.1.37) ... 79 3e-15 ROC2_MOUSE (P70336) Rho-associated protein kinase 2 (EC 2.7.1.37... 78 6e-15 ROC2_BOVIN (Q28021) Rho-associated protein kinase 2 (EC 2.7.1.37... 78 6e-15 ROC2_RAT (Q62868) Rho-associated protein kinase 2 (EC 2.7.1.37) ... 78 6e-15 ROC2_HUMAN (O75116) Rho-associated protein kinase 2 (EC 2.7.1.37... 77 1e-14 YPK1_YEAST (P12688) Serine/threonine-protein kinase YPK1 (EC 2.7... 75 5e-14 RI15_YEAST (P43565) Serine/threonine-protein kinase RIM15 (EC 2.... 75 7e-14 YPK2_YEAST (P18961) Serine/threonine-protein kinase YPK2/YKR2 (E... 74 9e-14 KAPC_CAEEL (P21137) cAMP-dependent protein kinase catalytic subu... 74 2e-13 DMK_MOUSE (P54265) Myotonin-protein kinase (EC 2.7.1.-) (Myotoni... 72 4e-13 KGP3_DROME (P32023) cGMP-dependent protein kinase, isozyme 2 for... 72 6e-13 KGP2_DROME (Q03043) cGMP-dependent protein kinase, isozyme 2 for... 72 6e-13 KN8R_YEAST (P53739) Probable serine/threonine-protein kinase YNR... 72 6e-13 KDC2_DROME (P16912) Protein kinase DC2 (EC 2.7.1.-) 71 8e-13 CDP2_PLAF7 (Q8ICR0) Calcium-dependent protein kinase 2 (EC 2.7.1... 71 8e-13 KAPC_DICDI (P34099) cAMP-dependent protein kinase catalytic subu... 71 8e-13 DMK_HUMAN (Q09013) Myotonin-protein kinase (EC 2.7.1.-) (Myotoni... 71 8e-13 PRKX_MOUSE (Q922R0) Serine/threonine-protein kinase PRKX (EC 2.7... 71 8e-13 CDP2_PLAFK (O15865) Calcium-dependent protein kinase 2 (EC 2.7.1... 71 8e-13 KAPA_CANFA (Q8MJ44) cAMP-dependent protein kinase, alpha-catalyt... 70 1e-12 PRKY_HUMAN (O43930) Serine/threonine-protein kinase PRKY (EC 2.7... 70 1e-12 KAPI_BOVIN (P24256) cAMP-dependent protein kinase, beta-2-cataly... 70 1e-12 KAPB_PIG (P05383) cAMP-dependent protein kinase, beta-catalytic ... 70 1e-12 KAPB_MOUSE (P05206) cAMP-dependent protein kinase, beta-catalyti... 70 1e-12 KAPB_HUMAN (P22694) cAMP-dependent protein kinase, beta-catalyti... 70 1e-12 KAPB_BOVIN (P05131) cAMP-dependent protein kinase, beta-1 cataly... 70 1e-12 KAPA_SHEEP (Q9MZD9) cAMP-dependent protein kinase, alpha-catalyt... 70 1e-12 KAPA_RAT (P27791) cAMP-dependent protein kinase, alpha-catalytic... 70 1e-12 KAPA_PIG (P36887) cAMP-dependent protein kinase, alpha-catalytic... 70 1e-12 KAPA_MOUSE (P05132) cAMP-dependent protein kinase, alpha-catalyt... 70 1e-12 KAPA_HUMAN (P17612) cAMP-dependent protein kinase, alpha-catalyt... 70 1e-12 KAPA_CRIGR (P25321) cAMP-dependent protein kinase, alpha-catalyt... 70 1e-12 KAPA_BOVIN (P00517) cAMP-dependent protein kinase, alpha-catalyt... 70 1e-12 PRKX_HUMAN (P51817) Serine/threonine-protein kinase PRKX (EC 2.7... 69 3e-12 KAPG_HUMAN (P22612) cAMP-dependent protein kinase, gamma-catalyt... 69 3e-12 KAPB_YEAST (P06245) cAMP-dependent protein kinase type 2 (EC 2.7... 69 3e-12 KRAC_DICDI (P54644) RAC-family serine/threonine-protein kinase h... 69 3e-12 PK2_DICDI (P28178) Protein kinase 2 (EC 2.7.1.-) 69 4e-12 KAPC_DROME (P12370) cAMP-dependent protein kinase catalytic subu... 69 5e-12 KGPB_MOUSE (Q9Z0Z0) cGMP-dependent protein kinase 1, beta isozym... 68 7e-12 KGPB_HUMAN (P14619) cGMP-dependent protein kinase 1, beta isozym... 68 7e-12 KGPB_BOVIN (P21136) cGMP-dependent protein kinase 1, beta isozym... 68 7e-12 KGPA_RABIT (O77676) cGMP-dependent protein kinase 1, alpha isozy... 68 7e-12 KGPA_HUMAN (Q13976) cGMP-dependent protein kinase 1, alpha isozy... 68 7e-12 KGPA_BOVIN (P00516) cGMP-dependent protein kinase 1, alpha isozy... 68 7e-12 KAPC_YEAST (P05986) cAMP-dependent protein kinase type 3 (EC 2.7... 68 7e-12 KAPA_YEAST (P06244) cAMP-dependent protein kinase type 1 (EC 2.7... 68 9e-12 SGK1_RAT (Q06226) Serine/threonine-protein kinase Sgk1 (EC 2.7.1... 68 9e-12 KGP2_HUMAN (Q13237) cGMP-dependent protein kinase 2 (EC 2.7.1.37... 68 9e-12 KPCN_HUMAN (O94806) Protein kinase C, nu type (EC 2.7.1.-) (nPKC... 67 1e-11 KGP2_RAT (Q64595) cGMP-dependent protein kinase 2 (EC 2.7.1.37) ... 67 1e-11 KGP2_MOUSE (Q61410) cGMP-dependent protein kinase 2 (EC 2.7.1.37... 67 1e-11 KAPB_SCHPO (P40376) cAMP-dependent protein kinase catalytic subu... 67 1e-11 DBF2_YEAST (P22204) Cell cycle protein kinase DBF2 (EC 2.7.1.37) 67 1e-11 DBFB_YEAST (P32328) Serine/threonine-protein kinase DBF20 (EC 2.... 67 2e-11 NPH1_ARATH (O48963) Nonphototropic hypocotyl protein 1 (EC 2.7.1... 66 3e-11 SGK1_RABIT (Q9XT18) Serine/threonine-protein kinase Sgk1 (EC 2.7... 66 3e-11 SGK1_MOUSE (Q9WVC6) Serine/threonine-protein kinase Sgk1 (EC 2.7... 66 3e-11 PLO1_SCHPO (P50528) Serine/threonine-protein kinase plo1 (EC 2.7... 65 4e-11 KI82_YEAST (P25341) Probable serine/threonine-protein kinase KIN... 65 6e-11 KPCD_MOUSE (P28867) Protein kinase C, delta type (EC 2.7.1.-) (n... 65 7e-11 SGK1_HUMAN (O00141) Serine/threonine-protein kinase Sgk1 (EC 2.7... 65 7e-11 KPCM_MOUSE (Q62101) Protein kinase C, mu type (EC 2.7.1.-) (nPKC... 64 1e-10 CEK1_SCHPO (P38938) Serine/threonine-protein kinase cek1 (EC 2.7... 64 1e-10 KPCM_HUMAN (Q15139) Protein kinase C, mu type (EC 2.7.1.-) (nPKC... 64 1e-10 CDP3_PLAYO (Q7RAV5) Calcium-dependent protein kinase 3 (EC 2.7.1... 64 1e-10 KPCT_HUMAN (Q04759) Protein kinase C, theta type (EC 2.7.1.-) (n... 64 2e-10 KMLC_DICDI (P25323) Myosin light chain kinase (EC 2.7.1.117) (MLCK) 64 2e-10 NRC2_NEUCR (O42626) Serine/threonine-protein kinase nrc-2 (EC 2.... 64 2e-10 SID2_SCHPO (Q09898) Serine/threonine-protein kinase sid2 (EC 2.7... 63 3e-10 KPK1_ARATH (P42818) Serine/threonine-protein kinase AtPK1/AtPK6 ... 63 3e-10 KP19_ARATH (Q39030) Serine/threonine-protein kinase AtPK19 (EC 2... 63 3e-10 KPCD_RAT (P09215) Protein kinase C, delta type (EC 2.7.1.-) (nPK... 63 3e-10 KPC1_CAEEL (P34722) Protein kinase C-like 1 (EC 2.7.1.-) (PKC) (... 63 3e-10 KGP1_DROME (Q03042) cGMP-dependent protein kinase, isozyme 1 (EC... 63 3e-10 KPCD_HUMAN (Q05655) Protein kinase C, delta type (EC 2.7.1.-) (n... 62 4e-10 KPCT_MOUSE (Q02111) Protein kinase C, theta type (EC 2.7.1.-) (n... 62 4e-10 SGK3_MOUSE (Q9ERE3) Serine/threonine-protein kinase Sgk3 (EC 2.7... 62 4e-10 SGK3_HUMAN (Q96BR1) Serine/threonine-protein kinase Sgk3 (EC 2.7... 62 4e-10 DUN1_YEAST (P39009) DNA damage response protein kinase DUN1 (EC ... 62 5e-10 CHK2_HUMAN (O96017) Serine/threonine-protein kinase Chk2 (EC 2.7... 62 5e-10 AKT3_RAT (Q63484) RAC-gamma serine/threonine-protein kinase (EC ... 62 6e-10 KCC1_HUMAN (Q14012) Calcium/calmodulin-dependent protein kinase ... 62 6e-10 SGK2_RAT (Q8R4U9) Serine/threonine-protein kinase Sgk2 (EC 2.7.1... 62 6e-10 MKK2_MOUSE (P49138) MAP kinase-activated protein kinase 2 (EC 2.... 62 6e-10 MKK2_CRILO (P49136) MAP kinase-activated protein kinase 2 (EC 2.... 62 6e-10 SGK2_MOUSE (Q9QZS5) Serine/threonine-protein kinase Sgk2 (EC 2.7... 62 6e-10 SGK2_HUMAN (Q9HBY8) Serine/threonine-protein kinase Sgk2 (EC 2.7... 62 6e-10 KAPC_ASCSU (P49673) cAMP-dependent protein kinase catalytic subu... 62 6e-10 CDP3_PLAF7 (Q9NJU9) Calcium-dependent protein kinase 3 (EC 2.7.1... 62 6e-10 KCC1_RAT (Q63450) Calcium/calmodulin-dependent protein kinase ty... 62 6e-10 KCC1_MOUSE (Q91YS8) Calcium/calmodulin-dependent protein kinase ... 62 6e-10 CHK2_MOUSE (Q9Z265) Serine/threonine-protein kinase Chk2 (EC 2.7... 62 6e-10 AKT3_MOUSE (Q9WUA6) RAC-gamma serine/threonine-protein kinase (E... 62 6e-10 AKT3_HUMAN (Q9Y243) RAC-gamma serine/threonine-protein kinase (E... 62 6e-10 MKK2_HUMAN (P49137) MAP kinase-activated protein kinase 2 (EC 2.... 62 6e-10 KPCO_HUMAN (Q9BZL6) Protein kinase C, D2 type (EC 2.7.1.-) (nPKC... 62 6e-10 KBN8_YEAST (P38070) Probable serine/threonine-protein kinase YBR... 61 8e-10 KRAC_BOVIN (Q01314) RAC-alpha serine/threonine-protein kinase (E... 61 1e-09 KPK7_ARATH (Q05999) Putative serine/threonine-protein kinase PK7... 61 1e-09 K6A6_HUMAN (Q9UK32) Ribosomal protein S6 kinase alpha 6 (EC 2.7.... 61 1e-09 CDP1_PLAFK (P62343) Calcium-dependent protein kinase 1 (EC 2.7.1... 61 1e-09 CDP1_PLAF7 (P62344) Calcium-dependent protein kinase 1 (EC 2.7.1... 61 1e-09 CDP1_PLAYO (Q7RAH3) Calcium-dependent protein kinase 1 (EC 2.7.1... 60 1e-09 K6A5_MOUSE (Q8C050) Ribosomal protein S6 kinase alpha 5 (EC 2.7.... 60 2e-09 APG1_YEAST (P53104) Autophagy serine/threonine-protein kinase AP... 60 2e-09 KPCA_RAT (P05696) Protein kinase C, alpha type (EC 2.7.1.37) (PK... 60 2e-09 KPCA_RABIT (P10102) Protein kinase C, alpha type (EC 2.7.1.37) (... 60 2e-09 KPCA_MOUSE (P20444) Protein kinase C, alpha type (EC 2.7.1.37) (... 60 2e-09 KPCA_HUMAN (P17252) Protein kinase C, alpha type (EC 2.7.1.37) (... 60 2e-09 KPCA_BOVIN (P04409) Protein kinase C, alpha type (EC 2.7.1.37) (... 60 2e-09 KPC2_APLCA (Q16975) Calcium-independent protein kinase C (EC 2.7... 60 2e-09 AKT2_HUMAN (P31751) RAC-beta serine/threonine-protein kinase (EC... 60 2e-09 CDP1_ORYSA (P53682) Calcium-dependent protein kinase, isoform 1 ... 60 2e-09 KRAC_RAT (P47196) RAC-alpha serine/threonine-protein kinase (EC ... 59 3e-09 KRAC_HUMAN (P31749) RAC-alpha serine/threonine-protein kinase (E... 59 3e-09 MKK2_RABIT (P49139) MAP kinase-activated protein kinase 2 (EC 2.... 59 3e-09 KPK1_PHAVU (P15792) Protein kinase PVPK-1 (EC 2.7.1.-) 59 3e-09 KAKT_MLVAT (P31748) AKT kinase transforming protein (EC 2.7.1.-) 59 3e-09 K6A5_HUMAN (O75582) Ribosomal protein S6 kinase alpha 5 (EC 2.7.... 59 3e-09 KPCZ_RAT (P09217) Protein kinase C, zeta type (EC 2.7.1.37) (nPK... 59 5e-09 KPCZ_MOUSE (Q02956) Protein kinase C, zeta type (EC 2.7.1.37) (n... 59 5e-09 KPCZ_HUMAN (Q05513) Protein kinase C, zeta type (EC 2.7.1.37) (n... 59 5e-09 PKC2_CAEEL (P90980) Protein kinase C-like 2 (EC 2.7.1.-) (PKC2) 59 5e-09 KPCG_BOVIN (P05128) Protein kinase C, gamma type (EC 2.7.1.37) (... 59 5e-09 KPCI_HUMAN (P41743) Protein kinase C, iota type (EC 2.7.1.37) (n... 59 5e-09 KPCG_RABIT (P10829) Protein kinase C, gamma type (EC 2.7.1.37) (... 59 5e-09 KPCG_MOUSE (P05697) Protein kinase C, gamma type (EC 2.7.1.37) (... 59 5e-09 KPCG_HUMAN (P05129) Protein kinase C, gamma type (EC 2.7.1.37) (... 59 5e-09 KPCI_BRARE (Q90XF2) Protein kinase C, iota type (EC 2.7.1.37) (n... 59 5e-09 KPCZ_RABIT (O19111) Protein kinase C, zeta type (EC 2.7.1.37) (n... 59 5e-09 KPCI_MOUSE (Q62074) Protein kinase C, iota type (EC 2.7.1.37) (n... 59 5e-09 KRAC_MOUSE (P31750) RAC-alpha serine/threonine-protein kinase (E... 58 7e-09 K6A1_RAT (Q63531) Ribosomal protein S6 kinase alpha 1 (EC 2.7.1.... 58 7e-09 KPC1_APLCA (Q16974) Calcium-dependent protein kinase C (EC 2.7.1... 58 7e-09 K6B2_HUMAN (Q9UBS0) Ribosomal protein S6 kinase beta 2 (EC 2.7.1... 58 7e-09 MKK2_DROME (P49071) MAP kinase-activated protein kinase 2 (EC 2.... 58 7e-09 K6B2_MOUSE (Q9Z1M4) Ribosomal protein S6 kinase beta 2 (EC 2.7.1... 58 7e-09 AKT2_RAT (P47197) RAC-beta serine/threonine-protein kinase (EC 2... 58 7e-09 AKT2_MOUSE (Q60823) RAC-beta serine/threonine-protein kinase (EC... 58 7e-09 SRK1_SCHPO (O94547) Serine/threonine-protein kinase srk1 (EC 2.7... 58 7e-09 K6B1_RAT (P21425) Ribosomal protein S6 kinase I (EC 2.7.1.37) (S... 58 9e-09 K6B1_HUMAN (P23443) Ribosomal protein S6 kinase (EC 2.7.1.37) (S... 58 9e-09 KDBE_SCHPO (Q10364) Putative serine/threonine-protein kinase C22... 58 9e-09 KPC1_DROME (P05130) Protein kinase C, brain isozyme (EC 2.7.1.-)... 58 9e-09 KPC1_CANAL (P43057) Protein kinase C-like 1 (EC 2.7.1.-) (PKC 1) 58 9e-09 KPC2_DROME (P13677) Protein kinase C, eye isozyme (EC 2.7.1.-) (... 57 1e-08 KPCB_CAEEL (P34885) Protein kinase C-like 1B (EC 2.7.1.-) (PKC1B) 57 1e-08 KCCA_MOUSE (P11798) Calcium/calmodulin-dependent protein kinase ... 57 1e-08 KPC3_DROME (P13678) Protein kinase C (EC 2.7.1.-) (PKC) (dPKC98F) 57 1e-08 G11A_ORYSA (P47997) Protein kinase G11A (EC 2.7.1.-) (Fragment) 57 1e-08 K6A1_HUMAN (Q15418) Ribosomal protein S6 kinase alpha 1 (EC 2.7.... 57 2e-08 K6A1_MOUSE (P18653) Ribosomal protein S6 kinase alpha 1 (EC 2.7.... 57 2e-08 KPCB_BOVIN (P05126) Protein kinase C, beta type (EC 2.7.1.37) (P... 57 2e-08 K6A2_MOUSE (Q9WUT3) Ribosomal protein S6 kinase alpha 2 (EC 2.7.... 57 2e-08 K6A2_HUMAN (Q15349) Ribosomal protein S6 kinase alpha 2 (EC 2.7.... 57 2e-08 KAD5_SCHPO (Q09831) Probable serine/threonine-protein kinase C4G... 57 2e-08 IPL1_YEAST (P38991) Serine/threonine-protein kinase IPL1 (EC 2.7... 57 2e-08 KPCE_RABIT (P10830) Protein kinase C, epsilon type (EC 2.7.1.-) ... 57 2e-08 KPCE_RAT (P09216) Protein kinase C, epsilon type (EC 2.7.1.-) (n... 57 2e-08 KPCE_MOUSE (P16054) Protein kinase C, epsilon type (EC 2.7.1.-) ... 57 2e-08 KPCE_HUMAN (Q02156) Protein kinase C, epsilon type (EC 2.7.1.-) ... 57 2e-08 K6AA_XENLA (P10665) Ribosomal protein S6 kinase II alpha (EC 2.7... 56 3e-08 KPSH_HUMAN (P11801) Serine/threonine-protein kinase H1 (EC 2.7.1... 56 3e-08 PKL1_MOUSE (P70268) Protein kinase C-like 1 (EC 2.7.1.-) (Protei... 56 3e-08 PKL1_HUMAN (Q16512) Protein kinase C-like 1 (EC 2.7.1.-) (Protei... 56 3e-08 KPC1_LYTPI (Q25378) Protein kinase C (EC 2.7.1.-) 56 3e-08 KPC4_DROME (P83099) Putative protein kinase C, delta type homolo... 56 3e-08 KPCB_RABIT (P05772) Protein kinase C, beta type (EC 2.7.1.37) (P... 56 3e-08 KPCB_MOUSE (P04410) Protein kinase C, beta type (EC 2.7.1.37) (P... 56 3e-08 KPCB_HUMAN (P05771) Protein kinase C, beta type (EC 2.7.1.37) (P... 56 3e-08 AURC_HUMAN (Q9UQB9) Serine/threonine-protein kinase 13 (EC 2.7.1... 55 4e-08 PKL1_RAT (Q63433) Protein kinase C-like 1 (EC 2.7.1.-) (Protein-... 55 4e-08 RCK1_YEAST (P38622) Serine/threonine-protein kinase RCK1 (EC 2.7... 55 6e-08 ST6L_XENLA (Q91819) Serine/threonine-protein kinase Eg2-like (EC... 55 6e-08 KCCD_HUMAN (Q13557) Calcium/calmodulin-dependent protein kinase ... 55 6e-08 KCCD_RAT (P15791) Calcium/calmodulin-dependent protein kinase ty... 55 6e-08 K6AA_CHICK (P18652) Ribosomal protein S6 kinase II alpha (EC 2.7... 55 6e-08 STK6_XENLA (Q91820) Serine/threonine-protein kinase Eg2 (EC 2.7.... 55 6e-08 AURB_MOUSE (O70126) Serine/threonine-protein kinase 12 (EC 2.7.1... 55 6e-08 CDP4_PLAYO (Q7RJG2) Calcium-dependent protein kinase 4 (EC 2.7.1... 55 6e-08 CDP4_PLAF7 (Q8IBS5) Calcium-dependent protein kinase 4 (EC 2.7.1... 55 6e-08 CDP4_PLABA (P62345) Calcium-dependent protein kinase 4 (EC 2.7.1... 55 6e-08 PKL2_RAT (O08874) Protein kinase C-like 2 (EC 2.7.1.-) (Protein-... 55 8e-08 KCCA_RAT (P11275) Calcium/calmodulin-dependent protein kinase ty... 55 8e-08 KCCA_HUMAN (Q9UQM7) Calcium/calmodulin-dependent protein kinase ... 55 8e-08 KCC4_MOUSE (P08414) Calcium/calmodulin-dependent protein kinase ... 55 8e-08 KCC4_RAT (P13234) Calcium/calmodulin-dependent protein kinase ty... 55 8e-08 K6A3_MOUSE (P18654) Ribosomal protein S6 kinase alpha 3 (EC 2.7.... 55 8e-08 K6A3_HUMAN (P51812) Ribosomal protein S6 kinase alpha 3 (EC 2.7.... 55 8e-08 PKL2_HUMAN (Q16513) Protein kinase C-like 2 (EC 2.7.1.-) (Protei... 55 8e-08 KCC4_HUMAN (Q16566) Calcium/calmodulin-dependent protein kinase ... 54 1e-07 RCK2_YEAST (P38623) Serine/threonine-protein kinase RCK2 (EC 2.7... 54 1e-07 KPCL_HUMAN (P24723) Protein kinase C, eta type (EC 2.7.1.-) (nPK... 54 1e-07 KML2_RAT (P20689) Myosin light chain kinase 2, skeletal/cardiac ... 54 1e-07 STK6_HUMAN (O14965) Serine/threonine-protein kinase 6 (EC 2.7.1.... 54 1e-07 KS6A_CAEEL (Q21734) Putative ribosomal protein S6 kinase alpha (... 54 1e-07 KCCA_DROME (Q00168) Calcium/calmodulin-dependent protein kinase ... 54 1e-07 KCCB_HUMAN (Q13554) Calcium/calmodulin-dependent protein kinase ... 54 1e-07 AURB_HUMAN (Q96GD4) Serine/threonine-protein kinase 12 (EC 2.7.1... 54 1e-07 KPCL_RAT (Q64617) Protein kinase C, eta type (EC 2.7.1.-) (nPKC-... 54 1e-07 KPCL_MOUSE (P23298) Protein kinase C, eta type (EC 2.7.1.-) (nPK... 54 1e-07 KCCB_RAT (P08413) Calcium/calmodulin-dependent protein kinase ty... 54 1e-07 KCCB_MOUSE (P28652) Calcium/calmodulin-dependent protein kinase ... 54 1e-07 KCC2_SCHPO (O42844) Calcium/calmodulin-dependent protein kinase ... 54 1e-07 S17A_RABIT (Q9GM70) Serine/threonine-protein kinase 17A (EC 2.7.... 53 2e-07 KML2_MOUSE (Q8VCR8) Myosin light chain kinase 2, skeletal/cardia... 53 2e-07 PCK2_SCHPO (P36583) Protein kinase C-like 2 (EC 2.7.1.-) 53 2e-07 K6AB_XENLA (P10666) Ribosomal protein S6 kinase II beta (EC 2.7.... 53 3e-07 PCK1_SCHPO (P36582) Protein kinase C-like 1 (EC 2.7.1.-) 53 3e-07 KCCG_MOUSE (Q923T9) Calcium/calmodulin-dependent protein kinase ... 52 4e-07 K6A4_HUMAN (O75676) Ribosomal protein S6 kinase alpha 4 (EC 2.7.... 52 4e-07 SCH9_YEAST (P11792) Serine/threonine-protein kinase SCH9 (EC 2.7... 52 4e-07 POLO_DROME (P52304) Serine/threonine-protein kinase polo (EC 2.7... 52 4e-07 KCCG_HUMAN (Q13555) Calcium/calmodulin-dependent protein kinase ... 52 4e-07 AURB_RAT (O55099) Serine/threonine-protein kinase 12 (EC 2.7.1.3... 52 4e-07 STK6_MOUSE (P97477) Serine/threonine-protein kinase 6 (EC 2.7.1.... 52 4e-07 PLK2_CAEEL (Q9N2L7) Serine/threonine-protein kinase plk-2 (EC 2.... 52 4e-07 KCCG_RAT (P11730) Calcium/calmodulin-dependent protein kinase ty... 52 4e-07 K6A4_MOUSE (Q9Z2B9) Ribosomal protein S6 kinase alpha 4 (EC 2.7.... 52 5e-07 PLK1_CAEEL (P34331) Serine/threonine-protein kinase plk-1 (EC 2.... 52 5e-07 AURB_PIG (Q9N0X0) Serine/threonine-protein kinase 12 (EC 2.7.1.3... 52 5e-07 KML2_HUMAN (Q9H1R3) Myosin light chain kinase 2, skeletal/cardia... 52 6e-07 UN51_CAEEL (Q23023) Serine/threonine-protein kinase unc-51 (EC 2... 52 6e-07 KML2_RABIT (P07313) Myosin light chain kinase 2, skeletal/cardia... 52 6e-07 CDP3_ORYSA (P53684) Calcium-dependent protein kinase, isoform 11... 52 6e-07 DCK1_RAT (O08875) Serine/threonine-protein kinase DCAMKL1 (EC 2.... 51 8e-07 KMLS_RABIT (P29294) Myosin light chain kinase, smooth muscle (EC... 51 8e-07 DCK1_MOUSE (Q9JLM8) Serine/threonine-protein kinase DCAMKL1 (EC ... 51 8e-07 CDPK_SOYBN (P28583) Calcium-dependent protein kinase SK5 (EC 2.7... 51 8e-07 SKM1_YEAST (Q12469) Serine/threonine-protein kinase SKM1 (EC 2.7... 51 8e-07 DCK1_HUMAN (O15075) Serine/threonine-protein kinase DCAMKL1 (EC ... 51 8e-07 KMLS_HUMAN (Q15746) Myosin light chain kinase, smooth muscle and... 51 1e-06 KMLS_SHEEP (O02827) Myosin light chain kinase, smooth muscle (EC... 51 1e-06 CDPK_DAUCA (P28582) Calcium-dependent protein kinase (EC 2.7.1.-... 51 1e-06 KCC2_YEAST (P22517) Calcium/calmodulin-dependent protein kinase ... 51 1e-06 ST2A_HUMAN (Q9BXA7) Serine/threonine-protein kinase 22A (EC 2.7.... 51 1e-06 PLK1_RAT (Q62673) Serine/threonine-protein kinase PLK1 (EC 2.7.1... 51 1e-06 PLK1_MOUSE (Q07832) Serine/threonine-protein kinase PLK1 (EC 2.7... 51 1e-06 PLK1_HUMAN (P53350) Serine/threonine-protein kinase PLK1 (EC 2.7... 51 1e-06 CDP2_ORYSA (P53683) Calcium-dependent protein kinase, isoform 2 ... 51 1e-06 KMLS_BOVIN (Q28824) Myosin light chain kinase, smooth muscle (EC... 51 1e-06 AURC_MOUSE (O88445) Serine/threonine-protein kinase 13 (EC 2.7.1... 51 1e-06 MEK1_SCHPO (Q10292) Meiosis-specific serine/threonine-protein ki... 50 1e-06 STK6_RAT (P59241) Serine/threonine-protein kinase 6 (EC 2.7.1.37... 50 1e-06 KMLS_CHICK (P11799) Myosin light chain kinase, smooth muscle and... 50 1e-06 SCK1_SCHPO (P50530) Serine/threonine-protein kinase sck1 (EC 2.7... 50 1e-06 ULK1_MOUSE (O70405) Serine/threonine-protein kinase ULK1 (EC 2.7... 50 2e-06 CDP2_MAIZE (P49101) Calcium-dependent protein kinase 2 (EC 2.7.1... 50 2e-06 CDC5_YEAST (P32562) Cell cycle serine/threonine-protein kinase C... 50 2e-06 KOK0_YEAST (Q12236) Probable serine/threonine-protein kinase YOL... 50 2e-06 PLK1_XENLA (P70032) Serine/threonine-protein kinase PLK1 (EC 2.7... 50 2e-06 ULK1_HUMAN (O75385) Serine/threonine-protein kinase ULK1 (EC 2.7... 50 2e-06 KPK2_PLAFK (Q02595) Probable serine/threonine-protein kinase 2 (... 50 2e-06 KKK1_YEAST (P34244) Probable serine/threonine-protein kinase YKL... 50 2e-06 KPBH_MOUSE (Q9DB30) Phosphorylase B kinase gamma catalytic chain... 49 3e-06 CDP1_ARATH (Q06850) Calcium-dependent protein kinase, isoform AK... 49 3e-06 GIN4_YEAST (Q12263) Serine/threonine-protein kinase GIN4 (EC 2.7... 49 3e-06 FUSE_DROME (P23647) Serine/threonine-protein kinase fused (EC 2.... 49 3e-06 PLK1_XENTR (P62205) Serine/threonine-protein kinase PLK1 (EC 2.7... 49 3e-06 PKSC_STRCO (Q9S2C0) Serine/threonine protein kinase pksC (EC 2.7... 49 3e-06 PLK3_CAEEL (Q20845) Serine/threonine-protein kinase plk-3 (EC 2.... 49 3e-06 CDR2_SCHPO (P87050) Mitosis inducer protein kinase cdr2 (EC 2.7.... 49 4e-06 KPC1_YEAST (P24583) Protein kinase C-like 1 (EC 2.7.1.-) (PKC 1) 49 4e-06 KPBH_HUMAN (P15735) Phosphorylase B kinase gamma catalytic chain... 49 4e-06 TRIO_HUMAN (O75962) Triple functional domain protein (PTPRF inte... 49 4e-06 MEK1_YEAST (P24719) Meiosis-specific serine/threonine-protein ki... 49 4e-06 CLA4_YEAST (P48562) Serine/threonine-protein kinase CLA4 (EC 2.7... 49 5e-06 KPC1_NEUCR (P87253) Protein kinase C-like (EC 2.7.1.-) 49 5e-06 GRK6_MOUSE (O70293) G protein-coupled receptor kinase 6 (EC 2.7.... 49 5e-06 KPC1_COCHE (O42632) Protein kinase C-like (EC 2.7.1.-) 49 5e-06 KPC1_ASPNG (Q00078) Protein kinase C-like (EC 2.7.1.-) 49 5e-06 KCC4_YEAST (P25389) Probable serine/threonine-protein kinase KCC... 49 5e-06 KPC1_TRIRE (Q99014) Protein kinase C-like (EC 2.7.1.-) 49 5e-06 S17A_HUMAN (Q9UEE5) Serine/threonine-protein kinase 17A (EC 2.7.... 48 7e-06 MNK1_HUMAN (Q9BUB5) MAP kinase-interacting serine/threonine kina... 48 7e-06 KIN4_YEAST (Q01919) Serine/threonine-protein kinase KIN4 (EC 2.7... 48 7e-06 KPBH_RAT (P31325) Phosphorylase B kinase gamma catalytic chain, ... 48 9e-06 GRK6_RAT (P97711) G protein-coupled receptor kinase 6 (EC 2.7.1.... 48 9e-06 GRK6_HUMAN (P43250) G protein-coupled receptor kinase 6 (EC 2.7.... 48 9e-06 ASK1_ARATH (P43291) Serine/threonine-protein kinase ASK1 (EC 2.7... 48 9e-06 ASK2_ARATH (P43292) Serine/threonine-protein kinase ASK2 (EC 2.7... 48 9e-06 RK_RAT (Q63651) Rhodopsin kinase (EC 2.7.1.125) (RK) (G protein-... 47 1e-05 RK_MOUSE (Q9WVL4) Rhodopsin kinase (EC 2.7.1.125) (RK) (G protei... 47 1e-05 RK_BOVIN (P28327) Rhodopsin kinase (EC 2.7.1.125) (RK) (G protei... 47 1e-05 GRK4_HUMAN (P32298) G protein-coupled receptor kinase 4 (EC 2.7.... 47 1e-05 KDC1_DROME (P16911) Protein kinase DC1 (EC 2.7.1.37) 47 1e-05 YQR1_CAEEL (Q09537) Probable G protein-coupled receptor kinase F... 47 1e-05 MNK1_MOUSE (O08605) MAP kinase-interacting serine/threonine kina... 47 1e-05 LOK_DROME (O61267) Ovarian-specific serine/threonine-protein kin... 47 1e-05 PLK3_MOUSE (Q60806) Serine/threonine-protein kinase PLK3 (EC 2.7... 47 2e-05 KCC1_EMENI (Q00771) Calcium/calmodulin-dependent protein kinase ... 47 2e-05 PLK3_RAT (Q9R011) Serine/threonine-protein kinase PLK3 (EC 2.7.1... 47 2e-05 PKN2_CLOPE (Q8XJL8) Probable serine/threonine protein kinase CPE... 47 2e-05 PLK3_HUMAN (Q9H4B4) Serine/threonine-protein kinase PLK3 (EC 2.7... 47 2e-05 KCC1_SCHPO (Q9P7I2) Calcium/calmodulin-dependent protein kinase ... 47 2e-05 MNK2_MOUSE (Q8CDB0) MAP kinase-interacting serine/threonine kina... 47 2e-05 PKN1_THETN (Q8R9T6) Probable serine/threonine-protein kinase Sps... 47 2e-05 GRK4_RAT (P70507) G protein-coupled receptor kinase 4 (EC 2.7.1.... 47 2e-05 ST2A_MOUSE (Q61241) Serine/threonine-protein kinase 22A (EC 2.7.... 47 2e-05 PK1_NPVHZ (P41719) Serine/threonine-protein kinase 1 (EC 2.7.1.37) 47 2e-05 MNK2_HUMAN (Q9HBH9) MAP kinase-interacting serine/threonine kina... 47 2e-05 ST2B_MOUSE (O54863) Serine/threonine-protein kinase 22B (EC 2.7.... 47 2e-05 CLA4_CANAL (O14427) Serine/threonine-protein kinase CLA4 (EC 2.7... 47 2e-05 ARK1_SCHPO (O59790) Serine/threonine-protein kinase ark1 (EC 2.7... 47 2e-05 PAK6_HUMAN (Q9NQU5) Serine/threonine-protein kinase PAK 6 (EC 2.... 46 3e-05 GRK4_MOUSE (O70291) G protein-coupled receptor kinase 4 (EC 2.7.... 46 3e-05 PR4B_MOUSE (Q61136) Serine/threonine-protein kinase PRP4 homolog... 46 3e-05 PR4B_HUMAN (Q13523) Serine/threonine-protein kinase PRP4 homolog... 46 3e-05 M3K2_ARATH (Q9FZ36) Mitogen-activated protein kinase kinase kina... 46 3e-05 YR22_CAEEL (Q09639) Putative G protein-coupled receptor kinase W... 46 3e-05 KSG1_SCHPO (Q12701) Serine/threonine-protein kinase ksg1 (EC 2.7... 46 4e-05 HUNK_MOUSE (O88866) Hormonally up-regulated neu tumor-associated... 46 4e-05 HUNK_HUMAN (P57058) Hormonally up-regulated neu tumor-associated... 46 4e-05 DUET_HUMAN (Q9Y2A5) Serine/threonine-protein kinase Duet (EC 2.7... 46 4e-05 DAK1_HUMAN (P53355) Death-associated protein kinase 1 (EC 2.7.1.... 46 4e-05 PKN3_MYXXA (Q9XBQ0) Serine/threonine-protein kinase pkn3 (EC 2.7... 46 4e-05 SHK1_SCHPO (P50527) Serine/threonine-protein kinase pak1/shk1 (E... 46 4e-05 AAIP_WHEAT (Q02066) Abscisic acid-inducible protein kinase (EC 2... 46 4e-05 RK_HUMAN (Q15835) Rhodopsin kinase (EC 2.7.1.125) (RK) (G protei... 46 4e-05 CC7_SCHPO (P41892) Cell division control protein 7 (EC 2.7.1.-) 45 5e-05 CHK2_CAEEL (Q9U1Y5) Serine/threonine-protein kinase chk-2 (EC 2.... 45 5e-05 KI11_HUMAN (Q8TDC3) Probable serine/threonine-protein kinase KIA... 45 5e-05 CRK_DAUCA (P53681) CDPK-related protein kinase (EC 2.7.1.-) (PK421) 45 5e-05 IKKB_MOUSE (O88351) Inhibitor of nuclear factor kappa B kinase b... 45 5e-05 NRKA_TRYBB (Q08942) Putative serine/threonine-protein kinase A (... 45 5e-05 ST2C_MOUSE (Q9D2E1) Serine/threonine-protein kinase 22C (EC 2.7.... 45 5e-05 ST2C_HUMAN (Q96PN8) Serine/threonine-protein kinase 22C (EC 2.7.... 45 5e-05 KCC1_YEAST (P27466) Calcium/calmodulin-dependent protein kinase ... 45 5e-05 ARK2_HUMAN (P35626) Beta-adrenergic receptor kinase 2 (EC 2.7.1.... 45 5e-05 ARK2_BOVIN (P26818) Beta-adrenergic receptor kinase 2 (EC 2.7.1.... 45 5e-05 KPBG_RAT (P13286) Phosphorylase B kinase gamma catalytic chain, ... 45 5e-05 KPBG_MOUSE (P07934) Phosphorylase B kinase gamma catalytic chain... 45 5e-05 ST20_CANAL (Q92212) Serine/threonine-protein kinase STE20 homolo... 45 6e-05 DAK2_MOUSE (Q8VDF3) Death-associated protein kinase 2 (EC 2.7.1.... 45 6e-05 DAK2_HUMAN (Q9UIK4) Death-associated protein kinase 2 (EC 2.7.1.... 45 6e-05 PAK7_HUMAN (Q9P286) Serine/threonine-protein kinase PAK 7 (EC 2.... 45 6e-05 M3K1_RAT (Q62925) Mitogen-activated protein kinase kinase kinase... 45 6e-05 M3K1_MOUSE (P53349) Mitogen-activated protein kinase kinase kina... 45 6e-05 ST29_HUMAN (Q8IWQ3) Serine/threonine-protein kinase 29 (EC 2.7.1... 45 6e-05 M3K1_HUMAN (Q13233) Mitogen-activated protein kinase kinase kina... 45 6e-05 DYRA_RAT (Q63470) Dual-specificity tyrosine-phosphorylation regu... 45 6e-05 DYRA_MOUSE (Q61214) Dual-specificity tyrosine-phosphorylation re... 45 6e-05 DYRA_HUMAN (Q13627) Dual-specificity tyrosine-phosphorylation re... 45 6e-05 KPBG_RABIT (P00518) Phosphorylase B kinase gamma catalytic chain... 45 8e-05 KPBG_HUMAN (Q16816) Phosphorylase B kinase gamma catalytic chain... 45 8e-05 M3K3_ARATH (O22042) Mitogen-activated protein kinase kinase kina... 45 8e-05 PAK1_MOUSE (O88643) Serine/threonine-protein kinase PAK 1 (EC 2.... 45 8e-05 PAK1_HUMAN (Q13153) Serine/threonine-protein kinase PAK 1 (EC 2.... 45 8e-05 ARK1_RAT (P26817) Beta-adrenergic receptor kinase 1 (EC 2.7.1.12... 45 8e-05 ARK1_MOUSE (Q99MK8) Beta-adrenergic receptor kinase 1 (EC 2.7.1.... 45 8e-05 ARK1_MESAU (Q64682) Beta-adrenergic receptor kinase 1 (EC 2.7.1.... 45 8e-05 ARK1_HUMAN (P25098) Beta-adrenergic receptor kinase 1 (EC 2.7.1.... 45 8e-05 ARK1_BOVIN (P21146) Beta-adrenergic receptor kinase 1 (EC 2.7.1.... 45 8e-05 PAK1_RAT (P35465) Serine/threonine-protein kinase PAK 1 (EC 2.7.... 45 8e-05 DYRB_MOUSE (Q9Z188) Dual-specificity tyrosine-phosphorylation re... 45 8e-05 AFC3_ARATH (P51568) Protein kinase AFC3 (EC 2.7.1.-) 45 8e-05 PK61_DROME (Q9W0V1) Serine/threonine-protein kinase Pk61C (EC 2.... 45 8e-05 NEK7_MOUSE (Q9ES74) Serine/threonine-protein kinase Nek7 (EC 2.7... 45 8e-05 NEK7_HUMAN (Q8TDX7) Serine/threonine-protein kinase Nek7 (EC 2.7... 45 8e-05 NEK6_RAT (P59895) Serine/threonine-protein kinase Nek6 (EC 2.7.1... 45 8e-05 NEK6_MOUSE (Q9ES70) Serine/threonine-protein kinase Nek6 (EC 2.7... 45 8e-05 NEK6_HUMAN (Q9HC98) Serine/threonine-protein kinase Nek6 (EC 2.7... 45 8e-05 DYRB_HUMAN (Q9Y463) Dual-specificity tyrosine-phosphorylation re... 45 8e-05 DAK3_RAT (O88764) Death-associated protein kinase 3 (EC 2.7.1.37... 45 8e-05 DAK3_MOUSE (O54784) Death-associated protein kinase 3 (EC 2.7.1.... 45 8e-05 DAK1_MOUSE (Q80YE7) Death-associated protein kinase 1 (EC 2.7.1.... 45 8e-05 ST20_YEAST (Q03497) Serine/threonine-protein kinase STE20 (EC 2.... 45 8e-05 PDPK_RAT (O55173) 3-phosphoinositide dependent protein kinase-1 ... 44 1e-04 PDPK_MOUSE (Q9Z2A0) 3-phosphoinositide dependent protein kinase-... 44 1e-04 PAK3_PONPY (Q7YQL3) Serine/threonine-protein kinase PAK 3 (EC 2.... 44 1e-04 PAK3_PANTR (Q7YQL4) Serine/threonine-protein kinase PAK 3 (EC 2.... 44 1e-04 PAK3_MOUSE (Q61036) Serine/threonine-protein kinase PAK 3 (EC 2.... 44 1e-04 PAK3_HUMAN (O75914) Serine/threonine-protein kinase PAK 3 (EC 2.... 44 1e-04 KIN3_YEAST (P22209) Serine/threonine-protein kinase KIN3 (EC 2.7... 44 1e-04 PDPK_HUMAN (O15530) 3-phosphoinositide dependent protein kinase-... 44 1e-04 PAK2_RAT (Q64303) Serine/threonine-protein kinase PAK 2 (EC 2.7.... 44 1e-04 PAK2_RABIT (Q29502) Serine/threonine-protein kinase PAK 2 (EC 2.... 44 1e-04 PAK2_MOUSE (Q8CIN4) Serine/threonine-protein kinase PAK 2 (EC 2.... 44 1e-04 PAK2_HUMAN (Q13177) Serine/threonine-protein kinase PAK 2 (EC 2.... 44 1e-04 SNK_HUMAN (Q9NYY3) Serine/threonine-protein kinase SNK (EC 2.7.1... 44 1e-04 PKN5_MYXXA (P54737) Serine/threonine-protein kinase pkn5 (EC 2.7... 44 1e-04 CSKP_MOUSE (O70589) Peripheral plasma membrane protein CASK (EC ... 44 1e-04 CSKP_RAT (Q62915) Peripheral plasma membrane protein CASK (EC 2.... 44 1e-04 CSKP_HUMAN (O14936) Peripheral plasma membrane protein CASK (EC ... 44 1e-04 IKKB_HUMAN (O14920) Inhibitor of nuclear factor kappa B kinase b... 44 1e-04 SNK_RAT (Q9R012) Serine/threonine-protein kinase SNK (EC 2.7.1.3... 44 1e-04 SNK_MOUSE (P53351) Serine/threonine-protein kinase SNK (EC 2.7.1... 44 1e-04 DYR4_HUMAN (Q9NR20) Dual-specificity tyrosine-phosphorylation re... 44 1e-04 ARK2_RAT (P26819) Beta-adrenergic receptor kinase 2 (EC 2.7.1.12... 44 1e-04 PAK3_RAT (Q62829) Serine/threonine-protein kinase PAK 3 (EC 2.7.... 44 1e-04 KOIA_SCHPO (Q9Y7J6) Putative serine/threonine-protein kinase C17... 44 1e-04 KAB7_YEAST (P31374) Probable serine/threonine-protein kinase YAL... 44 1e-04 NRKB_TRYBB (Q03428) Putative serine/threonine-protein kinase B (... 44 1e-04 AAK1_RAT (P54645) 5'-AMP-activated protein kinase, catalytic alp... 44 2e-04 GPK2_DROME (P32866) G protein-coupled receptor kinase 2 (EC 2.7.... 44 2e-04 KCC1_METAN (O14408) Calcium/calmodulin-dependent protein kinase ... 44 2e-04 DAK3_HUMAN (O43293) Death-associated protein kinase 3 (EC 2.7.1.... 44 2e-04 MNB_DROME (P49657) Serine/threonine-protein kinase minibrain (EC... 44 2e-04 PKAA_STRCO (P54739) Serine/threonine protein kinase pkaA (EC 2.7... 44 2e-04 M3K5_HUMAN (Q99683) Mitogen-activated protein kinase kinase kina... 44 2e-04 MRK3_HUMAN (P27448) MAP/microtubule affinity-regulating kinase 3... 44 2e-04 PAK4_MOUSE (Q8BTW9) Serine/threonine-protein kinase PAK 4 (EC 2.... 44 2e-04 AAK1_HUMAN (Q13131) 5'-AMP-activated protein kinase, catalytic a... 44 2e-04 CDS1_SCHPO (Q09170) Serine/threonine-protein kinase cds1 (EC 2.7... 44 2e-04 M3K5_MOUSE (O35099) Mitogen-activated protein kinase kinase kina... 44 2e-04 MKK2_YEAST (P32491) MAP kinase kinase MKK2/SSP33 (EC 2.7.1.-) 43 2e-04 PAK4_HUMAN (O96013) Serine/threonine-protein kinase PAK 4 (EC 2.... 43 2e-04 ST25_MOUSE (Q9Z2W1) Serine/threonine-protein kinase 25 (EC 2.7.1... 43 2e-04 ST25_HUMAN (O00506) Serine/threonine-protein kinase 25 (EC 2.7.1... 43 2e-04 IKKB_RAT (Q9QY78) Inhibitor of nuclear factor kappa B kinase bet... 43 2e-04 LKH1_SCHPO (Q10156) Protein kinase lkh1 (EC 2.7.1.37) (EC 2.7.1.... 43 3e-04 PKNB_MYCTU (P71584) Probable serine/threonine-protein kinase pkn... 43 3e-04 SPAK_HUMAN (Q9UEW8) STE20/SPS1-related proline-alanine rich prot... 43 3e-04 IKKA_MOUSE (Q60680) Inhibitor of nuclear factor kappa-B kinase a... 43 3e-04 IKKA_HUMAN (O15111) Inhibitor of nuclear factor kappa-B kinase a... 43 3e-04 SPAK_RAT (O88506) STE20/SPS1-related proline-alanine rich protei... 43 3e-04 M3K1_ARATH (O22040) Mitogen-activated protein kinase kinase kina... 43 3e-04 GRK7_HUMAN (Q8WTQ7) G protein-coupled receptor kinase 7 (EC 2.7.... 43 3e-04 PKNB_LACLA (Q9CEF5) Probable serine/threonine-protein kinase pkn... 43 3e-04 MRK4_HUMAN (Q96L34) MAP/microtubule affinity-regulating kinase 4... 43 3e-04 SPAK_MOUSE (Q9Z1W9) STE20/SPS1-related proline-alanine rich prot... 43 3e-04 AFC1_ARATH (P51566) Protein kinase AFC1 (EC 2.7.1.-) 43 3e-04 KCCS_MALDO (Q07250) Calcium/calmodulin-dependent serine/threonin... 43 3e-04 ARK5_HUMAN (O60285) AMPK-related protein kinase 5 (EC 2.7.1.37) 42 4e-04 GRK5_RAT (Q62833) G protein-coupled receptor kinase 5 (EC 2.7.1.... 42 4e-04 GRK5_MOUSE (Q8VEB1) G protein-coupled receptor kinase 5 (EC 2.7.... 42 4e-04 GRK5_HUMAN (P34947) G protein-coupled receptor kinase 5 (EC 2.7.... 42 4e-04 GRK5_BOVIN (P43249) G protein-coupled receptor kinase 5 (EC 2.7.... 42 4e-04 PKNJ_MYCTU (Q10697) Probable serine/threonine-protein kinase pkn... 42 4e-04 KI10_ARATH (Q38997) SNF1-related protein kinase KIN10 (EC 2.7.1.... 42 4e-04 AAK2_RAT (Q09137) 5'-AMP-activated protein kinase, catalytic alp... 42 4e-04 AAK2_HUMAN (P54646) 5'-AMP-activated protein kinase, catalytic a... 42 4e-04 PKN1_MYXXA (P33973) Serine/threonine-protein kinase pkn1 (EC 2.7... 42 4e-04 PKNB_BIFLO (Q8G6P9) Probable serine/threonine-protein kinase pkn... 42 4e-04 HPO_DROME (Q8T0S6) Serine/threonine-protein kinase hippo (EC 2.7... 42 4e-04 ST2B_HUMAN (Q96PF2) Serine/threonine-protein kinase 22B (EC 2.7.... 42 5e-04 GPK1_DROME (P32865) G protein-coupled receptor kinase 1 (EC 2.7.... 42 5e-04 PAK1_YEAST (P38990) Serine/threonine-protein kinase PAK1 (EC 2.7... 42 5e-04 YKT3_CAEEL (P34314) Putative serine/threonine-protein kinase C07... 42 5e-04 MY3B_HUMAN (Q8WXR4) Myosin IIIB (EC 2.7.1.37) 42 5e-04 MK08_XENLA (Q8QHK8) Mitogen-activated protein kinase 8 (EC 2.7.1... 42 5e-04 PKNB_MYCLE (P54744) Probable serine/threonine-protein kinase pkn... 42 5e-04 AFC2_ARATH (P51567) Protein kinase AFC2 (EC 2.7.1.-) 42 5e-04 MK8B_CYPCA (O42099) Mitogen-activated protein kinase 8B (EC 2.7.... 42 7e-04 CAKI_DROME (Q24210) Calcium/calmodulin-dependent protein kinase ... 42 7e-04 SNF1_CANTR (O94168) Carbon catabolite derepressing protein kinas... 42 7e-04 M3K3_HUMAN (Q99759) Mitogen-activated protein kinase kinase kina... 42 7e-04 DYR2_HUMAN (Q92630) Dual-specificity tyrosine-phosphorylation re... 42 7e-04 JNK_DROME (P92208) Stress-activated protein kinase JNK (EC 2.7.1... 42 7e-04 STKA_MOUSE (O55098) Serine/threonine-protein kinase 10 (EC 2.7.1... 41 9e-04 ST24_HUMAN (Q9Y6E0) Serine/threonine-protein kinase 24 (EC 2.7.1... 41 9e-04 M4K6_HUMAN (Q8N4C8) Mitogen-activated protein kinase kinase kina... 41 9e-04 M4K6_MOUSE (Q9JM52) Mitogen-activated protein kinase kinase kina... 41 9e-04 GRK7_SPETR (Q9Z2G7) G protein-coupled receptor kinase 7 (EC 2.7.... 41 0.001 DYR3_DROME (P83102) Putative dual-specificity tyrosine-phosphory... 41 0.001 SNF1_SCHPO (O74536) SNF1-like protein kinase (EC 2.7.1.-) 41 0.001 POM1_SCHPO (Q09690) Putative dual specificity protein kinase pom... 41 0.001 MK09_RAT (P49186) Mitogen-activated protein kinase 9 (EC 2.7.1.3... 41 0.001 MK09_HUMAN (P45984) Mitogen-activated protein kinase 9 (EC 2.7.1... 41 0.001 MK09_CHICK (P79996) Mitogen-activated protein kinase 9 (EC 2.7.1... 41 0.001 M3K3_MOUSE (Q61084) Mitogen-activated protein kinase kinase kina... 41 0.001 MK08_BRARE (Q9DGD9) Mitogen-activated protein kinase 8 (EC 2.7.1... 41 0.001 M4K4_HUMAN (O95819) Mitogen-activated protein kinase kinase kina... 41 0.001 SN1L_HUMAN (P57059) Probable serine/threonine-protein kinase SNF... 41 0.001 M3K2_HUMAN (Q9Y2U5) Mitogen-activated protein kinase kinase kina... 41 0.001 GCN2_YEAST (P15442) Serine/threonine-protein kinase GCN2 (EC 2.7... 41 0.001 STKA_HUMAN (O94804) Serine/threonine-protein kinase 10 (EC 2.7.1... 41 0.001 SN1L_RAT (Q9R1U5) Probable serine/threonine-protein kinase SNF1L... 41 0.001 MPS1_YEAST (P54199) Serine/threonine-protein kinase MPS1 (EC 2.7... 41 0.001 PKD1_DICDI (P34100) Developmentally regulated protein kinase 1 (... 41 0.001 NEK2_HUMAN (P51955) Serine/threonine-protein kinase Nek2 (EC 2.7... 41 0.001 SN1L_MOUSE (Q60670) Probable serine/threonine-protein kinase SNF... 41 0.001 SID1_SCHPO (O14305) Serine/threonine-protein kinase sid1 (EC 2.7... 41 0.001 MEK2_CAEEL (Q10664) Dual specificity mitogen-activated protein k... 41 0.001 STK4_HUMAN (Q13043) Serine/threonine-protein kinase 4 (EC 2.7.1.... 40 0.001 YX05_CAEEL (Q11112) Putative tyrosine-protein kinase C03B1.5 in ... 40 0.001 ELM1_YEAST (P32801) Protein kinase ELM1 (EC 2.7.1.-) 40 0.001 KGS9_YEAST (P43637) Probable serine/threonine-protein kinase YGL... 40 0.001 M4K4_MOUSE (P97820) Mitogen-activated protein kinase kinase kina... 40 0.001 RKI1_SECCE (Q02723) Carbon catabolite derepressing protein kinas... 40 0.001 MRK2_MOUSE (Q05512) MAP/microtubule affinity-regulating kinase 2... 40 0.001 SPS1_YEAST (P08458) Sporulation-specific protein 1 (EC 2.7.1.-) 40 0.001 YNA3_CAEEL (P45894) Putative serine/threonine-protein kinase PAR... 40 0.001 SPKA_SYNY3 (Q9FAB3) Serine/threonine-protein kinase A (EC 2.7.1.37) 40 0.001 TNIK_HUMAN (Q9UKE5) TRAF2 and NCK interacting kinase (EC 2.7.1.37) 40 0.001 PK1_NPVLD (P41720) Serine/threonine-protein kinase 1 (EC 2.7.1.37) 40 0.001 YAK1_YEAST (P14680) Protein kinase YAK1 (EC 2.7.1.-) 40 0.001 M3K2_MOUSE (Q61083) Mitogen-activated protein kinase kinase kina... 40 0.001 TNIK_MOUSE (P83510) Traf2 and NCK interacting kinase (EC 2.7.1.3... 40 0.001 STK3_MOUSE (Q9JI10) Serine/threonine-protein kinase 3 (EC 2.7.1.... 40 0.002 NEK9_HUMAN (Q8TD19) Serine/threonine-protein kinase Nek9 (EC 2.7... 40 0.002 STK3_HUMAN (Q13188) Serine/threonine-protein kinase 3 (EC 2.7.1.... 40 0.002 >ORB6_SCHPO (O13310) Serine/threonine-protein kinase orb6 (EC 2.7.1.37) Length = 469 Score = 90.9 bits (224), Expect = 1e-18 Identities = 44/95 (46%), Positives = 64/95 (67%) Frame = +3 Query: 159 WRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTG 338 W+ RV M G+P YIAPE+ + +GY CDWWS+G I+FE L G+PPF +++ Sbjct: 281 WKKNRRV-MAYSTVGTPDYIAPEIFLQQGYGQDCDWWSLGAIMFECLIGWPPFCSENSHE 339 Query: 339 TAKKIIQFREYLKFPNNVDNVSGKAVDLISNLITD 443 T +KII +RE L FPN++ ++S +A DL+ L+TD Sbjct: 340 TYRKIINWRETLTFPNDI-HLSIEARDLMDRLMTD 373 >CBK1_YEAST (P53894) Serine/threonine-protein kinase CBK1 (EC 2.7.1.37) (Cell wall biosynthesis kinase) Length = 756 Score = 86.3 bits (212), Expect = 2e-17 Identities = 40/94 (42%), Positives = 63/94 (67%) Frame = +3 Query: 159 WRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTG 338 WR R+ M G+P YIAPE+ + +GY CDWWS+G I++E L G+PPF +++ Sbjct: 560 WRKSRRL-MAYSTVGTPDYIAPEIFLYQGYGQECDWWSLGAIMYECLIGWPPFCSETPQE 618 Query: 339 TAKKIIQFREYLKFPNNVDNVSGKAVDLISNLIT 440 T +KI+ F + L+FP+++ ++S +A DLI L+T Sbjct: 619 TYRKIMNFEQTLQFPDDI-HISYEAEDLIRRLLT 651 >GAD8_SCHPO (Q9P7J8) Serine/threonine-protein kinase gad8 (EC 2.7.1.37) Length = 569 Score = 84.7 bits (208), Expect = 7e-17 Identities = 39/82 (47%), Positives = 59/82 (71%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APE+L+G GY DWW++GV+L+EM+ G PPFY+++ +KI+Q + L Sbjct: 388 FCGTPEYLAPELLLGHGYTKVVDWWTLGVLLYEMITGLPPFYDENINEMYRKILQ--DPL 445 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +FP+N+D KA DL+S L+T Sbjct: 446 RFPDNIDE---KAKDLLSGLLT 464 >COT1_NEUCR (P38679) Serine/threonine-protein kinase cot-1 (EC 2.7.1.37) (Colonial temperature-sensitive 1) Length = 598 Score = 82.8 bits (203), Expect = 3e-16 Identities = 40/93 (43%), Positives = 57/93 (61%) Frame = +3 Query: 159 WRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTG 338 WR R+ M G+P YIAPE+ G GY + CDWWS+G I+FE L G+PPF + Sbjct: 407 WRRSRRL-MAYSTVGTPDYIAPEIFTGHGYSFDCDWWSLGTIMFECLVGWPPFCAEDSHD 465 Query: 339 TAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 T +KI+ +R L FP+++ + A +LI +LI Sbjct: 466 TYRKIVNWRHSLYFPDDI-TLGVDAENLIRSLI 497 >ROC1_RABIT (O77819) Rho-associated protein kinase 1 (EC 2.7.1.37) (Rho-associated, coiled-coil containing protein kinase 1) (p160 ROCK-1) (p160ROCK) (cAMP dependent protein kinase ROCK-I) (CePKA) (Corneal epithelial Rho-associated-Ser/Thr kinase 1) (HEBM Length = 1354 Score = 79.3 bits (194), Expect = 3e-15 Identities = 42/85 (49%), Positives = 54/85 (63%), Gaps = 4/85 (4%) Frame = +3 Query: 201 GSPAYIAPEVLIGRG----YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFRE 368 G+P YI+PEVL +G Y CDWWSVGV L+EML G PFY DS GT KI+ + Sbjct: 236 GTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMNHKN 295 Query: 369 YLKFPNNVDNVSGKAVDLISNLITD 443 L FP++ D +S +A +LI +TD Sbjct: 296 SLTFPDDND-ISKEAKNLICAFLTD 319 >ROC1_MOUSE (P70335) Rho-associated protein kinase 1 (EC 2.7.1.37) (Rho-associated, coiled-coil containing protein kinase 1) (p160 ROCK-1) (p160ROCK) Length = 1354 Score = 79.3 bits (194), Expect = 3e-15 Identities = 42/85 (49%), Positives = 54/85 (63%), Gaps = 4/85 (4%) Frame = +3 Query: 201 GSPAYIAPEVLIGRG----YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFRE 368 G+P YI+PEVL +G Y CDWWSVGV L+EML G PFY DS GT KI+ + Sbjct: 236 GTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMNHKN 295 Query: 369 YLKFPNNVDNVSGKAVDLISNLITD 443 L FP++ D +S +A +LI +TD Sbjct: 296 SLTFPDDND-ISKEAKNLICAFLTD 319 >ROC1_HUMAN (Q13464) Rho-associated protein kinase 1 (EC 2.7.1.37) (Rho-associated, coiled-coil containing protein kinase 1) (p160 ROCK-1) (p160ROCK) Length = 1354 Score = 79.3 bits (194), Expect = 3e-15 Identities = 42/85 (49%), Positives = 54/85 (63%), Gaps = 4/85 (4%) Frame = +3 Query: 201 GSPAYIAPEVLIGRG----YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFRE 368 G+P YI+PEVL +G Y CDWWSVGV L+EML G PFY DS GT KI+ + Sbjct: 236 GTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMNHKN 295 Query: 369 YLKFPNNVDNVSGKAVDLISNLITD 443 L FP++ D +S +A +LI +TD Sbjct: 296 SLTFPDDND-ISKEAKNLICAFLTD 319 >ROC1_RAT (Q63644) Rho-associated protein kinase 1 (EC 2.7.1.37) (Rho-associated, coiled-coil containing protein kinase 1) (p160 ROCK-1) (p160ROCK) (p150 RhoA-binding kinase ROK beta) Length = 1369 Score = 79.3 bits (194), Expect = 3e-15 Identities = 42/85 (49%), Positives = 54/85 (63%), Gaps = 4/85 (4%) Frame = +3 Query: 201 GSPAYIAPEVLIGRG----YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFRE 368 G+P YI+PEVL +G Y CDWWSVGV L+EML G PFY DS GT KI+ + Sbjct: 236 GTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMNHKN 295 Query: 369 YLKFPNNVDNVSGKAVDLISNLITD 443 L FP++ D +S +A +LI +TD Sbjct: 296 SLTFPDDND-ISKEAKNLICAFLTD 319 >ROC2_MOUSE (P70336) Rho-associated protein kinase 2 (EC 2.7.1.37) (Rho-associated, coiled-coil containing protein kinase 2) (p164 ROCK-2) Length = 1388 Score = 78.2 bits (191), Expect = 6e-15 Identities = 42/85 (49%), Positives = 52/85 (61%), Gaps = 4/85 (4%) Frame = +3 Query: 201 GSPAYIAPEVLIGRG----YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFRE 368 G+P YI+PEVL +G Y CDWWSVGV LFEML G PFY DS GT KI+ + Sbjct: 252 GTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLFEMLVGDTPFYADSLVGTYSKIMDHKN 311 Query: 369 YLKFPNNVDNVSGKAVDLISNLITD 443 L FP + + +S A +LI +TD Sbjct: 312 SLCFPEDTE-ISKHAKNLICAFLTD 335 >ROC2_BOVIN (Q28021) Rho-associated protein kinase 2 (EC 2.7.1.37) (Rho-associated, coiled-coil containing protein kinase 2) (p164 ROCK-2) Length = 1388 Score = 78.2 bits (191), Expect = 6e-15 Identities = 42/85 (49%), Positives = 52/85 (61%), Gaps = 4/85 (4%) Frame = +3 Query: 201 GSPAYIAPEVLIGRG----YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFRE 368 G+P YI+PEVL +G Y CDWWSVGV LFEML G PFY DS GT KI+ + Sbjct: 252 GTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLFEMLVGDTPFYADSLVGTYSKIMDHKN 311 Query: 369 YLKFPNNVDNVSGKAVDLISNLITD 443 L FP + + +S A +LI +TD Sbjct: 312 SLCFPEDAE-ISKHAKNLICAFLTD 335 >ROC2_RAT (Q62868) Rho-associated protein kinase 2 (EC 2.7.1.37) (Rho-associated, coiled-coil containing protein kinase 2) (p164 ROCK-2) (RhoA-binding kinase 2) (p150 ROK-alpha) (ROKalpha) Length = 1379 Score = 78.2 bits (191), Expect = 6e-15 Identities = 42/85 (49%), Positives = 52/85 (61%), Gaps = 4/85 (4%) Frame = +3 Query: 201 GSPAYIAPEVLIGRG----YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFRE 368 G+P YI+PEVL +G Y CDWWSVGV LFEML G PFY DS GT KI+ + Sbjct: 243 GTPDYISPEVLKSQGGDGYYGRECDWWSVGVFLFEMLVGDTPFYADSLVGTYSKIMDHKN 302 Query: 369 YLKFPNNVDNVSGKAVDLISNLITD 443 L FP + + +S A +LI +TD Sbjct: 303 SLCFPEDTE-ISKHAKNLICAFLTD 326 >ROC2_HUMAN (O75116) Rho-associated protein kinase 2 (EC 2.7.1.37) (Rho-associated, coiled-coil containing protein kinase 2) (p164 ROCK-2) (Rho kinase 2) Length = 1388 Score = 77.0 bits (188), Expect = 1e-14 Identities = 41/85 (48%), Positives = 52/85 (61%), Gaps = 4/85 (4%) Frame = +3 Query: 201 GSPAYIAPEVLIGRG----YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFRE 368 G+P YI+PEVL +G Y CDWWSVGV L+EML G PFY DS GT KI+ + Sbjct: 252 GTPDYISPEVLKSQGGDGFYGRECDWWSVGVFLYEMLVGDTPFYADSLVGTYSKIMDHKN 311 Query: 369 YLKFPNNVDNVSGKAVDLISNLITD 443 L FP + + +S A +LI +TD Sbjct: 312 SLCFPEDAE-ISKHAKNLICAFLTD 335 >YPK1_YEAST (P12688) Serine/threonine-protein kinase YPK1 (EC 2.7.1.37) Length = 680 Score = 75.1 bits (183), Expect = 5e-14 Identities = 37/82 (45%), Positives = 54/82 (65%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APE+L+G GY + DWW++GV+L+EML G PP+Y++ KKI+Q E L Sbjct: 505 FCGTPEYLAPELLLGLGYTKAVDWWTLGVLLYEMLTGLPPYYDEDVPKMYKKILQ--EPL 562 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 FP+ D A DL+ L++ Sbjct: 563 VFPDGFDR---DAKDLLIGLLS 581 >RI15_YEAST (P43565) Serine/threonine-protein kinase RIM15 (EC 2.7.1.37) Length = 1770 Score = 74.7 bits (182), Expect = 7e-14 Identities = 38/86 (44%), Positives = 53/86 (61%), Gaps = 5/86 (5%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYS-CDWWSVGVILFEMLYGYPPFYNDSKTGTAKKI----IQ 359 FFG+P Y+APE + G+G D CDWWSVG I FE+L GYPPF+ ++ KKI IQ Sbjct: 1147 FFGTPDYLAPETIEGKGEDNKQCDWWSVGCIFFELLLGYPPFHAETPDAVFKKILSGVIQ 1206 Query: 360 FREYLKFPNNVDNVSGKAVDLISNLI 437 + E+ + ++ +A DLI L+ Sbjct: 1207 WPEFKNEEEEREFLTPEAKDLIEKLL 1232 >YPK2_YEAST (P18961) Serine/threonine-protein kinase YPK2/YKR2 (EC 2.7.1.37) Length = 677 Score = 74.3 bits (181), Expect = 9e-14 Identities = 34/82 (41%), Positives = 56/82 (68%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APE+L+G+GY + DWW++G++L+EM+ G PP+Y+++ KKI+Q + L Sbjct: 502 FCGTPEYLAPEILLGQGYTKTVDWWTLGILLYEMMTGLPPYYDENVPVMYKKILQ--QPL 559 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 FP+ D A DL+ L++ Sbjct: 560 LFPDGFDPA---AKDLLIGLLS 578 >KAPC_CAEEL (P21137) cAMP-dependent protein kinase catalytic subunit (EC 2.7.1.37) (PKA C) Length = 404 Score = 73.6 bits (179), Expect = 2e-13 Identities = 31/79 (39%), Positives = 54/79 (68%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + +KF Sbjct: 238 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VKF 295 Query: 381 PNNVDNVSGKAVDLISNLI 437 P++ N + DL+ NL+ Sbjct: 296 PSHFSN---ELKDLLKNLL 311 >DMK_MOUSE (P54265) Myotonin-protein kinase (EC 2.7.1.-) (Myotonic dystrophy protein kinase) (MDPK) (DM-kinase) (DMK) (DMPK) (MT-PK) Length = 631 Score = 72.4 bits (176), Expect = 4e-13 Identities = 37/86 (43%), Positives = 50/86 (58%), Gaps = 7/86 (8%) Frame = +3 Query: 201 GSPAYIAPEVL--IGRG-----YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 G+P Y++PE+L +G G Y CDWW++GV +EM YG PFY DS T KI+ Sbjct: 233 GTPDYLSPEILQAVGGGPGAGSYGPECDWWALGVFAYEMFYGQTPFYADSTAETYAKIVH 292 Query: 360 FREYLKFPNNVDNVSGKAVDLISNLI 437 +RE+L P V +A DLI L+ Sbjct: 293 YREHLSLPLADTVVPEEAQDLIRGLL 318 >KGP3_DROME (P32023) cGMP-dependent protein kinase, isozyme 2 forms cD5/T2 (EC 2.7.1.37) (CGK) (Foraging protein) Length = 934 Score = 71.6 bits (174), Expect = 6e-13 Identities = 34/83 (40%), Positives = 52/83 (62%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEV++ RG+D S D+WS+GV++FE+L G PPF T I++ + + Sbjct: 781 FCGTPEYVAPEVILNRGHDISADYWSLGVLMFELLTGTPPFTGSDPMRTYNIILKGIDAI 840 Query: 375 KFPNNVDNVSGKAVDLISNLITD 443 +FP N++ A +LI L D Sbjct: 841 EFPR---NITRNASNLIKKLCRD 860 >KGP2_DROME (Q03043) cGMP-dependent protein kinase, isozyme 2 forms cD4/T1/T3A/T3B (EC 2.7.1.37) (CGK) (Foraging protein) Length = 1088 Score = 71.6 bits (174), Expect = 6e-13 Identities = 34/83 (40%), Positives = 52/83 (62%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEV++ RG+D S D+WS+GV++FE+L G PPF T I++ + + Sbjct: 935 FCGTPEYVAPEVILNRGHDISADYWSLGVLMFELLTGTPPFTGSDPMRTYNIILKGIDAI 994 Query: 375 KFPNNVDNVSGKAVDLISNLITD 443 +FP N++ A +LI L D Sbjct: 995 EFPR---NITRNASNLIKKLCRD 1014 >KN8R_YEAST (P53739) Probable serine/threonine-protein kinase YNR047W (EC 2.7.1.37) Length = 893 Score = 71.6 bits (174), Expect = 6e-13 Identities = 33/82 (40%), Positives = 52/82 (63%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+ YIAPEV+ G G+ + DWW++G++++EML+G+ PF D+ T I+ + + Sbjct: 677 FVGTEEYIAPEVIRGNGHTAAVDWWTLGILIYEMLFGFTPFKGDNTNETFTNIL--KNEV 734 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 FPNN + +S DLI L+T Sbjct: 735 SFPNN-NEISRTCKDLIKKLLT 755 >KDC2_DROME (P16912) Protein kinase DC2 (EC 2.7.1.-) Length = 502 Score = 71.2 bits (173), Expect = 8e-13 Identities = 31/81 (38%), Positives = 56/81 (69%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P YIAPE++ +G++ + DWW++GV+++EML GYPPFY++ G +KI+ + +++ Sbjct: 350 GTPEYIAPEIIQSKGHNKAVDWWALGVLIYEMLVGYPPFYDEQPFGIYEKILSGK--IEW 407 Query: 381 PNNVDNVSGKAVDLISNLITD 443 ++D + A DLI L+ + Sbjct: 408 ERHMDPI---AKDLIKKLLVN 425 >CDP2_PLAF7 (Q8ICR0) Calcium-dependent protein kinase 2 (EC 2.7.1.37) (PfCDPK2) Length = 508 Score = 71.2 bits (173), Expect = 8e-13 Identities = 35/80 (43%), Positives = 53/80 (66%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+AP+VL G+ YD CD WS GVI++ +L GYPPFY D+ KK ++ E+ + Sbjct: 230 GTPYYVAPQVLDGK-YDKKCDIWSSGVIMYTLLCGYPPFYGDTDNEVLKK-VKKGEFCFY 287 Query: 381 PNNVDNVSGKAVDLISNLIT 440 N+ ++S A +LI+ L+T Sbjct: 288 ENDWGSISSDAKNLITKLLT 307 >KAPC_DICDI (P34099) cAMP-dependent protein kinase catalytic subunit (EC 2.7.1.37) Length = 648 Score = 71.2 bits (173), Expect = 8e-13 Identities = 34/80 (42%), Positives = 50/80 (62%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE++ +G+ + DWW++G+++FEML GYPPFY+D KI+ R + F Sbjct: 493 GTPEYLAPEIIQSKGHGKAVDWWALGILIFEMLAGYPPFYDDDTFAIYNKILAGR--ITF 550 Query: 381 PNNVDNVSGKAVDLISNLIT 440 P D A DLI L+T Sbjct: 551 PLGFD---VDAKDLIKRLLT 567 >DMK_HUMAN (Q09013) Myotonin-protein kinase (EC 2.7.1.-) (Myotonic dystrophy protein kinase) (MDPK) (DM-kinase) (DMK) (DMPK) (MT-PK) Length = 639 Score = 71.2 bits (173), Expect = 8e-13 Identities = 35/86 (40%), Positives = 50/86 (58%), Gaps = 7/86 (8%) Frame = +3 Query: 201 GSPAYIAPEVL--IGRG-----YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 G+P Y++PE+L +G G Y CDWW++GV +EM YG PFY DS T KI+ Sbjct: 243 GTPDYLSPEILQAVGGGPGTGSYGPECDWWALGVFAYEMFYGQTPFYADSTAETYGKIVH 302 Query: 360 FREYLKFPNNVDNVSGKAVDLISNLI 437 ++E+L P + V +A D I L+ Sbjct: 303 YKEHLSLPLVDEGVPEEARDFIQRLL 328 >PRKX_MOUSE (Q922R0) Serine/threonine-protein kinase PRKX (EC 2.7.1.37) (PKA-related protein kinase) Length = 355 Score = 71.2 bits (173), Expect = 8e-13 Identities = 32/79 (40%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APEV+ +G+ + DWW++G+++FEML G+PPF++D+ G +KI+ + + F Sbjct: 203 GTPEYLAPEVIQSKGHGRAVDWWALGILIFEMLSGFPPFFDDNPFGIYQKILACK--IDF 260 Query: 381 PNNVDNVSGKAVDLISNLI 437 P +D S DLI L+ Sbjct: 261 PRQLDFTS---KDLIKKLL 276 >CDP2_PLAFK (O15865) Calcium-dependent protein kinase 2 (EC 2.7.1.37) (PfCDPK2) Length = 512 Score = 71.2 bits (173), Expect = 8e-13 Identities = 35/80 (43%), Positives = 53/80 (66%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+AP+VL G+ YD CD WS GVI++ +L GYPPFY D+ KK ++ E+ + Sbjct: 230 GTPYYVAPQVLDGK-YDKKCDIWSSGVIMYTLLCGYPPFYGDTDNEVLKK-VKKGEFCFY 287 Query: 381 PNNVDNVSGKAVDLISNLIT 440 N+ ++S A +LI+ L+T Sbjct: 288 ENDWGSISSDAKNLITKLLT 307 >KAPA_CANFA (Q8MJ44) cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) (PKA C-alpha) Length = 349 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 199 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 256 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 257 PS---HFSSDLKDLLRNLL 272 >PRKY_HUMAN (O43930) Serine/threonine-protein kinase PRKY (EC 2.7.1.37) Length = 277 Score = 70.5 bits (171), Expect = 1e-12 Identities = 28/65 (43%), Positives = 48/65 (73%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APEV+ +G+ + DWW++G+++FEML G+PPF++D+ G +KI+ + Y F Sbjct: 206 GTPEYLAPEVIQSKGHGRAVDWWALGILIFEMLSGFPPFFDDNPFGIYQKILAGKLY--F 263 Query: 381 PNNVD 395 P ++D Sbjct: 264 PRHLD 268 >KAPI_BOVIN (P24256) cAMP-dependent protein kinase, beta-2-catalytic subunit (EC 2.7.1.37) (PKA C-beta-2) Length = 397 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 247 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 304 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 305 PS---HFSSDLKDLLRNLL 320 >KAPB_PIG (P05383) cAMP-dependent protein kinase, beta-catalytic subunit (EC 2.7.1.37) (PKA C-beta) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >KAPB_MOUSE (P05206) cAMP-dependent protein kinase, beta-catalytic subunit (EC 2.7.1.37) (PKA C-beta) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >KAPB_HUMAN (P22694) cAMP-dependent protein kinase, beta-catalytic subunit (EC 2.7.1.37) (PKA C-beta) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >KAPB_BOVIN (P05131) cAMP-dependent protein kinase, beta-1 catalytic subunit (EC 2.7.1.37) (PKA C-beta-1) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >KAPA_SHEEP (Q9MZD9) cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) (PKA C-alpha) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >KAPA_RAT (P27791) cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) (PKA C-alpha) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >KAPA_PIG (P36887) cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) (PKA C-alpha) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >KAPA_MOUSE (P05132) cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) (PKA C-alpha) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >KAPA_HUMAN (P17612) cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) (PKA C-alpha) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >KAPA_CRIGR (P25321) cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) (PKA C-alpha) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >KAPA_BOVIN (P00517) cAMP-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) (PKA C-alpha) Length = 350 Score = 70.5 bits (171), Expect = 1e-12 Identities = 30/79 (37%), Positives = 53/79 (67%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 257 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + S DL+ NL+ Sbjct: 258 PS---HFSSDLKDLLRNLL 273 >PRKX_HUMAN (P51817) Serine/threonine-protein kinase PRKX (EC 2.7.1.37) (Protein kinase PKX1) Length = 358 Score = 69.3 bits (168), Expect = 3e-12 Identities = 27/65 (41%), Positives = 48/65 (73%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APEV+ +G+ + DWW++G+++FEML G+PPF++D+ G +KI+ + + F Sbjct: 206 GTPEYLAPEVIQSKGHGRAVDWWALGILIFEMLSGFPPFFDDNPFGIYQKILAGK--IDF 263 Query: 381 PNNVD 395 P ++D Sbjct: 264 PRHLD 268 >KAPG_HUMAN (P22612) cAMP-dependent protein kinase, gamma-catalytic subunit (EC 2.7.1.37) (PKA C-gamma) Length = 350 Score = 69.3 bits (168), Expect = 3e-12 Identities = 26/66 (39%), Positives = 47/66 (71%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM G+PPFY D +KI+ R ++F Sbjct: 200 GTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAVGFPPFYADQPIQIYEKIVSGR--VRF 257 Query: 381 PNNVDN 398 P+ + + Sbjct: 258 PSKLSS 263 >KAPB_YEAST (P06245) cAMP-dependent protein kinase type 2 (EC 2.7.1.37) (PKA 2) Length = 380 Score = 69.3 bits (168), Expect = 3e-12 Identities = 36/80 (45%), Positives = 52/80 (65%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P YIAPEV+ + Y+ S DWWS+GV+++EML GY PFY+ + T +KI+Q + + + Sbjct: 227 GTPDYIAPEVITTKPYNKSVDWWSLGVLIYEMLAGYTPFYDTTPMKTYEKILQGK--VVY 284 Query: 381 PNNVDNVSGKAVDLISNLIT 440 P VDL+S LIT Sbjct: 285 P---PYFHPDVVDLLSKLIT 301 >KRAC_DICDI (P54644) RAC-family serine/threonine-protein kinase homolog (EC 2.7.1.37) Length = 444 Score = 69.3 bits (168), Expect = 3e-12 Identities = 33/64 (51%), Positives = 40/64 (62%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL G GY DWWS G +L+EML G PPFYN +KI+ E L Sbjct: 279 FCGTPEYLAPEVLQGNGYGKQVDWWSFGSLLYEMLTGLPPFYNQDVQEMYRKIMM--EKL 336 Query: 375 KFPN 386 FP+ Sbjct: 337 SFPH 340 >PK2_DICDI (P28178) Protein kinase 2 (EC 2.7.1.-) Length = 479 Score = 68.9 bits (167), Expect = 4e-12 Identities = 35/82 (42%), Positives = 51/82 (62%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL G G+ + DWWS+G +L+EML G PPFY+ + + +KI+ L Sbjct: 310 FCGTPEYLAPEVLNGHGHGCAVDWWSLGTLLYEMLTGLPPFYSQNVSTMYQKILNGE--L 367 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 K P +S +A L+ L+T Sbjct: 368 KIPT---YISPEAKSLLEGLLT 386 >KAPC_DROME (P12370) cAMP-dependent protein kinase catalytic subunit (EC 2.7.1.37) (PKA C) Length = 352 Score = 68.6 bits (166), Expect = 5e-12 Identities = 29/79 (36%), Positives = 52/79 (65%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+++ +GY+ + DWW++GV+++EM GYPPF+ D +KI+ + ++F Sbjct: 202 GTPEYLAPEIILSKGYNKAVDWWALGVLVYEMAAGYPPFFADQPIQIYEKIVSGK--VRF 259 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ + DL+ NL+ Sbjct: 260 PS---HFGSDLKDLLRNLL 275 >KGPB_MOUSE (Q9Z0Z0) cGMP-dependent protein kinase 1, beta isozyme (EC 2.7.1.37) (CGK 1 beta) (cGKI-beta) Length = 686 Score = 68.2 bits (165), Expect = 7e-12 Identities = 34/114 (29%), Positives = 61/114 (53%), Gaps = 3/114 (2%) Frame = +3 Query: 111 PQKPFASARAAFERVGWRCGARVGMGAP---FFGSPAYIAPEVLIGRGYDYSCDWWSVGV 281 P+ R + V + ++G G F G+P Y+APE+++ +G+D S D+WS+G+ Sbjct: 502 PENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISADYWSLGI 561 Query: 282 ILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLITD 443 +++E+L G PPF T I++ + ++FP ++ A +LI L D Sbjct: 562 LMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPK---KIAKNAANLIKKLCRD 612 >KGPB_HUMAN (P14619) cGMP-dependent protein kinase 1, beta isozyme (EC 2.7.1.37) (cGK 1 beta) (cGKI-beta) Length = 686 Score = 68.2 bits (165), Expect = 7e-12 Identities = 34/114 (29%), Positives = 61/114 (53%), Gaps = 3/114 (2%) Frame = +3 Query: 111 PQKPFASARAAFERVGWRCGARVGMGAP---FFGSPAYIAPEVLIGRGYDYSCDWWSVGV 281 P+ R + V + ++G G F G+P Y+APE+++ +G+D S D+WS+G+ Sbjct: 502 PENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISADYWSLGI 561 Query: 282 ILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLITD 443 +++E+L G PPF T I++ + ++FP ++ A +LI L D Sbjct: 562 LMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPK---KIAKNAANLIKKLCRD 612 >KGPB_BOVIN (P21136) cGMP-dependent protein kinase 1, beta isozyme (EC 2.7.1.37) (CGK 1 beta) (cGKI-beta) Length = 686 Score = 68.2 bits (165), Expect = 7e-12 Identities = 34/114 (29%), Positives = 61/114 (53%), Gaps = 3/114 (2%) Frame = +3 Query: 111 PQKPFASARAAFERVGWRCGARVGMGAP---FFGSPAYIAPEVLIGRGYDYSCDWWSVGV 281 P+ R + V + ++G G F G+P Y+APE+++ +G+D S D+WS+G+ Sbjct: 502 PENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISADYWSLGI 561 Query: 282 ILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLITD 443 +++E+L G PPF T I++ + ++FP ++ A +LI L D Sbjct: 562 LMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPK---KIAKNAANLIKKLCRD 612 >KGPA_RABIT (O77676) cGMP-dependent protein kinase 1, alpha isozyme (EC 2.7.1.37) (CGK 1 alpha) (cGKI-alpha) Length = 670 Score = 68.2 bits (165), Expect = 7e-12 Identities = 34/114 (29%), Positives = 61/114 (53%), Gaps = 3/114 (2%) Frame = +3 Query: 111 PQKPFASARAAFERVGWRCGARVGMGAP---FFGSPAYIAPEVLIGRGYDYSCDWWSVGV 281 P+ R + V + ++G G F G+P Y+APE+++ +G+D S D+WS+G+ Sbjct: 486 PENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISADYWSLGI 545 Query: 282 ILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLITD 443 +++E+L G PPF T I++ + ++FP ++ A +LI L D Sbjct: 546 LMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPK---KIAKNAANLIKKLCRD 596 >KGPA_HUMAN (Q13976) cGMP-dependent protein kinase 1, alpha isozyme (EC 2.7.1.37) (CGK 1 alpha) (cGKI-alpha) Length = 670 Score = 68.2 bits (165), Expect = 7e-12 Identities = 34/114 (29%), Positives = 61/114 (53%), Gaps = 3/114 (2%) Frame = +3 Query: 111 PQKPFASARAAFERVGWRCGARVGMGAP---FFGSPAYIAPEVLIGRGYDYSCDWWSVGV 281 P+ R + V + ++G G F G+P Y+APE+++ +G+D S D+WS+G+ Sbjct: 486 PENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISADYWSLGI 545 Query: 282 ILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLITD 443 +++E+L G PPF T I++ + ++FP ++ A +LI L D Sbjct: 546 LMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPK---KIAKNAANLIKKLCRD 596 >KGPA_BOVIN (P00516) cGMP-dependent protein kinase 1, alpha isozyme (EC 2.7.1.37) (CGK 1 alpha) (CGKI-alpha) Length = 670 Score = 68.2 bits (165), Expect = 7e-12 Identities = 34/114 (29%), Positives = 61/114 (53%), Gaps = 3/114 (2%) Frame = +3 Query: 111 PQKPFASARAAFERVGWRCGARVGMGAP---FFGSPAYIAPEVLIGRGYDYSCDWWSVGV 281 P+ R + V + ++G G F G+P Y+APE+++ +G+D S D+WS+G+ Sbjct: 486 PENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISADYWSLGI 545 Query: 282 ILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLITD 443 +++E+L G PPF T I++ + ++FP ++ A +LI L D Sbjct: 546 LMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPK---KIAKNAANLIKKLCRD 596 >KAPC_YEAST (P05986) cAMP-dependent protein kinase type 3 (EC 2.7.1.37) (PKA 3) Length = 398 Score = 68.2 bits (165), Expect = 7e-12 Identities = 37/80 (46%), Positives = 48/80 (60%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P YIAPEV+ + Y+ S DWWS GV+++EML GY PFYN + T + I+ LKF Sbjct: 245 GTPDYIAPEVVSTKPYNKSVDWWSFGVLIYEMLAGYTPFYNSNTMKTYENILNAE--LKF 302 Query: 381 PNNVDNVSGKAVDLISNLIT 440 P A DL+ LIT Sbjct: 303 P---PFFHPDAQDLLKKLIT 319 >KAPA_YEAST (P06244) cAMP-dependent protein kinase type 1 (EC 2.7.1.37) (PKA 1) (CDC25 suppressing protein kinase) (PK-25) Length = 397 Score = 67.8 bits (164), Expect = 9e-12 Identities = 35/80 (43%), Positives = 50/80 (62%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P YIAPEV+ + Y+ S DWWS G++++EML GY PFY+ + T +KI+ L+F Sbjct: 244 GTPDYIAPEVVSTKPYNKSIDWWSFGILIYEMLAGYTPFYDSNTMKTYEKILNAE--LRF 301 Query: 381 PNNVDNVSGKAVDLISNLIT 440 P + DL+S LIT Sbjct: 302 PPFFNE---DVKDLLSRLIT 318 >SGK1_RAT (Q06226) Serine/threonine-protein kinase Sgk1 (EC 2.7.1.37) (Serum/glucocorticoid-regulated kinase 1) Length = 430 Score = 67.8 bits (164), Expect = 9e-12 Identities = 34/86 (39%), Positives = 50/86 (58%) Frame = +3 Query: 180 GMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 G + F G+P Y+APEVL + YD + DWW +G +L+EMLYG PPFY+ TA+ Sbjct: 252 GTTSTFCGTPEYLAPEVLHKQPYDRTVDWWCLGAVLYEMLYGLPPFYS---RNTAE---M 305 Query: 360 FREYLKFPNNVDNVSGKAVDLISNLI 437 + L P + N++ A L+ L+ Sbjct: 306 YDNILNKPLQLKNITNSARHLLEGLL 331 >KGP2_HUMAN (Q13237) cGMP-dependent protein kinase 2 (EC 2.7.1.37) (CGK 2) (cGKII) (Type II cGMP-dependent protein kinase) Length = 762 Score = 67.8 bits (164), Expect = 9e-12 Identities = 35/111 (31%), Positives = 61/111 (54%), Gaps = 3/111 (2%) Frame = +3 Query: 111 PQKPFASARAAFERVGWRCGARVGMGAP---FFGSPAYIAPEVLIGRGYDYSCDWWSVGV 281 P+ A + V + ++G G F G+P Y+APEV++ +G+D+S D+WS+G+ Sbjct: 579 PENLILDAEGYLKLVDFGFAKKIGSGQKTWTFCGTPEYVAPEVILNKGHDFSVDFWSLGI 638 Query: 282 ILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFPNNVDNVSGKAVDLISNL 434 +++E+L G PPF + T I++ E + FP ++ + DLI L Sbjct: 639 LVYELLTGNPPFSGVDQMMTYNLILKGIEKMDFPR---KITRRPEDLIRRL 686 >KPCN_HUMAN (O94806) Protein kinase C, nu type (EC 2.7.1.-) (nPKC-nu) (Protein kinase EPK2) Length = 890 Score = 67.4 bits (163), Expect = 1e-11 Identities = 36/79 (45%), Positives = 49/79 (62%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+PAY+APEVL +GY+ S D WSVGVI++ L G PF D IQ ++ Sbjct: 738 GTPAYLAPEVLRSKGYNRSLDMWSVGVIIYVSLSGTFPFNEDEDINDQ---IQNAAFMYP 794 Query: 381 PNNVDNVSGKAVDLISNLI 437 PN +SG+A+DLI+NL+ Sbjct: 795 PNPWREISGEAIDLINNLL 813 >KGP2_RAT (Q64595) cGMP-dependent protein kinase 2 (EC 2.7.1.37) (CGK 2) (cGKII) (Type II cGMP-dependent protein kinase) Length = 762 Score = 67.0 bits (162), Expect = 1e-11 Identities = 35/111 (31%), Positives = 61/111 (54%), Gaps = 3/111 (2%) Frame = +3 Query: 111 PQKPFASARAAFERVGWRCGARVGMGAP---FFGSPAYIAPEVLIGRGYDYSCDWWSVGV 281 P+ A + V + ++G G F G+P Y+APEV++ +G+D+S D+WS+G+ Sbjct: 579 PENLILDADGYLKLVDFGFAKKIGSGQKTWTFCGTPEYVAPEVILNKGHDFSVDFWSLGI 638 Query: 282 ILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFPNNVDNVSGKAVDLISNL 434 +++E+L G PPF + T I++ E + FP ++ + DLI L Sbjct: 639 LVYELLTGNPPFSGIDQMMTYNLILKGIEKMDFPR---KITRRPEDLIRRL 686 >KGP2_MOUSE (Q61410) cGMP-dependent protein kinase 2 (EC 2.7.1.37) (CGK 2) (cGKII) (Type II cGMP-dependent protein kinase) Length = 762 Score = 67.0 bits (162), Expect = 1e-11 Identities = 35/111 (31%), Positives = 61/111 (54%), Gaps = 3/111 (2%) Frame = +3 Query: 111 PQKPFASARAAFERVGWRCGARVGMGAP---FFGSPAYIAPEVLIGRGYDYSCDWWSVGV 281 P+ A + V + ++G G F G+P Y+APEV++ +G+D+S D+WS+G+ Sbjct: 579 PENLILDADGYLKLVDFGFAKKIGSGQKTWTFCGTPEYVAPEVILNKGHDFSVDFWSLGI 638 Query: 282 ILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFPNNVDNVSGKAVDLISNL 434 +++E+L G PPF + T I++ E + FP ++ + DLI L Sbjct: 639 LVYELLTGNPPFSGIDQMMTYNLILKGIEKMDFPR---KITRRPEDLIRRL 686 >KAPB_SCHPO (P40376) cAMP-dependent protein kinase catalytic subunit (EC 2.7.1.37) Length = 512 Score = 67.0 bits (162), Expect = 1e-11 Identities = 29/79 (36%), Positives = 55/79 (69%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE++ + Y+ + DWWS+G+++FEML GYPPFY+++ + I++ + + + Sbjct: 359 GTPDYLAPEIISLKPYNKAADWWSLGILIFEMLAGYPPFYSENPMKLYENILEGK--VNY 416 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ S ++DL+S+L+ Sbjct: 417 PS---YFSPASIDLLSHLL 432 >DBF2_YEAST (P22204) Cell cycle protein kinase DBF2 (EC 2.7.1.37) Length = 572 Score = 67.0 bits (162), Expect = 1e-11 Identities = 35/84 (41%), Positives = 50/84 (59%), Gaps = 3/84 (3%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 GSP Y+A EVL G+ YD++ D+WS+G +LFE L GY PF S T + ++++ L+ Sbjct: 377 GSPDYMALEVLEGKKYDFTVDYWSLGCMLFESLVGYTPFSGSSTNETYDNLRRWKQTLRR 436 Query: 381 PNNVDN---VSGKAVDLISNLITD 443 P D S + DLI+ LI D Sbjct: 437 PRQSDGRAAFSDRTWDLITRLIAD 460 >DBFB_YEAST (P32328) Serine/threonine-protein kinase DBF20 (EC 2.7.1.37) Length = 564 Score = 66.6 bits (161), Expect = 2e-11 Identities = 35/84 (41%), Positives = 50/84 (59%), Gaps = 3/84 (3%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 GSP Y+A EVL G+ YD++ D+WS+G +LFE L GY PF S T + + +++ L+ Sbjct: 369 GSPDYMALEVLEGKKYDFTVDYWSLGCMLFESLVGYTPFSGSSTNETYENLRYWKKTLRR 428 Query: 381 PNNVDN---VSGKAVDLISNLITD 443 P D S + DLI+ LI D Sbjct: 429 PRTEDRRAAFSDRTWDLITRLIAD 452 >NPH1_ARATH (O48963) Nonphototropic hypocotyl protein 1 (EC 2.7.1.37) (Phototropin) Length = 996 Score = 66.2 bits (160), Expect = 3e-11 Identities = 27/66 (40%), Positives = 45/66 (68%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+ YIAPE++ G G+ + DWW++G++++EMLYGY PF ++ T ++Q + L Sbjct: 852 FVGTEEYIAPEIISGAGHTSAVDWWALGILMYEMLYGYTPFRGKTRQKTFTNVLQ--KDL 909 Query: 375 KFPNNV 392 KFP ++ Sbjct: 910 KFPASI 915 >SGK1_RABIT (Q9XT18) Serine/threonine-protein kinase Sgk1 (EC 2.7.1.37) (Serum/glucocorticoid-regulated kinase 1) Length = 431 Score = 65.9 bits (159), Expect = 3e-11 Identities = 33/86 (38%), Positives = 48/86 (55%) Frame = +3 Query: 180 GMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 G + F G+P Y+APEVL + YD + DWW +G +L+EMLYG PPFY+ + I+ Sbjct: 252 GTTSTFCGTPEYLAPEVLHKQPYDRTVDWWCLGAVLYEMLYGLPPFYSRNTAEMYDNILN 311 Query: 360 FREYLKFPNNVDNVSGKAVDLISNLI 437 LK N++ A L+ L+ Sbjct: 312 KPLQLK-----PNITNSARHLLEGLL 332 >SGK1_MOUSE (Q9WVC6) Serine/threonine-protein kinase Sgk1 (EC 2.7.1.37) (Serum/glucocorticoid-regulated kinase 1) Length = 431 Score = 65.9 bits (159), Expect = 3e-11 Identities = 33/86 (38%), Positives = 48/86 (55%) Frame = +3 Query: 180 GMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 G + F G+P Y+APEVL + YD + DWW +G +L+EMLYG PPFY+ + I+ Sbjct: 252 GTTSTFCGTPEYLAPEVLHKQPYDRTVDWWCLGAVLYEMLYGLPPFYSRNTAEMYDNILN 311 Query: 360 FREYLKFPNNVDNVSGKAVDLISNLI 437 LK N++ A L+ L+ Sbjct: 312 KPLQLK-----PNITNSARHLLEGLL 332 >PLO1_SCHPO (P50528) Serine/threonine-protein kinase plo1 (EC 2.7.1.37) Length = 683 Score = 65.5 bits (158), Expect = 4e-11 Identities = 36/82 (43%), Positives = 52/82 (63%), Gaps = 2/82 (2%) Frame = +3 Query: 201 GSPAYIAPEVLIG--RGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 G+P YIAPE+L G+ + D WS GV+++ +L G PPF D + T + I+ Y Sbjct: 200 GTPNYIAPEILFNSKEGHSFEVDLWSAGVVMYALLIGKPPF-QDKEVKTIYRKIKANSY- 257 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 FP+NVD +S +A DLIS+L+T Sbjct: 258 SFPSNVD-ISAEAKDLISSLLT 278 >KI82_YEAST (P25341) Probable serine/threonine-protein kinase KIN82 (EC 2.7.1.37) Length = 720 Score = 65.1 bits (157), Expect = 6e-11 Identities = 31/81 (38%), Positives = 51/81 (62%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+ Y+APEV+ G G+ + DWW++G++++EML+G PF D+ T I+ + + Sbjct: 502 FVGTEEYLAPEVIRGNGHTAAVDWWTLGILIYEMLFGCTPFKGDNSNETFSNIL--TKDV 559 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 KFP++ + VS DLI L+ Sbjct: 560 KFPHDKE-VSKNCKDLIKKLL 579 >KPCD_MOUSE (P28867) Protein kinase C, delta type (EC 2.7.1.-) (nPKC-delta) Length = 674 Score = 64.7 bits (156), Expect = 7e-11 Identities = 27/51 (52%), Positives = 35/51 (68%) Frame = +3 Query: 180 GMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSK 332 G + F G+P YIAPE+L G Y +S DWWS GV+L+EML G PF+ D + Sbjct: 501 GRASTFCGTPDYIAPEILQGLKYSFSVDWWSFGVLLYEMLIGQSPFHGDDE 551 >SGK1_HUMAN (O00141) Serine/threonine-protein kinase Sgk1 (EC 2.7.1.37) (Serum/glucocorticoid-regulated kinase 1) Length = 431 Score = 64.7 bits (156), Expect = 7e-11 Identities = 32/81 (39%), Positives = 46/81 (56%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL + YD + DWW +G +L+EMLYG PPFY+ + I+ L Sbjct: 257 FCGTPEYLAPEVLHKQPYDRTVDWWCLGAVLYEMLYGLPPFYSRNTAEMYDNILNKPLQL 316 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 K N++ A L+ L+ Sbjct: 317 K-----PNITNSARHLLEGLL 332 >KPCM_MOUSE (Q62101) Protein kinase C, mu type (EC 2.7.1.-) (nPKC-mu) (Protein kinase D) Length = 918 Score = 63.9 bits (154), Expect = 1e-10 Identities = 35/79 (44%), Positives = 48/79 (60%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+PAY+APEVL +GY+ S D WSVGVI++ L G PF D IQ ++ Sbjct: 751 GTPAYLAPEVLRNKGYNRSLDMWSVGVIIYVSLSGTFPFNEDEDIHDQ---IQNAAFMYP 807 Query: 381 PNNVDNVSGKAVDLISNLI 437 PN +S +A+DLI+NL+ Sbjct: 808 PNPWKEISHEAIDLINNLL 826 >CEK1_SCHPO (P38938) Serine/threonine-protein kinase cek1 (EC 2.7.1.37) Length = 1338 Score = 63.9 bits (154), Expect = 1e-10 Identities = 33/82 (40%), Positives = 49/82 (59%), Gaps = 1/82 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPEV++G + DWWS+G ++FE L+GYPPF ++ + I+ R + Sbjct: 857 FIGTPDYIAPEVILGNPGIKASDWWSLGCVVFEFLFGYPPFNAETPDQVFQNILARR--I 914 Query: 375 KFPNNVDNV-SGKAVDLISNLI 437 +P V S A+DLI L+ Sbjct: 915 NWPAEVFTAESSVALDLIDRLL 936 >KPCM_HUMAN (Q15139) Protein kinase C, mu type (EC 2.7.1.-) (nPKC-mu) (Protein kinase D) Length = 912 Score = 63.9 bits (154), Expect = 1e-10 Identities = 35/79 (44%), Positives = 48/79 (60%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+PAY+APEVL +GY+ S D WSVGVI++ L G PF D IQ ++ Sbjct: 745 GTPAYLAPEVLRNKGYNRSLDMWSVGVIIYVSLSGTFPFNEDEDIHDQ---IQNAAFMYP 801 Query: 381 PNNVDNVSGKAVDLISNLI 437 PN +S +A+DLI+NL+ Sbjct: 802 PNPWKEISHEAIDLINNLL 820 >CDP3_PLAYO (Q7RAV5) Calcium-dependent protein kinase 3 (EC 2.7.1.37) Length = 538 Score = 63.9 bits (154), Expect = 1e-10 Identities = 33/80 (41%), Positives = 47/80 (58%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+AP+VL G YDY CD WS GV+ + +L GYPPFY +S + + + K Sbjct: 272 GTPYYVAPQVLTGC-YDYKCDLWSAGVLFYIILCGYPPFYGESDHEILSMVKKGKYNFK- 329 Query: 381 PNNVDNVSGKAVDLISNLIT 440 +N+S +A DLI +T Sbjct: 330 GKEWNNISDEAKDLIKRCLT 349 >KPCT_HUMAN (Q04759) Protein kinase C, theta type (EC 2.7.1.-) (nPKC-theta) Length = 706 Score = 63.5 bits (153), Expect = 2e-10 Identities = 25/46 (54%), Positives = 35/46 (76%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSK 332 F G+P YIAPE+L+G+ Y++S DWWS GV+L+EML G PF+ + Sbjct: 539 FCGTPDYIAPEILLGQKYNHSVDWWSFGVLLYEMLIGQSPFHGQDE 584 >KMLC_DICDI (P25323) Myosin light chain kinase (EC 2.7.1.117) (MLCK) Length = 295 Score = 63.5 bits (153), Expect = 2e-10 Identities = 32/80 (40%), Positives = 48/80 (60%), Gaps = 1/80 (1%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P+Y+APEVL GYD D WS+GVI + +L G+PPFY D+ ++I++ +F Sbjct: 169 GTPSYVAPEVLNATGYDKEVDMWSIGVITYILLCGFPPFYGDTVPEIFEQIMEAN--YEF 226 Query: 381 PNNV-DNVSGKAVDLISNLI 437 P +S +A D I L+ Sbjct: 227 PEEYWGGISKEAKDFIGKLL 246 >NRC2_NEUCR (O42626) Serine/threonine-protein kinase nrc-2 (EC 2.7.1.37) (Nonrepressible conidiation protein 2) Length = 623 Score = 63.5 bits (153), Expect = 2e-10 Identities = 31/83 (37%), Positives = 49/83 (59%), Gaps = 2/83 (2%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+ YIAPEV+ G G+ + DWW++G++++EMLYG PF ++ T I+ RE + Sbjct: 429 FVGTEEYIAPEVIKGSGHTSAVDWWTLGILIYEMLYGTTPFKGKNRNATFANIL--REDI 486 Query: 375 KFPNN--VDNVSGKAVDLISNLI 437 FP++ +S LI L+ Sbjct: 487 PFPDHAGAPQISNLCKSLIRKLL 509 >SID2_SCHPO (Q09898) Serine/threonine-protein kinase sid2 (EC 2.7.1.37) Length = 607 Score = 62.8 bits (151), Expect = 3e-10 Identities = 33/87 (37%), Positives = 49/87 (56%), Gaps = 6/87 (6%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 GSP Y+APEVL G Y++S D+WS+G I++E L G+PPF + T + +R+ + Sbjct: 405 GSPDYMAPEVLRGENYNHSVDYWSLGCIMYECLSGFPPFSGSNVNETWSNLKNWRKCFQR 464 Query: 381 PNNVD------NVSGKAVDLISNLITD 443 P+ D N A D + + ITD Sbjct: 465 PHYDDPRDLEFNWRDDAWDFVCHCITD 491 >KPK1_ARATH (P42818) Serine/threonine-protein kinase AtPK1/AtPK6 (EC 2.7.1.37) Length = 465 Score = 62.8 bits (151), Expect = 3e-10 Identities = 29/66 (43%), Positives = 45/66 (68%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ Y+APE++ G+G+D + DWWSVG++L+EML G PPF SK +KI+ ++ +K Sbjct: 293 GTTEYMAPEIVRGKGHDKAADWWSVGILLYEMLTGKPPFLG-SKGKIQQKIV--KDKIKL 349 Query: 381 PNNVDN 398 P + N Sbjct: 350 PQFLSN 355 >KP19_ARATH (Q39030) Serine/threonine-protein kinase AtPK19 (EC 2.7.1.37) (Ribosomal-protein S6 kinase homolog) Length = 471 Score = 62.8 bits (151), Expect = 3e-10 Identities = 29/66 (43%), Positives = 45/66 (68%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ Y+APE++ G+G+D + DWWSVG++L+EML G PPF SK +KI+ ++ +K Sbjct: 299 GTTEYMAPEIVRGKGHDKAADWWSVGILLYEMLTGKPPFLG-SKGKIQQKIV--KDKIKL 355 Query: 381 PNNVDN 398 P + N Sbjct: 356 PQFLSN 361 >KPCD_RAT (P09215) Protein kinase C, delta type (EC 2.7.1.-) (nPKC-delta) Length = 673 Score = 62.8 bits (151), Expect = 3e-10 Identities = 26/46 (56%), Positives = 33/46 (71%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSK 332 F G+P YIAPE+L G Y +S DWWS GV+L+EML G PF+ D + Sbjct: 506 FCGTPDYIAPEILQGLKYSFSVDWWSFGVLLYEMLIGQSPFHGDDE 551 >KPC1_CAEEL (P34722) Protein kinase C-like 1 (EC 2.7.1.-) (PKC) (Tetradecanoyl phorbol acetate resistant protein 1) Length = 704 Score = 62.8 bits (151), Expect = 3e-10 Identities = 28/82 (34%), Positives = 48/82 (58%) Frame = +3 Query: 180 GMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 GM + F G+P YI+PE++ G+ Y+ + D+WS GV+++EML G PF+ + + I+ Sbjct: 530 GMASTFCGTPDYISPEIIKGQLYNEAVDFWSFGVLMYEMLVGQSPFHGEGEDELFDSILN 589 Query: 360 FREYLKFPNNVDNVSGKAVDLI 425 R Y FP + + K + + Sbjct: 590 ERPY--FPKTISKEAAKCLSAL 609 >KGP1_DROME (Q03042) cGMP-dependent protein kinase, isozyme 1 (EC 2.7.1.37) (CGK) Length = 768 Score = 62.8 bits (151), Expect = 3e-10 Identities = 29/83 (34%), Positives = 50/83 (60%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APE+++ +G+D + D+W++G+++ E+L G PPF T I++ + + Sbjct: 616 FCGTPEYVAPEIILNKGHDRAVDYWALGILIHELLNGTPPFSAPDPMQTYNLILKGIDMI 675 Query: 375 KFPNNVDNVSGKAVDLISNLITD 443 FP ++S AV LI L D Sbjct: 676 AFPK---HISRWAVQLIKRLCRD 695 >KPCD_HUMAN (Q05655) Protein kinase C, delta type (EC 2.7.1.-) (nPKC-delta) Length = 676 Score = 62.4 bits (150), Expect = 4e-10 Identities = 26/46 (56%), Positives = 33/46 (71%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSK 332 F G+P YIAPE+L G Y +S DWWS GV+L+EML G PF+ D + Sbjct: 508 FCGTPDYIAPEILQGLKYTFSVDWWSFGVLLYEMLIGQSPFHGDDE 553 >KPCT_MOUSE (Q02111) Protein kinase C, theta type (EC 2.7.1.-) (nPKC-theta) Length = 707 Score = 62.4 bits (150), Expect = 4e-10 Identities = 24/46 (52%), Positives = 35/46 (76%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSK 332 F G+P YIAPE+L+G+ Y++S DWWS GV+++EML G PF+ + Sbjct: 539 FCGTPDYIAPEILLGQKYNHSVDWWSFGVLVYEMLIGQSPFHGQDE 584 >SGK3_MOUSE (Q9ERE3) Serine/threonine-protein kinase Sgk3 (EC 2.7.1.37) (Serum/glucocorticoid regulated kinase 3) (Serum/glucocorticoid regulated kinase-like) (Cytokine independent survival kinase) Length = 496 Score = 62.4 bits (150), Expect = 4e-10 Identities = 24/42 (57%), Positives = 32/42 (76%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFY 320 F G+P Y+APEV+ + YD + DWW +G +L+EMLYG PPFY Sbjct: 321 FCGTPEYLAPEVIRKQPYDNTVDWWCLGAVLYEMLYGLPPFY 362 >SGK3_HUMAN (Q96BR1) Serine/threonine-protein kinase Sgk3 (EC 2.7.1.37) (Serum/glucocorticoid regulated kinase 3) (Serum/glucocorticoid regulated kinase-like) Length = 496 Score = 62.4 bits (150), Expect = 4e-10 Identities = 24/42 (57%), Positives = 32/42 (76%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFY 320 F G+P Y+APEV+ + YD + DWW +G +L+EMLYG PPFY Sbjct: 321 FCGTPEYLAPEVIRKQPYDNTVDWWCLGAVLYEMLYGLPPFY 362 >DUN1_YEAST (P39009) DNA damage response protein kinase DUN1 (EC 2.7.1.-) Length = 513 Score = 62.0 bits (149), Expect = 5e-10 Identities = 31/79 (39%), Positives = 45/79 (56%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P+Y+APEVL +GY D WS GVIL+ L G+PPF + + K+ I +Y + Sbjct: 383 GTPSYVAPEVLTKKGYTSKVDLWSAGVILYVCLCGFPPFSDQLGPPSLKEQILQAKYAFY 442 Query: 381 PNNVDNVSGKAVDLISNLI 437 D + + LISNL+ Sbjct: 443 SPYWDKIDDSVLHLISNLL 461 >CHK2_HUMAN (O96017) Serine/threonine-protein kinase Chk2 (EC 2.7.1.37) (Cds1) Length = 543 Score = 62.0 bits (149), Expect = 5e-10 Identities = 35/82 (42%), Positives = 46/82 (56%), Gaps = 3/82 (3%) Frame = +3 Query: 201 GSPAYIAPEVLIG---RGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREY 371 G+P Y+APEVL+ GY+ + D WS+GVILF L GYPPF + K I +Y Sbjct: 386 GTPTYLAPEVLVSVGTAGYNRAVDCWSLGVILFICLSGYPPFSEHRTQVSLKDQITSGKY 445 Query: 372 LKFPNNVDNVSGKAVDLISNLI 437 P VS KA+DL+ L+ Sbjct: 446 NFIPEVWAEVSEKALDLVKKLL 467 >AKT3_RAT (Q63484) RAC-gamma serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-gamma) (Protein kinase Akt-3) (Protein kinase B, gamma) (PKB gamma) Length = 454 Score = 61.6 bits (148), Expect = 6e-10 Identities = 32/81 (39%), Positives = 46/81 (56%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 306 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILM--EDI 363 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 KFP +S A L+S L+ Sbjct: 364 KFPR---TLSSDAKSLLSGLL 381 >KCC1_HUMAN (Q14012) Calcium/calmodulin-dependent protein kinase type I (EC 2.7.1.123) (CaM kinase I) Length = 370 Score = 61.6 bits (148), Expect = 6e-10 Identities = 31/79 (39%), Positives = 49/79 (62%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APEVL + Y + D WS+GVI + +L GYPPFY+++ ++I++ EY Sbjct: 180 GTPGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDAKLFEQILK-AEYEFD 238 Query: 381 PNNVDNVSGKAVDLISNLI 437 D++S A D I +L+ Sbjct: 239 SPYWDDISDSAKDFIRHLM 257 >SGK2_RAT (Q8R4U9) Serine/threonine-protein kinase Sgk2 (EC 2.7.1.37) (Serum/glucocorticoid regulated kinase 2) (Fragment) Length = 302 Score = 61.6 bits (148), Expect = 6e-10 Identities = 24/43 (55%), Positives = 32/43 (74%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYN 323 F G+P Y+APEVL YD + DWW +G +L+EML+G PPF+N Sbjct: 177 FCGTPEYLAPEVLRKEPYDRAVDWWCLGAVLYEMLHGLPPFFN 219 >MKK2_MOUSE (P49138) MAP kinase-activated protein kinase 2 (EC 2.7.1.-) (MAPK-activated protein kinase 2) (MAPKAP kinase 2) (MAPKAPK-2) (Fragment) Length = 385 Score = 61.6 bits (148), Expect = 6e-10 Identities = 36/82 (43%), Positives = 50/82 (60%), Gaps = 4/82 (4%) Frame = +3 Query: 204 SPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTA---KKIIQFREYL 374 +P Y+APEVL YD SCD WS+GVI++ +L GYPPFY++ + K I+ +Y Sbjct: 211 TPYYVAPEVLGPEKYDKSCDMWSLGVIMYILLCGYPPFYSNHGLAISPGMKTRIRMGQY- 269 Query: 375 KFPN-NVDNVSGKAVDLISNLI 437 +FPN VS + LI NL+ Sbjct: 270 EFPNPEWSEVSEEVKMLIRNLL 291 >MKK2_CRILO (P49136) MAP kinase-activated protein kinase 2 (EC 2.7.1.-) (MAPK-activated protein kinase 2) (MAPKAP kinase 2) (MAPKAPK-2) (P45-54 HSP27 kinase) (Fragment) Length = 329 Score = 61.6 bits (148), Expect = 6e-10 Identities = 36/82 (43%), Positives = 50/82 (60%), Gaps = 4/82 (4%) Frame = +3 Query: 204 SPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTA---KKIIQFREYL 374 +P Y+APEVL YD SCD WS+GVI++ +L GYPPFY++ + K I+ +Y Sbjct: 155 TPYYVAPEVLGPEKYDKSCDMWSLGVIMYILLCGYPPFYSNHGLAISPGMKTRIRMGQY- 213 Query: 375 KFPN-NVDNVSGKAVDLISNLI 437 +FPN VS + LI NL+ Sbjct: 214 EFPNPEWSEVSEEVKMLIRNLL 235 >SGK2_MOUSE (Q9QZS5) Serine/threonine-protein kinase Sgk2 (EC 2.7.1.37) (Serum/glucocorticoid regulated kinase 2) Length = 367 Score = 61.6 bits (148), Expect = 6e-10 Identities = 24/43 (55%), Positives = 32/43 (74%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYN 323 F G+P Y+APEVL YD + DWW +G +L+EML+G PPF+N Sbjct: 194 FCGTPEYLAPEVLRKEPYDRAVDWWCLGAVLYEMLHGLPPFFN 236 >SGK2_HUMAN (Q9HBY8) Serine/threonine-protein kinase Sgk2 (EC 2.7.1.37) (Serum/glucocorticoid regulated kinase 2) Length = 427 Score = 61.6 bits (148), Expect = 6e-10 Identities = 25/54 (46%), Positives = 36/54 (66%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKII 356 F G+P Y+APEVL YD + DWW +G +L+EML+G PPFY+ + + I+ Sbjct: 254 FCGTPEYLAPEVLRKEPYDRAVDWWCLGAVLYEMLHGLPPFYSQDVSQMYENIL 307 >KAPC_ASCSU (P49673) cAMP-dependent protein kinase catalytic subunit (EC 2.7.1.37) (PKA C) Length = 337 Score = 61.6 bits (148), Expect = 6e-10 Identities = 31/79 (39%), Positives = 49/79 (62%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APEV+ +G+D + DWWS+GV+++EM+ G PPF + +KII + L+F Sbjct: 186 GTPEYLAPEVIGNKGHDTAVDWWSLGVLIYEMMIGIPPFRGKTLDEIYEKIILGK--LRF 243 Query: 381 PNNVDNVSGKAVDLISNLI 437 + D A DL+ L+ Sbjct: 244 TRSFDLF---AKDLVKKLL 259 >CDP3_PLAF7 (Q9NJU9) Calcium-dependent protein kinase 3 (EC 2.7.1.37) (PfCDPK3) Length = 562 Score = 61.6 bits (148), Expect = 6e-10 Identities = 31/80 (38%), Positives = 47/80 (58%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+AP+VL G Y+Y CD WS GV+ + +L GYPPF+ +S + + + K Sbjct: 278 GTPYYVAPQVLTG-SYNYKCDMWSSGVLFYILLCGYPPFFGESDHEILSMVKKGKYQFK- 335 Query: 381 PNNVDNVSGKAVDLISNLIT 440 +N+S +A DLI +T Sbjct: 336 GKEWNNISEEAKDLIKRCLT 355 >KCC1_RAT (Q63450) Calcium/calmodulin-dependent protein kinase type I (EC 2.7.1.123) (CaM kinase I) Length = 374 Score = 61.6 bits (148), Expect = 6e-10 Identities = 31/79 (39%), Positives = 49/79 (62%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APEVL + Y + D WS+GVI + +L GYPPFY+++ ++I++ EY Sbjct: 180 GTPGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDAKLFEQILK-AEYEFD 238 Query: 381 PNNVDNVSGKAVDLISNLI 437 D++S A D I +L+ Sbjct: 239 SPYWDDISDSAKDFIRHLM 257 >KCC1_MOUSE (Q91YS8) Calcium/calmodulin-dependent protein kinase type I (EC 2.7.1.123) (CaM kinase I) Length = 374 Score = 61.6 bits (148), Expect = 6e-10 Identities = 31/79 (39%), Positives = 49/79 (62%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APEVL + Y + D WS+GVI + +L GYPPFY+++ ++I++ EY Sbjct: 180 GTPGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDAKLFEQILK-AEYEFD 238 Query: 381 PNNVDNVSGKAVDLISNLI 437 D++S A D I +L+ Sbjct: 239 SPYWDDISDSAKDFIRHLM 257 >CHK2_MOUSE (Q9Z265) Serine/threonine-protein kinase Chk2 (EC 2.7.1.37) Length = 546 Score = 61.6 bits (148), Expect = 6e-10 Identities = 34/82 (41%), Positives = 46/82 (56%), Gaps = 3/82 (3%) Frame = +3 Query: 201 GSPAYIAPEVLIGRG---YDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREY 371 G+P Y+APEVL+ G Y + D WS+GVILF L GYPPF + K I +Y Sbjct: 390 GTPTYLAPEVLVSNGTAGYSRAVDCWSLGVILFICLSGYPPFSEHKTQVSLKDQITSGKY 449 Query: 372 LKFPNNVDNVSGKAVDLISNLI 437 P +VS +A+DL+ L+ Sbjct: 450 NFIPEVWTDVSEEALDLVKKLL 471 >AKT3_MOUSE (Q9WUA6) RAC-gamma serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-gamma) (Protein kinase Akt-3) (Protein kinase B, gamma) (PKB gamma) Length = 479 Score = 61.6 bits (148), Expect = 6e-10 Identities = 32/81 (39%), Positives = 46/81 (56%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 306 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILM--EDI 363 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 KFP +S A L+S L+ Sbjct: 364 KFPR---TLSSDAKSLLSGLL 381 >AKT3_HUMAN (Q9Y243) RAC-gamma serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-gamma) (Protein kinase Akt-3) (Protein kinase B, gamma) (PKB gamma) (STK-2) Length = 479 Score = 61.6 bits (148), Expect = 6e-10 Identities = 32/81 (39%), Positives = 46/81 (56%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 306 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILM--EDI 363 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 KFP +S A L+S L+ Sbjct: 364 KFPR---TLSSDAKSLLSGLL 381 >MKK2_HUMAN (P49137) MAP kinase-activated protein kinase 2 (EC 2.7.1.-) (MAPK-activated protein kinase 2) (MAPKAP kinase 2) (MAPKAPK-2) Length = 400 Score = 61.6 bits (148), Expect = 6e-10 Identities = 36/82 (43%), Positives = 50/82 (60%), Gaps = 4/82 (4%) Frame = +3 Query: 204 SPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTA---KKIIQFREYL 374 +P Y+APEVL YD SCD WS+GVI++ +L GYPPFY++ + K I+ +Y Sbjct: 226 TPYYVAPEVLGPEKYDKSCDMWSLGVIMYILLCGYPPFYSNHGLAISPGMKTRIRMGQY- 284 Query: 375 KFPN-NVDNVSGKAVDLISNLI 437 +FPN VS + LI NL+ Sbjct: 285 EFPNPEWSEVSEEVKMLIRNLL 306 >KPCO_HUMAN (Q9BZL6) Protein kinase C, D2 type (EC 2.7.1.-) (nPKC-D2) (Protein kinase D2) (HSPC187) Length = 878 Score = 61.6 bits (148), Expect = 6e-10 Identities = 33/79 (41%), Positives = 48/79 (60%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+PAY+APEVL+ +GY+ S D WSVGVI++ L G PF D IQ ++ Sbjct: 713 GTPAYLAPEVLLNQGYNRSLDMWSVGVIMYVSLSGTFPFNEDEDINDQ---IQNAAFMYP 769 Query: 381 PNNVDNVSGKAVDLISNLI 437 + ++S A+DLI+NL+ Sbjct: 770 ASPWSHISAGAIDLINNLL 788 >KBN8_YEAST (P38070) Probable serine/threonine-protein kinase YBR028C (EC 2.7.1.37) Length = 525 Score = 61.2 bits (147), Expect = 8e-10 Identities = 25/61 (40%), Positives = 39/61 (63%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y APE+L+G+ Y +CDW+S+G +L++ML G PP+ + KI Q ++ K Sbjct: 324 GTPEYCAPEILLGKAYSQNCDWYSLGCLLYDMLVGKPPYTGSNHKVIINKIQQNKQGPKI 383 Query: 381 P 383 P Sbjct: 384 P 384 >KRAC_BOVIN (Q01314) RAC-alpha serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-alpha) (Protein kinase B) (PKB) Length = 480 Score = 60.8 bits (146), Expect = 1e-09 Identities = 31/81 (38%), Positives = 47/81 (58%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 309 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILM--EEI 366 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 +FP +S +A L+S L+ Sbjct: 367 RFPR---TLSPEAKSLLSGLL 384 >KPK7_ARATH (Q05999) Putative serine/threonine-protein kinase PK7 (EC 2.7.1.37) Length = 578 Score = 60.8 bits (146), Expect = 1e-09 Identities = 30/81 (37%), Positives = 47/81 (58%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+ Y+APE++ G G+ + DWW+ G+ L+E+L+G PF T ++ + L Sbjct: 416 FVGTHEYLAPEIIKGEGHGSAVDWWTFGIFLYELLFGITPFRGGDNRATLFNVV--GQPL 473 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 +FP + NVS A DLI L+ Sbjct: 474 RFPEH-PNVSFAARDLIRGLL 493 >K6A6_HUMAN (Q9UK32) Ribosomal protein S6 kinase alpha 6 (EC 2.7.1.37) (S6K-alpha 6) (90 kDa ribosomal protein S6 kinase 6) (p90-RSK 6) (Ribosomal S6 kinase 4) (RSK-4) (pp90RSK4) Length = 745 Score = 60.8 bits (146), Expect = 1e-09 Identities = 33/78 (42%), Positives = 49/78 (62%), Gaps = 3/78 (3%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFP--- 383 ++APEVL+ +GYD +CD WS+GV+ + ML GY PF N T ++I+ KF Sbjct: 588 FVAPEVLMQQGYDAACDIWSLGVLFYTMLAGYTPFAN-GPNDTPEEILLRIGNGKFSLSG 646 Query: 384 NNVDNVSGKAVDLISNLI 437 N DN+S A DL+S+++ Sbjct: 647 GNWDNISDGAKDLLSHML 664 Score = 55.8 bits (133), Expect = 3e-08 Identities = 25/55 (45%), Positives = 34/55 (61%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ RG+ S DWWS GV++FEML G PF + T I++ Sbjct: 233 FCGTVEYMAPEVVNRRGHSQSADWWSYGVLMFEMLTGTLPFQGKDRNETMNMILK 287 >CDP1_PLAFK (P62343) Calcium-dependent protein kinase 1 (EC 2.7.1.37) (PfCPK) (PfCDPK1) Length = 523 Score = 60.8 bits (146), Expect = 1e-09 Identities = 34/80 (42%), Positives = 49/80 (61%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ YIAPEVL + Y+ CD WS GVIL+ +L GYPPF + KK+ + + Y F Sbjct: 229 GTAYYIAPEVL-RKKYNEKCDVWSCGVILYILLCGYPPFGGQNDQDIIKKVEKGKYYFDF 287 Query: 381 PNNVDNVSGKAVDLISNLIT 440 N+ N+S +A +LI ++T Sbjct: 288 -NDWKNISEEAKELIKLMLT 306 >CDP1_PLAF7 (P62344) Calcium-dependent protein kinase 1 (EC 2.7.1.37) Length = 523 Score = 60.8 bits (146), Expect = 1e-09 Identities = 34/80 (42%), Positives = 49/80 (61%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ YIAPEVL + Y+ CD WS GVIL+ +L GYPPF + KK+ + + Y F Sbjct: 229 GTAYYIAPEVL-RKKYNEKCDVWSCGVILYILLCGYPPFGGQNDQDIIKKVEKGKYYFDF 287 Query: 381 PNNVDNVSGKAVDLISNLIT 440 N+ N+S +A +LI ++T Sbjct: 288 -NDWKNISEEAKELIKLMLT 306 >CDP1_PLAYO (Q7RAH3) Calcium-dependent protein kinase 1 (EC 2.7.1.37) Length = 534 Score = 60.5 bits (145), Expect = 1e-09 Identities = 33/80 (41%), Positives = 49/80 (61%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ YIAPEVL + Y+ CD WS GVI++ +L GYPPF + KK+ + + Y F Sbjct: 228 GTAYYIAPEVL-KKKYNEKCDVWSCGVIMYILLCGYPPFGGQNDQDIIKKVEKGKYYFDF 286 Query: 381 PNNVDNVSGKAVDLISNLIT 440 N+ N+S +A +LI ++T Sbjct: 287 -NDWKNISDEAKELIKLMLT 305 >K6A5_MOUSE (Q8C050) Ribosomal protein S6 kinase alpha 5 (EC 2.7.1.37) (Nuclear mitogen-and stress-activated protein kinase-1) (90 kDa ribosomal protein S6 kinase 5) (RSK-like protein kinase) (RLSK) Length = 863 Score = 60.1 bits (144), Expect = 2e-09 Identities = 34/82 (41%), Positives = 46/82 (56%), Gaps = 6/82 (7%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLK----- 377 Y APE+L GYD SCD WS+GVIL+ ML G PF + ++ T ++ + +K Sbjct: 652 YAAPELLTHNGYDESCDLWSLGVILYTMLSGQVPFQSHDRSLTCTSAVEIMKKIKKGDFS 711 Query: 378 FPNNV-DNVSGKAVDLISNLIT 440 F NVS +A DLI L+T Sbjct: 712 FEGEAWKNVSQEAKDLIQGLLT 733 Score = 50.4 bits (119), Expect = 1e-06 Identities = 30/84 (35%), Positives = 48/84 (57%), Gaps = 3/84 (3%) Frame = +3 Query: 195 FFGSPAYIAPEVLIG--RGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFRE 368 F G+ Y+AP+++ G G+D + DWWS+GV+++E+L G PF D + + +I R Sbjct: 212 FCGTIEYMAPDIVRGGDSGHDKAVDWWSLGVLMYELLTGASPFTVDGEKNSQAEI--SRR 269 Query: 369 YLKF-PNNVDNVSGKAVDLISNLI 437 LK P +S A DL+ L+ Sbjct: 270 ILKSEPPYPQEMSTVAKDLLQRLL 293 >APG1_YEAST (P53104) Autophagy serine/threonine-protein kinase APG1 (EC 2.7.1.37) Length = 897 Score = 59.7 bits (143), Expect = 2e-09 Identities = 31/80 (38%), Positives = 47/80 (58%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 GSP Y+APE+L + Y+ D WSVG ++FEM G PPF + KKI + + + F Sbjct: 229 GSPLYMAPEILNYQKYNAKADLWSVGTVVFEMCCGTPPFRASNHLELFKKIKRANDVITF 288 Query: 381 PNNVDNVSGKAVDLISNLIT 440 P+ N+ + +LI +L+T Sbjct: 289 PSYC-NIEPELKELICSLLT 307 >KPCA_RAT (P05696) Protein kinase C, alpha type (EC 2.7.1.37) (PKC-alpha) (PKC-A) Length = 672 Score = 59.7 bits (143), Expect = 2e-09 Identities = 30/82 (36%), Positives = 49/82 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWW+ GV+L+EML G PPF + + + I++ + Sbjct: 498 FCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEMLAGQPPFDGEDEDELFQSIMEHN--V 555 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + L+T Sbjct: 556 SYPK---SLSKEAVSICKGLMT 574 >KPCA_RABIT (P10102) Protein kinase C, alpha type (EC 2.7.1.37) (PKC-alpha) (PKC-A) Length = 672 Score = 59.7 bits (143), Expect = 2e-09 Identities = 30/82 (36%), Positives = 49/82 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWW+ GV+L+EML G PPF + + + I++ + Sbjct: 498 FCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEMLAGQPPFDGEDEDELFQSIMEHN--V 555 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + L+T Sbjct: 556 SYPK---SLSKEAVSICKGLMT 574 >KPCA_MOUSE (P20444) Protein kinase C, alpha type (EC 2.7.1.37) (PKC-alpha) (PKC-A) Length = 672 Score = 59.7 bits (143), Expect = 2e-09 Identities = 30/82 (36%), Positives = 49/82 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWW+ GV+L+EML G PPF + + + I++ + Sbjct: 498 FCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEMLAGQPPFDGEDEDELFQSIMEHN--V 555 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + L+T Sbjct: 556 SYPK---SLSKEAVSICKGLMT 574 >KPCA_HUMAN (P17252) Protein kinase C, alpha type (EC 2.7.1.37) (PKC-alpha) (PKC-A) Length = 672 Score = 59.7 bits (143), Expect = 2e-09 Identities = 30/82 (36%), Positives = 49/82 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWW+ GV+L+EML G PPF + + + I++ + Sbjct: 498 FCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEMLAGQPPFDGEDEDELFQSIMEHN--V 555 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + L+T Sbjct: 556 SYPK---SLSKEAVSICKGLMT 574 >KPCA_BOVIN (P04409) Protein kinase C, alpha type (EC 2.7.1.37) (PKC-alpha) (PKC-A) Length = 672 Score = 59.7 bits (143), Expect = 2e-09 Identities = 30/82 (36%), Positives = 49/82 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWW+ GV+L+EML G PPF + + + I++ + Sbjct: 498 FCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEMLAGQPPFDGEDEDELFQSIMEHN--V 555 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + L+T Sbjct: 556 SYPK---SLSKEAVSICKGLMT 574 >KPC2_APLCA (Q16975) Calcium-independent protein kinase C (EC 2.7.1.-) (APL II) Length = 743 Score = 59.7 bits (143), Expect = 2e-09 Identities = 25/54 (46%), Positives = 37/54 (68%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKII 356 F G+P YIAPE+L YD S DWW++GV+++EM+ G PPF D++ + I+ Sbjct: 562 FCGTPDYIAPEILQELKYDASVDWWALGVLMYEMMAGQPPFEADNEDDLFESIL 615 >AKT2_HUMAN (P31751) RAC-beta serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-beta) (Protein kinase Akt-2) (Protein kinase B, beta) (PKB beta) Length = 481 Score = 59.7 bits (143), Expect = 2e-09 Identities = 30/81 (37%), Positives = 47/81 (58%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 310 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILM--EEI 367 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 +FP +S +A L++ L+ Sbjct: 368 RFPR---TLSPEAKSLLAGLL 385 >CDP1_ORYSA (P53682) Calcium-dependent protein kinase, isoform 1 (EC 2.7.1.-) (CDPK 1) Length = 534 Score = 59.7 bits (143), Expect = 2e-09 Identities = 34/79 (43%), Positives = 47/79 (59%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 GSP YIAPEVL R Y D W+ GVIL+ +L G PPF+ D+++G +K++ R K Sbjct: 236 GSPYYIAPEVLEKR-YGPEADIWTAGVILYVLLTGVPPFWADTQSGIYEKVLDGRIDFK- 293 Query: 381 PNNVDNVSGKAVDLISNLI 437 N +S A DLI ++ Sbjct: 294 SNRWPRISDSAKDLIKKML 312 >KRAC_RAT (P47196) RAC-alpha serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-alpha) (Protein kinase B) (PKB) Length = 480 Score = 59.3 bits (142), Expect = 3e-09 Identities = 30/81 (37%), Positives = 46/81 (56%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 309 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILM--EEI 366 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 +FP + +A L+S L+ Sbjct: 367 RFPR---TLGPEAKSLLSGLL 384 >KRAC_HUMAN (P31749) RAC-alpha serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-alpha) (Protein kinase B) (PKB) (C-AKT) Length = 480 Score = 59.3 bits (142), Expect = 3e-09 Identities = 30/81 (37%), Positives = 46/81 (56%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 309 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILM--EEI 366 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 +FP + +A L+S L+ Sbjct: 367 RFPR---TLGPEAKSLLSGLL 384 >MKK2_RABIT (P49139) MAP kinase-activated protein kinase 2 (EC 2.7.1.-) (MAPK-activated protein kinase 2) (MAPKAP kinase 2) (MAPKAPK-2) (Fragments) Length = 330 Score = 59.3 bits (142), Expect = 3e-09 Identities = 30/64 (46%), Positives = 42/64 (65%), Gaps = 3/64 (4%) Frame = +3 Query: 204 SPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTA---KKIIQFREYL 374 +P Y+APEVL YD SCD WS+GVI++ +L GYPPFY++ + K I+ +Y Sbjct: 192 TPYYVAPEVLGPEKYDKSCDMWSLGVIMYILLCGYPPFYSNHGLAISPGMKTRIRMGQY- 250 Query: 375 KFPN 386 +FPN Sbjct: 251 EFPN 254 >KPK1_PHAVU (P15792) Protein kinase PVPK-1 (EC 2.7.1.-) Length = 609 Score = 59.3 bits (142), Expect = 3e-09 Identities = 30/81 (37%), Positives = 47/81 (58%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+ Y+APE++ G G+ + DWW+ G+ L+E+L+G PF + T +I + L Sbjct: 465 FVGTHEYLAPEIIKGEGHGSAVDWWTFGIFLYELLFGRTPFKGSANRATLFNVI--GQPL 522 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 +FP + VS A DLI L+ Sbjct: 523 RFPES-PTVSFAARDLIRGLL 542 >KAKT_MLVAT (P31748) AKT kinase transforming protein (EC 2.7.1.-) Length = 501 Score = 59.3 bits (142), Expect = 3e-09 Identities = 30/81 (37%), Positives = 46/81 (56%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 330 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILM--EEI 387 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 +FP + +A L+S L+ Sbjct: 388 RFPR---TLGPEAKSLLSGLL 405 >K6A5_HUMAN (O75582) Ribosomal protein S6 kinase alpha 5 (EC 2.7.1.37) (Nuclear mitogen-and stress-activated protein kinase-1) (90 kDa ribosomal protein S6 kinase 5) (RSK-like protein kinase) (RLSK) Length = 802 Score = 59.3 bits (142), Expect = 3e-09 Identities = 34/82 (41%), Positives = 46/82 (56%), Gaps = 6/82 (7%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLK----- 377 Y APE+L GYD SCD WS+GVIL+ ML G PF + ++ T ++ + +K Sbjct: 588 YAAPELLNQNGYDESCDLWSLGVILYTMLSGQVPFQSHDRSLTCTSAVEIMKKIKKGDFS 647 Query: 378 FPNNV-DNVSGKAVDLISNLIT 440 F NVS +A DLI L+T Sbjct: 648 FEGEAWKNVSQEAKDLIQGLLT 669 Score = 52.0 bits (123), Expect = 5e-07 Identities = 31/84 (36%), Positives = 48/84 (57%), Gaps = 3/84 (3%) Frame = +3 Query: 195 FFGSPAYIAPEVLIG--RGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFRE 368 F G+ Y+AP+++ G G+D + DWWS+GV+++E+L G PF D + + +I R Sbjct: 213 FCGTIEYMAPDIVRGGDSGHDKAVDWWSLGVLMYELLTGASPFTVDGEKNSQAEI--SRR 270 Query: 369 YLKF-PNNVDNVSGKAVDLISNLI 437 LK P +S A DLI L+ Sbjct: 271 ILKSEPPYPQEMSALAKDLIQRLL 294 >KPCZ_RAT (P09217) Protein kinase C, zeta type (EC 2.7.1.37) (nPKC-zeta) Length = 592 Score = 58.5 bits (140), Expect = 5e-09 Identities = 26/54 (48%), Positives = 36/54 (66%), Gaps = 3/54 (5%) Frame = +3 Query: 165 CGARVGMG---APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 C +G G + F G+P YIAPE+L G Y +S DWW++GV++FEM+ G PF Sbjct: 398 CKEGLGPGDTTSTFCGTPNYIAPEILRGEEYGFSVDWWALGVLMFEMMAGRSPF 451 >KPCZ_MOUSE (Q02956) Protein kinase C, zeta type (EC 2.7.1.37) (nPKC-zeta) Length = 592 Score = 58.5 bits (140), Expect = 5e-09 Identities = 26/54 (48%), Positives = 36/54 (66%), Gaps = 3/54 (5%) Frame = +3 Query: 165 CGARVGMG---APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 C +G G + F G+P YIAPE+L G Y +S DWW++GV++FEM+ G PF Sbjct: 398 CKEGLGPGDTTSTFCGTPNYIAPEILRGEEYGFSVDWWALGVLMFEMMAGRSPF 451 >KPCZ_HUMAN (Q05513) Protein kinase C, zeta type (EC 2.7.1.37) (nPKC-zeta) Length = 592 Score = 58.5 bits (140), Expect = 5e-09 Identities = 26/54 (48%), Positives = 36/54 (66%), Gaps = 3/54 (5%) Frame = +3 Query: 165 CGARVGMG---APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 C +G G + F G+P YIAPE+L G Y +S DWW++GV++FEM+ G PF Sbjct: 398 CKEGLGPGDTTSTFCGTPNYIAPEILRGEEYGFSVDWWALGVLMFEMMAGRSPF 451 >PKC2_CAEEL (P90980) Protein kinase C-like 2 (EC 2.7.1.-) (PKC2) Length = 682 Score = 58.5 bits (140), Expect = 5e-09 Identities = 24/41 (58%), Positives = 31/41 (75%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 F G+P YIAPE+++ + Y S DWW+ GV+LFEML G PPF Sbjct: 507 FCGTPDYIAPEIILYQPYGKSVDWWAYGVLLFEMLAGQPPF 547 >KPCG_BOVIN (P05128) Protein kinase C, gamma type (EC 2.7.1.37) (PKC-gamma) (Fragment) Length = 682 Score = 58.5 bits (140), Expect = 5e-09 Identities = 30/82 (36%), Positives = 49/82 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWWS GV+L+EML G PPF + + + I++ + + Sbjct: 500 FCGTPDYIAPEIIAYQPYGKSVDWWSFGVLLYEMLAGQPPFDGEDEEELFQAIME--QTV 557 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + +T Sbjct: 558 TYPK---SLSREAVAICKGFLT 576 >KPCI_HUMAN (P41743) Protein kinase C, iota type (EC 2.7.1.37) (nPKC-iota) (Atypical protein kinase C-lambda/iota) (aPKC-lambda/iota) Length = 587 Score = 58.5 bits (140), Expect = 5e-09 Identities = 23/41 (56%), Positives = 31/41 (75%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 F G+P YIAPE+L G Y +S DWW++GV++FEM+ G PF Sbjct: 404 FCGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPF 444 >KPCG_RABIT (P10829) Protein kinase C, gamma type (EC 2.7.1.37) (PKC-gamma) (PKC-delta) Length = 697 Score = 58.5 bits (140), Expect = 5e-09 Identities = 30/82 (36%), Positives = 49/82 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWWS GV+L+EML G PPF + + + I++ + + Sbjct: 515 FCGTPDYIAPEIIAYQPYGKSVDWWSFGVLLYEMLAGQPPFDGEDEEELFQAIME--QTV 572 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + +T Sbjct: 573 TYPK---SLSREAVAICKGFLT 591 >KPCG_MOUSE (P05697) Protein kinase C, gamma type (EC 2.7.1.37) (PKC-gamma) Length = 697 Score = 58.5 bits (140), Expect = 5e-09 Identities = 30/82 (36%), Positives = 49/82 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWWS GV+L+EML G PPF + + + I++ + + Sbjct: 515 FCGTPDYIAPEIIAYQPYGKSVDWWSFGVLLYEMLAGQPPFDGEDEEELFQAIME--QTV 572 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + +T Sbjct: 573 TYPK---SLSREAVAICKGFLT 591 >KPCG_HUMAN (P05129) Protein kinase C, gamma type (EC 2.7.1.37) (PKC-gamma) Length = 697 Score = 58.5 bits (140), Expect = 5e-09 Identities = 30/82 (36%), Positives = 49/82 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWWS GV+L+EML G PPF + + + I++ + + Sbjct: 515 FCGTPDYIAPEIIAYQPYGKSVDWWSFGVLLYEMLAGQPPFDGEDEEELFQAIME--QTV 572 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + +T Sbjct: 573 TYPK---SLSREAVAICKGFLT 591 >KPCI_BRARE (Q90XF2) Protein kinase C, iota type (EC 2.7.1.37) (nPKC-iota) (Atypical protein kinase C-lambda/iota) (aPKC-lambda/iota) (Heart and soul protein) Length = 588 Score = 58.5 bits (140), Expect = 5e-09 Identities = 23/41 (56%), Positives = 31/41 (75%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 F G+P YIAPE+L G Y +S DWW++GV++FEM+ G PF Sbjct: 405 FCGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPF 445 >KPCZ_RABIT (O19111) Protein kinase C, zeta type (EC 2.7.1.37) (nPKC-zeta) Length = 591 Score = 58.5 bits (140), Expect = 5e-09 Identities = 26/54 (48%), Positives = 36/54 (66%), Gaps = 3/54 (5%) Frame = +3 Query: 165 CGARVGMG---APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 C +G G + F G+P YIAPE+L G Y +S DWW++GV++FEM+ G PF Sbjct: 397 CKEGLGPGDTTSTFCGTPNYIAPEILRGEEYGFSVDWWALGVLMFEMMAGRSPF 450 >KPCI_MOUSE (Q62074) Protein kinase C, iota type (EC 2.7.1.37) (nPKC-iota) (Atypical protein kinase C-lambda/iota) (aPKC-lambda/iota) Length = 586 Score = 58.5 bits (140), Expect = 5e-09 Identities = 23/41 (56%), Positives = 31/41 (75%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 F G+P YIAPE+L G Y +S DWW++GV++FEM+ G PF Sbjct: 403 FCGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPF 443 >KRAC_MOUSE (P31750) RAC-alpha serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-alpha) (AKT1 kinase) (Protein kinase B) (PKB) (C-AKT) (Thymoma viral proto-oncogene) Length = 480 Score = 58.2 bits (139), Expect = 7e-09 Identities = 30/81 (37%), Positives = 45/81 (55%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 309 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILM--EEI 366 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 FP + +A L+S L+ Sbjct: 367 AFPR---TLGPEAKSLLSGLL 384 >K6A1_RAT (Q63531) Ribosomal protein S6 kinase alpha 1 (EC 2.7.1.37) (S6K-alpha 1) (90 kDa ribosomal protein S6 kinase 1) (p90-RSK 1) (Ribosomal S6 kinase 1) (RSK-1) (pp90RSK1) (MAP kinase-activated protein kinase 1a) (MAPKAPK1A) Length = 735 Score = 58.2 bits (139), Expect = 7e-09 Identities = 33/78 (42%), Positives = 47/78 (60%), Gaps = 3/78 (3%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFP--- 383 ++APEVL +GYD CD WS+GV+L+ ML GY PF N + T ++I+ KF Sbjct: 580 FVAPEVLKRQGYDEGCDIWSLGVLLYTMLAGYTPFAN-GPSDTPEEILTRISSGKFTLSG 638 Query: 384 NNVDNVSGKAVDLISNLI 437 N + VS A DL+S ++ Sbjct: 639 GNWNTVSETAKDLVSKML 656 Score = 53.9 bits (128), Expect = 1e-07 Identities = 24/55 (43%), Positives = 35/55 (63%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ +G+ +S DWWS GV++FEML G PF + T I++ Sbjct: 222 FCGTVEYMAPEVVNRQGHTHSADWWSYGVLMFEMLTGSLPFQGKDRKETMTLILK 276 >KPC1_APLCA (Q16974) Calcium-dependent protein kinase C (EC 2.7.1.-) (APL I) Length = 649 Score = 58.2 bits (139), Expect = 7e-09 Identities = 31/82 (37%), Positives = 46/82 (56%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE+++ + Y S DWW+ GV+L+EML G PPF + + I + Sbjct: 479 FCGTPDYIAPEIVLYQPYGRSVDWWAYGVLLYEMLAGQPPFDGEDEEELFTSITDHN--V 536 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P +S +AV L L+T Sbjct: 537 SYPK---ALSREAVSLCKGLLT 555 >K6B2_HUMAN (Q9UBS0) Ribosomal protein S6 kinase beta 2 (EC 2.7.1.37) (S6K-beta 2) (70 kDa ribosomal protein S6 kinase 2) (p70-S6KB) (p70 ribosomal S6 kinase beta) (p70 S6Kbeta) (S6K2) (S6 kinase-related kinase) (SRK) (Serine/threonine-protein kinase 14 b Length = 482 Score = 58.2 bits (139), Expect = 7e-09 Identities = 23/55 (41%), Positives = 39/55 (70%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APE+L+ G++ + DWWS+G ++++ML G PPF +++ T KII+ Sbjct: 229 FCGTIEYMAPEILVRSGHNRAVDWWSLGALMYDMLTGSPPFTAENRKKTMDKIIR 283 >MKK2_DROME (P49071) MAP kinase-activated protein kinase 2 (EC 2.7.1.-) (MAPK-activated protein kinase 2) (MAPKAP kinase 2) (MAPKAPK-2) Length = 359 Score = 58.2 bits (139), Expect = 7e-09 Identities = 33/82 (40%), Positives = 50/82 (60%), Gaps = 4/82 (4%) Frame = +3 Query: 204 SPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTA---KKIIQFREYL 374 +P Y+APEVL YD SCD WS+GV+++ ++ G+PPFY++ + K I+ +Y Sbjct: 182 TPYYVAPEVLGPEKYDKSCDIWSLGVVMYIIMCGFPPFYSNHGLAISPGMKNRIRTGQY- 240 Query: 375 KFPN-NVDNVSGKAVDLISNLI 437 FP+ NVS A DLI ++ Sbjct: 241 DFPDPEWTNVSQAAKDLIKGML 262 >K6B2_MOUSE (Q9Z1M4) Ribosomal protein S6 kinase beta 2 (EC 2.7.1.37) (S6K-beta 2) (70 kDa ribosomal protein S6 kinase 2) (p70-S6KB) (p70 ribosomal S6 kinase beta) (p70 S6Kbeta) (S6K2) Length = 485 Score = 58.2 bits (139), Expect = 7e-09 Identities = 23/55 (41%), Positives = 39/55 (70%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APE+L+ G++ + DWWS+G ++++ML G PPF +++ T KII+ Sbjct: 229 FCGTIEYMAPEILVRTGHNRAVDWWSLGALMYDMLTGSPPFTAENRKKTMDKIIK 283 >AKT2_RAT (P47197) RAC-beta serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-beta) (Protein kinase Akt-2) (Protein kinase B, beta) (PKB beta) Length = 481 Score = 58.2 bits (139), Expect = 7e-09 Identities = 26/66 (39%), Positives = 39/66 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 310 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILM--EEI 367 Query: 375 KFPNNV 392 +FP + Sbjct: 368 RFPRTL 373 >AKT2_MOUSE (Q60823) RAC-beta serine/threonine-protein kinase (EC 2.7.1.37) (RAC-PK-beta) (Protein kinase Akt-2) (Protein kinase B, beta) (PKB beta) Length = 481 Score = 58.2 bits (139), Expect = 7e-09 Identities = 26/66 (39%), Positives = 39/66 (59%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APEVL Y + DWW +GV+++EM+ G PFYN + I+ E + Sbjct: 310 FCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILM--EEI 367 Query: 375 KFPNNV 392 +FP + Sbjct: 368 RFPRTL 373 >SRK1_SCHPO (O94547) Serine/threonine-protein kinase srk1 (EC 2.7.1.37) (Sty1-regulated kinase 1) Length = 580 Score = 58.2 bits (139), Expect = 7e-09 Identities = 30/80 (37%), Positives = 48/80 (60%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ Y APE++ Y D W++G +L+ +L G+PPFY++S + KK+ + EY Sbjct: 325 GTMGYTAPEIVRDERYSKGVDMWALGCVLYTILCGFPPFYDESISLLTKKVSR-GEYSFL 383 Query: 381 PNNVDNVSGKAVDLISNLIT 440 D++S A DLIS+L+T Sbjct: 384 SPWWDDISKSAKDLISHLLT 403 >K6B1_RAT (P21425) Ribosomal protein S6 kinase I (EC 2.7.1.37) (S6K) (P70-S6K) Length = 502 Score = 57.8 bits (138), Expect = 9e-09 Identities = 28/81 (34%), Positives = 51/81 (62%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+ Y+APE+L+ G++ + DWWS+G ++++ML G PPF +++ T KI++ + L Sbjct: 230 FCGTIEYMAPEILMRSGHNRAVDWWSLGALMYDMLTGAPPFTGENRKKTIDKILKCK--L 287 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 P ++ +A DL+ L+ Sbjct: 288 NLP---PYLTQEARDLLKKLL 305 >K6B1_HUMAN (P23443) Ribosomal protein S6 kinase (EC 2.7.1.37) (S6K) (p70-S6K) Length = 502 Score = 57.8 bits (138), Expect = 9e-09 Identities = 28/81 (34%), Positives = 51/81 (62%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+ Y+APE+L+ G++ + DWWS+G ++++ML G PPF +++ T KI++ + L Sbjct: 230 FCGTIEYMAPEILMRSGHNRAVDWWSLGALMYDMLTGAPPFTGENRKKTIDKILKCK--L 287 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 P ++ +A DL+ L+ Sbjct: 288 NLP---PYLTQEARDLLKKLL 305 >KDBE_SCHPO (Q10364) Putative serine/threonine-protein kinase C22E12.14c (EC 2.7.1.37) Length = 646 Score = 57.8 bits (138), Expect = 9e-09 Identities = 33/82 (40%), Positives = 51/82 (62%), Gaps = 1/82 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGR-GYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREY 371 F G+ Y+APEV++ GYD D+WS+GV+L+EM G+ PFY D+ K I+ + Sbjct: 427 FCGTTDYLAPEVILDEAGYDMMVDFWSLGVLLYEMTCGWSPFYADNTQQLYKNIVFGK-- 484 Query: 372 LKFPNNVDNVSGKAVDLISNLI 437 ++FP + +S +A DLI L+ Sbjct: 485 VRFPRGL--LSVEARDLIKLLL 504 >KPC1_DROME (P05130) Protein kinase C, brain isozyme (EC 2.7.1.-) (PKC) (dPKC53E(BR)) Length = 679 Score = 57.8 bits (138), Expect = 9e-09 Identities = 23/41 (56%), Positives = 31/41 (75%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 F G+P YIAPE+++ + Y S DWW+ GV+L+EML G PPF Sbjct: 509 FCGTPDYIAPEIILYQPYGKSVDWWAYGVLLYEMLVGQPPF 549 >KPC1_CANAL (P43057) Protein kinase C-like 1 (EC 2.7.1.-) (PKC 1) Length = 1097 Score = 57.8 bits (138), Expect = 9e-09 Identities = 30/82 (36%), Positives = 48/82 (58%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P ++APE++ G+ YD S DWW+ GV+LF+ML PF D + I + + Sbjct: 930 FCGTPEFMAPEIVAGKAYDRSVDWWAFGVLLFQMLLCQSPFKGDDEDDIFNAI--ENDEV 987 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 K+P N+S + V ++ L+T Sbjct: 988 KYP---INLSRQTVLVLQALLT 1006 >KPC2_DROME (P13677) Protein kinase C, eye isozyme (EC 2.7.1.-) (PKC) (dPKC53E(EY)) (Protein INAC) (Inactivation no after-potential C protein) (Photoreceptor-specific PKC) (Eye-PKC) Length = 700 Score = 57.4 bits (137), Expect = 1e-08 Identities = 30/82 (36%), Positives = 47/82 (57%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y+APE++ Y + DWWS GV+LFE + G PF D +T + I + Sbjct: 530 FCGTPNYMAPEIVSYDPYSIAADWWSFGVLLFEFMAGQAPFEGDDETTVFRNIKDKKAV- 588 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 FP + S +A+D+I++ +T Sbjct: 589 -FPK---HFSVEAMDIITSFLT 606 >KPCB_CAEEL (P34885) Protein kinase C-like 1B (EC 2.7.1.-) (PKC1B) Length = 707 Score = 57.4 bits (137), Expect = 1e-08 Identities = 24/54 (44%), Positives = 36/54 (66%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKII 356 F G+P YIAPE+L Y S DWW++GV+++EM+ G PPF D++ + I+ Sbjct: 537 FCGTPDYIAPEILQEMEYGVSVDWWALGVLMYEMMAGQPPFEADNEDDLFEAIL 590 >KCCA_MOUSE (P11798) Calcium/calmodulin-dependent protein kinase type II alpha chain (EC 2.7.1.123) (CaM-kinase II alpha chain) (CaM kinase II alpha subunit) (CaMK-II alpha subunit) Length = 478 Score = 57.4 bits (137), Expect = 1e-08 Identities = 33/83 (39%), Positives = 52/83 (62%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ R Y Sbjct: 173 FAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYQQ-IKARAY- 230 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A DLI+ ++T Sbjct: 231 DFPSPEWDTVTPEAKDLINKMLT 253 >KPC3_DROME (P13678) Protein kinase C (EC 2.7.1.-) (PKC) (dPKC98F) Length = 634 Score = 57.4 bits (137), Expect = 1e-08 Identities = 23/46 (50%), Positives = 34/46 (73%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSK 332 F G+P YIAPE+L + Y S DWW++GV+++EM+ G PPF D++ Sbjct: 462 FCGTPDYIAPEILKEQEYGASVDWWALGVLMYEMMAGQPPFEADNE 507 >G11A_ORYSA (P47997) Protein kinase G11A (EC 2.7.1.-) (Fragment) Length = 531 Score = 57.4 bits (137), Expect = 1e-08 Identities = 30/81 (37%), Positives = 45/81 (55%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+ Y+APE++ G G+ + DWW+ G+ L+E+L+G PF T +I + L Sbjct: 380 FVGTHEYLAPEIIKGEGHGSAVDWWTFGIFLYELLFGKTPFKGSGNRATLFNVI--GQPL 437 Query: 375 KFPNNVDNVSGKAVDLISNLI 437 +FP VS A DLI L+ Sbjct: 438 RFP-EYPVVSFSARDLIRGLL 457 >K6A1_HUMAN (Q15418) Ribosomal protein S6 kinase alpha 1 (EC 2.7.1.37) (S6K-alpha 1) (90 kDa ribosomal protein S6 kinase 1) (p90-RSK 1) (Ribosomal S6 kinase 1) (RSK-1) (pp90RSK1) Length = 735 Score = 57.0 bits (136), Expect = 2e-08 Identities = 32/78 (41%), Positives = 47/78 (60%), Gaps = 3/78 (3%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFP--- 383 ++APEVL +GYD CD WS+G++L+ ML GY PF N + T ++I+ KF Sbjct: 580 FVAPEVLKRQGYDEGCDIWSLGILLYTMLAGYTPFAN-GPSDTPEEILTRIGSGKFTLSG 638 Query: 384 NNVDNVSGKAVDLISNLI 437 N + VS A DL+S ++ Sbjct: 639 GNWNTVSETAKDLVSKML 656 Score = 54.3 bits (129), Expect = 1e-07 Identities = 24/55 (43%), Positives = 35/55 (63%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ +G+ +S DWWS GV++FEML G PF + T I++ Sbjct: 222 FCGTVEYMAPEVVNRQGHSHSADWWSYGVLMFEMLTGSLPFQGKDRKETMTLILK 276 >K6A1_MOUSE (P18653) Ribosomal protein S6 kinase alpha 1 (EC 2.7.1.37) (S6K-alpha 1) (90 kDa ribosomal protein S6 kinase 1) (p90-RSK 1) (Ribosomal S6 kinase 1) (RSK-1) (pp90RSK1) (MAP kinase-activated protein kinase 1a) (MAPKAPK1A) Length = 724 Score = 57.0 bits (136), Expect = 2e-08 Identities = 32/78 (41%), Positives = 47/78 (60%), Gaps = 3/78 (3%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFP--- 383 ++APEVL +GYD CD WS+G++L+ ML GY PF N + T ++I+ KF Sbjct: 569 FVAPEVLKRQGYDEGCDIWSLGILLYTMLAGYTPFAN-GPSDTPEEILTRIGSGKFTLSG 627 Query: 384 NNVDNVSGKAVDLISNLI 437 N + VS A DL+S ++ Sbjct: 628 GNWNTVSETAKDLVSKML 645 Score = 39.7 bits (91), Expect = 0.003 Identities = 15/31 (48%), Positives = 23/31 (74%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVIL 287 F G+ Y+APEV+ +G+ +S DWWS GV++ Sbjct: 222 FCGTVEYMAPEVVNRQGHTHSADWWSYGVLM 252 >KPCB_BOVIN (P05126) Protein kinase C, beta type (EC 2.7.1.37) (PKC-beta) (PKC-B) Length = 673 Score = 57.0 bits (136), Expect = 2e-08 Identities = 30/82 (36%), Positives = 48/82 (58%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWW+ GV+L+EML G PF + + + I++ + Sbjct: 501 FCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAPFEGEDEDELFQSIMEHN--V 558 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + LIT Sbjct: 559 AYPK---SMSKEAVAICKGLIT 577 >K6A2_MOUSE (Q9WUT3) Ribosomal protein S6 kinase alpha 2 (EC 2.7.1.37) (S6K-alpha 2) (90 kDa ribosomal protein S6 kinase 2) (p90-RSK 2) (Ribosomal S6 kinase 3) (RSK-3) (pp90RSK3) (Protein-tyrosine kinase Mpk-9) (MAP kinase-activated protein kinase 1c) (MA Length = 733 Score = 57.0 bits (136), Expect = 2e-08 Identities = 29/77 (37%), Positives = 45/77 (58%), Gaps = 2/77 (2%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYN--DSKTGTAKKIIQFREYLKFPN 386 ++APEVL +GYD +CD WS+G++L+ ML G+ PF N D I +Y Sbjct: 577 FVAPEVLKRQGYDAACDVWSLGILLYTMLAGFTPFANGPDDTPEEILARIGSGKYALSGG 636 Query: 387 NVDNVSGKAVDLISNLI 437 N D++S A D++S ++ Sbjct: 637 NWDSISDAAKDVVSKML 653 Score = 53.9 bits (128), Expect = 1e-07 Identities = 25/55 (45%), Positives = 34/55 (61%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ RG+ S DWWS GV++FEML G PF + T I++ Sbjct: 219 FCGTIEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGSLPFQGKDRKETMALILK 273 >K6A2_HUMAN (Q15349) Ribosomal protein S6 kinase alpha 2 (EC 2.7.1.37) (S6K-alpha 2) (90 kDa ribosomal protein S6 kinase 2) (p90-RSK 2) (Ribosomal S6 kinase 3) (RSK-3) (pp90RSK3) Length = 733 Score = 57.0 bits (136), Expect = 2e-08 Identities = 29/77 (37%), Positives = 45/77 (58%), Gaps = 2/77 (2%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYN--DSKTGTAKKIIQFREYLKFPN 386 ++APEVL +GYD +CD WS+G++L+ ML G+ PF N D I +Y Sbjct: 577 FVAPEVLKRQGYDAACDIWSLGILLYTMLAGFTPFANGPDDTPEEILARIGSGKYALSGG 636 Query: 387 NVDNVSGKAVDLISNLI 437 N D++S A D++S ++ Sbjct: 637 NWDSISDAAKDVVSKML 653 Score = 53.9 bits (128), Expect = 1e-07 Identities = 25/55 (45%), Positives = 34/55 (61%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ RG+ S DWWS GV++FEML G PF + T I++ Sbjct: 219 FCGTIEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGSLPFQGKDRKETMALILK 273 >KAD5_SCHPO (Q09831) Probable serine/threonine-protein kinase C4G8.05 (EC 2.7.1.37) Length = 566 Score = 57.0 bits (136), Expect = 2e-08 Identities = 30/85 (35%), Positives = 46/85 (54%), Gaps = 4/85 (4%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ----F 362 F G+ YIAPEV+ G G+ + DWW++G++ +EMLY PF ++ T I+ F Sbjct: 382 FVGTEEYIAPEVIKGCGHTSAVDWWTLGILFYEMLYATTPFKGKNRNMTFSNILHKDVIF 441 Query: 363 REYLKFPNNVDNVSGKAVDLISNLI 437 EY P ++S +LI L+ Sbjct: 442 PEYADAP----SISSLCKNLIRKLL 462 >IPL1_YEAST (P38991) Serine/threonine-protein kinase IPL1 (EC 2.7.1.37) Length = 367 Score = 57.0 bits (136), Expect = 2e-08 Identities = 31/79 (39%), Positives = 48/79 (60%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ Y++PE++ R YD++ D W++GV+ FE+L G PPF + K T K+I +K Sbjct: 263 GTIDYLSPEMVESREYDHTIDAWALGVLAFELLTGAPPFEEEMKDTTYKRIAALD--IKM 320 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ N+S A DLI L+ Sbjct: 321 PS---NISQDAQDLILKLL 336 >KPCE_RABIT (P10830) Protein kinase C, epsilon type (EC 2.7.1.-) (nPKC-epsilon) Length = 736 Score = 56.6 bits (135), Expect = 2e-08 Identities = 24/54 (44%), Positives = 36/54 (66%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKII 356 F G+P YIAPE+L Y S DWW++GV+++EM+ G PPF D++ + I+ Sbjct: 566 FCGTPDYIAPEILQELEYGPSVDWWALGVLMYEMMAGQPPFEADNEDDLFESIL 619 >KPCE_RAT (P09216) Protein kinase C, epsilon type (EC 2.7.1.-) (nPKC-epsilon) Length = 737 Score = 56.6 bits (135), Expect = 2e-08 Identities = 24/54 (44%), Positives = 36/54 (66%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKII 356 F G+P YIAPE+L Y S DWW++GV+++EM+ G PPF D++ + I+ Sbjct: 567 FCGTPDYIAPEILQELEYGPSVDWWALGVLMYEMMAGQPPFEADNEDDLFESIL 620 >KPCE_MOUSE (P16054) Protein kinase C, epsilon type (EC 2.7.1.-) (nPKC-epsilon) Length = 737 Score = 56.6 bits (135), Expect = 2e-08 Identities = 24/54 (44%), Positives = 36/54 (66%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKII 356 F G+P YIAPE+L Y S DWW++GV+++EM+ G PPF D++ + I+ Sbjct: 567 FCGTPDYIAPEILQELEYGPSVDWWALGVLMYEMMAGQPPFEADNEDDLFESIL 620 >KPCE_HUMAN (Q02156) Protein kinase C, epsilon type (EC 2.7.1.-) (nPKC-epsilon) Length = 737 Score = 56.6 bits (135), Expect = 2e-08 Identities = 24/54 (44%), Positives = 36/54 (66%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKII 356 F G+P YIAPE+L Y S DWW++GV+++EM+ G PPF D++ + I+ Sbjct: 567 FCGTPDYIAPEILQELEYGPSVDWWALGVLMYEMMAGQPPFEADNEDDLFESIL 620 >K6AA_XENLA (P10665) Ribosomal protein S6 kinase II alpha (EC 2.7.1.37) (S6KII-alpha) (P90-RSK) (MAP kinase-activated protein kinase 1) (MAPK-activated protein kinase 1) (MAPKAP kinase 1) (MAPKAPK-1) Length = 733 Score = 56.2 bits (134), Expect = 3e-08 Identities = 32/78 (41%), Positives = 46/78 (58%), Gaps = 3/78 (3%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFP--- 383 ++APEVL +GYD CD WS+G++L+ ML GY PF N T ++I+ KF Sbjct: 578 FVAPEVLKRQGYDEGCDIWSLGILLYTMLAGYTPFAN-GLGDTPEEILARIGSGKFTLRG 636 Query: 384 NNVDNVSGKAVDLISNLI 437 N + VS A DL+S ++ Sbjct: 637 GNWNTVSAAAKDLVSRML 654 Score = 54.3 bits (129), Expect = 1e-07 Identities = 24/55 (43%), Positives = 35/55 (63%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ +G+ +S DWWS GV++FEML G PF + T I++ Sbjct: 222 FCGTVEYMAPEVVNRQGHSHSADWWSYGVLMFEMLTGSLPFQGKDRKETMTLILK 276 >KPSH_HUMAN (P11801) Serine/threonine-protein kinase H1 (EC 2.7.1.37) (PSK-H1) Length = 424 Score = 56.2 bits (134), Expect = 3e-08 Identities = 31/80 (38%), Positives = 48/80 (60%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P YIAPEVL+ + Y S D W++GVI + +L G PF +D++T ++I++ +Y Sbjct: 259 GTPEYIAPEVLVRKPYTNSVDMWALGVIAYILLSGTMPFEDDNRTRLYRQILR-GKYSYS 317 Query: 381 PNNVDNVSGKAVDLISNLIT 440 +VS A D I L+T Sbjct: 318 GEPWPSVSNLAKDFIDRLLT 337 >PKL1_MOUSE (P70268) Protein kinase C-like 1 (EC 2.7.1.-) (Protein-kinase C-related kinase 1) (Protein kinase C-like PKN) (Serine-threonine protein kinase N) (Fragment) Length = 283 Score = 56.2 bits (134), Expect = 3e-08 Identities = 30/94 (31%), Positives = 51/94 (54%), Gaps = 3/94 (3%) Frame = +3 Query: 165 CGARVGMG---APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 C +G G + F G+P ++APEVL Y + DWW +GV+L+EML G PF D + Sbjct: 103 CKEGMGYGDRTSTFCGTPEFLAPEVLTDTSYTRAVDWWGLGVLLYEMLVGESPFPGDDEE 162 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 I+ + +++P +S +A+ ++ L+ Sbjct: 163 EVFDSIV--NDEVRYPR---FLSAEAIGIMRRLL 191 >PKL1_HUMAN (Q16512) Protein kinase C-like 1 (EC 2.7.1.-) (Protein-kinase C-related kinase 1) (Protein kinase C-like PKN) (Serine-threonine protein kinase N) Length = 942 Score = 56.2 bits (134), Expect = 3e-08 Identities = 30/94 (31%), Positives = 51/94 (54%), Gaps = 3/94 (3%) Frame = +3 Query: 165 CGARVGMG---APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 C +G G + F G+P ++APEVL Y + DWW +GV+L+EML G PF D + Sbjct: 762 CKEGMGYGDRTSTFCGTPEFLAPEVLTDTSYTRAVDWWGLGVLLYEMLVGESPFPGDDEE 821 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 I+ + +++P +S +A+ ++ L+ Sbjct: 822 EVFDSIV--NDEVRYPR---FLSAEAIGIMRRLL 850 >KPC1_LYTPI (Q25378) Protein kinase C (EC 2.7.1.-) Length = 658 Score = 56.2 bits (134), Expect = 3e-08 Identities = 27/82 (32%), Positives = 47/82 (57%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y + DWW+ GV+L+EML G PPF + + + I++ Sbjct: 484 FCGTPDYIAPEIVAYQPYGKAVDWWAFGVLLYEMLAGQPPFDGEDEDELFQSIME----- 538 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 P+ ++S ++V + +T Sbjct: 539 HVPSYPKSMSRESVTMCKGFLT 560 >KPC4_DROME (P83099) Putative protein kinase C, delta type homolog (EC 2.7.1.37) Length = 643 Score = 55.8 bits (133), Expect = 3e-08 Identities = 22/41 (53%), Positives = 30/41 (73%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 F G+P Y+APE++ G Y+ + DWWS GV+L+EML G PF Sbjct: 474 FCGTPDYMAPEIIKGEKYNQNVDWWSFGVLLYEMLIGQSPF 514 >KPCB_RABIT (P05772) Protein kinase C, beta type (EC 2.7.1.37) (PKC-beta) (PKC-B) Length = 671 Score = 55.8 bits (133), Expect = 3e-08 Identities = 29/82 (35%), Positives = 48/82 (58%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWW+ GV+L+EML G PF + + + I++ + Sbjct: 501 FCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAPFEGEDEDELFQSIMEHN--V 558 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + L+T Sbjct: 559 AYPK---SMSKEAVAICKGLMT 577 >KPCB_MOUSE (P04410) Protein kinase C, beta type (EC 2.7.1.37) (PKC-beta) (PKC-B) Length = 671 Score = 55.8 bits (133), Expect = 3e-08 Identities = 29/82 (35%), Positives = 48/82 (58%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWW+ GV+L+EML G PF + + + I++ + Sbjct: 501 FCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAPFEGEDEDELFQSIMEHN--V 558 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + L+T Sbjct: 559 AYPK---SMSKEAVAICKGLMT 577 >KPCB_HUMAN (P05771) Protein kinase C, beta type (EC 2.7.1.37) (PKC-beta) (PKC-B) Length = 671 Score = 55.8 bits (133), Expect = 3e-08 Identities = 29/82 (35%), Positives = 48/82 (58%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P YIAPE++ + Y S DWW+ GV+L+EML G PF + + + I++ + Sbjct: 501 FCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAPFEGEDEDELFQSIMEHN--V 558 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 +P ++S +AV + L+T Sbjct: 559 AYPK---SMSKEAVAICKGLMT 577 >AURC_HUMAN (Q9UQB9) Serine/threonine-protein kinase 13 (EC 2.7.1.37) (Aurora/Ipl1/Eg2 protein 2) (Aurora/Ipl1-related kinase 3) (Aurora-C) Length = 309 Score = 55.5 bits (132), Expect = 4e-08 Identities = 30/79 (37%), Positives = 49/79 (62%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ Y+ PE++ GR YD D W +GV+ +E+L GYPPF + S + T ++I++ ++F Sbjct: 201 GTLDYLPPEMIEGRTYDEKVDLWCIGVLCYELLVGYPPFESASHSETYRRILKVD--VRF 258 Query: 381 PNNVDNVSGKAVDLISNLI 437 P ++ A DLIS L+ Sbjct: 259 PLSMPL---GARDLISRLL 274 >PKL1_RAT (Q63433) Protein kinase C-like 1 (EC 2.7.1.-) (Protein-kinase C-related kinase 1) (Protein kinase C-like PKN) (Serine-threonine protein kinase N) (Protease-activated kinase 1) (PAK-1) Length = 946 Score = 55.5 bits (132), Expect = 4e-08 Identities = 30/94 (31%), Positives = 50/94 (53%), Gaps = 3/94 (3%) Frame = +3 Query: 165 CGARVGMG---APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 C +G G + F G+P ++APEVL Y + DWW +GV L+EML G PF D + Sbjct: 766 CKEGMGYGDRTSTFCGTPEFLAPEVLTDTSYTRAVDWWGLGVFLYEMLVGESPFPGDDEE 825 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 I+ + +++P +S +A+ ++ L+ Sbjct: 826 EVFDSIV--NDEVRYPR---FLSAEAIGIMRRLL 854 >RCK1_YEAST (P38622) Serine/threonine-protein kinase RCK1 (EC 2.7.1.37) Length = 512 Score = 55.1 bits (131), Expect = 6e-08 Identities = 28/79 (35%), Positives = 44/79 (55%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ Y+A EV + Y D WS+G +LF +L GYPPFY ++ KKI + +Y Sbjct: 318 GTIEYVASEVFTSKRYSMKVDMWSIGCVLFTLLCGYPPFYEKNEKTLLKKISR-GDYEFL 376 Query: 381 PNNVDNVSGKAVDLISNLI 437 DN+S A + +++L+ Sbjct: 377 APWWDNISSGAKNAVTHLL 395 >ST6L_XENLA (Q91819) Serine/threonine-protein kinase Eg2-like (EC 2.7.1.37) (p46XlEg22) Length = 408 Score = 55.1 bits (131), Expect = 6e-08 Identities = 32/94 (34%), Positives = 49/94 (52%) Frame = +3 Query: 156 GWRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 GW A G+ Y+ PE++ GR +D D WS+GV+ +E L G PPF D+ Sbjct: 283 GWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFETDTHQ 342 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 T ++I + ++P VS +A DL+S L+ Sbjct: 343 ETYRRISKVE--FQYP---PYVSEEAKDLVSKLL 371 >KCCD_HUMAN (Q13557) Calcium/calmodulin-dependent protein kinase type II delta chain (EC 2.7.1.123) (CaM-kinase II delta chain) (CaM kinase II delta subunit) (CaMK-II delta subunit) Length = 499 Score = 55.1 bits (131), Expect = 6e-08 Identities = 32/83 (38%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ Y Sbjct: 174 FAGTPGYLSPEVLRKDPYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQ-IKAGAY- 231 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A DLI+ ++T Sbjct: 232 DFPSPEWDTVTPEAKDLINKMLT 254 >KCCD_RAT (P15791) Calcium/calmodulin-dependent protein kinase type II delta chain (EC 2.7.1.123) (CaM-kinase II delta chain) (CaM kinase II delta subunit) (CaMK-II delta subunit) Length = 533 Score = 55.1 bits (131), Expect = 6e-08 Identities = 32/83 (38%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ Y Sbjct: 174 FAGTPGYLSPEVLRKDPYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQ-IKAGAY- 231 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A DLI+ ++T Sbjct: 232 DFPSPEWDTVTPEAKDLINKMLT 254 >K6AA_CHICK (P18652) Ribosomal protein S6 kinase II alpha (EC 2.7.1.37) (S6KII-alpha) (P90-RSK) (MAP kinase-activated protein kinase 1) (MAPK-activated protein kinase 1) (MAPKAP kinase 1) (MAPKAPK-1) Length = 752 Score = 55.1 bits (131), Expect = 6e-08 Identities = 32/78 (41%), Positives = 46/78 (58%), Gaps = 3/78 (3%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFP--- 383 ++APEVL +GYD CD WS+GV+L+ ML G PF N + T ++I+ KF Sbjct: 597 FVAPEVLKRQGYDEGCDIWSLGVLLYTMLAGCTPFAN-GPSDTPEEILTRIGGGKFSVNG 655 Query: 384 NNVDNVSGKAVDLISNLI 437 N D +S A DL+S ++ Sbjct: 656 GNWDTISDVAKDLVSKML 673 Score = 54.3 bits (129), Expect = 1e-07 Identities = 24/55 (43%), Positives = 35/55 (63%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ +G+ +S DWWS GV++FEML G PF + T I++ Sbjct: 240 FCGTVEYMAPEVVNRQGHSHSADWWSYGVLMFEMLTGSLPFQGKDRKETMTLILK 294 >STK6_XENLA (Q91820) Serine/threonine-protein kinase Eg2 (EC 2.7.1.37) (pEg2) (p46Eg265) Length = 407 Score = 55.1 bits (131), Expect = 6e-08 Identities = 32/94 (34%), Positives = 50/94 (53%) Frame = +3 Query: 156 GWRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 GW A G+ Y+ PE++ GR +D + D WS+GV+ +E L G PPF D+ Sbjct: 283 GWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDETVDLWSLGVLCYEFLVGKPPFETDTHQ 342 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 T ++I + ++P VS +A DL+S L+ Sbjct: 343 ETYRRISKVE--FQYP---PYVSEEARDLVSKLL 371 >AURB_MOUSE (O70126) Serine/threonine-protein kinase 12 (EC 2.7.1.37) (Aurora-related kinase 2) (Serine/threonine-protein kinase 5) (STK-1) (Aurora-B) Length = 345 Score = 55.1 bits (131), Expect = 6e-08 Identities = 32/94 (34%), Positives = 53/94 (56%) Frame = +3 Query: 156 GWRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 GW A G+ Y+ PE++ GR ++ D W +GV+ +E++ G PPF + S + Sbjct: 225 GWSVHAPSLRRKTMCGTLDYLPPEMIEGRMHNEMVDLWCIGVLCYELMVGNPPFESPSHS 284 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 T ++I++ LKFP++V + A DLIS L+ Sbjct: 285 ETYRRIVKVD--LKFPSSVPS---GAQDLISKLL 313 >CDP4_PLAYO (Q7RJG2) Calcium-dependent protein kinase 4 (EC 2.7.1.37) Length = 527 Score = 55.1 bits (131), Expect = 6e-08 Identities = 32/79 (40%), Positives = 43/79 (54%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ YIAP+VL G YD CD WS GVIL+ +L G PPF ++ KK+ + Sbjct: 232 GTAYYIAPDVLHGT-YDEKCDIWSCGVILYILLSGCPPFNGSNEYDILKKVETGKYTFDL 290 Query: 381 PNNVDNVSGKAVDLISNLI 437 P +S KA DLI ++ Sbjct: 291 P-QFKKISDKAKDLIKKML 308 >CDP4_PLAF7 (Q8IBS5) Calcium-dependent protein kinase 4 (EC 2.7.1.37) Length = 527 Score = 55.1 bits (131), Expect = 6e-08 Identities = 32/79 (40%), Positives = 43/79 (54%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ YIAP+VL G YD CD WS GVIL+ +L G PPF ++ KK+ + Sbjct: 232 GTAYYIAPDVLHGT-YDEKCDIWSCGVILYILLSGCPPFNGSNEYDILKKVEAGKYTFDL 290 Query: 381 PNNVDNVSGKAVDLISNLI 437 P +S KA DLI ++ Sbjct: 291 P-QFKKISDKAKDLIKKML 308 >CDP4_PLABA (P62345) Calcium-dependent protein kinase 4 (EC 2.7.1.37) (PbCDPK4) Length = 527 Score = 55.1 bits (131), Expect = 6e-08 Identities = 32/79 (40%), Positives = 43/79 (54%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ YIAP+VL G YD CD WS GVIL+ +L G PPF ++ KK+ + Sbjct: 232 GTAYYIAPDVLHGT-YDEKCDIWSCGVILYILLSGCPPFNGSNEYDILKKVETGKYTFDL 290 Query: 381 PNNVDNVSGKAVDLISNLI 437 P +S KA DLI ++ Sbjct: 291 P-QFKKISDKAKDLIKKML 308 >PKL2_RAT (O08874) Protein kinase C-like 2 (EC 2.7.1.-) (Protein-kinase C-related kinase 2) (Protease-activated kinase 2) (PAK-2) (Fragment) Length = 842 Score = 54.7 bits (130), Expect = 8e-08 Identities = 29/94 (30%), Positives = 51/94 (54%), Gaps = 3/94 (3%) Frame = +3 Query: 165 CGARVGMG---APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 C +G G + F G+P ++APEVL Y + DWW +GV+++EML G PF D + Sbjct: 668 CKEGMGYGDRTSTFCGTPEFLAPEVLTETSYTRAVDWWGLGVLIYEMLVGESPFPGDDEE 727 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 I+ + +++P +S +A+ ++ L+ Sbjct: 728 EVFDSIV--NDEVRYPR---FLSTEAISIMRRLL 756 >KCCA_RAT (P11275) Calcium/calmodulin-dependent protein kinase type II alpha chain (EC 2.7.1.123) (CaM-kinase II alpha chain) (CaM kinase II alpha subunit) (CaMK-II alpha subunit) Length = 478 Score = 54.7 bits (130), Expect = 8e-08 Identities = 32/83 (38%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ Y Sbjct: 173 FAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYQQ-IKAGAY- 230 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A DLI+ ++T Sbjct: 231 DFPSPEWDTVTPEAKDLINKMLT 253 >KCCA_HUMAN (Q9UQM7) Calcium/calmodulin-dependent protein kinase type II alpha chain (EC 2.7.1.123) (CaM-kinase II alpha chain) (CaM kinase II alpha subunit) (CaMK-II alpha subunit) Length = 478 Score = 54.7 bits (130), Expect = 8e-08 Identities = 32/83 (38%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ Y Sbjct: 173 FAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYQQ-IKAGAY- 230 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A DLI+ ++T Sbjct: 231 DFPSPEWDTVTPEAKDLINKMLT 253 >KCC4_MOUSE (P08414) Calcium/calmodulin-dependent protein kinase type IV catalytic chain (EC 2.7.1.123) (CAM kinase-GR) (CaMK IV) Length = 469 Score = 54.7 bits (130), Expect = 8e-08 Identities = 31/79 (39%), Positives = 41/79 (51%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y APE+L G Y D WSVG+I + +L G+ PFY++ + I EY Sbjct: 199 GTPGYCAPEILRGCAYGPEVDMWSVGIITYILLCGFEPFYDERGDQFMFRRILNCEYYFI 258 Query: 381 PNNVDNVSGKAVDLISNLI 437 D VS A DL+ LI Sbjct: 259 SPWWDEVSLNAKDLVKKLI 277 >KCC4_RAT (P13234) Calcium/calmodulin-dependent protein kinase type IV catalytic chain (EC 2.7.1.123) (CAM kinase-GR) (CaMK IV) (Calspermin) Length = 474 Score = 54.7 bits (130), Expect = 8e-08 Identities = 31/79 (39%), Positives = 41/79 (51%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y APE+L G Y D WSVG+I + +L G+ PFY++ + I EY Sbjct: 199 GTPGYCAPEILRGCAYGPEVDMWSVGIITYILLCGFEPFYDERGDQFMFRRILNCEYYFI 258 Query: 381 PNNVDNVSGKAVDLISNLI 437 D VS A DL+ LI Sbjct: 259 SPWWDEVSLNAKDLVKKLI 277 >K6A3_MOUSE (P18654) Ribosomal protein S6 kinase alpha 3 (EC 2.7.1.37) (S6K-alpha 3) (90 kDa ribosomal protein S6 kinase 3) (p90-RSK 3) (Ribosomal S6 kinase 2) (RSK-2) (pp90RSK2) (MAP kinase-activated protein kinase 1b) (MAPKAPK1B) Length = 740 Score = 54.7 bits (130), Expect = 8e-08 Identities = 32/78 (41%), Positives = 47/78 (60%), Gaps = 3/78 (3%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFP--- 383 ++APEVL +GYD +CD WS+GV+L+ ML GY PF N T ++I+ KF Sbjct: 584 FVAPEVLKRQGYDAACDIWSLGVLLYTMLTGYTPFAN-GPDDTPEEILARIGSGKFSLSG 642 Query: 384 NNVDNVSGKAVDLISNLI 437 ++VS A DL+S ++ Sbjct: 643 GYWNSVSDTAKDLVSKML 660 Score = 54.7 bits (130), Expect = 8e-08 Identities = 25/55 (45%), Positives = 34/55 (61%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ RG+ S DWWS GV++FEML G PF + T I++ Sbjct: 228 FCGTVEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGTLPFQGKDRKETMTMILK 282 >K6A3_HUMAN (P51812) Ribosomal protein S6 kinase alpha 3 (EC 2.7.1.37) (S6K-alpha 3) (90 kDa ribosomal protein S6 kinase 3) (p90-RSK 3) (Ribosomal S6 kinase 2) (RSK-2) (pp90RSK2) (Insulin-stimulated protein kinase 1) (ISPK-1) Length = 740 Score = 54.7 bits (130), Expect = 8e-08 Identities = 32/78 (41%), Positives = 47/78 (60%), Gaps = 3/78 (3%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKFP--- 383 ++APEVL +GYD +CD WS+GV+L+ ML GY PF N T ++I+ KF Sbjct: 584 FVAPEVLKRQGYDAACDIWSLGVLLYTMLTGYTPFAN-GPDDTPEEILARIGSGKFSLSG 642 Query: 384 NNVDNVSGKAVDLISNLI 437 ++VS A DL+S ++ Sbjct: 643 GYWNSVSDTAKDLVSKML 660 Score = 54.7 bits (130), Expect = 8e-08 Identities = 25/55 (45%), Positives = 34/55 (61%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ RG+ S DWWS GV++FEML G PF + T I++ Sbjct: 228 FCGTVEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGTLPFQGKDRKETMTMILK 282 >PKL2_HUMAN (Q16513) Protein kinase C-like 2 (EC 2.7.1.-) (Protein-kinase C-related kinase 2) Length = 984 Score = 54.7 bits (130), Expect = 8e-08 Identities = 29/94 (30%), Positives = 51/94 (54%), Gaps = 3/94 (3%) Frame = +3 Query: 165 CGARVGMG---APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 C +G G + F G+P ++APEVL Y + DWW +GV+++EML G PF D + Sbjct: 804 CKEGMGYGDRTSTFCGTPEFLAPEVLTETSYTRAVDWWGLGVLIYEMLVGESPFPGDDEE 863 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 I+ + +++P +S +A+ ++ L+ Sbjct: 864 EVFDSIV--NDEVRYPR---FLSTEAISIMRRLL 892 >KCC4_HUMAN (Q16566) Calcium/calmodulin-dependent protein kinase type IV catalytic chain (EC 2.7.1.123) (CAM kinase-GR) (CaMK IV) Length = 473 Score = 54.3 bits (129), Expect = 1e-07 Identities = 31/79 (39%), Positives = 41/79 (51%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y APE+L G Y D WSVG+I + +L G+ PFY++ + I EY Sbjct: 203 GTPGYCAPEILRGCAYGPEVDMWSVGIITYILLCGFEPFYDERGDQFMFRRILNCEYYFI 262 Query: 381 PNNVDNVSGKAVDLISNLI 437 D VS A DL+ LI Sbjct: 263 SPWWDEVSLNAKDLVRKLI 281 >RCK2_YEAST (P38623) Serine/threonine-protein kinase RCK2 (EC 2.7.1.37) (CAM kinase-like protein kinase CLK1) Length = 610 Score = 53.9 bits (128), Expect = 1e-07 Identities = 29/79 (36%), Positives = 40/79 (50%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ Y APEV+ Y D W +G +L+ ML G+PPFY D K T + I EY Sbjct: 382 GTVGYTAPEVVKDEHYSMKVDMWGIGCVLYTMLCGFPPFY-DEKIDTLTEKISRGEYTFL 440 Query: 381 PNNVDNVSGKAVDLISNLI 437 D +S A + +S L+ Sbjct: 441 KPWWDEISAGAKNAVSKLL 459 >KPCL_HUMAN (P24723) Protein kinase C, eta type (EC 2.7.1.-) (nPKC-eta) (PKC-L) Length = 682 Score = 53.9 bits (128), Expect = 1e-07 Identities = 24/56 (42%), Positives = 37/56 (66%) Frame = +3 Query: 189 APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKII 356 A F G+P YIAPE+L Y + DWW++GV+L+EML G+ PF +++ + I+ Sbjct: 511 ATFCGTPDYIAPEILQEMLYGPAVDWWAMGVLLYEMLCGHAPFEAENEDDLFEAIL 566 >KML2_RAT (P20689) Myosin light chain kinase 2, skeletal/cardiac muscle (EC 2.7.1.117) (MLCK2) Length = 609 Score = 53.9 bits (128), Expect = 1e-07 Identities = 29/81 (35%), Positives = 42/81 (51%) Frame = +3 Query: 198 FGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLK 377 FG+P +++PEV+ D WS+GVI + +L G PF D T T ++ Y Sbjct: 456 FGTPEFLSPEVVNYDQISDKTDMWSLGVITYMLLSGLSPFLGDDDTETLNNVLSANWYFD 515 Query: 378 FPNNVDNVSGKAVDLISNLIT 440 + VS +A D +SNLIT Sbjct: 516 -EETFEAVSDEAKDFVSNLIT 535 >STK6_HUMAN (O14965) Serine/threonine-protein kinase 6 (EC 2.7.1.37) (Serine/threonine kinase 15) (Aurora/IPL1-related kinase 1) (Aurora-related kinase 1) (hARK1) (Aurora-A) (Breast-tumor-amplified kinase) Length = 403 Score = 53.9 bits (128), Expect = 1e-07 Identities = 35/94 (37%), Positives = 48/94 (51%) Frame = +3 Query: 156 GWRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 GW A G+ Y+ PE++ GR +D D WS+GV+ +E L G PPF ++ Sbjct: 276 GWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQ 335 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 T K+I R FP D V+ A DLIS L+ Sbjct: 336 ETYKRI--SRVEFTFP---DFVTEGARDLISRLL 364 >KS6A_CAEEL (Q21734) Putative ribosomal protein S6 kinase alpha (EC 2.7.1.37) Length = 784 Score = 53.9 bits (128), Expect = 1e-07 Identities = 23/55 (41%), Positives = 37/55 (67%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ RG+ + D+WS+GV++FEML G+ PF + T +I++ Sbjct: 264 FCGTVEYMAPEVINRRGHSMAADFWSLGVLMFEMLTGHLPFQGRDRNDTMTQILK 318 Score = 50.4 bits (119), Expect = 1e-06 Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 3/78 (3%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFY---NDSKTGTAKKIIQFREYLKFP 383 ++APEVL +GYD SCD WS+GV+L ML G PF ND+ +++ + + P Sbjct: 617 FVAPEVLRKQGYDRSCDVWSLGVLLHTMLTGCTPFAMGPNDTPDQILQRVGDGKISMTHP 676 Query: 384 NNVDNVSGKAVDLISNLI 437 D +S +A DL+ ++ Sbjct: 677 -VWDTISDEAKDLVRKML 693 >KCCA_DROME (Q00168) Calcium/calmodulin-dependent protein kinase type II alpha chain (EC 2.7.1.123) (CaM-kinase II alpha chain) Length = 530 Score = 53.9 bits (128), Expect = 1e-07 Identities = 30/82 (36%), Positives = 48/82 (58%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y S D W+ GVIL+ +L GYPPF+++ + + I+ Y Sbjct: 174 FAGTPGYLSPEVLKKEPYGKSVDIWACGVILYILLVGYPPFWDEDQHRLYSQ-IKAGAYD 232 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 D V+ +A +LI+ ++T Sbjct: 233 YPSPEWDTVTPEAKNLINQMLT 254 >KCCB_HUMAN (Q13554) Calcium/calmodulin-dependent protein kinase type II beta chain (EC 2.7.1.123) (CaM-kinase II beta chain) (CaM kinase II beta subunit) (CaMK-II beta subunit) Length = 664 Score = 53.9 bits (128), Expect = 1e-07 Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ Y Sbjct: 174 FAGTPGYLSPEVLRKEAYGKPVDIWACGVILYILLVGYPPFWDEDQHKLYQQ-IKAGAY- 231 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A +LI+ ++T Sbjct: 232 DFPSPEWDTVTPEAKNLINQMLT 254 >AURB_HUMAN (Q96GD4) Serine/threonine-protein kinase 12 (EC 2.7.1.37) (Aurora- and Ipl1-like midbody-associated protein 1) (AIM-1) (Aurora/IPL1-related kinase 2) (Aurora-related kinase 2) (STK-1) (Aurora-B) Length = 344 Score = 53.9 bits (128), Expect = 1e-07 Identities = 33/94 (35%), Positives = 50/94 (53%) Frame = +3 Query: 156 GWRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 GW A G+ Y+ PE++ GR ++ D W +GV+ +E+L G PPF + S Sbjct: 220 GWSVHAPSLRRKTMCGTLDYLPPEMIEGRMHNEKVDLWCIGVLCYELLVGNPPFESASHN 279 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 T ++I++ LKFP +V A DLIS L+ Sbjct: 280 ETYRRIVKVD--LKFPASVPT---GAQDLISKLL 308 >KPCL_RAT (Q64617) Protein kinase C, eta type (EC 2.7.1.-) (nPKC-eta) (PKC-L) Length = 683 Score = 53.9 bits (128), Expect = 1e-07 Identities = 24/56 (42%), Positives = 37/56 (66%) Frame = +3 Query: 189 APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKII 356 A F G+P YIAPE+L Y + DWW++GV+L+EML G+ PF +++ + I+ Sbjct: 512 ATFCGTPDYIAPEILQEMLYGPAVDWWAMGVLLYEMLCGHAPFEAENEDDLFEAIL 567 >KPCL_MOUSE (P23298) Protein kinase C, eta type (EC 2.7.1.-) (nPKC-eta) (PKC-L) Length = 683 Score = 53.9 bits (128), Expect = 1e-07 Identities = 24/56 (42%), Positives = 37/56 (66%) Frame = +3 Query: 189 APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKII 356 A F G+P YIAPE+L Y + DWW++GV+L+EML G+ PF +++ + I+ Sbjct: 512 ATFCGTPDYIAPEILQEMLYGPAVDWWAMGVLLYEMLCGHAPFEAENEDDLFEAIL 567 >KCCB_RAT (P08413) Calcium/calmodulin-dependent protein kinase type II beta chain (EC 2.7.1.123) (CaM-kinase II beta chain) (CaM kinase II beta subunit) (CaMK-II beta subunit) Length = 542 Score = 53.9 bits (128), Expect = 1e-07 Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ Y Sbjct: 174 FAGTPGYLSPEVLRKEAYGKPVDIWACGVILYILLVGYPPFWDEDQHKLYQQ-IKAGAY- 231 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A +LI+ ++T Sbjct: 232 DFPSPEWDTVTPEAKNLINQMLT 254 >KCCB_MOUSE (P28652) Calcium/calmodulin-dependent protein kinase type II beta chain (EC 2.7.1.123) (CaM-kinase II beta chain) (CaM kinase II beta subunit) (CaMK-II beta subunit) Length = 542 Score = 53.9 bits (128), Expect = 1e-07 Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ Y Sbjct: 174 FAGTPGYLSPEVLRKEAYGKPVDIWACGVILYILLVGYPPFWDEDQHKLYQQ-IKAGAY- 231 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A +LI+ ++T Sbjct: 232 DFPSPEWDTVTPEAKNLINQMLT 254 >KCC2_SCHPO (O42844) Calcium/calmodulin-dependent protein kinase type II (EC 2.7.1.123) (CAM kinase II) Length = 504 Score = 53.9 bits (128), Expect = 1e-07 Identities = 27/80 (33%), Positives = 47/80 (58%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ Y APE++ Y + D W++G +L ML G+PPF++++ A K++ E+ Sbjct: 255 GTVGYAAPEIVNDELYSKNVDMWAMGCVLHTMLCGFPPFFDENIKDLASKVVN-GEFEFL 313 Query: 381 PNNVDNVSGKAVDLISNLIT 440 D++S A DLI++L+T Sbjct: 314 SPWWDDISDSAKDLITHLLT 333 >S17A_RABIT (Q9GM70) Serine/threonine-protein kinase 17A (EC 2.7.1.37) (DAP kinase-related apoptosis-inducing protein kinase 1) (rDRAK1) Length = 397 Score = 53.1 bits (126), Expect = 2e-07 Identities = 30/79 (37%), Positives = 39/79 (49%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P Y+APE+L + D WS+GV+ + ML G PF D+K T I Q Sbjct: 208 GTPEYVAPEILSYDPISMATDMWSIGVLTYVMLTGISPFLGDNKQETFLNISQMNLSYS- 266 Query: 381 PNNVDNVSGKAVDLISNLI 437 D VS AVD I L+ Sbjct: 267 EEEFDTVSESAVDFIKKLL 285 >KML2_MOUSE (Q8VCR8) Myosin light chain kinase 2, skeletal/cardiac muscle (EC 2.7.1.117) (MLCK2) (Fragment) Length = 240 Score = 53.1 bits (126), Expect = 2e-07 Identities = 28/81 (34%), Positives = 42/81 (51%) Frame = +3 Query: 198 FGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLK 377 FG+P +++PEV+ D WS+GVI + +L G PF D T T ++ Y Sbjct: 87 FGTPEFLSPEVVNYDQISDKTDMWSLGVITYMLLSGLSPFLGDDDTETLNNVLSANWYFD 146 Query: 378 FPNNVDNVSGKAVDLISNLIT 440 + VS +A D +SNL+T Sbjct: 147 -EETFEAVSDEAKDFVSNLLT 166 >PCK2_SCHPO (P36583) Protein kinase C-like 2 (EC 2.7.1.-) Length = 1016 Score = 53.1 bits (126), Expect = 2e-07 Identities = 20/48 (41%), Positives = 33/48 (68%) Frame = +3 Query: 189 APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSK 332 A F G+P ++APE+L+ + Y S DWW+ GV++++ML G PF + + Sbjct: 841 ATFCGTPEFMAPEILLEQQYTRSVDWWAFGVLIYQMLLGQSPFRGEDE 888 >K6AB_XENLA (P10666) Ribosomal protein S6 kinase II beta (EC 2.7.1.37) (S6KII-beta) (P90-RSK) Length = 629 Score = 52.8 bits (125), Expect = 3e-07 Identities = 23/55 (41%), Positives = 34/55 (61%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQ 359 F G+ Y+APEV+ +G+ + DWWS GV++FEML G PF + T I++ Sbjct: 222 FCGTVEYMAPEVVNRQGHSHGADWWSYGVLMFEMLTGSLPFQGKDRKETMTLILK 276 Score = 52.4 bits (124), Expect = 4e-07 Identities = 21/37 (56%), Positives = 28/37 (75%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYN 323 ++APEVL +GYD CD WS+G++L+ ML GY PF N Sbjct: 578 FVAPEVLKRQGYDEGCDIWSLGILLYTMLAGYTPFAN 614 >PCK1_SCHPO (P36582) Protein kinase C-like 1 (EC 2.7.1.-) Length = 988 Score = 52.8 bits (125), Expect = 3e-07 Identities = 27/82 (32%), Positives = 45/82 (54%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P ++APE+L+ + Y DWW+ GV++++ML G PF + + I+ + Sbjct: 824 FCGTPEFMAPEILLEQQYSKDVDWWAFGVLMYQMLLGQSPFKGEDEEEIFDAILS--DEP 881 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 FP N+ AV L+ L+T Sbjct: 882 LFP---INMPADAVSLLRGLLT 900 >KCCG_MOUSE (Q923T9) Calcium/calmodulin-dependent protein kinase type II gamma chain (EC 2.7.1.123) (CaM-kinase II gamma chain) (CaM kinase II gamma subunit) (CaMK-II gamma subunit) Length = 529 Score = 52.4 bits (124), Expect = 4e-07 Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ Y Sbjct: 174 FAGTPGYLSPEVLRKDPYGKPVDIWACGVILYILLVGYPPFWDEDQHKLYQQ-IKAGAY- 231 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A +LI+ ++T Sbjct: 232 DFPSPEWDTVTPEAKNLINQMLT 254 >K6A4_HUMAN (O75676) Ribosomal protein S6 kinase alpha 4 (EC 2.7.1.37) (Nuclear mitogen-and stress-activated protein kinase-2) (90 kDa ribosomal protein S6 kinase 4) (Ribosomal protein kinase B) (RSKB) Length = 772 Score = 52.4 bits (124), Expect = 4e-07 Identities = 37/94 (39%), Positives = 50/94 (53%), Gaps = 6/94 (6%) Frame = +3 Query: 177 VGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTG----TA 344 V M P F + Y APE+L +GYD SCD WS+GVIL+ ML G PF S G A Sbjct: 564 VPMQTPCF-TLQYAAPELLAQQGYDESCDLWSLGVILYMMLSGQVPFQGASGQGGQSQAA 622 Query: 345 KKIIQFRE--YLKFPNNVDNVSGKAVDLISNLIT 440 + + + RE + VS +A +L+ L+T Sbjct: 623 EIMCKIREGRFSLDGEAWQGVSEEAKELVRGLLT 656 Score = 48.9 bits (115), Expect = 4e-06 Identities = 30/86 (34%), Positives = 48/86 (55%), Gaps = 5/86 (5%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGR-GYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREY 371 F G+ Y+APE++ + G+ + DWWS+G++LFE+L G PF + + T ++ R Sbjct: 197 FCGTIEYMAPEIIRSKTGHGKAVDWWSLGILLFELLTGASPFTLEGERNTQAEV--SRRI 254 Query: 372 LK----FPNNVDNVSGKAVDLISNLI 437 LK FP + V A DL+ L+ Sbjct: 255 LKCSPPFPPRIGPV---AQDLLQRLL 277 >SCH9_YEAST (P11792) Serine/threonine-protein kinase SCH9 (EC 2.7.1.37) Length = 823 Score = 52.4 bits (124), Expect = 4e-07 Identities = 27/74 (36%), Positives = 46/74 (62%), Gaps = 1/74 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGR-GYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREY 371 F G+ Y+APE+L+ GY D+WS+GV++FEM G+ PF+ ++ +KI + Sbjct: 570 FCGTTEYLAPELLLDETGYTKMVDFWSLGVLIFEMCCGWSPFFAENNQKMYQKIAFGK-- 627 Query: 372 LKFPNNVDNVSGKA 413 +KFP +V + G++ Sbjct: 628 VKFPRDVLSQEGRS 641 >POLO_DROME (P52304) Serine/threonine-protein kinase polo (EC 2.7.1.37) Length = 576 Score = 52.4 bits (124), Expect = 4e-07 Identities = 21/51 (41%), Positives = 32/51 (62%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKI 353 G+P YIAPE+L +G+ + D WS+G +++ +L G PPF + T KI Sbjct: 185 GTPNYIAPEILTKKGHSFEVDIWSIGCVMYTLLVGQPPFETKTLKDTYSKI 235 >KCCG_HUMAN (Q13555) Calcium/calmodulin-dependent protein kinase type II gamma chain (EC 2.7.1.123) (CaM-kinase II gamma chain) (CaM kinase II gamma subunit) (CaMK-II gamma subunit) (Fragment) Length = 472 Score = 52.4 bits (124), Expect = 4e-07 Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ Y Sbjct: 174 FAGTPGYLSPEVLRKDPYGKPVDIWACGVILYILLVGYPPFWDEDQHKLYQQ-IKAGAY- 231 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A +LI+ ++T Sbjct: 232 DFPSPEWDTVTPEAKNLINQMLT 254 >AURB_RAT (O55099) Serine/threonine-protein kinase 12 (EC 2.7.1.37) (Aurora- and Ipl1-like midbody-associated protein 1) (AIM-1) (Aurora-B) Length = 343 Score = 52.4 bits (124), Expect = 4e-07 Identities = 31/94 (32%), Positives = 52/94 (55%) Frame = +3 Query: 156 GWRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 GW A G+ Y+ PE++ GR ++ D W +GV+ +E++ G PPF + S + Sbjct: 223 GWSVHAPSLRRKTMCGTLDYLPPEMIEGRMHNEMVDLWCIGVLCYELMVGNPPFESPSHS 282 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 T ++I++ LKFP+++ A DLIS L+ Sbjct: 283 ETYRRIVKVD--LKFPSSMPL---GAKDLISKLL 311 >STK6_MOUSE (P97477) Serine/threonine-protein kinase 6 (EC 2.7.1.37) (Aurora-family kinase 1) (Aurora/IPL1-related kinase 1) (Ipl1- and aurora-related kinase 1) (Aurora-A) (Serine/threonine kinase Ayk1) Length = 395 Score = 52.4 bits (124), Expect = 4e-07 Identities = 34/94 (36%), Positives = 47/94 (50%) Frame = +3 Query: 156 GWRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 GW A G+ Y+ PE++ GR +D D WS+GV+ +E L G PPF + Sbjct: 267 GWSVHAPSSRRTTMCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGMPPFEAHTYQ 326 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLISNLI 437 T ++I R FP D V+ A DLIS L+ Sbjct: 327 ETYRRI--SRVEFTFP---DFVTEGARDLISRLL 355 >PLK2_CAEEL (Q9N2L7) Serine/threonine-protein kinase plk-2 (EC 2.7.1.37) (Polo-like kinase-2) Length = 632 Score = 52.4 bits (124), Expect = 4e-07 Identities = 23/51 (45%), Positives = 34/51 (66%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKI 353 G+P YIAPEVL G+ + D W++G IL+ +L+G+PPF + S T +I Sbjct: 195 GTPNYIAPEVLNKIGHSFEVDLWAIGCILYILLFGHPPFESKSLEETYSRI 245 >KCCG_RAT (P11730) Calcium/calmodulin-dependent protein kinase type II gamma chain (EC 2.7.1.123) (CaM-kinase II gamma chain) (CaM kinase II gamma subunit) (CaMK-II gamma subunit) Length = 527 Score = 52.4 bits (124), Expect = 4e-07 Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYL 374 F G+P Y++PEVL Y D W+ GVIL+ +L GYPPF+++ + ++ I+ Y Sbjct: 174 FAGTPGYLSPEVLRKDPYGKPVDIWACGVILYILLVGYPPFWDEDQHKLYQQ-IKAGAY- 231 Query: 375 KFPN-NVDNVSGKAVDLISNLIT 440 FP+ D V+ +A +LI+ ++T Sbjct: 232 DFPSPEWDTVTPEAKNLINQMLT 254 >K6A4_MOUSE (Q9Z2B9) Ribosomal protein S6 kinase alpha 4 (EC 2.7.1.37) (Nuclear mitogen-and stress-activated protein kinase-2) (90 kDa ribosomal protein S6 kinase 4) (RSK-like protein kinase) (RLSK) Length = 773 Score = 52.0 bits (123), Expect = 5e-07 Identities = 33/82 (40%), Positives = 45/82 (54%), Gaps = 6/82 (7%) Frame = +3 Query: 213 YIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTG----TAKKIIQFRE--YL 374 Y APE+L +GYD SCD WS+GVIL+ ML G PF S G A+ + + RE + Sbjct: 575 YAAPELLAQQGYDESCDLWSLGVILYMMLSGQVPFQGASGQGGQSQAAEIMCKIREGRFS 634 Query: 375 KFPNNVDNVSGKAVDLISNLIT 440 VS +A +L+ L+T Sbjct: 635 LDGEAWQGVSEEAKELVRGLLT 656 Score = 48.5 bits (114), Expect = 5e-06 Identities = 30/86 (34%), Positives = 48/86 (55%), Gaps = 5/86 (5%) Frame = +3 Query: 195 FFGSPAYIAPEVLIGR-GYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREY 371 F G+ Y+APE++ + G+ + DWWS+G++LFE+L G PF + + T ++ R Sbjct: 197 FCGTIEYMAPEIIRSKAGHGKAVDWWSLGILLFELLTGASPFTLEGERNTQAEV--SRRI 254 Query: 372 LK----FPNNVDNVSGKAVDLISNLI 437 LK FP + V A DL+ L+ Sbjct: 255 LKCSPPFPLRIGPV---AQDLLQRLL 277 >PLK1_CAEEL (P34331) Serine/threonine-protein kinase plk-1 (EC 2.7.1.37) (Polo-like kinase-1) Length = 649 Score = 52.0 bits (123), Expect = 5e-07 Identities = 24/51 (47%), Positives = 33/51 (64%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKI 353 G+P YIAPEVL G+ + D W+VG IL+ +L+G PPF + S T +I Sbjct: 198 GTPNYIAPEVLNKAGHSFEVDIWAVGCILYILLFGQPPFESKSLEETYSRI 248 >AURB_PIG (Q9N0X0) Serine/threonine-protein kinase 12 (EC 2.7.1.37) (Aurora-B) (Fragment) Length = 156 Score = 52.0 bits (123), Expect = 5e-07 Identities = 32/91 (35%), Positives = 48/91 (52%) Frame = +3 Query: 156 GWRCGARVGMGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKT 335 GW A G+ Y+ PE++ GR ++ D W +GV+ +E+L G PPF + S Sbjct: 71 GWSVHAPSLRRKTMRGTLDYLPPEMIEGRTHNEKVDLWCIGVLCYELLVGNPPFESASHN 130 Query: 336 GTAKKIIQFREYLKFPNNVDNVSGKAVDLIS 428 T ++I++ LKFP +V A DLIS Sbjct: 131 ETYRRIVKVD--LKFP---PSVPAGAQDLIS 156 >KML2_HUMAN (Q9H1R3) Myosin light chain kinase 2, skeletal/cardiac muscle (EC 2.7.1.117) (MLCK2) Length = 595 Score = 51.6 bits (122), Expect = 6e-07 Identities = 28/80 (35%), Positives = 41/80 (51%) Frame = +3 Query: 198 FGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLK 377 FG+P +++PEV+ D WS+GVI + +L G PF D T T ++ Y Sbjct: 442 FGTPEFLSPEVVNYDQISDKTDMWSMGVITYMLLSGLSPFLGDDDTETLNNVLSGNWYFD 501 Query: 378 FPNNVDNVSGKAVDLISNLI 437 + VS +A D +SNLI Sbjct: 502 -EETFEAVSDEAKDFVSNLI 520 >UN51_CAEEL (Q23023) Serine/threonine-protein kinase unc-51 (EC 2.7.1.37) (Uncoordinated protein 51) Length = 856 Score = 51.6 bits (122), Expect = 6e-07 Identities = 23/45 (51%), Positives = 28/45 (62%) Frame = +3 Query: 183 MGAPFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF 317 M A GSP Y+APEV++ YD D WS+G ILF+ L G PF Sbjct: 174 MAATLCGSPMYMAPEVIMSMQYDAKADLWSIGTILFQCLTGKAPF 218 >KML2_RABIT (P07313) Myosin light chain kinase 2, skeletal/cardiac muscle (EC 2.7.1.117) (MLCK2) Length = 607 Score = 51.6 bits (122), Expect = 6e-07 Identities = 28/80 (35%), Positives = 41/80 (51%) Frame = +3 Query: 198 FGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLK 377 FG+P +++PEV+ D WS+GVI + +L G PF D T T ++ Y Sbjct: 454 FGTPEFLSPEVVNYDQISDKTDMWSLGVITYMLLSGLSPFLGDDDTETLNNVLSGNWYFD 513 Query: 378 FPNNVDNVSGKAVDLISNLI 437 + VS +A D +SNLI Sbjct: 514 -EETFEAVSDEAKDFVSNLI 532 >CDP3_ORYSA (P53684) Calcium-dependent protein kinase, isoform 11 (EC 2.7.1.-) (CDPK 11) Length = 542 Score = 51.6 bits (122), Expect = 6e-07 Identities = 30/81 (37%), Positives = 48/81 (59%), Gaps = 1/81 (1%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 GSP Y+APEVL R Y D WS GVIL+ +L G PPF+ +++ G ++ + ++ F Sbjct: 242 GSPYYVAPEVLHKR-YGPESDVWSAGVILYVLLSGVPPFWAETQQGIFDAVL--KGHIDF 298 Query: 381 PNNV-DNVSGKAVDLISNLIT 440 ++ +S A DLI +++ Sbjct: 299 QSDPWPKISDSAKDLIRKMLS 319 >DCK1_RAT (O08875) Serine/threonine-protein kinase DCAMKL1 (EC 2.7.1.37) (Doublecortin-like and CAM kinase-like 1) (Calcium/calmodulin-dependent protein kinase type I-like CPG16) Length = 433 Score = 51.2 bits (121), Expect = 8e-07 Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 3/82 (3%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF--YNDSKTGTAKKIIQFREYL 374 G+P Y+APE++ GY D W+ GVI + +L G+PPF D + +I+ + + Sbjct: 242 GTPTYVAPEIIAETGYGLKVDIWAAGVITYILLCGFPPFRGSGDDQEVLFDQILMGQ--V 299 Query: 375 KFPNNV-DNVSGKAVDLISNLI 437 FP+ DNVS A +LI+ ++ Sbjct: 300 DFPSPYWDNVSDSAKELINMML 321 >KMLS_RABIT (P29294) Myosin light chain kinase, smooth muscle (EC 2.7.1.117) (MLCK) [Contains: Telokin] Length = 1147 Score = 51.2 bits (121), Expect = 8e-07 Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 1/81 (1%) Frame = +3 Query: 198 FGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLK 377 FG+P ++APEV+ Y+ D WS+GVI + ++ G PF D+ T + Sbjct: 854 FGTPEFVAPEVINYEPISYATDMWSIGVICYILVSGLSPFMGDNDNETLANVTS--ATWD 911 Query: 378 FPNNV-DNVSGKAVDLISNLI 437 F + D +S A D ISNL+ Sbjct: 912 FDDEAFDEISDDAKDFISNLL 932 >DCK1_MOUSE (Q9JLM8) Serine/threonine-protein kinase DCAMKL1 (EC 2.7.1.37) (Doublecortin-like and CAM kinase-like 1) Length = 756 Score = 51.2 bits (121), Expect = 8e-07 Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 3/82 (3%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF--YNDSKTGTAKKIIQFREYL 374 G+P Y+APE++ GY D W+ GVI + +L G+PPF D + +I+ + + Sbjct: 565 GTPTYVAPEIIAETGYGLKVDIWAAGVITYILLCGFPPFRGSGDDQEVLFDQILMGQ--V 622 Query: 375 KFPNNV-DNVSGKAVDLISNLI 437 FP+ DNVS A +LI+ ++ Sbjct: 623 DFPSPYWDNVSDSAKELINMML 644 >CDPK_SOYBN (P28583) Calcium-dependent protein kinase SK5 (EC 2.7.1.-) (CDPK) Length = 508 Score = 51.2 bits (121), Expect = 8e-07 Identities = 32/80 (40%), Positives = 48/80 (60%), Gaps = 1/80 (1%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 GSP Y+APEVL + Y D WS GVIL+ +L G PPF+ +S+ G ++I+ + L F Sbjct: 197 GSPYYVAPEVL-RKLYGPESDVWSAGVILYILLSGVPPFWAESEPGIFRQILLGK--LDF 253 Query: 381 PNNV-DNVSGKAVDLISNLI 437 + ++S A DLI ++ Sbjct: 254 HSEPWPSISDSAKDLIRKML 273 >SKM1_YEAST (Q12469) Serine/threonine-protein kinase SKM1 (EC 2.7.1.37) (Protein kinase 75490 D) Length = 655 Score = 51.2 bits (121), Expect = 8e-07 Identities = 20/46 (43%), Positives = 32/46 (69%) Frame = +3 Query: 189 APFFGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYND 326 A G+P ++APE++ +GYD D WS+G++L EM+ G PP+ N+ Sbjct: 540 ATMVGTPYWMAPEIVNQKGYDEKVDVWSLGIMLIEMIEGEPPYLNE 585 >DCK1_HUMAN (O15075) Serine/threonine-protein kinase DCAMKL1 (EC 2.7.1.37) (Doublecortin-like and CAM kinase-like 1) Length = 740 Score = 51.2 bits (121), Expect = 8e-07 Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 3/82 (3%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPF--YNDSKTGTAKKIIQFREYL 374 G+P Y+APE++ GY D W+ GVI + +L G+PPF D + +I+ + + Sbjct: 549 GTPTYVAPEIIAETGYGLKVDIWAAGVITYILLCGFPPFRGSGDDQEVLFDQILMGQ--V 606 Query: 375 KFPNNV-DNVSGKAVDLISNLI 437 FP+ DNVS A +LI+ ++ Sbjct: 607 DFPSPYWDNVSDSAKELITMML 628 >KMLS_HUMAN (Q15746) Myosin light chain kinase, smooth muscle and non-muscle isozymes (EC 2.7.1.117) (MLCK) [Contains: Telokin (Kinase related protein) (KRP)] Length = 1914 Score = 50.8 bits (120), Expect = 1e-06 Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 1/81 (1%) Frame = +3 Query: 198 FGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLK 377 FG+P ++APEV+ Y+ D WS+GVI + ++ G PF D+ T + Sbjct: 1622 FGTPEFVAPEVINYEPIGYATDMWSIGVICYILVSGLSPFMGDNDNETLANVTS--ATWD 1679 Query: 378 FPNNV-DNVSGKAVDLISNLI 437 F + D +S A D ISNL+ Sbjct: 1680 FDDEAFDEISDDAKDFISNLL 1700 >KMLS_SHEEP (O02827) Myosin light chain kinase, smooth muscle (EC 2.7.1.117) (MLCK) [Contains: Telokin] (Fragment) Length = 438 Score = 50.8 bits (120), Expect = 1e-06 Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 1/81 (1%) Frame = +3 Query: 198 FGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLK 377 FG+P ++APEV+ Y+ D WS+GVI + ++ G PF D+ T + Sbjct: 144 FGTPEFVAPEVINYEPIGYATDMWSIGVICYILVSGLSPFMGDNDNETLANVTS--ATWD 201 Query: 378 FPNNV-DNVSGKAVDLISNLI 437 F + D +S A D ISNL+ Sbjct: 202 FDDEAFDEISDDAKDFISNLL 222 >CDPK_DAUCA (P28582) Calcium-dependent protein kinase (EC 2.7.1.-) (CDPK) Length = 532 Score = 50.8 bits (120), Expect = 1e-06 Identities = 31/81 (38%), Positives = 46/81 (56%), Gaps = 1/81 (1%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 GS Y+APEVL R Y D WS GVIL+ +L G PPF+ +++ G I++ + F Sbjct: 244 GSAYYVAPEVL-RRSYGKEIDIWSAGVILYILLSGVPPFWAENEKGIFDAILE--GVIDF 300 Query: 381 PNNV-DNVSGKAVDLISNLIT 440 + +VS A DL+ ++T Sbjct: 301 ESEPWPSVSNSAKDLVRKMLT 321 >KCC2_YEAST (P22517) Calcium/calmodulin-dependent protein kinase II (EC 2.7.1.123) Length = 447 Score = 50.8 bits (120), Expect = 1e-06 Identities = 23/46 (50%), Positives = 29/46 (63%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTG 338 GS Y+APEVL G+ CD WS+GVI + +L GY PF +S G Sbjct: 211 GSLGYVAPEVLTQDGHGKPCDIWSIGVITYTLLCGYSPFIAESVEG 256 >ST2A_HUMAN (Q9BXA7) Serine/threonine-protein kinase 22A (EC 2.7.1.37) (Testis-specific kinase 1) (TSK-1) (Testis-specific serine kinase 1) (TSSK-1) (Serine/threonine-protein kinase FKSG81) Length = 367 Score = 50.8 bits (120), Expect = 1e-06 Identities = 35/89 (39%), Positives = 51/89 (57%), Gaps = 1/89 (1%) Frame = +3 Query: 174 RVGMGAPFFGSPAYIAPEVLIGRGYDYSC-DWWSVGVILFEMLYGYPPFYNDSKTGTAKK 350 R+ + F GSPAY APEVL G Y D WS+GVIL+ M+ G P Y+DS + Sbjct: 168 RMALSKTFCGSPAYAAPEVLQGIPYQPKVYDIWSLGVILYIMVCGSMP-YDDSNIKKMLR 226 Query: 351 IIQFREYLKFPNNVDNVSGKAVDLISNLI 437 IQ + FP + +++G+ DLI +++ Sbjct: 227 -IQKEHRVNFPRS-KHLTGECKDLIYHML 253 >PLK1_RAT (Q62673) Serine/threonine-protein kinase PLK1 (EC 2.7.1.37) (Polo-like kinase 1) (PLK-1) Length = 603 Score = 50.8 bits (120), Expect = 1e-06 Identities = 26/72 (36%), Positives = 41/72 (56%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P YIAPEVL +G+ + D WS+G I++ +L G PPF T + I+ EY Sbjct: 213 GTPNYIAPEVLSKKGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLR-IKKNEY-SI 270 Query: 381 PNNVDNVSGKAV 416 P +++ V+ + Sbjct: 271 PKHINPVAASLI 282 >PLK1_MOUSE (Q07832) Serine/threonine-protein kinase PLK1 (EC 2.7.1.37) (Polo-like kinase 1) (PLK-1) (Serine-threonine protein kinase 13) (STPK13) Length = 603 Score = 50.8 bits (120), Expect = 1e-06 Identities = 26/72 (36%), Positives = 41/72 (56%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P YIAPEVL +G+ + D WS+G I++ +L G PPF T + I+ EY Sbjct: 213 GTPNYIAPEVLSKKGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLR-IKKNEY-SI 270 Query: 381 PNNVDNVSGKAV 416 P +++ V+ + Sbjct: 271 PKHINPVAASLI 282 >PLK1_HUMAN (P53350) Serine/threonine-protein kinase PLK1 (EC 2.7.1.37) (Polo-like kinase 1) (PLK-1) (Serine-threonine protein kinase 13) (STPK13) Length = 603 Score = 50.8 bits (120), Expect = 1e-06 Identities = 26/72 (36%), Positives = 41/72 (56%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+P YIAPEVL +G+ + D WS+G I++ +L G PPF T + I+ EY Sbjct: 213 GTPNYIAPEVLSKKGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLR-IKKNEY-SI 270 Query: 381 PNNVDNVSGKAV 416 P +++ V+ + Sbjct: 271 PKHINPVAASLI 282 >CDP2_ORYSA (P53683) Calcium-dependent protein kinase, isoform 2 (EC 2.7.1.-) (CDPK 2) Length = 533 Score = 50.8 bits (120), Expect = 1e-06 Identities = 31/81 (38%), Positives = 46/81 (56%), Gaps = 1/81 (1%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 GS Y+APEVL R Y D WS GVIL+ +L G PPF+ +++ G I+Q + F Sbjct: 248 GSAYYVAPEVL-RRNYGKEIDVWSAGVILYILLSGVPPFWAETEKGIFDAILQGE--IDF 304 Query: 381 PNNV-DNVSGKAVDLISNLIT 440 + ++S A DL+ ++T Sbjct: 305 ESQPWPSISESAKDLVRKMLT 325 >KMLS_BOVIN (Q28824) Myosin light chain kinase, smooth muscle (EC 2.7.1.117) (MLCK) [Contains: Telokin] Length = 1176 Score = 50.8 bits (120), Expect = 1e-06 Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 1/81 (1%) Frame = +3 Query: 198 FGSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLK 377 FG+P ++APEV+ Y+ D WS+GVI + ++ G PF D+ T + Sbjct: 883 FGTPEFVAPEVINYEPIGYATDMWSIGVICYILVSGLSPFMGDNDNETLANVTS--ATWD 940 Query: 378 FPNNV-DNVSGKAVDLISNLI 437 F + D +S A D ISNL+ Sbjct: 941 FDDEAFDEISDDAKDFISNLL 961 >AURC_MOUSE (O88445) Serine/threonine-protein kinase 13 (EC 2.7.1.37) (Aurora/Ipl1/Eg2 protein 1) (Aurora-C) Length = 282 Score = 50.8 bits (120), Expect = 1e-06 Identities = 28/79 (35%), Positives = 46/79 (58%) Frame = +3 Query: 201 GSPAYIAPEVLIGRGYDYSCDWWSVGVILFEMLYGYPPFYNDSKTGTAKKIIQFREYLKF 380 G+ Y+ PE++ + Y+ D W +GV+ +E+L G PPF + + + T ++I Q KF Sbjct: 174 GTLDYLPPEMIAQKPYNEMVDLWCIGVLCYELLVGKPPFESSTSSETYRRIRQVD--FKF 231 Query: 381 PNNVDNVSGKAVDLISNLI 437 P+ +V A DLIS L+ Sbjct: 232 PS---SVPAGAQDLISKLL 247 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 51,749,274 Number of Sequences: 153871 Number of extensions: 1159514 Number of successful extensions: 4673 Number of sequences better than 1.0e-01: 500 Number of HSP's better than 0.1 without gapping: 4419 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 4558 length of database: 56,608,159 effective HSP length: 99 effective length of database: 41,374,930 effective search space used: 1985996640 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 367 (414 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 41,850,356 Number of Sequences: 153871 Number of extensions: 786713 Number of successful extensions: 1678 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1607 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1677 length of database: 56,608,159 effective HSP length: 98 effective length of database: 41,528,801 effective search space used: 1619623239 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 368 (157 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 13,639,257 Number of Sequences: 153871 Number of extensions: 168621 Number of successful extensions: 227 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 227 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 227 length of database: 56,608,159 effective HSP length: 24 effective length of database: 52,915,255 effective search space used: 1428711885 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 369 (422 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 38,271,321 Number of Sequences: 153871 Number of extensions: 617972 Number of successful extensions: 1992 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1950 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1992 length of database: 56,608,159 effective HSP length: 98 effective length of database: 41,528,801 effective search space used: 1744209642 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 370 (618 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value UBIQ_TRYBB (P15174) Ubiquitin 64 3e-10 UBIQ_TRYCR (P08565) Ubiquitin 62 8e-10 UBIQ_SOYBN (P03993) Ubiquitin 62 8e-10 UBIQ_LEIMA (Q05550) Ubiquitin 62 8e-10 UBIQ_EUPEU (P23324) Ubiquitin 62 8e-10 UBIQ_CHLRE (P14624) Ubiquitin 62 8e-10 UBIQ_ARATH (P59263) Ubiquitin 62 8e-10 UBIQ_ACECL (P42739) Ubiquitin 62 8e-10 UBIQ_ACACA (P49634) Ubiquitin 62 8e-10 UBIQ_YEAST (P61864) Ubiquitin 61 2e-09 UBIQ_TETPY (P20685) Ubiquitin 61 2e-09 UBIQ_STRPU (P23398) Ubiquitin 61 2e-09 UBIQ_PHYIN (P22589) Ubiquitin 61 2e-09 UBIQ_NEUCR (P13117) Ubiquitin 61 2e-09 UBIQ_HUMAN (P02248) Ubiquitin 61 2e-09 UBIQ_GEOCY (P59669) Ubiquitin 61 2e-09 UBIQ_EIMBO (P46574) Ubiquitin 61 2e-09 UBIQ_DROME (Q9VZL4) Ubiquitin 61 2e-09 UBIQ_DICDI (P08618) Ubiquitin 61 2e-09 UBIQ_CRYNE (P61863) Ubiquitin 61 2e-09 UBIQ_COPCO (P19848) Ubiquitin 61 2e-09 UBIQ_CANAL (P61862) Ubiquitin 61 2e-09 UBIQ_CAEEL (P14792) Ubiquitin 61 2e-09 UBIQ_AGLNE (P42740) Ubiquitin 61 2e-09 UBIQ_LEITA (P49635) Ubiquitin 60 5e-09 UBIL_NPVAC (P16709) Ubiquitin-like protein 57 2e-08 UBIL_NPVOP (Q05120) Ubiquitin-like protein 57 4e-08 RUB1_ARATH (Q9SHE7) Ubiquitin-related protein 1 precursor (AtRUB1) 40 0.003 RUB2_ARATH (Q8RUC6) Ubiquitin-related protein 2 precursor (AtRUB2) 37 0.026 NED8_MOUSE (P29595) Ubiquitin-like protein NEDD8 37 0.044 NED8_HUMAN (Q15843) Ubiquitin-like protein NEDD8 37 0.044 NED8_BOVIN (P61282) Ubiquitin-like protein NEDD8 37 0.044 >UBIQ_TRYBB (P15174) Ubiquitin Length = 76 Score = 63.5 bits (153), Expect = 3e-10 Identities = 31/31 (100%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 74 >UBIQ_TRYCR (P08565) Ubiquitin Length = 76 Score = 62.4 bits (150), Expect = 8e-10 Identities = 30/31 (96%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTLADYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 >UBIQ_SOYBN (P03993) Ubiquitin Length = 76 Score = 62.4 bits (150), Expect = 8e-10 Identities = 30/31 (96%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTLADYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 >UBIQ_LEIMA (Q05550) Ubiquitin Length = 76 Score = 62.4 bits (150), Expect = 8e-10 Identities = 30/31 (96%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLEEGRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEEGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_EUPEU (P23324) Ubiquitin Length = 76 Score = 62.4 bits (150), Expect = 8e-10 Identities = 30/31 (96%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTLADYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 >UBIQ_CHLRE (P14624) Ubiquitin Length = 76 Score = 62.4 bits (150), Expect = 8e-10 Identities = 30/31 (96%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTLADYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 >UBIQ_ARATH (P59263) Ubiquitin Length = 76 Score = 62.4 bits (150), Expect = 8e-10 Identities = 30/31 (96%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTLADYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 >UBIQ_ACECL (P42739) Ubiquitin Length = 76 Score = 62.4 bits (150), Expect = 8e-10 Identities = 30/31 (96%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTLADYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 >UBIQ_ACACA (P49634) Ubiquitin Length = 76 Score = 62.4 bits (150), Expect = 8e-10 Identities = 30/31 (96%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTLADYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 >UBIQ_YEAST (P61864) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_TETPY (P20685) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_STRPU (P23398) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_PHYIN (P22589) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_NEUCR (P13117) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_HUMAN (P02248) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_GEOCY (P59669) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_EIMBO (P46574) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_DROME (Q9VZL4) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_DICDI (P08618) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_CRYNE (P61863) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_COPCO (P19848) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_CANAL (P61862) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_CAEEL (P14792) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_AGLNE (P42740) Ubiquitin Length = 76 Score = 61.2 bits (147), Expect = 2e-09 Identities = 29/31 (93%), Positives = 31/31 (100%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+GRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 >UBIQ_LEITA (P49635) Ubiquitin Length = 76 Score = 59.7 bits (143), Expect = 5e-09 Identities = 29/31 (93%), Positives = 30/31 (96%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFA KQLEEGRTL+DYNIQKESTLHLVLRLR Sbjct: 44 IFADKQLEEGRTLSDYNIQKESTLHLVLRLR 74 >UBIL_NPVAC (P16709) Ubiquitin-like protein Length = 77 Score = 57.4 bits (137), Expect = 2e-08 Identities = 26/31 (83%), Positives = 30/31 (96%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 IFAGKQLE+ +T+ADYNIQKESTLH+VLRLR Sbjct: 44 IFAGKQLEDSKTMADYNIQKESTLHMVLRLR 74 >UBIL_NPVOP (Q05120) Ubiquitin-like protein Length = 93 Score = 56.6 bits (135), Expect = 4e-08 Identities = 26/31 (83%), Positives = 30/31 (96%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 I+AGKQLE+ +TLADYNIQKESTLH+VLRLR Sbjct: 44 IYAGKQLEDAQTLADYNIQKESTLHMVLRLR 74 >RUB1_ARATH (Q9SHE7) Ubiquitin-related protein 1 precursor (AtRUB1) Length = 80 Score = 40.4 bits (93), Expect = 0.003 Identities = 19/31 (61%), Positives = 23/31 (74%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 I+AGKQL + +T DYNI+ S LHLVL LR Sbjct: 44 IYAGKQLADDKTAKDYNIEGGSVLHLVLALR 74 >RUB2_ARATH (Q8RUC6) Ubiquitin-related protein 2 precursor (AtRUB2) Length = 78 Score = 37.4 bits (85), Expect = 0.026 Identities = 18/31 (58%), Positives = 22/31 (70%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 I+AGKQL + +T DY I+ S LHLVL LR Sbjct: 44 IYAGKQLADDKTAKDYAIEGGSVLHLVLALR 74 >NED8_MOUSE (P29595) Ubiquitin-like protein NEDD8 Length = 81 Score = 36.6 bits (83), Expect = 0.044 Identities = 17/31 (54%), Positives = 22/31 (70%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 I++GKQ+ + +T ADY I S LHLVL LR Sbjct: 44 IYSGKQMNDEKTAADYKILGGSVLHLVLALR 74 >NED8_HUMAN (Q15843) Ubiquitin-like protein NEDD8 Length = 81 Score = 36.6 bits (83), Expect = 0.044 Identities = 17/31 (54%), Positives = 22/31 (70%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 I++GKQ+ + +T ADY I S LHLVL LR Sbjct: 44 IYSGKQMNDEKTAADYKILGGSVLHLVLALR 74 >NED8_BOVIN (P61282) Ubiquitin-like protein NEDD8 Length = 81 Score = 36.6 bits (83), Expect = 0.044 Identities = 17/31 (54%), Positives = 22/31 (70%) Frame = -3 Query: 94 IFAGKQLEEGRTLADYNIQKESTLHLVLRLR 2 I++GKQ+ + +T ADY I S LHLVL LR Sbjct: 44 IYSGKQMNDEKTAADYKILGGSVLHLVLALR 74 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 51,524,064 Number of Sequences: 153871 Number of extensions: 985661 Number of successful extensions: 2171 Number of sequences better than 1.0e-01: 32 Number of HSP's better than 0.1 without gapping: 2098 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2168 length of database: 56,608,159 effective HSP length: 104 effective length of database: 40,605,575 effective search space used: 4101163075 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 371 (485 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 49,363,264 Number of Sequences: 153871 Number of extensions: 987384 Number of successful extensions: 3447 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 3246 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 3442 length of database: 56,608,159 effective HSP length: 101 effective length of database: 41,067,188 effective search space used: 2464031280 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 372 (240 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ZIP3_ARATH (Q9SLG3) Zinc transporter 3 precursor (ZRT/IRT-like p... 42 4e-04 ZIP5_ARATH (O23039) Zinc transporter 5 precursor (ZRT/IRT-like p... 41 8e-04 ZIP4_ARATH (O04089) Zinc transporter 4, chloroplast precursor (Z... 40 0.002 ZIP1_ARATH (O81123) Zinc transporter 1 precursor (ZRT/IRT-like p... 39 0.003 IRT3_ARATH (Q8LE59) Fe(II) transport protein 3, chloroplast prec... 38 0.005 ZIP8_ARATH (Q8S3W4) Probable zinc transporter 8 precursor (ZRT/I... 38 0.007 IRT2_ARATH (O81850) Fe(II) transport protein 2 precursor (Iron-r... 37 0.012 ZIP7_ARATH (Q8W246) Probable zinc transporter 7 precursor (ZRT/I... 37 0.012 IRT1_ARATH (Q38856) Fe(II) transport protein 1 precursor (Iron-r... 36 0.020 ZRT2_YEAST (Q12436) Zinc-regulated transporter 2 (Low-affinity z... 36 0.026 ZRT1_YEAST (P32804) Zinc-regulated transporter 1 (High-affinity ... 35 0.034 ZP10_ARATH (Q8W245) Probable zinc transporter 10 precursor (ZRT/... 35 0.058 >ZIP3_ARATH (Q9SLG3) Zinc transporter 3 precursor (ZRT/IRT-like protein 3) Length = 339 Score = 42.0 bits (97), Expect = 4e-04 Identities = 20/48 (41%), Positives = 28/48 (58%) Frame = +3 Query: 6 VLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMI 149 VL+A +IG PL+GK P+LR F V K A GV+L +H++ Sbjct: 61 VLIAGIIGVLFPLLGKVFPSLRPETCFFFVTKAFAAGVILATGFMHVL 108 >ZIP5_ARATH (O23039) Zinc transporter 5 precursor (ZRT/IRT-like protein 5) Length = 360 Score = 40.8 bits (94), Expect = 8e-04 Identities = 19/48 (39%), Positives = 28/48 (58%) Frame = +3 Query: 6 VLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMI 149 VL A +IG PL+GK+ P+L+ F V K A GV+L +H++ Sbjct: 56 VLAAGVIGVMFPLLGKFFPSLKPETTFFFVTKAFAAGVILATGFMHVL 103 >ZIP4_ARATH (O04089) Zinc transporter 4, chloroplast precursor (ZRT/IRT-like protein 4) Length = 374 Score = 39.7 bits (91), Expect = 0.002 Identities = 19/48 (39%), Positives = 26/48 (54%) Frame = +3 Query: 6 VLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMI 149 +LLA G AIPL+G+ L+ FV K A GV+L +HM+ Sbjct: 35 ILLAGAAGVAIPLIGRNRRFLQTEGNLFVAAKAFAAGVILATGFVHML 82 >ZIP1_ARATH (O81123) Zinc transporter 1 precursor (ZRT/IRT-like protein 1) Length = 355 Score = 38.9 bits (89), Expect = 0.003 Identities = 20/55 (36%), Positives = 33/55 (60%) Frame = +3 Query: 3 VVLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMITLPAFE 167 ++L+A +G ++PL+GK PAL+ F + K A GV+L +H++ AFE Sbjct: 57 LLLVAGGVGVSLPLIGKRIPALQPENDIFFMVKAFAAGVILCTGFVHILP-DAFE 110 >IRT3_ARATH (Q8LE59) Fe(II) transport protein 3, chloroplast precursor (Iron-regulated transporter 3) Length = 389 Score = 38.1 bits (87), Expect = 0.005 Identities = 18/48 (37%), Positives = 25/48 (52%) Frame = +3 Query: 6 VLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMI 149 +LLA G IPL+G+ L+ FV K A GV+L +HM+ Sbjct: 35 ILLAGAAGVTIPLIGRNRRFLQTDGNLFVTAKAFAAGVILATGFVHML 82 >ZIP8_ARATH (Q8S3W4) Probable zinc transporter 8 precursor (ZRT/IRT-like protein 8) Length = 347 Score = 37.7 bits (86), Expect = 0.007 Identities = 16/48 (33%), Positives = 28/48 (58%) Frame = +3 Query: 6 VLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMI 149 +L+ S+IG A PL +Y L F++ KC A+G++L +H++ Sbjct: 58 ILVTSMIGVAAPLFSRYVTFLHPDGKIFMIIKCFASGIILGTGFMHVL 105 >IRT2_ARATH (O81850) Fe(II) transport protein 2 precursor (Iron-regulated transporter 2) Length = 350 Score = 37.0 bits (84), Expect = 0.012 Identities = 16/48 (33%), Positives = 27/48 (56%) Frame = +3 Query: 6 VLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMI 149 +L SLIG PL +Y LR F++ KC ++G++L +H++ Sbjct: 54 ILTTSLIGVTSPLFSRYISFLRPDGNGFMIVKCFSSGIILGTGFMHVL 101 >ZIP7_ARATH (Q8W246) Probable zinc transporter 7 precursor (ZRT/IRT-like protein 7) Length = 365 Score = 37.0 bits (84), Expect = 0.012 Identities = 17/48 (35%), Positives = 30/48 (62%) Frame = +3 Query: 6 VLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMI 149 +L+AS+IG ++PL + PAL V+ K +A+GV+L +H++ Sbjct: 63 ILVASMIGVSLPLFSRSIPALGPDREMSVIVKTLASGVILATGFMHVL 110 >IRT1_ARATH (Q38856) Fe(II) transport protein 1 precursor (Iron-regulated transporter 1) Length = 339 Score = 36.2 bits (82), Expect = 0.020 Identities = 16/49 (32%), Positives = 28/49 (57%) Frame = +3 Query: 3 VVLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMI 149 V+L+AS+IG PL + L+ F + KC A+G++L +H++ Sbjct: 50 VILIASMIGVGAPLFSRNVSFLQPDGNIFTIIKCFASGIILGTGFMHVL 98 >ZRT2_YEAST (Q12436) Zinc-regulated transporter 2 (Low-affinity zinc transport protein ZRT2) Length = 422 Score = 35.8 bits (81), Expect = 0.026 Identities = 15/55 (27%), Positives = 32/55 (58%) Frame = +3 Query: 3 VVLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMITLPAFE 167 ++L++S +G P++ +R+P + F + K +GV++ A +H++ PA E Sbjct: 33 IILISSGLGVYFPILSSRYSFIRLPNWCFFIAKFFGSGVIVATAFVHLLQ-PAAE 86 >ZRT1_YEAST (P32804) Zinc-regulated transporter 1 (High-affinity zinc transport protein ZRT1) Length = 376 Score = 35.4 bits (80), Expect = 0.034 Identities = 17/54 (31%), Positives = 29/54 (53%) Frame = +3 Query: 3 VVLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMITLPAF 164 V+L S T PL+ LR+P + ++ K +GV++ A IH++ PA+ Sbjct: 56 VILFVSTFFTMFPLISTKVKRLRIPLYVYLFAKYFGSGVIVATAFIHLMD-PAY 108 >ZP10_ARATH (Q8W245) Probable zinc transporter 10 precursor (ZRT/IRT-like protein 10) Length = 364 Score = 34.7 bits (78), Expect = 0.058 Identities = 14/48 (29%), Positives = 27/48 (56%) Frame = +3 Query: 6 VLLASLIGTAIPLVGKYAPALRMPPFAFVVGKCMATGVVLVVATIHMI 149 +L+ SLIG +P + PA + F++ K A+G++L +H++ Sbjct: 59 ILITSLIGVCLPFFARSIPAFQPEKSHFLIVKSFASGIILSTGFMHVL 106 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 29,560,342 Number of Sequences: 153871 Number of extensions: 635009 Number of successful extensions: 2375 Number of sequences better than 1.0e-01: 12 Number of HSP's better than 0.1 without gapping: 2278 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2366 length of database: 56,608,159 effective HSP length: 50 effective length of database: 48,914,609 effective search space used: 1418523661 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 373 (228 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 26,046,626 Number of Sequences: 153871 Number of extensions: 464569 Number of successful extensions: 1030 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1019 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1030 length of database: 56,608,159 effective HSP length: 47 effective length of database: 49,376,222 effective search space used: 1382534216 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 374 (352 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 37,508,918 Number of Sequences: 153871 Number of extensions: 721804 Number of successful extensions: 2796 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2637 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2793 length of database: 56,608,159 effective HSP length: 84 effective length of database: 43,682,995 effective search space used: 1397855840 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 375 (105 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 9,284,894 Number of Sequences: 153871 Number of extensions: 76546 Number of successful extensions: 151 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 151 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 151 length of database: 56,608,159 effective HSP length: 8 effective length of database: 55,377,191 effective search space used: 1439806966 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 376 (503 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 39,134,953 Number of Sequences: 153871 Number of extensions: 665371 Number of successful extensions: 2602 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2413 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2595 length of database: 56,608,159 effective HSP length: 101 effective length of database: 41,067,188 effective search space used: 2710434408 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 377 (793 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 67,855,164 Number of Sequences: 153871 Number of extensions: 1242623 Number of successful extensions: 4338 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 4129 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 4337 length of database: 56,608,159 effective HSP length: 107 effective length of database: 40,143,962 effective search space used: 6262458072 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 378 (185 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 17,523,960 Number of Sequences: 153871 Number of extensions: 264246 Number of successful extensions: 656 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 637 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 656 length of database: 56,608,159 effective HSP length: 34 effective length of database: 51,376,545 effective search space used: 1387166715 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 379 (416 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 44,532,081 Number of Sequences: 153871 Number of extensions: 936611 Number of successful extensions: 2317 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2269 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2317 length of database: 56,608,159 effective HSP length: 98 effective length of database: 41,528,801 effective search space used: 1661152040 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 449 (529 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 53,033,181 Number of Sequences: 153871 Number of extensions: 1102541 Number of successful extensions: 2956 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2885 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2953 length of database: 56,608,159 effective HSP length: 102 effective length of database: 40,913,317 effective search space used: 2986672141 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 450 (192 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 20,578,409 Number of Sequences: 153871 Number of extensions: 346878 Number of successful extensions: 850 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 841 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 850 length of database: 56,608,159 effective HSP length: 35 effective length of database: 51,222,674 effective search space used: 1434234872 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 451 (344 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 30,826,364 Number of Sequences: 153871 Number of extensions: 499087 Number of successful extensions: 1237 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1222 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1237 length of database: 56,608,159 effective HSP length: 82 effective length of database: 43,990,737 effective search space used: 1407703584 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 452 (277 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 31,394,734 Number of Sequences: 153871 Number of extensions: 590725 Number of successful extensions: 1777 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1746 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1777 length of database: 56,608,159 effective HSP length: 61 effective length of database: 47,222,028 effective search space used: 1416660840 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 453 (115 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 10,886,277 Number of Sequences: 153871 Number of extensions: 108004 Number of successful extensions: 408 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 394 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 408 length of database: 56,608,159 effective HSP length: 11 effective length of database: 54,915,578 effective search space used: 1427805028 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 454 (399 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 38,986,008 Number of Sequences: 153871 Number of extensions: 697829 Number of successful extensions: 2329 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2236 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2324 length of database: 56,608,159 effective HSP length: 97 effective length of database: 41,682,672 effective search space used: 1458893520 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 455 (562 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 45,109,499 Number of Sequences: 153871 Number of extensions: 733051 Number of successful extensions: 2202 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 2116 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2202 length of database: 56,608,159 effective HSP length: 103 effective length of database: 40,759,446 effective search space used: 3383034018 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 456 (456 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 50,396,854 Number of Sequences: 153871 Number of extensions: 1095724 Number of successful extensions: 3968 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 3713 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 3959 length of database: 56,608,159 effective HSP length: 100 effective length of database: 41,221,059 effective search space used: 2102274009 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 457 (580 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 59,408,433 Number of Sequences: 153871 Number of extensions: 1184612 Number of successful extensions: 3552 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 3370 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 3542 length of database: 56,608,159 effective HSP length: 103 effective length of database: 40,759,446 effective search space used: 3627590694 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 458 (407 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 28,894,928 Number of Sequences: 153871 Number of extensions: 410658 Number of successful extensions: 1717 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1640 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1716 length of database: 56,608,159 effective HSP length: 97 effective length of database: 41,682,672 effective search space used: 1583941536 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 459 (451 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value HS70_TRYCR (P05456) Heat shock 70 kDa protein 34 0.023 HS70_LEIDO (P17804) Heat shock 70 kDa protein 32 0.049 HS74_TRYBB (P11145) Heat shock 70 kDa protein 4 (HSP70) 32 0.064 HS70_LEIAM (Q07437) Heat shock 70 kDa protein 32 0.064 HS70_LEIMA (P14834) Heat shock 70 kDa protein (Fragment) 32 0.065 >HS70_TRYCR (P05456) Heat shock 70 kDa protein Length = 680 Score = 33.9 bits (76), Expect(2) = 0.023 Identities = 15/17 (88%), Positives = 17/17 (100%) Frame = -1 Query: 79 IDALFDSVDFQSTITRA 29 IDALFD+VDFQ+TITRA Sbjct: 287 IDALFDNVDFQATITRA 303 Score = 21.6 bits (44), Expect(2) = 0.023 Identities = 8/9 (88%), Positives = 8/9 (88%) Frame = -2 Query: 27 RFEELCGNL 1 RFEELCG L Sbjct: 304 RFEELCGEL 312 >HS70_LEIDO (P17804) Heat shock 70 kDa protein Length = 653 Score = 32.3 bits (72), Expect(2) = 0.049 Identities = 14/17 (82%), Positives = 17/17 (100%) Frame = -1 Query: 79 IDALFDSVDFQSTITRA 29 IDALF++VDFQ+TITRA Sbjct: 286 IDALFENVDFQATITRA 302 Score = 21.9 bits (45), Expect(2) = 0.049 Identities = 8/9 (88%), Positives = 9/9 (100%) Frame = -2 Query: 27 RFEELCGNL 1 RFEELCG+L Sbjct: 303 RFEELCGDL 311 >HS74_TRYBB (P11145) Heat shock 70 kDa protein 4 (HSP70) Length = 661 Score = 32.0 bits (71), Expect(2) = 0.064 Identities = 13/17 (76%), Positives = 17/17 (100%) Frame = -1 Query: 79 IDALFDSVDFQSTITRA 29 IDALF+++DFQ+TITRA Sbjct: 287 IDALFENIDFQATITRA 303 Score = 21.9 bits (45), Expect(2) = 0.064 Identities = 8/9 (88%), Positives = 9/9 (100%) Frame = -2 Query: 27 RFEELCGNL 1 RFEELCG+L Sbjct: 304 RFEELCGDL 312 >HS70_LEIAM (Q07437) Heat shock 70 kDa protein Length = 652 Score = 32.0 bits (71), Expect(2) = 0.064 Identities = 14/17 (82%), Positives = 16/17 (94%) Frame = -1 Query: 79 IDALFDSVDFQSTITRA 29 IDALFD+VDFQ+TI RA Sbjct: 287 IDALFDNVDFQATINRA 303 Score = 21.9 bits (45), Expect(2) = 0.064 Identities = 8/9 (88%), Positives = 9/9 (100%) Frame = -2 Query: 27 RFEELCGNL 1 RFEELCG+L Sbjct: 304 RFEELCGDL 312 >HS70_LEIMA (P14834) Heat shock 70 kDa protein (Fragment) Length = 516 Score = 32.0 bits (71), Expect(2) = 0.065 Identities = 13/17 (76%), Positives = 17/17 (100%) Frame = -1 Query: 79 IDALFDSVDFQSTITRA 29 IDALF+++DFQ+TITRA Sbjct: 287 IDALFENIDFQATITRA 303 Score = 21.9 bits (45), Expect(2) = 0.065 Identities = 8/9 (88%), Positives = 9/9 (100%) Frame = -2 Query: 27 RFEELCGNL 1 RFEELCG+L Sbjct: 304 RFEELCGDL 312 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 43,832,529 Number of Sequences: 153871 Number of extensions: 926140 Number of successful extensions: 2669 Number of sequences better than 1.0e-01: 5 Number of HSP's better than 0.1 without gapping: 2312 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2668 length of database: 56,608,159 effective HSP length: 99 effective length of database: 41,374,930 effective search space used: 2068746500 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 460 (202 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 17,446,939 Number of Sequences: 153871 Number of extensions: 227127 Number of successful extensions: 544 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 543 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 544 length of database: 56,608,159 effective HSP length: 38 effective length of database: 50,761,061 effective search space used: 1421309708 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 461 (337 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ACO1_YEAST (P21147) Acyl-CoA desaturase 1 (EC 1.14.19.1) (Stearo... 36 0.026 >ACO1_YEAST (P21147) Acyl-CoA desaturase 1 (EC 1.14.19.1) (Stearoyl-CoA desaturase 1) (Fatty acid desaturase 1) Length = 510 Score = 35.8 bits (81), Expect = 0.026 Identities = 14/35 (40%), Positives = 23/35 (65%) Frame = +3 Query: 36 VDGVYYDTAKLAALHPGGETMVKMVNGLDSTRASS 140 + G+ +D + + HPGGET++K G D+T+A S Sbjct: 430 ISGIVHDVSGYISEHPGGETLIKTALGKDATKAFS 464 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 34,946,656 Number of Sequences: 153871 Number of extensions: 662625 Number of successful extensions: 1940 Number of sequences better than 1.0e-01: 1 Number of HSP's better than 0.1 without gapping: 1902 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1939 length of database: 56,608,159 effective HSP length: 79 effective length of database: 44,452,350 effective search space used: 1422475200 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 462 (382 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 36,718,939 Number of Sequences: 153871 Number of extensions: 676885 Number of successful extensions: 2154 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1997 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 2133 length of database: 56,608,159 effective HSP length: 93 effective length of database: 42,298,156 effective search space used: 1395839148 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 463 (357 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 27,704,605 Number of Sequences: 153871 Number of extensions: 466114 Number of successful extensions: 1148 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 1101 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 1144 length of database: 56,608,159 effective HSP length: 86 effective length of database: 43,375,253 effective search space used: 1388008096 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 464 (106 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 11,995,413 Number of Sequences: 153871 Number of extensions: 132524 Number of successful extensions: 592 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 563 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 592 length of database: 56,608,159 effective HSP length: 8 effective length of database: 55,377,191 effective search space used: 1439806966 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 465 (193 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done ***** No hits found ****** Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 19,393,970 Number of Sequences: 153871 Number of extensions: 272407 Number of successful extensions: 673 Number of sequences better than 1.0e-01: 0 Number of HSP's better than 0.1 without gapping: 671 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 673 length of database: 56,608,159 effective HSP length: 35 effective length of database: 51,222,674 effective search space used: 1434234872 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) BLASTX 2.2.9 [May-01-2004] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= 466 (470 letters) Database: uniprot_sprot.fasta 153,871 sequences; 56,608,159 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value MDR_LEITA (P21441) Multidrug resistance protein (P-glycoprotein) 160 3e-44 MRP3_RAT (O88563) Canalicular multispecific organic anion transp... 129 2e-34 MRP3_HUMAN (O15438) Canalicular multispecific organic anion tran... 124 3e-33 MRP2_MOUSE (Q8VI47) Canalicular multispecific organic anion tran... 124 1e-32 MRP2_RAT (Q63120) Canalicular multispecific organic anion transp... 124 2e-32 MRP1_HUMAN (P33527) Multidrug resistance-associated protein 1 123 6e-32 MRP2_RABIT (Q28689) Canalicular multispecific organic anion tran... 121 3e-31 MRP2_HUMAN (Q92887) Canalicular multispecific organic anion tran... 120 3e-30 MRP5_HUMAN (O15440) Multidrug resistance-associated protein 5 (M... 124 9e-29 MRP6_HUMAN (O95255) Multidrug resistance-associated protein 6 (A... 110 2e-28 MRP5_RAT (Q9QYM0) Multidrug resistance-associated protein 5 123 2e-28 MRP5_MOUSE (Q9R1X5) Multidrug resistance-associated protein 5 (A... 123 2e-28 MRP4_HUMAN (O15439) Multidrug resistance-associated protein 4 (M... 114 6e-28 YCFI_YEAST (P39109) Metal resistance protein YCF1 (Yeast cadmium... 120 1e-27 YAWB_SCHPO (Q10185) Probable ATP-dependent permease C3F10.11c 119 3e-27 YOR1_YEAST (P53049) Oligomycin resistance ATP-dependent permease... 119 3e-27 MRP6_RAT (O88269) Multidrug resistance-associated protein 6 (MRP... 109 3e-27 BPT1_YEAST (P14772) Bile pigment transporter 1 117 9e-27 YH85_SCHPO (Q9P5N0) Probable ATP-dependent permease C359.05 112 5e-25 ACC8_HUMAN (Q09428) Sulfonylurea receptor 1 110 1e-24 ACC8_CRICR (Q09427) Sulfonylurea receptor 1 110 2e-24 ACC8_RAT (Q09429) Sulfonylurea receptor 1 109 2e-24 CFTR_MOUSE (P26361) Cystic fibrosis transmembrane conductance re... 99 4e-24 CFTR_RAT (P34158) Cystic fibrosis transmembrane conductance regu... 98 4e-24 L259_DROME (P91660) Probable multidrug resistance-associated pro... 108 5e-24 ACC9_HUMAN (O60706) Sulfonylurea receptor 2 108 5e-24 ACC9_MOUSE (P70170) Sulfonylurea receptor 2 108 7e-24 CFTR_BOVIN (P35071) Cystic fibrosis transmembrane conductance re... 96 8e-24 ACC9_RABIT (P82451) Sulfonylurea receptor 2 107 1e-23 CFTR_SHEEP (Q00555) Cystic fibrosis transmembrane conductance re... 94 2e-23 CFTR_HUMAN (P13569) Cystic fibrosis transmembrane conductance re... 96 2e-23 CFTR_RABIT (Q00554) Cystic fibrosis transmembrane conductance re... 96 2e-23 YBT1_YEAST (P32386) ATP-dependent bile acid permease 106 3e-23 CFTR_SQUAC (P26362) Cystic fibrosis transmembrane conductance re... 97 5e-23 ACC9_RAT (Q63563) Sulfonylurea receptor 2 105 6e-23 ABC1_SCHPO (Q92337) ATP-binding cassette transporter abc1 100 1e-21 YHD5_YEAST (P38735) Probable ATP-dependent permease YHL035C 100 2e-21 YK83_YEAST (P36028) Probable ATP-dependent permease YKR103W/YKR104W 94 2e-19 CFTR_XENLA (P26363) Cystic fibrosis transmembrane conductance re... 93 2e-19 HEPA_ANASP (P22638) Heterocyst differentiation ATP-binding prote... 75 2e-16 PEDD_PEDAC (P36497) Pediocin PA-1 transport/processing ATP-bindi... 73 5e-16 MESD_LEUME (Q10418) Mesentericin Y105 transport/processing ATP-b... 72 2e-15 MDLA_ECOLI (P77265) Multidrug resistance-like ATP-binding protei... 78 7e-15 MSBA_COXBU (Q83D84) Lipid A export ATP-binding/permease protein ... 68 2e-14 MSBA_NEIMA (Q9JW59) Lipid A export ATP-binding/permease protein ... 69 4e-14 MSBA_NEIMB (Q9JXR3) Lipid A export ATP-binding/permease protein ... 67 2e-13 CYDC_ECOLI (P23886) Transport ATP-binding protein cydC 65 3e-13 MDR3_CAEEL (P34713) Multidrug resistance protein 3 (P-glycoprote... 73 3e-13 PMD1_SCHPO (P36619) Leptomycin B resistance protein pmd1 73 3e-13 COMA_STRPN (Q03727) Transport/processing ATP-binding protein com... 72 7e-13 Y742_STRCO (Q9ZNB0) Hypothetical ABC transporter ATP-binding pro... 63 7e-13 YD49_MYCTU (Q11019) Hypothetical ABC transporter ATP-binding pro... 67 1e-12 MDLA_BUCAP (Q8K985) Multidrug resistance-like ATP-binding protei... 70 2e-12 AB10_MOUSE (Q9JI39) ATP-binding cassette, sub-family B, member 1... 70 2e-12 MDR1_CAEEL (P34712) Multidrug resistance protein 1 (P-glycoprote... 70 2e-12 COMA_STRR6 (P59653) Transport/processing ATP-binding protein com... 70 3e-12 MDLA_BUCAI (P57551) Multidrug resistance-like ATP-binding protei... 70 3e-12 AB10_HUMAN (Q9NRK6) ATP-binding cassette, sub-family B, member 1... 70 3e-12 MSBA_VIBPA (Q87R16) Lipid A export ATP-binding/permease protein ... 63 3e-12 MDL1_CANAL (P97998) ATP-dependent permease MDL1 69 5e-12 MSBA_SHEON (Q8EDF0) Lipid A export ATP-binding/permease protein ... 69 5e-12 YFIB_BACSU (P54718) Hypothetical ABC transporter ATP-binding pro... 69 6e-12 HLYB_PASHA (P16532) Leukotoxin secretion/processing ATP-binding ... 58 6e-12 ABC8_HUMAN (Q9NUT2) ATP-binding cassette, sub-family B, member 8... 68 8e-12 CYDD_ECOLI (P29018) Transport ATP-binding protein cydD 68 8e-12 MSBA_RALSO (Q8XXB6) Lipid A export ATP-binding/permease protein ... 68 8e-12 MDR4_DROME (Q00449) Multidrug resistance protein homolog 49 (P-g... 68 1e-11 MDL1_YEAST (P33310) ATP-dependent permease MDL1 68 1e-11 HLYB_PASSP (P55122) Leukotoxin secretion/processing ATP-binding ... 57 1e-11 RT1B_ACTPL (P26760) Toxin RTX-I secretion/processing ATP-binding... 57 2e-11 LCNC_LACLA (Q00564) Lactococcin A transport/processing ATP-bindi... 67 2e-11 PRTD_ERWCH (P23596) Proteases secretion ATP-binding protein prtD 67 2e-11 MSBA_WIGBR (Q8D2U8) Lipid A export ATP-binding/permease protein ... 59 3e-11 RT3B_ACTPL (Q04473) Toxin RTX-III secretion/processing ATP-bindi... 56 5e-11 MDLA_BUCBP (Q89A97) Multidrug resistance-like ATP-binding protei... 65 5e-11 LCCL_LACLA (Q9CJB8) Lactococcin transport/processing ATP-binding... 65 7e-11 Y4GM_RHISN (P55469) Probable ABC transporter ATP-binding protein... 65 7e-11 HLYB_ACTAC (P23702) Leukotoxin secretion/processing ATP-binding ... 57 8e-11 YWJA_BACSU (P45861) Hypothetical ABC transporter ATP-binding pro... 64 1e-10 MAM1_SCHPO (P78966) Mating factor M secretion protein mam1 (Mult... 58 1e-10 MSBA_VIBCH (Q9KQW9) Lipid A export ATP-binding/permease protein ... 64 1e-10 MSBA_SALTY (Q8XFG5) Lipid A export ATP-binding/permease protein ... 64 1e-10 MDR1_HUMAN (P08183) Multidrug resistance protein 1 (P-glycoprote... 64 2e-10 AARD_PROST (Q52402) Transport ATP-binding protein aarD 64 2e-10 YC73_MYCTU (Q11046) Hypothetical ABC transporter ATP-binding pro... 64 2e-10 MSBA_SHIFL (Q83LP0) Lipid A export ATP-binding/permease protein ... 64 2e-10 MSBA_ECOLI (P60752) Lipid A export ATP-binding/permease protein ... 64 2e-10 MSBA_ECOL6 (Q8FJB1) Lipid A export ATP-binding/permease protein ... 64 2e-10 MSBA_ECO57 (P60753) Lipid A export ATP-binding/permease protein ... 64 2e-10 CYDD_HAEIN (P45082) Transport ATP-binding protein cydD 55 2e-10 HMT1_SCHPO (Q02592) Heavy metal tolerance protein precursor 63 2e-10 MSBA_PSEAE (Q9HUG8) Lipid A export ATP-binding/permease protein ... 63 2e-10 MDR2_MOUSE (P21440) Multidrug resistance protein 2 (P-glycoprote... 63 2e-10 MDR3_HUMAN (P21439) Multidrug resistance protein 3 (P-glycoprote... 63 3e-10 MSBA_PASMU (Q9CMG7) Lipid A export ATP-binding/permease protein ... 63 3e-10 MSBA_VIBVU (Q8DAV2) Lipid A export ATP-binding/permease protein ... 63 3e-10 HLYB_PROVU (P11599) Hemolysin secretion/processing ATP-binding p... 53 4e-10 MDR2_CRIGR (P21449) Multidrug resistance protein 2 (P-glycoprote... 62 4e-10 MDR1_CRIGR (P21448) Multidrug resistance protein 1 (P-glycoprote... 62 4e-10 HLYB_ECOLI (P08716) Hemolysin secretion/processing ATP-binding p... 52 5e-10 HLY2_ECOLI (P10089) Hemolysin secretion/processing ATP-binding p... 52 5e-10 MDR3_MOUSE (P21447) Multidrug resistance protein 3 (P-glycoprote... 62 6e-10 CYAB_BORPE (P18770) Cyclolysin secretion/processing ATP-binding ... 62 7e-10 MDR1_LEIEN (Q06034) Multidrug resistance protein 1 (P-glycoprote... 62 7e-10 MSBA_YERPE (Q8ZGA9) Lipid A export ATP-binding/permease protein ... 62 7e-10 ABC9_RAT (Q9QYJ4) ATP-binding cassette, sub-family B, member 9 p... 61 9e-10 ABC9_MOUSE (Q9JJ59) ATP-binding cassette, sub-family B, member 9... 61 9e-10 MDR1_MOUSE (P06795) Multidrug resistance protein 1 (P-glycoprote... 61 9e-10 CYDC_BACSU (P94366) Transport ATP-binding protein cydC 61 9e-10 ABC9_HUMAN (Q9NP78) ATP-binding cassette, sub-family B, member 9... 61 9e-10 TAGB_DICDI (P54683) Prestalk-specific protein tagB precursor (EC... 59 1e-09 STE6_YEAST (P12866) Mating factor A secretion protein STE6 (Mult... 61 1e-09 MDR2_RAT (Q08201) Multidrug resistance protein 2 (P-glycoprotein 2) 60 2e-09 SUNT_BACSU (O30671) Sublancin 168 processing and transport ATP-b... 60 2e-09 Y664_HAEIN (Q57538) Probable ABC transporter ATP-binding protein... 60 2e-09 MDR5_DROME (Q00748) Multidrug resistance protein homolog 65 (P-g... 60 2e-09 MDR3_CRIGR (P23174) Multidrug resistance protein 3 (P-glycoprote... 60 2e-09 TAP1_HUMAN (Q03518) Antigen peptide transporter 1 (APT1) (Peptid... 56 2e-09 LMRA_LACLA (Q9CHL8) Multidrug resistance ABC transporter ATP-bin... 59 4e-09 MDR1_RAT (P43245) Multidrug resistance protein 1 (P-glycoprotein 1) 59 4e-09 MDR_PLAFF (P13568) Multidrug resistance protein (Chloroquine res... 56 4e-09 YNT9_SCHPO (Q9Y7M7) Probable ATP-dependent permease C9B6.09c 52 4e-09 MSBA_XANAC (Q8PKS5) Lipid A export ATP-binding/permease protein ... 59 5e-09 MSBA_XANCP (Q8P8W4) Lipid A export ATP-binding/permease protein ... 58 8e-09 TAP2_HUMAN (Q03519) Antigen peptide transporter 2 (APT2) (Peptid... 58 8e-09 MDLB_ECOLI (P75706) Multidrug resistance-like ATP-binding protei... 58 1e-08 APRD_PSEAE (Q03024) Alkaline protease secretion ATP-binding prot... 58 1e-08 CVAB_ECOLI (P22520) Colicin V secretion/processing ATP-binding p... 57 1e-08 MSBA_HAEIN (P44407) Lipid A export ATP-binding/permease protein ... 57 1e-08 LMRA_LACLC (P97046) Multidrug resistance ABC transporter ATP-bin... 57 2e-08 MCHF_ECOLI (Q9EXN5) Probable microcin H47 secretion/processing A... 57 2e-08 MSBA_FRANO (Q47908) Lipid A export ATP-binding/permease protein ... 57 2e-08 TAP2_RAT (P36372) Antigen peptide transporter 2 (APT2) 57 2e-08 AB11_HUMAN (O95342) Bile salt export pump (ATP-binding cassette,... 57 2e-08 CHVA_AGRT5 (P18768) Beta-(1-->2)glucan export ATP-binding protei... 56 3e-08 ATM1_YEAST (P40416) Transporter ATM1, mitochondrial precursor 56 3e-08 TAGC_DICDI (Q23868) Prestalk-specific protein tagC precursor (EC... 54 4e-08 AB11_RAT (O70127) Bile salt export pump (ATP-binding cassette, s... 56 4e-08 CYDD_BACSU (P94367) Transport ATP-binding protein cydD 56 4e-08 TAP2_MOUSE (P36371) Antigen peptide transporter 2 (APT2) (Histoc... 55 7e-08 ABC7_HUMAN (O75027) ATP-binding cassette, sub-family B, member 7... 55 9e-08 MSBA_PSEPK (Q88D92) Lipid A export ATP-binding/permease protein ... 55 9e-08 MSBA_PSESM (Q87VF3) Lipid A export ATP-binding/permease protein ... 55 9e-08 MDL2_YEAST (P33311) ATP-dependent permease MDL2 55 9e-08 AB11_RABIT (Q9N0V3) Bile salt export pump (ATP-binding cassette,... 54 1e-07 YA51_HAEIN (Q57180) Hypothetical ABC transporter ATP-binding pro... 54 1e-07 Y663_HAEIN (P71355) Hypothetical ABC transporter ATP-binding pro... 51 1e-07 TAP1_RAT (P36370) Antigen peptide transporter 1 (APT1) 54 2e-07 AB11_MOUSE (Q9QY30) Bile salt export pump (ATP-binding cassette,... 54 2e-07 YFIC_BACSU (P54719) Hypothetical ABC transporter ATP-binding pro... 54 2e-07 NDVA_RHIME (P18767) Beta-(1-->2)glucan export ATP-binding protei... 53 3e-07 YC72_MYCTU (Q11047) Hypothetical ABC transporter ATP-binding pro... 53 3e-07 ABC6_HUMAN (Q9NP58) ATP-binding cassette, sub-family B, member 6... 53 3e-07 TAP1_MOUSE (P21958) Antigen peptide transporter 1 (APT1) (Histoc... 53 3e-07 CYS2_RHIME (Q92VJ2) Sulfate/thiosulfate import ATP-binding prote... 44 3e-07 MSBA_XYLFA (Q9PEE7) Lipid A export ATP-binding/permease protein ... 52 4e-07 ABC7_MOUSE (Q61102) ATP-binding cassette, sub-family B, member 7... 52 4e-07 YD01_SCHPO (O14286) Putative ABC transporter C15A10.01 in chromo... 52 4e-07 CYS1_RHIME (Q92XW1) Sulfate/thiosulfate import ATP-binding prote... 44 6e-07 LAGD_LACLA (P59852) Lactococcin G processing and transport ATP-b... 52 6e-07 MSBA_XYLFT (Q87EF0) Lipid A export ATP-binding/permease protein ... 51 1e-06 MDLB_BUCBP (Q89A96) Multidrug resistance-like ATP-binding protei... 51 1e-06 CYDC_HAEIN (P45081) Transport ATP-binding protein cydC 50 2e-06 EXP8_STRPN (P35598) Putative ABC transporter ATP-binding protein... 50 2e-06 Y288_THEMA (Q9WYC4) Hypothetical ABC transporter ATP-binding pro... 50 3e-06 Y015_MYCPN (P75094) Hypothetical ABC transporter ATP-binding pro... 50 3e-06 PSTB_XANAC (Q8PM59) Phosphate import ATP-binding protein pstB (E... 49 4e-06 YD48_MYCTU (Q11018) Hypothetical ABC transporter ATP-binding pro... 49 4e-06 CYSA_BRAJA (Q89UD2) Sulfate/thiosulfate import ATP-binding prote... 42 4e-06 FBC2_HAEIN (P44513) Ferric cations import ATP-binding protein fb... 49 6e-06 PSTB_XANCP (Q8PAG0) Phosphate import ATP-binding protein pstB (E... 49 6e-06 CYSA_SYNY3 (P74548) Sulfate/thiosulfate import ATP-binding prote... 49 6e-06 SPAT_BACSU (P33116) Subtilin transport ATP-binding protein spaT 43 7e-06 PSTB_THEMA (Q9X0Y8) Phosphate import ATP-binding protein pstB (E... 48 8e-06 PSB1_PSEPK (Q88JJ0) Phosphate import ATP-binding protein pstB 1 ... 48 1e-05 TROB_TREPA (P96117) Zinc transport system ATP-binding protein troB 48 1e-05 PSB2_LISMO (Q8Y4E9) Phosphate import ATP-binding protein pstB 2 ... 48 1e-05 PSB2_LISIN (Q927Z7) Phosphate import ATP-binding protein pstB 2 ... 48 1e-05 PSTB_RHILO (Q98FL5) Phosphate import ATP-binding protein pstB (E... 47 1e-05 CMA2_SALTY (P61378) Cytochrome c biogenesis ATP-binding export p... 47 1e-05 CMA1_SALTY (Q8ZKZ9) Cytochrome c biogenesis ATP-binding export p... 47 1e-05 CCMA_SALTI (P61377) Cytochrome c biogenesis ATP-binding export p... 47 1e-05 MDLB_BUCAP (Q8K984) Multidrug resistance-like ATP-binding protei... 47 1e-05 POTA_MYCGE (P47288) Spermidine/putrescine transport ATP-binding ... 47 1e-05 MSMX_BACSU (P94360) Probable multiple sugar-binding transport AT... 47 1e-05 LCN3_LACLA (P37608) Lacticin 481/lactococcin transport/processin... 44 2e-05 CYSA_SYNP7 (P14788) Sulfate/thiosulfate import ATP-binding prote... 47 2e-05 CYS2_AGRT5 (Q8UA73) Sulfate/thiosulfate import ATP-binding prote... 47 2e-05 CYSA_MYCTU (P71747) Sulfate/thiosulfate import ATP-binding prote... 47 2e-05 PSTB_TROW8 (Q83HT1) Phosphate import ATP-binding protein pstB (E... 47 2e-05 PSTB_BIFLO (Q8G7F4) Phosphate import ATP-binding protein pstB (E... 47 2e-05 PSTB_NITEU (Q82VR4) Phosphate import ATP-binding protein pstB (E... 47 2e-05 Y4FO_RHISN (P55453) Putative ABC transporter ATP-binding protein... 47 2e-05 HST6_CANAL (P53706) ATP-dependent permease HST6 (STE6 homolog) 46 3e-05 PSB2_SHEON (Q8E9I8) Phosphate import ATP-binding protein pstB 2 ... 46 4e-05 POTA_MYCPN (P75059) Spermidine/putrescine transport ATP-binding ... 46 4e-05 PSB1_ENTFA (Q834B4) Phosphate import ATP-binding protein pstB 1 ... 46 4e-05 PSB2_LACPL (Q88YK7) Phosphate import ATP-binding protein pstB 2 ... 46 4e-05 SSUB_ECOLI (P38053) Putative aliphatic sulfonates transport ATP-... 46 4e-05 THIQ_HAEIN (P44986) Thiamine transport ATP-binding protein thiQ 45 5e-05 PSB1_HALN1 (Q9HS13) Phosphate import ATP-binding protein pstB 1 ... 45 5e-05 MACB_ECOLI (P75831) Macrolide-specific ABC-type efflux carrier 45 5e-05 YTMN_BACSU (O34900) Probable amino-acid ABC transporter ATP-bind... 45 5e-05 NODI_RHIGA (P50332) Nod factor export ATP-binding protein I (Nod... 45 5e-05 PSTB_BRAJA (Q89VF2) Phosphate import ATP-binding protein pstB (E... 45 5e-05 PSB2_VIBCH (Q9KU04) Phosphate import ATP-binding protein pstB 2 ... 45 5e-05 CYSA_CHLVU (P56344) Probable sulfate/thiosulfate import ATP-bind... 45 5e-05 PSB1_THETN (Q8RCU0) Phosphate import ATP-binding protein pstB 1 ... 45 7e-05 CYSA_SALTY (P40860) Sulfate/thiosulfate import ATP-binding prote... 45 7e-05 CYSA_SALTI (Q8Z4V6) Sulfate/thiosulfate import ATP-binding prote... 45 7e-05 CYSA_ECOLI (P16676) Sulfate/thiosulfate import ATP-binding prote... 45 7e-05 CYSA_ECOL6 (Q8FFB3) Sulfate/thiosulfate import ATP-binding prote... 45 7e-05 CYSA_ECO57 (Q8XBJ8) Sulfate/thiosulfate import ATP-binding prote... 45 7e-05 MCJD_ECOLI (Q9X2W0) Microcin J25 export ATP-binding/permease pro... 45 7e-05 PSB2_ENTFA (Q834B3) Phosphate import ATP-binding protein pstB 2 ... 45 7e-05 CYSA_YERPE (Q8D0W8) Sulfate/thiosulfate import ATP-binding prote... 45 7e-05 Y014_MYCPN (P75095) Hypothetical ABC transporter ATP-binding pro... 45 7e-05 PSB2_HALN1 (Q9HML8) Phosphate import ATP-binding protein pstB 2 ... 45 7e-05 PSTB_CAUCR (Q9ABD6) Phosphate import ATP-binding protein pstB (E... 45 7e-05 PSB1_YERPE (Q8ZCX5) Phosphate import ATP-binding protein pstB 1 ... 45 7e-05 PSB1_STRMU (Q8DU24) Phosphate import ATP-binding protein pstB 1 ... 45 7e-05 CYSA_VIBCH (Q9KUI0) Sulfate/thiosulfate import ATP-binding prote... 45 7e-05 CYS1_SHEON (Q8EBC3) Sulfate/thiosulfate import ATP-binding prote... 45 7e-05 Y4OS_RHISN (P55604) Probable ABC transporter ATP-binding protein... 45 7e-05 PSTB_CHLTE (Q8KDZ5) Phosphate import ATP-binding protein pstB (E... 45 7e-05 Y015_MYCGE (P47261) Hypothetical ABC transporter ATP-binding pro... 45 9e-05 PSB1_VIBVU (Q8DEW5) Phosphate import ATP-binding protein pstB 1 ... 45 9e-05 PSB1_VIBPA (Q87S48) Phosphate import ATP-binding protein pstB 1 ... 45 9e-05 HISP_ECOLI (P07109) Histidine transport ATP-binding protein hisP 45 9e-05 PSTB_METJA (Q58418) Phosphate import ATP-binding protein pstB (E... 45 9e-05 PSB1_STRPN (Q97Q35) Phosphate import ATP-binding protein pstB 1 ... 45 9e-05 PSTB_AGRT5 (Q8UI76) Phosphate import ATP-binding protein pstB (E... 45 9e-05 MSMK_STRMU (Q00752) Multiple sugar-binding transport ATP-binding... 45 9e-05 PSTB_METTH (O27764) Phosphate import ATP-binding protein pstB (E... 45 9e-05 YD67_METJA (Q58762) Hypothetical ABC transporter ATP-binding pro... 44 1e-04 PSTB_XYLFT (Q87C88) Phosphate import ATP-binding protein pstB (E... 44 1e-04 CYSA_ANASP (Q8Z0H0) Sulfate/thiosulfate import ATP-binding prote... 44 1e-04 PSTB_TROWT (Q83GE8) Phosphate import ATP-binding protein pstB (E... 44 1e-04 PSTB_AQUAE (O67154) Phosphate import ATP-binding protein pstB (E... 44 1e-04 CYSA_NITEU (Q82WT5) Sulfate/thiosulfate import ATP-binding prote... 44 1e-04 MDR1_ENTHI (P16875) Multidrug resistance protein 1 (P-glycoprote... 44 1e-04 CYS1_AGRT5 (Q8UH62) Sulfate/thiosulfate import ATP-binding prote... 44 1e-04 UGPC_ECOLI (P10907) SN-glycerol-3-phosphate transport ATP-bindin... 44 1e-04 YQIZ_BACSU (P54537) Probable amino-acid ABC transporter ATP-bind... 44 1e-04 CYSA_MESVI (Q9MUN1) Probable sulfate/thiosulfate import ATP-bind... 44 1e-04 NIST_LACLA (Q03203) Nisin transport ATP-binding protein nisT 39 1e-04 PSTB_XYLFA (Q9PBK0) Phosphate import ATP-binding protein pstB (E... 44 2e-04 MDLB_BUCAI (P57552) Multidrug resistance-like ATP-binding protei... 44 2e-04 PSTB_EDWTA (Q9AML4) Phosphate import ATP-binding protein pstB (E... 44 2e-04 PSTB_ARCFU (O28912) Phosphate import ATP-binding protein pstB (E... 44 2e-04 POTG_ECOLI (P31134) Putrescine transport ATP-binding protein potG 44 2e-04 CYSA_CAUCR (Q9A7X1) Sulfate/thiosulfate import ATP-binding prote... 44 2e-04 PSB2_PSESM (Q87U31) Phosphate import ATP-binding protein pstB 2 ... 44 2e-04 TAUB_ECOLI (Q47538) Taurine transport ATP-binding protein tauB 44 2e-04 CYSA_NEPOL (Q9TKX3) Sulfate/thiosulfate import ATP-binding prote... 44 2e-04 HISP_SALTY (P02915) Histidine transport ATP-binding protein hisP 44 2e-04 CYSA_VIBVU (Q8D653) Sulfate/thiosulfate import ATP-binding prote... 44 2e-04 CYSA_SYNEL (Q8DIA0) Sulfate/thiosulfate import ATP-binding prote... 44 2e-04 ABCR_MOUSE (O35600) Retinal-specific ATP-binding cassette transp... 44 2e-04 MDR3_ENTHI (P16876) Multidrug resistance protein 3 (P-glycoprote... 44 2e-04 CYSA_RHILO (Q98K23) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 YCJV_ECOLI (P77481) Hypothetical ABC transporter ATP-binding pro... 43 3e-04 CYSA_XYLFT (Q87DT9) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 CYSA_XYLFA (Q9PDN2) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 YDCT_ECOLI (P77795) Hypothetical ABC transporter ATP-binding pro... 43 3e-04 OCCP_RHIME (P72297) Octopine permease ATP-binding protein P 43 3e-04 CYSA_BRUME (Q8G342) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 PSTB_RHIME (Q92SA1) Phosphate import ATP-binding protein pstB (E... 43 3e-04 PSB1_SHEON (Q8EG82) Phosphate import ATP-binding protein pstB 1 ... 43 3e-04 CYSA_BURCE (Q93DX8) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 CYSA_PSEPK (Q88CL2) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 PTB3_ANASP (Q8YNJ3) Phosphate import ATP-binding protein pstB 3 ... 43 3e-04 MODC_HAEIN (P45321) Molybdenum import ATP-binding protein modC (... 43 3e-04 CYSA_PSESM (Q88AS5) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 ARTP_ECOLI (P30858) Arginine transport ATP-binding protein artP 43 3e-04 CYSA_XANCP (Q8PC11) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 CYSA_XANAC (Q8PNN4) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 Y014_MYCGE (P47260) Hypothetical ABC transporter ATP-binding pro... 43 3e-04 PTB1_SYNY3 (Q55196) Phosphate import ATP-binding protein pstB 1 ... 43 3e-04 PSB2_LACLA (Q9CEW7) Phosphate import ATP-binding protein pstB 2 ... 43 3e-04 CYSA_NEIMB (Q9JZW0) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 CYSA_NEIMA (Q9JUX4) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 CYSA_BACHD (Q9K876) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 CYSA_BACCR (Q81GU1) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 CYSA_BACC1 (O31339) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 ABG8_MOUSE (Q9DBM0) ATP-binding cassette, sub-family G, member 8... 43 3e-04 THIQ_ECOLI (P31548) Thiamine transport ATP-binding protein thiQ 43 3e-04 CYSA_RALSO (Q8XZP8) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 POTA_ECOLI (P23858) Spermidine/putrescine transport ATP-binding ... 43 3e-04 CYSA_CUCSA (Q9G4F5) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 ABCR_HUMAN (P78363) Retinal-specific ATP-binding cassette transp... 43 3e-04 CYS2_SHEON (Q8E8K8) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 NRTD_SYNP7 (P38046) Nitrate transport ATP-binding protein nrtD 43 3e-04 ABG8_RAT (P58428) ATP-binding cassette, sub-family G, member 8 (... 43 3e-04 PSTB_PSEPU (Q9Z411) Phosphate import ATP-binding protein pstB (E... 43 3e-04 PSB2_PSEPK (Q88C57) Phosphate import ATP-binding protein pstB 2 ... 43 3e-04 NODI_RHIS3 (P72335) Nod factor export ATP-binding protein I (Nod... 43 3e-04 CYSA_PSEAE (Q9I6L0) Sulfate/thiosulfate import ATP-binding prote... 43 3e-04 PSTB_MYCGE (P47650) Phosphate import ATP-binding protein pstB (E... 42 5e-04 PSTB_ENTCL (O32487) Phosphate import ATP-binding protein pstB (E... 42 5e-04 PSTB_PASMU (Q9CNJ7) Phosphate import ATP-binding protein pstB (E... 42 5e-04 NDI2_RHIME (Q8GNH6) Nod factor export ATP-binding protein I (Nod... 42 5e-04 PTB2_SYNY3 (Q55195) Phosphate import ATP-binding protein pstB 2 ... 42 5e-04 PSTB_SALTY (P58656) Phosphate import ATP-binding protein pstB (E... 42 5e-04 PSTB_ECOLI (P07655) Phosphate import ATP-binding protein pstB (E... 42 5e-04 MALK_SALTY (P19566) Maltose/maltodextrin transport ATP-binding p... 42 5e-04 MALK_SALTI (Q8Z1U0) Maltose/maltodextrin transport ATP-binding p... 42 5e-04 Y354_HAEIN (P44656) Hypothetical ABC transporter ATP-binding pro... 42 5e-04 MALK_ECOLI (P02914) Maltose/maltodextrin transport ATP-binding p... 42 5e-04 MODC_RHOCA (Q08381) Molybdenum import ATP-binding protein modC (... 42 6e-04 METN_PASMU (Q9CK97) Probable D-methionine transport ATP-binding ... 42 6e-04 LACK_AGRRD (Q01937) Lactose transport ATP-binding protein lacK 42 6e-04 PSTB_PSEAE (Q51546) Phosphate import ATP-binding protein pstB (E... 42 6e-04 LOLD_SHEON (Q8EEV5) Lipoprotein releasing system ATP-binding pro... 42 6e-04 LOD1_CAUCR (Q9A9P4) Lipoprotein releasing system ATP-binding pro... 42 6e-04 Y467_MYCGE (P47705) Hypothetical ABC transporter ATP-binding pro... 42 6e-04 PSB1_LACLA (Q9CEW8) Phosphate import ATP-binding protein pstB 1 ... 42 6e-04 LOLD_NITEU (Q82VL9) Lipoprotein releasing system ATP-binding pro... 36 6e-04 UVRA_DEIRA (Q46577) UvrABC system protein A (UvrA protein) (Exci... 38 7e-04 Y187_MYCPN (P75264) ABC transporter ATP-binding protein MG187 ho... 42 8e-04 PSTB_RALSO (Q8XZ72) Phosphate import ATP-binding protein pstB (E... 42 8e-04 LOLD_PSEAE (Q9HZL7) Lipoprotein releasing system ATP-binding pro... 42 8e-04 Y467_MYCPN (P75110) Hypothetical ABC transporter ATP-binding pro... 42 8e-04 Y796_METJA (Q58206) ABC transporter ATP-binding protein MJ0796 42 8e-04 METN_VIBCH (Q9KTJ5) Probable D-methionine transport ATP-binding ... 42 8e-04 NDI1_RHIME (O52618) Nod factor export ATP-binding protein I (Nod... 42 8e-04 METN_HAEIN (P44785) Probable D-methionine transport ATP-binding ... 42 8e-04 YF72_METJA (Q58967) Hypothetical ABC transporter ATP-binding pro... 42 8e-04 PSTB_HELMO (Q8GDV4) Phosphate import ATP-binding protein pstB (E... 42 8e-04 PSTB_BRUME (Q8YE92) Phosphate import ATP-binding protein pstB (E... 41 0.001 METN_SALTY (Q8ZRM9) D-methionine transport ATP-binding protein metN 41 0.001 METN_SALTI (Q8Z990) D-methionine transport ATP-binding protein metN 41 0.001 PSB2_THETN (Q8R9I2) Phosphate import ATP-binding protein pstB 2 ... 41 0.001 PSB1_LACPL (Q88YK8) Phosphate import ATP-binding protein pstB 1 ... 41 0.001 OCCP_AGRTU (P35117) Octopine permease ATP-binding protein P 41 0.001 AGLK_RHIME (Q9Z3R9) Alpha-glucoside transport ATP-binding protei... 41 0.001 YEHX_ECOLI (P33360) Hypothetical ABC transporter ATP-binding pro... 41 0.001 PSTB_MYCIT (Q49588) Phosphate import ATP-binding protein pstB (E... 41 0.001 Y352_THEMA (Q9WYI7) Hypothetical ABC transporter ATP-binding pro... 41 0.001 NODI_RHILV (P08720) Nod factor export ATP-binding protein I (Nod... 41 0.001 PSTB_MYCPN (P75186) Phosphate import ATP-binding protein pstB (E... 41 0.001 POTA_HAEIN (P45171) Spermidine/putrescine transport ATP-binding ... 41 0.001 PSTB_CLOPE (Q8XMP8) Phosphate import ATP-binding protein pstB (E... 41 0.001 ELF1_SCHPO (O14134) mRNA export factor elf1 38 0.001 PSTB_UREPA (Q9PQU3) Phosphate import ATP-binding protein pstB (E... 41 0.001 YHES_ECOLI (P45535) Hypothetical ABC transporter ATP-binding pro... 41 0.001 METN_ECOLI (P30750) D-methionine transport ATP-binding protein metN 41 0.001 METN_ECOL6 (Q8X7Z9) D-methionine transport ATP-binding protein metN 41 0.001 PSTB_STRGR (Q9EUS2) Phosphate import ATP-binding protein pstB (E... 41 0.001 PSB2_YERPE (Q8Z9T1) Phosphate import ATP-binding protein pstB 2 ... 41 0.001 PSTB_CAMJE (Q9PHQ1) Phosphate import ATP-binding protein pstB (E... 41 0.001 OPPF_BACSU (P24137) Oligopeptide transport ATP-binding protein oppF 41 0.001 PSB1_STRA3 (Q8E5K6) Phosphate import ATP-binding protein pstB 1 ... 41 0.001 PSTB_STAAM (Q9EX64) Phosphate import ATP-binding protein pstB (E... 41 0.001 MODC_MYCTU (P95155) Molybdenum import ATP-binding protein modC (... 41 0.001 Y412_METJA (Q57855) Hypothetical ABC transporter ATP-binding pro... 41 0.001 PSB2_STRA3 (Q8E5K5) Phosphate import ATP-binding protein pstB 2 ... 41 0.001 ARTP_HAEIN (P45092) Arginine transport ATP-binding protein artP 41 0.001 YBXA_BACSU (P40735) Hypothetical ABC transporter ATP-binding pro... 36 0.002 CYSA_LEPIN (Q8F6Z1) Sulfate/thiosulfate import ATP-binding prote... 40 0.002 FBPC_ACTPL (Q57293) Ferric cations import ATP-binding protein fb... 40 0.002 WHIT_LUCCU (Q05360) White protein 40 0.002 PSTB_CORGL (Q8NMK1) Phosphate import ATP-binding protein pstB (E... 40 0.002 YNJD_ECOLI (P76909) Hypothetical ABC transporter ATP-binding pro... 40 0.002 PSTB_MYCSM (O68469) Phosphate import ATP-binding protein pstB (E... 40 0.002 WHIT_CERCA (Q17320) White protein 40 0.002 ABG8_HUMAN (Q9H221) ATP-binding cassette, sub-family G, member 8... 40 0.002 YA78_HAEIN (P45022) Probable amino-acid ABC transporter ATP-bind... 40 0.002 PSTB_BACAN (Q81LW6) Phosphate import ATP-binding protein pstB (E... 40 0.002 NRTC_SYNY3 (P73450) Nitrate transport ATP-binding protein nrtC 40 0.002 MNTB_BACSU (O34338) Manganese transport system ATP-binding prote... 40 0.002 PSB2_STRR6 (Q8DPB4) Phosphate import ATP-binding protein pstB 2 ... 40 0.002 PSB2_STRPN (Q97Q34) Phosphate import ATP-binding protein pstB 2 ... 40 0.002 GC20_YEAST (P43535) GCN20 protein 40 0.002 YCKI_BACSU (P39456) Probable amino-acid ABC transporter ATP-bind... 40 0.002 PSTB_OCEIH (Q8ELT4) Phosphate import ATP-binding protein pstB (E... 40 0.002 PSTB_SYNEL (Q8DGZ3) Phosphate import ATP-binding protein pstB (E... 40 0.002 PSTB_STRCO (Q9KZW2) Phosphate import ATP-binding protein pstB (E... 40 0.002 PSTB_STRAW (Q82G23) Phosphate import ATP-binding protein pstB (E... 40 0.002 YDDO_ECOLI (P77622) Hypothetical ABC transporter ATP-binding pro... 40 0.002 UVRA_BRUSU (Q8G0I9) UvrABC system protein A (UvrA protein) (Exci... 40 0.002 UVRA_BRUME (Q8YHC4) UvrABC system protein A (UvrA protein) (Exci... 40 0.002 POTA_SALTY (P40790) Spermidine/putrescine transport ATP-binding ... 40 0.002 PSTB_BACHD (Q9K8L5) Phosphate import ATP-binding protein pstB (E... 40 0.002 PSB1_STRPY (Q99ZG5) Phosphate import ATP-binding protein pstB 1 ... 40 0.002 ALD_MOUSE (P48410) Adrenoleukodystrophy protein homolog (ALDP) 40 0.002 WHIT_ANOGA (Q27256) White protein 40 0.002 LOD1_RHOBA (Q7UX73) Lipoprotein releasing system ATP-binding pro... 40 0.002 CCMA_ARATH (Q9C8T1) Putative cytochrome c biogenesis ATP-binding... 40 0.002 PSB3_STRPN (Q9X4T3) Phosphate import ATP-binding protein pstB 3 ... 40 0.002 LOLD_BRAJA (Q89KN0) Lipoprotein releasing system ATP-binding pro... 40 0.003 ADCC_STRPN (O87862) Zinc transport system ATP-binding protein adcC 40 0.003 PSB1_VIBCH (Q9KN92) Phosphate import ATP-binding protein pstB 1 ... 40 0.003 YECC_ECOLI (P37774) Hypothetical amino-acid ABC transporter ATP-... 40 0.003 PSTB_PYRAB (Q9UZU7) Phosphate import ATP-binding protein pstB (E... 40 0.003 Y361_HAEIN (P44662) Probable iron transport system ATP-binding p... 40 0.003 AOTP_PSEAE (O30506) Arginine/ornithine transport ATP-binding pro... 40 0.003 PTB2_MYCTU (P95302) Phosphate import ATP-binding protein pstB 2 ... 40 0.003 FBC1_HAEIN (P44531) Ferric cations import ATP-binding protein fb... 40 0.003 PSB1_PSESM (Q880A6) Phosphate import ATP-binding protein pstB 1 ... 40 0.003 PSTB_BACCR (Q818I7) Phosphate import ATP-binding protein pstB (E... 40 0.003 FBPC_ECOLI (P37009) Ferric cations import ATP-binding protein fb... 40 0.003 GLUA_CORGL (P48243) Glutamate transport ATP-binding protein gluA 40 0.003 YOH5_YEAST (Q08234) Probable ATP-dependent transporter YOL074C/Y... 40 0.003 PSTB_COREF (Q8FMN9) Phosphate import ATP-binding protein pstB (E... 40 0.003 HFAC_CAUCR (Q45978) Holdfast attachment protein C (HfaC protein) 40 0.003 LOLD_COXBU (Q83CV2) Lipoprotein releasing system ATP-binding pro... 35 0.004 GLUA_COREF (Q8RQL7) Glutamate transport ATP-binding protein gluA 39 0.004 YC81_MYCTU (Q11040) Hypothetical ABC transporter ATP-binding pro... 39 0.004 YBBA_ECOLI (P31219) Hypothetical ABC transporter ATP-binding pro... 39 0.004 METN_YERPE (Q8ZH38) D-methionine transport ATP-binding protein metN 39 0.004 YXEO_BACSU (P54954) Probable amino-acid ABC transporter ATP-bind... 39 0.004 SMOK_RHOSH (P54933) ATP-binding transport protein smoK (PolK) 39 0.004 PSTB_CLOAB (Q97IE0) Phosphate import ATP-binding protein pstB (E... 39 0.004 PSB2_VIBVU (Q8D3X4) Phosphate import ATP-binding protein pstB 2 ... 39 0.004 LOLD_FUSNN (Q8RFV0) Lipoprotein releasing system ATP-binding pro... 39 0.004 DPPF_ECOLI (P37313) Dipeptide transport ATP-binding protein dppF 39 0.004 CED7_CAEEL (P34358) ABC transporter ced-7 (Cell death protein 7) 39 0.004 OPAA_LACLA (Q9KIF7) Glycine betaine transport ATP-binding protei... 39 0.004 PSB1_BACSU (P46342) Phosphate import ATP-binding protein pstB 1 ... 39 0.004 LOLD_PSESM (Q884I3) Lipoprotein releasing system ATP-binding pro... 39 0.004 LOLD_PSEPK (Q88KY4) Lipoprotein releasing system ATP-binding pro... 39 0.004 PSTB_STAEP (Q8CPA1) Phosphate import ATP-binding protein pstB (E... 39 0.004 LOLD_BORPE (Q7VZ31) Lipoprotein releasing system ATP-binding pro... 34 0.005 LOLD_BORPA (Q7W8T0) Lipoprotein releasing system ATP-binding pro... 34 0.005 LOLD_BORBR (Q7WK40) Lipoprotein releasing system ATP-binding pro... 34 0.005 DPPF_HAEIN (P45094) Dipeptide transport ATP-binding protein dppF 39 0.005 PTB2_ANASP (Q8YYE2) Phosphate import ATP-binding protein pstB 2 ... 39 0.005 PSTB_BORBU (O51236) Phosphate import ATP-binding protein pstB (E... 39 0.005 PSB3_STRA3 (Q8E313) Phosphate import ATP-binding protein pstB 3 ... 39 0.005 PSTB_DEIRA (Q9RYZ3) Phosphate import ATP-binding protein pstB (E... 39 0.005 PSTB_CLOTE (Q895Y0) Phosphate import ATP-binding protein pstB (E... 39 0.005 PSB2_VIBPA (Q87G59) Phosphate import ATP-binding protein pstB 2 ... 39 0.005 MODC_AZOVI (P37732) Molybdenum import ATP-binding protein modC (... 39 0.005 FBPC_SERMA (P21410) Ferric cations import ATP-binding protein fb... 39 0.005 NASD_KLEOX (P39459) Nitrate transport protein nasD 39 0.005 PTB3_SYNY3 (P73788) Phosphate import ATP-binding protein pstB 3 ... 39 0.005 NRTD_SYNY3 (P73265) Putative nitrate transport ATP-binding prote... 39 0.005 PSTB_MYCPE (Q8EUJ1) Phosphate import ATP-binding protein pstB (E... 39 0.005 PSB2_STRPY (Q99ZG4) Phosphate import ATP-binding protein pstB 2 ... 39 0.005 PSB2_STRP8 (Q8P0V3) Phosphate import ATP-binding protein pstB 2 ... 39 0.005 PSB2_STRMU (Q8DU23) Phosphate import ATP-binding protein pstB 2 ... 39 0.005 YBBL_ECOLI (P77279) Hypothetical ABC transporter ATP-binding pro... 39 0.005 Y179_MYCGE (P47425) Hypothetical ABC transporter ATP-binding pro... 30 0.006 MODC_SHIFL (P59738) Molybdenum import ATP-binding protein modC (... 39 0.007 MODC_SALTY (Q8ZQR6) Molybdenum import ATP-binding protein modC (... 39 0.007 MODC_SALTI (Q8Z8A4) Molybdenum import ATP-binding protein modC (... 39 0.007 MODC_ECOLI (P09833) Molybdenum import ATP-binding protein modC (... 39 0.007 MODC_ECOL6 (Q8FJR4) Molybdenum import ATP-binding protein modC (... 39 0.007 MODC_ECO57 (Q8X4V7) Molybdenum import ATP-binding protein modC (... 39 0.007 FHUC_ECOLI (P07821) Ferrichrome transport ATP-binding protein fhuC 39 0.007 PHNC_ECOLI (P16677) Phosphonates transport ATP-binding protein phnC 39 0.007 CCMA_RHOSH (O33570) Cytochrome c biogenesis ATP-binding export p... 39 0.007 SSUB_BACSU (P97027) Putative aliphatic sulfonates transport ATP-... 39 0.007 CCMA_NITEU (Q82WC8) Cytochrome c biogenesis ATP-binding export p... 39 0.007 APPF_BACSU (P42065) Oligopeptide transport ATP-binding protein appF 39 0.007 CCMA_ALCEU (Q7WXC1) Cytochrome c biogenesis ATP-binding export p... 39 0.007 NODI_BRAJA (P26050) Nod factor export ATP-binding protein I (Nod... 39 0.007 Y179_MYCPN (Q50294) Hypothetical ABC transporter ATP-binding pro... 32 0.008 LOLD_CHRVO (Q7NTU0) Lipoprotein releasing system ATP-binding pro... 38 0.009 CYSA_MARPO (P10091) Probable sulfate/thiosulfate import ATP-bind... 38 0.009 CYSA_ANTFO (Q85A69) Probable sulfate/thiosulfate import ATP-bind... 38 0.009 OPPF_STRPY (Q9F5U1) Oligopeptide transport ATP-binding protein oppF 38 0.009 OPPF_STRP8 (Q8P2L5) Oligopeptide transport ATP-binding protein oppF 38 0.009 Y187_MYCGE (P47433) Hypothetical ABC transporter ATP-binding pro... 38 0.009 P29_MYCPN (P75370) Probable ABC transporter ATP-binding protein p29 38 0.009 PSTB_BACTN (Q8A853) Phosphate import ATP-binding protein pstB (E... 38 0.009 ABD4_HUMAN (O14678) ATP-binding cassette, sub-family D, member 4... 38 0.009 YDIF_BACSU (O05519) Hypothetical ABC transporter ATP-binding pro... 38 0.009 GLTL_ECOLI (P41076) Glutamate/aspartate transport ATP-binding pr... 38 0.009 CCMA_SHIFL (Q83KD5) Cytochrome c biogenesis ATP-binding export p... 38 0.011 YE74_HAEIN (Q57213) Hypothetical ABC transporter ATP-binding pro... 38 0.011 UVRA_AGRT5 (Q8UF86) UvrABC system protein A (UvrA protein) (Exci... 38 0.011 YEJF_ECOLI (P33916) Hypothetical ABC transporter ATP-binding pro... 38 0.011 NODI_RHISN (P55476) Nod factor export ATP-binding protein I (Nod... 38 0.011 PTB1_MYCTU (O53832) Phosphate import ATP-binding protein pstB 1 ... 38 0.011 PSTB_MYCLE (Q50046) Phosphate import ATP-binding protein pstB (E... 38 0.011 EF3B_YEAST (P53978) Elongation factor 3B (EF-3B) 38 0.011 NOCP_AGRT5 (P35116) Nopaline permease ATP-binding protein P 38 0.011 OPPF_STRMU (P72479) Oligopeptide transport ATP-binding protein oppF 38 0.011 YFEB_YERPE (Q56953) Chelated iron transport system membrane prot... 38 0.011 OPAA_BACSU (P46920) Glycine betaine transport ATP-binding protei... 38 0.011 Y124_THEMA (Q9WXX8) Probable metal transport system ATP-binding ... 37 0.015 GLNQ_ECOLI (P10346) Glutamine transport ATP-binding protein glnQ 37 0.015 YHBG_THIFE (P24693) Probable ABC transporter ATP-binding protein... 37 0.015 CCMA_BRAJA (P30963) Cytochrome c biogenesis ATP-binding export p... 37 0.015 Y065_MYCGE (P47311) Hypothetical ABC transporter ATP-binding pro... 37 0.015 Y180_MYCPN (Q50293) Hypothetical ABC transporter ATP-binding pro... 37 0.015 PSTB_SULSO (Q97ZT9) Phosphate import ATP-binding protein pstB (E... 37 0.015 CBIO_METJA (Q58488) Probable cobalt transport ATP-binding protei... 37 0.015 ABD4_MOUSE (O89016) ATP-binding cassette, sub-family D, member 4... 37 0.015 NODI_BRASS (Q9Z3I3) Nod factor export ATP-binding protein I (Nod... 37 0.015 MNTB_BACHD (Q9KD30) Manganese transport system ATP-binding prote... 37 0.015 Y888_HELPY (O05732) Probable iron chelatin transport ATP-binding... 37 0.015 Y888_HELPJ (Q9ZKW3) Probable iron chelatin transport ATP-binding... 37 0.015 YTRE_BACSU (O34392) Hypothetical ABC transporter ATP-binding pro... 37 0.019 MNTA_SYNY3 (Q55281) Manganese transport system ATP-binding prote... 37 0.019 CCMA_CAUCR (Q9A298) Cytochrome c biogenesis ATP-binding export p... 37 0.019 NRTC_SYNP7 (P38045) Nitrate transport ATP-binding protein nrtC 37 0.019 PSTB_METAC (Q8TSA8) Phosphate import ATP-binding protein pstB (E... 37 0.019 >MDR_LEITA (P21441) Multidrug resistance protein (P-glycoprotein) Length = 1548 Score = 160 bits (404), Expect(2) = 3e-44 Identities = 79/114 (69%), Positives = 90/114 (78%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G WA +SIAYV QQ WIMNATLR N+LFF LQ+ +R CQLEADL G+ T Sbjct: 689 GELWAERSIAYVPQQAWIMNATLRGNILFFDEERAEDLQDVIRCCQLEADLAQFCGGLDT 748 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 EIGE G+NLSGGQKARVSLARAVYA+R+VYLLDDPLSALDAHVG+RIV +V+ G Sbjct: 749 EIGEMGVNLSGGQKARVSLARAVYANRDVYLLDDPLSALDAHVGQRIVQDVILG 802 Score = 37.4 bits (85), Expect = 0.015 Identities = 26/102 (25%), Positives = 50/102 (49%), Gaps = 1/102 (0%) Frame = -1 Query: 437 VSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGINLSG 258 + Q P + + T+R+NV F A + A+ + L + + G+ + + E G N S Sbjct: 1366 IPQDPVLFDGTVRQNVDPFLEASSAEVWAALELVGLRERVASESEGIDSRVLEGGSNYSV 1425 Query: 257 GQKARVSLARAVYADREVYLLDDPLSA-LDAHVGERIVTEVL 135 GQ+ + +ARA+ ++L D +A +D + +I V+ Sbjct: 1426 GQRQLMCMARALLKRGSGFILMDEATANIDPALDRQIQATVM 1467 Score = 37.0 bits (84), Expect(2) = 3e-44 Identities = 16/33 (48%), Positives = 24/33 (72%) Frame = -2 Query: 133 LVHLAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 L L KTR+L THQI +L AD++VV++ G++ Sbjct: 801 LGRLRGKTRVLATHQIHLLPLADYIVVLQHGSI 833 >MRP3_RAT (O88563) Canalicular multispecific organic anion transporter 2 (Multidrug resistance-associated protein 3) (MRP-like protein-2) (MLP-2) Length = 1522 Score = 129 bits (323), Expect(2) = 2e-34 Identities = 64/105 (60%), Positives = 78/105 (74%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 S+AYV QQ WI N TL+ENVLF P + R Q+A+ C L ADL VL G TEIGE GI Sbjct: 688 SVAYVPQQAWIQNCTLQENVLFGQPMNPKRYQQALETCALLADLDVLPGGDQTEIGEKGI 747 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 NLSGGQ+ RVSLARAVY+D ++LLDDPLSA+D+HV + I +V+ Sbjct: 748 NLSGGQRQRVSLARAVYSDANIFLLDDPLSAVDSHVAKHIFDQVI 792 Score = 47.0 bits (110), Expect = 2e-05 Identities = 28/99 (28%), Positives = 47/99 (47%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 + + Q P + + TLR N+ F + + + + L A + G+ + E G N Sbjct: 1361 LTIIPQDPILFSGTLRMNLDPFGRYSDEDIWRTLELSHLSAFVSSQPTGLDFQCSEGGDN 1420 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LS GQ+ V LARA+ V +LD+ +A+D + I Sbjct: 1421 LSVGQRQLVCLARALLRKSRVLVLDEATAAIDLETDDLI 1459 Score = 35.4 bits (80), Expect(2) = 2e-34 Identities = 15/30 (50%), Positives = 21/30 (70%) Frame = -2 Query: 124 LAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 LA KTR+LVTH I L + DF++V+ G + Sbjct: 798 LAGKTRVLVTHGISFLPQTDFIIVLADGQI 827 >MRP3_HUMAN (O15438) Canalicular multispecific organic anion transporter 2 (Multidrug resistance-associated protein 3) (Multi-specific organic anion tranporter-D) (MOAT-D) Length = 1527 Score = 124 bits (310), Expect(2) = 3e-33 Identities = 61/105 (58%), Positives = 76/105 (72%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 S+AYV QQ WI N TL+ENVLF + R Q+ + C L ADL +L G TEIGE GI Sbjct: 690 SVAYVPQQAWIQNCTLQENVLFGKALNPKRYQQTLEACALLADLEMLPGGDQTEIGEKGI 749 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 NLSGGQ+ RVSLARAVY+D +++LLDDPLSA+D+HV + I V+ Sbjct: 750 NLSGGQRQRVSLARAVYSDADIFLLDDPLSAVDSHVAKHIFDHVI 794 Score = 47.8 bits (112), Expect = 1e-05 Identities = 28/92 (30%), Positives = 46/92 (50%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 + + Q P + + TLR N+ F E + A+ + L + AG+ + E G N Sbjct: 1366 LTIIPQDPILFSGTLRMNLDPFGSYSEEDIWWALELSHLHTFVSSQPAGLDFQCSEGGEN 1425 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LS GQ+ V LARA+ + +LD+ +A+D Sbjct: 1426 LSVGQRQLVCLARALLRKSRILVLDEATAAID 1457 Score = 36.6 bits (83), Expect(2) = 3e-33 Identities = 17/35 (48%), Positives = 23/35 (65%) Frame = -2 Query: 124 LAQKTRILVTHQIDVLSRADFVVVMEKGAVQLL*P 20 LA KTR+LVTH I L + DF++V+ G V + P Sbjct: 800 LAGKTRVLVTHGISFLPQTDFIIVLADGQVSEMGP 834 >MRP2_MOUSE (Q8VI47) Canalicular multispecific organic anion transporter 1 (ATP-binding cassette, sub-family C, member 2) Length = 1543 Score = 124 bits (312), Expect(2) = 1e-32 Identities = 61/112 (54%), Positives = 76/112 (67%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G+ SIAYV QQ WI N T+++N+LF S DE + Q + C L DL +L G Sbjct: 691 GHITIKGSIAYVPQQAWIQNGTIKDNILFGSEYDEKKYQRVIEACALLPDLEMLPGGDMA 750 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 EIGE GINLSGGQK RVSLARA Y D ++Y+LDDPLSA+D HVG+ I +V+ Sbjct: 751 EIGEKGINLSGGQKHRVSLARATYQDADIYILDDPLSAVDTHVGKHIFNKVV 802 Score = 48.9 bits (115), Expect = 5e-06 Identities = 28/103 (27%), Positives = 52/103 (50%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 + + Q P + + LR N+ F+ + + A+ + L++ + L G+ E+ E G N Sbjct: 1375 LTIIPQDPILFSGNLRMNLDPFNKYSDEEIWRALELAHLKSFVAGLQLGLLHEVTEGGDN 1434 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 LS GQ+ + L RAV ++ +LD+ +A+D I T + Sbjct: 1435 LSIGQRQLLCLGRAVLRKSKILVLDEATAAVDLETDSLIQTTI 1477 Score = 33.5 bits (75), Expect(2) = 1e-32 Identities = 16/30 (53%), Positives = 21/30 (70%) Frame = -2 Query: 124 LAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 L+ KTRILVTH I L + D +VV+ KG + Sbjct: 808 LSGKTRILVTHGIHFLPQVDEIVVLGKGTI 837 >MRP2_RAT (Q63120) Canalicular multispecific organic anion transporter 1 (ATP-binding cassette, sub-family C, member 2) (Multidrug resistance-associated protein 2) (Canalicular multidrug resistance protein) Length = 1541 Score = 124 bits (311), Expect(2) = 2e-32 Identities = 60/112 (53%), Positives = 78/112 (69%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G+ S AYV QQ WI N T+++N+LF S +E + Q+ ++ C L DL +L G Sbjct: 689 GHITIQGSTAYVPQQSWIQNGTIKDNILFGSEYNEKKYQQVLKACALLPDLEILPGGDMA 748 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 EIGE GINLSGGQK RVSLARA Y D ++Y+LDDPLSA+DAHVG+ I +V+ Sbjct: 749 EIGEKGINLSGGQKQRVSLARAAYQDADIYILDDPLSAVDAHVGKHIFNKVV 800 Score = 50.1 bits (118), Expect = 2e-06 Identities = 28/105 (26%), Positives = 54/105 (51%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 + + + Q P + + +LR N+ F+ + + A+ + L + + L G+ +E+ E G Sbjct: 1371 ERLTIIPQDPILFSGSLRMNLDPFNKYSDEEVWRALELAHLRSFVSGLQLGLLSEVTEGG 1430 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 NLS GQ+ + L RAV ++ +LD+ +A+D I T + Sbjct: 1431 DNLSIGQRQLLCLGRAVLRKSKILVLDEATAAVDLETDSLIQTTI 1475 Score = 33.1 bits (74), Expect(2) = 2e-32 Identities = 16/30 (53%), Positives = 20/30 (66%) Frame = -2 Query: 124 LAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 LA KTRI VTH I L + D +VV+ KG + Sbjct: 806 LAGKTRIFVTHGIHFLPQVDEIVVLGKGTI 835 >MRP1_HUMAN (P33527) Multidrug resistance-associated protein 1 Length = 1531 Score = 123 bits (308), Expect(2) = 6e-32 Identities = 60/112 (53%), Positives = 78/112 (69%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G+ S+AYV QQ WI N +LREN+LF +E + ++ C L DL +L +G T Sbjct: 700 GHVAIKGSVAYVPQQAWIQNDSLRENILFGCQLEEPYYRSVIQACALLPDLEILPSGDRT 759 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 EIGE G+NLSGGQK RVSLARAVY++ ++YL DDPLSA+DAHVG+ I V+ Sbjct: 760 EIGEKGVNLSGGQKQRVSLARAVYSNADIYLFDDPLSAVDAHVGKHIFENVI 811 Score = 47.4 bits (111), Expect = 1e-05 Identities = 28/103 (27%), Positives = 52/103 (50%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 I + Q P + + +LR N+ FS + + ++ + L+ + L + E E G N Sbjct: 1370 ITIIPQDPVLFSGSLRMNLDPFSQYSDEEVWTSLELAHLKDFVSALPDKLDHECAEGGEN 1429 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 LS GQ+ V LARA+ ++ +LD+ +A+D + I + + Sbjct: 1430 LSVGQRQLVCLARALLRKTKILVLDEATAAVDLETDDLIQSTI 1472 Score = 32.7 bits (73), Expect(2) = 6e-32 Identities = 14/30 (46%), Positives = 19/30 (63%) Frame = -2 Query: 124 LAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 L KTRILVTH + L + D ++VM G + Sbjct: 817 LKNKTRILVTHSMSYLPQVDVIIVMSGGKI 846 >MRP2_RABIT (Q28689) Canalicular multispecific organic anion transporter 1 (ATP-binding cassette, sub-family C, member 2) (Multidrug resistance-associated protein 2) (Canalicular multidrug resistance protein) (Epithelial basolateral chloride conductance r Length = 1564 Score = 121 bits (304), Expect(2) = 3e-31 Identities = 59/112 (52%), Positives = 76/112 (67%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G+ + AYV QQ WI N T+++N+LF + DE R Q + C L DL +L G Sbjct: 691 GHITIKGTTAYVPQQSWIQNGTIKDNILFGAEFDERRYQRVLEACALLPDLEILPGGDLA 750 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 EIGE GINLSGGQK R+SLARA Y + ++Y+LDDPLSA+DAHVG+ I +VL Sbjct: 751 EIGEKGINLSGGQKQRISLARASYQNSDIYILDDPLSAVDAHVGKHIFNKVL 802 Score = 46.2 bits (108), Expect = 3e-05 Identities = 26/103 (25%), Positives = 52/103 (50%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 + + Q P + + +LR N+ F+ + + A+ + L++ + L G+ E+ E N Sbjct: 1375 LTIIPQDPVLFSGSLRMNLDPFNNYSDEEIWRALELAHLKSFVAGLQHGLSREVSEAEDN 1434 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 LS GQ+ + L RA+ ++ +LD+ +A+D I T + Sbjct: 1435 LSIGQRQLLCLGRALLRKSKILVLDEATAAVDLETDHLIQTTI 1477 Score = 32.0 bits (71), Expect(2) = 3e-31 Identities = 13/27 (48%), Positives = 19/27 (70%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 KTR+LVTH + L + D +VV+E G + Sbjct: 811 KTRLLVTHSLHFLPQVDEIVVVENGTI 837 >MRP2_HUMAN (Q92887) Canalicular multispecific organic anion transporter 1 (ATP-binding cassette, sub-family C, member 2) (Multidrug resistance-associated protein 2) (Canalicular multidrug resistance protein) Length = 1545 Score = 120 bits (301), Expect(2) = 3e-30 Identities = 59/112 (52%), Positives = 77/112 (68%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G+ + AYV QQ WI N T+++N+LF + +E R Q+ + C L DL +L G Sbjct: 693 GHITIKGTTAYVPQQSWIQNGTIKDNILFGTEFNEKRYQQVLEACALLPDLEMLPGGDLA 752 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 EIGE GINLSGGQK R+SLARA Y + ++YLLDDPLSA+DAHVG+ I +VL Sbjct: 753 EIGEKGINLSGGQKQRISLARATYQNLDIYLLDDPLSAVDAHVGKHIFNKVL 804 Score = 50.4 bits (119), Expect = 2e-06 Identities = 34/123 (27%), Positives = 62/123 (50%), Gaps = 3/123 (2%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 + + + Q P + + +LR N+ F+ + + +A+ + L++ + L G+ E+ E G Sbjct: 1375 EKLTIIPQDPILFSGSLRMNLDPFNNYSDEEIWKALELAHLKSFVASLQLGLSHEVTEAG 1434 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG-APCTKDT--HP 102 NLS GQ+ + L RA+ ++ +LD+ +A+D I T + A CT T H Sbjct: 1435 GNLSIGQRQLLCLGRALLRKSKILVLDEATAAVDLETDNLIQTTIQNEFAHCTVITIAHR 1494 Query: 101 CHT 93 HT Sbjct: 1495 LHT 1497 Score = 29.6 bits (65), Expect(2) = 3e-30 Identities = 13/30 (43%), Positives = 19/30 (63%) Frame = -2 Query: 124 LAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 L KTR+LVTH + L + D +VV+ G + Sbjct: 810 LKGKTRLLVTHSMHFLPQVDEIVVLGNGTI 839 >MRP5_HUMAN (O15440) Multidrug resistance-associated protein 5 (Multi-specific organic anion tranporter-C) (MOAT-C) (pABC11) (SMRP) Length = 1437 Score = 124 bits (311), Expect = 9e-29 Identities = 60/107 (56%), Positives = 75/107 (70%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S + AYV+QQ WI+NATLR+N+LF DE R + C L DL +L + TEIGE Sbjct: 622 SGTFAYVAQQAWILNATLRDNILFGKEYDEERYNSVLNSCCLRPDLAILPSSDLTEIGER 681 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G NLSGGQ+ R+SLARA+Y+DR +Y+LDDPLSALDAHVG I + Sbjct: 682 GANLSGGQRQRISLARALYSDRSIYILDDPLSALDAHVGNHIFNSAI 728 Score = 48.9 bits (115), Expect = 5e-06 Identities = 33/130 (25%), Positives = 67/130 (51%), Gaps = 4/130 (3%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G A ++ + Q+P + + T+R N+ F+ E ++ +A+ ++ + L + + Sbjct: 1262 GLADLRSKLSIIPQEPVLFSGTVRSNLDPFNQYTEDQIWDALERTHMKECIAQLPLKLES 1321 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL--FGAPCT 117 E+ ENG N S G++ + +ARA+ ++ +LD+ +A+D + ++ E + A CT Sbjct: 1322 EVMENGDNFSVGERQLLCIARALLRHCKILILDEATAAMDTET-DLLIQETIREAFADCT 1380 Query: 116 KDT--HPCHT 93 T H HT Sbjct: 1381 MLTIAHRLHT 1390 >MRP6_HUMAN (O95255) Multidrug resistance-associated protein 6 (Anthracycline resistance-associated protein) (Multi-specific organic anion tranporter-E) (MOAT-E) Length = 1503 Score = 110 bits (274), Expect(2) = 2e-28 Identities = 53/112 (47%), Positives = 72/112 (64%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G+ ++AYV Q+ W+ N ++ ENV F D L+ + C L+ D+ G+ T Sbjct: 685 GFVSIEGAVAYVPQEAWVQNTSVVENVCFGQELDPPWLERVLEACALQPDVDSFPEGIHT 744 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 IGE G+NLSGGQK R+SLARAVY VYLLDDPL+ALDAHVG+ + +V+ Sbjct: 745 SIGEQGMNLSGGQKQRLSLARAVYRKAAVYLLDDPLAALDAHVGQHVFNQVI 796 Score = 44.3 bits (103), Expect = 1e-04 Identities = 30/113 (26%), Positives = 55/113 (48%), Gaps = 3/113 (2%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 I+ + Q P + +LR N+ + + A+ QL+A + L + + + G + Sbjct: 1342 ISIIPQDPILFPGSLRMNLDLLQEHSDEAIWAALETVQLKALVASLPGQLQYKCADRGED 1401 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG---APCT 117 LS GQK + LARA+ ++ +LD+ +A+D G + + + G A CT Sbjct: 1402 LSVGQKQLLCLARALLRKTQILILDEATAAVDP--GTELQMQAMLGSWFAQCT 1452 Score = 34.3 bits (77), Expect(2) = 2e-28 Identities = 13/26 (50%), Positives = 21/26 (80%) Frame = -2 Query: 112 TRILVTHQIDVLSRADFVVVMEKGAV 35 TRILVTH + +L +AD+++V+ GA+ Sbjct: 806 TRILVTHALHILPQADWIIVLANGAI 831 >MRP5_RAT (Q9QYM0) Multidrug resistance-associated protein 5 Length = 1436 Score = 123 bits (308), Expect = 2e-28 Identities = 60/107 (56%), Positives = 74/107 (69%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S + AYV+QQ WI+NATLR+N+LF DE R + C L DL +L TEIGE Sbjct: 622 SGTFAYVAQQAWILNATLRDNILFGKEFDEERYNSVLNSCCLRPDLAILPNSDLTEIGER 681 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G NLSGGQ+ R+SLARA+Y+DR +Y+LDDPLSALDAHVG I + Sbjct: 682 GANLSGGQRQRISLARALYSDRSIYILDDPLSALDAHVGNHIFNSAI 728 Score = 48.9 bits (115), Expect = 5e-06 Identities = 33/130 (25%), Positives = 66/130 (50%), Gaps = 4/130 (3%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G A + + Q+P + + T+R N+ F+ E ++ +A+ ++ + L + + Sbjct: 1261 GLADLRSKLTIIPQEPVLFSGTVRSNLDPFNQYTEEQIWDALERTHMKECIAQLPLKLES 1320 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL--FGAPCT 117 E+ ENG N S G++ + +ARA+ ++ +LD+ +A+D + ++ E + A CT Sbjct: 1321 EVMENGDNFSVGERQLLCIARALLRHCKILILDEATAAMDTET-DLLIQETIREAFADCT 1379 Query: 116 KDT--HPCHT 93 T H HT Sbjct: 1380 MLTIAHRLHT 1389 >MRP5_MOUSE (Q9R1X5) Multidrug resistance-associated protein 5 (ABC transporter MOAT-C) (SMRP) Length = 1436 Score = 123 bits (308), Expect = 2e-28 Identities = 60/107 (56%), Positives = 74/107 (69%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S + AYV+QQ WI+NATLR+N+LF DE R + C L DL +L TEIGE Sbjct: 622 SGTFAYVAQQAWILNATLRDNILFGKEFDEERYNSVLNSCCLRPDLAILPNSDLTEIGER 681 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G NLSGGQ+ R+SLARA+Y+DR +Y+LDDPLSALDAHVG I + Sbjct: 682 GANLSGGQRQRISLARALYSDRSIYILDDPLSALDAHVGNHIFNSAI 728 Score = 50.1 bits (118), Expect = 2e-06 Identities = 34/130 (26%), Positives = 67/130 (51%), Gaps = 4/130 (3%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G A +A + Q+P + + T+R N+ F+ E ++ +A+ ++ + L + + Sbjct: 1261 GLADLRSKLAIIPQEPVLFSGTVRSNLDPFNQYTEDQIWDALERTHMKECIAQLPLKLES 1320 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL--FGAPCT 117 E+ ENG N S G++ + +ARA+ ++ +LD+ +A+D + ++ E + A CT Sbjct: 1321 EVMENGDNFSVGERQLLCIARALLRHCKILILDEATAAMDTET-DLLIQETIREAFADCT 1379 Query: 116 KDT--HPCHT 93 T H HT Sbjct: 1380 MLTIAHRLHT 1389 >MRP4_HUMAN (O15439) Multidrug resistance-associated protein 4 (MRP/cMOAT-related ABC transporter) (Multi-specific organic anion tranporter-B) (MOAT-B) Length = 1325 Score = 114 bits (285), Expect(2) = 6e-28 Identities = 54/99 (54%), Positives = 72/99 (72%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 IAYVSQQPW+ + TLR N+LF ++ R ++ ++ C L+ DL++L G T IG+ G Sbjct: 475 IAYVSQQPWVFSGTLRSNILFGKKYEKERYEKVIKACALKKDLQLLEDGDLTVIGDRGTT 534 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQKARV+LARAVY D ++YLLDDPLSA+DA V + Sbjct: 535 LSGGQKARVNLARAVYQDADIYLLDDPLSAVDAEVSRHL 573 Score = 56.6 bits (135), Expect = 2e-08 Identities = 29/105 (27%), Positives = 56/105 (53%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 + ++ + Q+P + T+R+N+ F + L A++ QL+ + L M TE+ E+G Sbjct: 1115 KKMSIIPQEPVLFTGTMRKNLDPFKEHTDEELWNALQEVQLKETIEDLPGKMDTELAESG 1174 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 N S GQ+ V LARA+ ++ ++D+ + +D E I ++ Sbjct: 1175 SNFSVGQRQLVCLARAILRKNQILIIDEATANVDPRTDELIQKKI 1219 Score = 28.1 bits (61), Expect(2) = 6e-28 Identities = 12/33 (36%), Positives = 21/33 (63%) Frame = -2 Query: 139 CYLVHLAQKTRILVTHQIDVLSRADFVVVMEKG 41 C ++H +K ILVTHQ+ L A +++++ G Sbjct: 579 CQILH--EKITILVTHQLQYLKAASQILILKDG 609 >YCFI_YEAST (P39109) Metal resistance protein YCF1 (Yeast cadmium factor 1) Length = 1515 Score = 120 bits (302), Expect = 1e-27 Identities = 59/112 (52%), Positives = 77/112 (68%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G+A S+AYVSQ PWIMN T++EN+LF D ++ ++ C L DL +L G T Sbjct: 685 GFATVHGSVAYVSQVPWIMNGTVKENILFGHRYDAEFYEKTIKACALTIDLAILMDGDKT 744 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +GE GI+LSGGQKAR+SLARAVYA + YLLDDPL+A+D HV ++ VL Sbjct: 745 LVGEKGISLSGGQKARLSLARAVYARADTYLLDDPLAAVDEHVARHLIEHVL 796 Score = 43.9 bits (102), Expect = 2e-04 Identities = 27/105 (25%), Positives = 55/105 (52%), Gaps = 1/105 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQL-EADLRVLAAGMGTEIGENGI 270 ++ + Q + T+REN+ + + + A+ + L E L + G+ ++ E G Sbjct: 1349 LSIIPQDSQVFEGTVRENIDPINQYTDEAIWRALELSHLKEHVLSMSNDGLDAQLTEGGG 1408 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 NLS GQ+ + LARA+ ++ +LD+ +A+D +++V E + Sbjct: 1409 NLSVGQRQLLCLARAMLVPSKILVLDEATAAVDVET-DKVVQETI 1452 >YAWB_SCHPO (Q10185) Probable ATP-dependent permease C3F10.11c Length = 1478 Score = 119 bits (298), Expect = 3e-27 Identities = 59/112 (52%), Positives = 78/112 (69%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G + SIAY +QQPWI+NAT++EN+LF D ++ +R C L D +LA G T Sbjct: 653 GSVFRCGSIAYAAQQPWILNATIQENILFGLELDPEFYEKTIRACCLLRDFEILADGDQT 712 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 E+GE GI+LSGGQKAR+SLARAVY+ ++YLLDD LSA+D HV +V +L Sbjct: 713 EVGEKGISLSGGQKARISLARAVYSRSDIYLLDDILSAVDQHVNRDLVRNLL 764 Score = 50.1 bits (118), Expect = 2e-06 Identities = 27/92 (29%), Positives = 48/92 (52%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 +A + Q+ T+REN+ + A + + A+ L+ ++ L G+ + + E G N Sbjct: 1316 LAIIPQENQAFEGTIRENLDPNANATDEEIWHALEAASLKQFIQTLDGGLYSRVTEGGAN 1375 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LS GQ+ + L RA+ V LLD+ +A+D Sbjct: 1376 LSSGQRQLMCLTRALLTPTRVLLLDEATAAVD 1407 >YOR1_YEAST (P53049) Oligomycin resistance ATP-dependent permease YOR1 Length = 1477 Score = 119 bits (298), Expect = 3e-27 Identities = 57/104 (54%), Positives = 77/104 (74%) Frame = -1 Query: 425 PWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGINLSGGQKA 246 PWI NA++R+N++F SP ++ + E VRVC L+ADL +L AG TEIGE GI LSGGQKA Sbjct: 657 PWIQNASVRDNIIFGSPFNKEKYDEVVRVCSLKADLDILPAGDMTEIGERGITLSGGQKA 716 Query: 245 RVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGAPCTK 114 R++LAR+VY +++YL DD LSA+D+ VG+ I+ E L G K Sbjct: 717 RINLARSVYKKKDIYLFDDVLSAVDSRVGKHIMDECLTGMLANK 760 >MRP6_RAT (O88269) Multidrug resistance-associated protein 6 (MRP-like protein-1) (MLP-1) Length = 1502 Score = 109 bits (272), Expect(2) = 3e-27 Identities = 53/105 (50%), Positives = 71/105 (67%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 S+AYV Q+ W+ N ++ ENV F D LQE + C L +D+ AG+ T +GE G+ Sbjct: 690 SVAYVPQEAWVQNTSVVENVCFRQELDLPWLQEVLEACALGSDVASFPAGVHTPVGEQGM 749 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 NLSGGQK R+SLARAVY VYL+DDPL+ALDAHV + + +V+ Sbjct: 750 NLSGGQKQRLSLARAVYRRAAVYLMDDPLAALDAHVSQEVFKQVI 794 Score = 41.2 bits (95), Expect = 0.001 Identities = 25/92 (27%), Positives = 45/92 (48%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 I + Q P + +LR N+ + + A+ QL+A + L + E G + Sbjct: 1341 ITIIPQDPVLFPGSLRMNLDLLQENTDEGIWAALETVQLKAFVTSLPGQLQYECSGQGDD 1400 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LS GQK + LARA+ ++ +LD+ +++D Sbjct: 1401 LSVGQKQLLCLARALLRKTQILILDEATASVD 1432 Score = 30.8 bits (68), Expect(2) = 3e-27 Identities = 13/26 (50%), Positives = 19/26 (73%) Frame = -2 Query: 112 TRILVTHQIDVLSRADFVVVMEKGAV 35 TRILVTH + VL +AD ++V+ G + Sbjct: 804 TRILVTHTLHVLPQADQILVLANGTI 829 >BPT1_YEAST (P14772) Bile pigment transporter 1 Length = 1559 Score = 117 bits (294), Expect = 9e-27 Identities = 59/109 (54%), Positives = 78/109 (71%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S S+AY SQ+ WIMNA++REN+LF D+ ++ CQL DL++L G T +GE Sbjct: 707 SSSVAYCSQESWIMNASVRENILFGHKFDQDYYDLTIKACQLLPDLKILPDGDETLVGEK 766 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 GI+LSGGQKAR+SLARAVY+ ++YLLDD LSA+DA V + I+ VL G Sbjct: 767 GISLSGGQKARLSLARAVYSRADIYLLDDILSAVDAEVSKNIIEYVLIG 815 Score = 37.7 bits (86), Expect = 0.011 Identities = 28/121 (23%), Positives = 54/121 (44%), Gaps = 17/121 (14%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAG----------- 300 +A + Q T++ N+ F+ E L+ AV L+ L + Sbjct: 1379 LAIIPQDAQAFEGTVKTNLDPFNRYSEDELKRAVEQAHLKPHLEKMLHSKPRGDDSNEED 1438 Query: 299 ------MGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 + +I ENG NLS GQ+ + LARA+ ++ +LD+ +++D ++I+ + Sbjct: 1439 GNVNDILDVKINENGSNLSVGQRQLLCLARALLNRSKILVLDEATASVDMET-DKIIQDT 1497 Query: 137 L 135 + Sbjct: 1498 I 1498 >YH85_SCHPO (Q9P5N0) Probable ATP-dependent permease C359.05 Length = 1465 Score = 112 bits (279), Expect = 5e-25 Identities = 54/122 (44%), Positives = 78/122 (63%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G + S+AY +QQPWI +AT+REN+LF S D ++ + C L+ D + G T Sbjct: 636 GSVFQCGSLAYAAQQPWIFDATIRENILFGSEFDPELYEKTIHACCLKRDFEIFTEGDQT 695 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGAPCTKD 111 E+G+ G +LSGGQK+R+SLARA+Y+ ++YLLDD LS++D HV ++ LFG Sbjct: 696 EVGQKGASLSGGQKSRISLARAIYSQADIYLLDDVLSSVDQHVSRDLIKN-LFGPEGFLR 754 Query: 110 TH 105 TH Sbjct: 755 TH 756 Score = 43.9 bits (102), Expect = 2e-04 Identities = 22/93 (23%), Positives = 46/93 (49%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 ++ + Q+ I +REN+ + ++ E + + L+ + L G+ + + E G N Sbjct: 1303 LSIIPQESQIFEGNIRENLDPNHRLTDKKIWEVLEIASLKNCISQLEDGLYSRVAEGGAN 1362 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDA 168 S GQ+ + LAR + + LLD+ +++ A Sbjct: 1363 FSSGQRQLICLARVLLTSTRILLLDEATASVHA 1395 >ACC8_HUMAN (Q09428) Sulfonylurea receptor 1 Length = 1580 Score = 110 bits (275), Expect = 1e-24 Identities = 48/100 (48%), Positives = 71/100 (71%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 +AY SQ+PW++NAT+ EN++F SP ++ R + + C L+ D+ +L G T+IGE GIN Sbjct: 768 VAYASQKPWLLNATVEENIIFESPFNKQRYKMVIEACSLQPDIDILPHGDQTQIGERGIN 827 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 LSGGQ+ R+S+ARA+Y V LDDP SALD H+ + ++ Sbjct: 828 LSGGQRQRISVARALYQHANVVFLDDPFSALDIHLSDHLM 867 Score = 48.9 bits (115), Expect(2) = 5e-09 Identities = 29/107 (27%), Positives = 55/107 (51%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 ++ + Q P + + T+R N+ + L EA+ + QL+ ++ L G+ I E G N Sbjct: 1420 LSIILQDPVLFSGTIRFNLDPERKCSDSTLWEALEIAQLKLVVKALPGGLDAIITEGGEN 1479 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGA 126 S GQ+ LARA ++++D+ +++D E I+ +V+ A Sbjct: 1480 FSQGQRQLFCLARAFVRKTSIFIMDEATASIDM-ATENILQKVVMTA 1525 Score = 29.6 bits (65), Expect(2) = 5e-09 Identities = 10/36 (27%), Positives = 22/36 (61%) Frame = -2 Query: 142 KCYLVHLAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 K + A +T + + H++ + AD V+V+++GA+ Sbjct: 1520 KVVMTAFADRTVVTIAHRVHTILSADLVIVLKRGAI 1555 >ACC8_CRICR (Q09427) Sulfonylurea receptor 1 Length = 1581 Score = 110 bits (274), Expect = 2e-24 Identities = 48/100 (48%), Positives = 70/100 (70%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 +AY SQ+PW++NAT+ EN+ F SP ++ R + + C L+ D+ +L G T+IGE GIN Sbjct: 769 VAYASQKPWLLNATVEENITFESPFNKQRYKMVIEACSLQPDIDILPHGDQTQIGERGIN 828 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 LSGGQ+ R+S+ARA+Y V LDDP SALD H+ + ++ Sbjct: 829 LSGGQRQRISVARALYQQTNVVFLDDPFSALDVHLSDHLM 868 Score = 49.3 bits (116), Expect(2) = 6e-09 Identities = 29/107 (27%), Positives = 55/107 (51%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 ++ + Q P + + T+R N+ + L EA+ + QL+ ++ L G+ I E G N Sbjct: 1421 LSIILQDPVLFSGTIRFNLDPEKKCSDSTLWEALEIAQLKLVVKALPGGLDAIITEGGEN 1480 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGA 126 S GQ+ LARA ++++D+ +++D E I+ +V+ A Sbjct: 1481 FSQGQRQLFCLARAFVRKTSIFIMDEATASIDM-ATENILQKVVMTA 1526 Score = 28.9 bits (63), Expect(2) = 6e-09 Identities = 10/36 (27%), Positives = 22/36 (61%) Frame = -2 Query: 142 KCYLVHLAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 K + A +T + + H++ + AD V+V+++GA+ Sbjct: 1521 KVVMTAFADRTVVTIAHRVHTILSADLVMVLKRGAI 1556 >ACC8_RAT (Q09429) Sulfonylurea receptor 1 Length = 1581 Score = 109 bits (273), Expect = 2e-24 Identities = 48/100 (48%), Positives = 70/100 (70%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 +AY SQ+PW++NAT+ EN+ F SP ++ R + + C L+ D+ +L G T+IGE GIN Sbjct: 769 VAYASQKPWLLNATVEENITFESPFNKQRYKMVIEACSLQPDIDILPHGDQTQIGERGIN 828 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 LSGGQ+ R+S+ARA+Y V LDDP SALD H+ + ++ Sbjct: 829 LSGGQRQRISVARALYQHTNVVFLDDPFSALDVHLSDHLM 868 Score = 49.3 bits (116), Expect(2) = 6e-09 Identities = 29/107 (27%), Positives = 55/107 (51%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 ++ + Q P + + T+R N+ + L EA+ + QL+ ++ L G+ I E G N Sbjct: 1421 LSIILQDPVLFSGTIRFNLDPEKKCSDSTLWEALEIAQLKLVVKALPGGLDAIITEGGEN 1480 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGA 126 S GQ+ LARA ++++D+ +++D E I+ +V+ A Sbjct: 1481 FSQGQRQLFCLARAFVRKTSIFIMDEATASIDM-ATENILQKVVMTA 1526 Score = 28.9 bits (63), Expect(2) = 6e-09 Identities = 10/36 (27%), Positives = 22/36 (61%) Frame = -2 Query: 142 KCYLVHLAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 K + A +T + + H++ + AD V+V+++GA+ Sbjct: 1521 KVVMTAFADRTVVTIAHRVHTILSADLVMVLKRGAI 1556 >CFTR_MOUSE (P26361) Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) Length = 1476 Score = 98.6 bits (244), Expect(2) = 4e-24 Identities = 46/102 (45%), Positives = 66/102 (64%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S +++ SQ WIM T++EN++F DE+R + V+ CQL+ D+ A T +GE Sbjct: 485 SGRVSFCSQFSWIMPGTIKENIIFGVSYDEYRYKSVVKACQLQQDITKFAEQDNTVLGEG 544 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 G+ LSGGQ+AR+SLARAVY D ++YLLD P LD E++ Sbjct: 545 GVTLSGGQRARISLARAVYKDADLYLLDSPFGYLDVFTEEQV 586 Score = 36.2 bits (82), Expect = 0.033 Identities = 27/110 (24%), Positives = 54/110 (49%), Gaps = 10/110 (9%) Frame = -1 Query: 470 GYAWAS-------QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQ---LEAD 321 G +W S ++ ++Q+ +I + T R+N+ P + + +E +V L++ Sbjct: 1267 GVSWNSVTLQEWRKAFGVITQKVFIFSGTFRQNL---DPNGKWKDEEIWKVADEVGLKSV 1323 Query: 320 LRVLAAGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + + + + G LS G K + LAR+V + ++ LLD+P + LD Sbjct: 1324 IEQFPGQLNFTLVDGGYVLSHGHKQLMCLARSVLSKAKIILLDEPSAHLD 1373 Score = 31.2 bits (69), Expect(2) = 4e-24 Identities = 13/34 (38%), Positives = 24/34 (70%) Frame = -2 Query: 139 CYLVHLAQKTRILVTHQIDVLSRADFVVVMEKGA 38 C +A KTRILVT +++ L +AD ++++ +G+ Sbjct: 590 CVCKLMANKTRILVTSKMEHLRKADKILILHQGS 623 >CFTR_RAT (P34158) Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (Fragments) Length = 524 Score = 97.8 bits (242), Expect(2) = 4e-24 Identities = 47/102 (46%), Positives = 66/102 (64%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S +++ SQ WIM T++EN++F DE+R + V+ CQL+ D+ A T +GE Sbjct: 21 SGRVSFSSQISWIMPGTIKENIIFGVSYDEYRYKSVVKACQLQEDITKFAEQDNTVLGEG 80 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 G+ LSGGQ+AR+SLARAVY D ++YLLD P LD E+I Sbjct: 81 GVTLSGGQRARISLARAVYKDADLYLLDSPFGYLDVLTEEQI 122 Score = 32.0 bits (71), Expect(2) = 4e-24 Identities = 13/34 (38%), Positives = 24/34 (70%) Frame = -2 Query: 139 CYLVHLAQKTRILVTHQIDVLSRADFVVVMEKGA 38 C +A KTRILVT +++ L +AD ++++ +G+ Sbjct: 126 CVCKLMASKTRILVTSKMEQLKKADKILILHEGS 159 >L259_DROME (P91660) Probable multidrug resistance-associated protein lethal(2)03659 (Wunen region A protein) Length = 1290 Score = 108 bits (270), Expect = 5e-24 Identities = 52/114 (45%), Positives = 72/114 (63%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 G + S++Y SQ+ W+ + T+R+N+LF P D R +E V+ C LE D +L T Sbjct: 473 GQLQVNGSLSYTSQESWLFSGTVRQNILFGQPMDSQRYEEVVKKCALERDFDLLPLRDNT 532 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 +GE G LSGGQKAR+SLAR+VY +YLLDDPLSA+DA V + + + G Sbjct: 533 IVGERGATLSGGQKARISLARSVYRKASIYLLDDPLSAVDASVARHLFDQCVRG 586 Score = 49.3 bits (116), Expect = 4e-06 Identities = 25/94 (26%), Positives = 51/94 (54%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 + I+ + Q+P + + T+R N+ F + +L + +L+ + L G+ ++I E G Sbjct: 1110 RQISIIPQEPVLFSGTMRYNLDPFDEYSDEKLWGCLEEVKLKEVVSDLPDGLASKISEGG 1169 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 N S GQ+ V LARA+ + + ++D+ + +D Sbjct: 1170 TNFSVGQRQLVCLARAILRENRILVMDEATANVD 1203 >ACC9_HUMAN (O60706) Sulfonylurea receptor 2 Length = 1549 Score = 108 bits (270), Expect = 5e-24 Identities = 48/103 (46%), Positives = 71/103 (68%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 S+AY +Q+PW++NAT+ EN+ F SP ++ R + C L+ D+ +L G TEIGE GI Sbjct: 751 SVAYAAQKPWLLNATVEENITFGSPFNKQRYKAVTDACSLQPDIDLLPFGDQTEIGERGI 810 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTE 141 NLSGGQ+ R+ +ARA+Y + + LDDP SALD H+ + ++ E Sbjct: 811 NLSGGQRQRICVARALYQNTNIVFLDDPFSALDIHLSDHLMQE 853 Score = 46.2 bits (108), Expect = 3e-05 Identities = 28/107 (26%), Positives = 55/107 (51%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 ++ + Q P + + ++R N+ + RL EA+ + QL+ ++ L G+ + E G N Sbjct: 1389 LSIILQDPILFSGSIRFNLDPECKCTDDRLWEALEIAQLKNMVKSLPGGLDAVVTEGGEN 1448 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGA 126 S GQ+ LARA + ++D+ +++D E I+ +V+ A Sbjct: 1449 FSVGQRQLFCLARAFVRKSSILIMDEATASIDM-ATENILQKVVMTA 1494 >ACC9_MOUSE (P70170) Sulfonylurea receptor 2 Length = 1546 Score = 108 bits (269), Expect = 7e-24 Identities = 48/103 (46%), Positives = 70/103 (67%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 S+AY +Q+PW++NAT+ EN+ F SP + R + C L+ D+ +L G TEIGE GI Sbjct: 748 SVAYAAQKPWLLNATVEENITFGSPFNRQRYKAVTDACSLQPDIDLLPFGDQTEIGERGI 807 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTE 141 NLSGGQ+ R+ +ARA+Y + + LDDP SALD H+ + ++ E Sbjct: 808 NLSGGQRQRICVARALYQNTNIVFLDDPFSALDIHLSDHLMQE 850 Score = 46.6 bits (109), Expect = 2e-05 Identities = 28/107 (26%), Positives = 55/107 (51%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 ++ + Q P + + ++R N+ + RL EA+ + QL+ ++ L G+ + E G N Sbjct: 1386 LSIILQDPILFSGSIRFNLDPECKCTDDRLWEALEIAQLKNMVKSLPGGLDATVTEGGEN 1445 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGA 126 S GQ+ LARA + ++D+ +++D E I+ +V+ A Sbjct: 1446 FSVGQRQLFCLARAFVRKSSILIMDEATASIDM-ATENILQKVVMTA 1491 >CFTR_BOVIN (P35071) Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) Length = 1481 Score = 95.5 bits (236), Expect(2) = 8e-24 Identities = 45/95 (47%), Positives = 62/95 (65%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S I++ SQ WIM T+++N++F DE+R + ++ CQLE D+ A +GE Sbjct: 484 SGRISFCSQYSWIMPGTIKDNIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNVVLGEG 543 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GI LSGGQ+AR+SLARAVY D ++YLLD P LD Sbjct: 544 GITLSGGQRARISLARAVYKDADLYLLDSPFGYLD 578 Score = 37.0 bits (84), Expect = 0.019 Identities = 25/107 (23%), Positives = 49/107 (45%), Gaps = 7/107 (6%) Frame = -1 Query: 470 GYAWAS-------QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRV 312 G +W S ++ + Q+ +I + T R+N+ + + + + L A + Sbjct: 1272 GVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLDPYGQWSDQEIWKVADEVGLRAVIEQ 1331 Query: 311 LAAGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + + + G LS G K + LAR+V + ++ LLD+P + LD Sbjct: 1332 FPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLD 1378 Score = 33.1 bits (74), Expect(2) = 8e-24 Identities = 15/46 (32%), Positives = 28/46 (60%) Frame = -2 Query: 139 CYLVHLAQKTRILVTHQIDVLSRADFVVVMEKGAVQLL*PLGYLQH 2 C +A KTRILVT +++ L +AD ++++ +G++ LQ+ Sbjct: 589 CICKLMANKTRILVTSKMEHLKKADKILILHEGSIYFYGTFSELQN 634 >ACC9_RABIT (P82451) Sulfonylurea receptor 2 Length = 1549 Score = 107 bits (267), Expect = 1e-23 Identities = 48/103 (46%), Positives = 70/103 (67%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 S+AY +Q+PW++NAT+ EN+ F SP ++ R + C L+ D+ +L G TEIGE GI Sbjct: 751 SVAYAAQKPWLLNATVEENITFGSPFNKQRYKAVTDACSLQPDIDLLPFGDQTEIGERGI 810 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTE 141 NLSGGQ R+ +ARA+Y + + LDDP SALD H+ + ++ E Sbjct: 811 NLSGGQTERICVARALYQNTNIVFLDDPFSALDIHLSDHLMQE 853 Score = 47.0 bits (110), Expect = 2e-05 Identities = 28/107 (26%), Positives = 56/107 (52%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 ++ + Q P + + ++R N+ + RL EA+ + QL+ ++ L+ G+ + E G N Sbjct: 1389 LSIILQDPILFSGSIRFNLDPECKCTDDRLWEALEIAQLKNMVKSLSGGLDAVVTEGGEN 1448 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGA 126 S GQ+ LARA + ++D+ +++D E I+ +V+ A Sbjct: 1449 FSVGQRQLFCLARAFVRKSSILIMDEATASIDM-ATENILQKVVMTA 1494 >CFTR_SHEEP (Q00555) Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) Length = 1481 Score = 94.0 bits (232), Expect(2) = 2e-23 Identities = 44/95 (46%), Positives = 62/95 (65%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S I++ SQ WIM T+++N++F DE+R + ++ CQLE D+ + +GE Sbjct: 484 SGRISFCSQYSWIMPGTIKDNIIFGVSYDEYRYRSVIKACQLEEDISKFSEKDNIVLGEG 543 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GI LSGGQ+AR+SLARAVY D ++YLLD P LD Sbjct: 544 GITLSGGQRARISLARAVYKDADLYLLDSPFGYLD 578 Score = 35.8 bits (81), Expect = 0.043 Identities = 24/107 (22%), Positives = 49/107 (45%), Gaps = 7/107 (6%) Frame = -1 Query: 470 GYAWAS-------QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRV 312 G +W S ++ + Q+ +I + T R+N+ + + + + L + + Sbjct: 1272 GVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLDPYEQWSDQEIWKVADEVGLRSVIEQ 1331 Query: 311 LAAGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + + + G LS G K + LAR+V + ++ LLD+P + LD Sbjct: 1332 FPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLD 1378 Score = 33.5 bits (75), Expect(2) = 2e-23 Identities = 16/46 (34%), Positives = 28/46 (60%) Frame = -2 Query: 139 CYLVHLAQKTRILVTHQIDVLSRADFVVVMEKGAVQLL*PLGYLQH 2 C +A KTRILVT +++ L +AD ++++ +G+V LQ+ Sbjct: 589 CVCKLMANKTRILVTSKMEHLKKADKILILHEGSVYFYGTFSELQN 634 >CFTR_HUMAN (P13569) Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) Length = 1480 Score = 95.5 bits (236), Expect(2) = 2e-23 Identities = 46/95 (48%), Positives = 62/95 (65%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S I++ SQ WIM T++EN++F DE+R + ++ CQLE D+ A +GE Sbjct: 485 SGRISFCSQFSWIMPGTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIVLGEG 544 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GI LSGGQ+AR+SLARAVY D ++YLLD P LD Sbjct: 545 GITLSGGQRARISLARAVYKDADLYLLDSPFGYLD 579 Score = 35.8 bits (81), Expect = 0.043 Identities = 24/107 (22%), Positives = 49/107 (45%), Gaps = 7/107 (6%) Frame = -1 Query: 470 GYAWAS-------QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRV 312 G +W S ++ + Q+ +I + T R+N+ + + + + L + + Sbjct: 1271 GVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLDPYEQWSDQEIWKVADEVGLRSVIEQ 1330 Query: 311 LAAGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + + + G LS G K + LAR+V + ++ LLD+P + LD Sbjct: 1331 FPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLD 1377 Score = 31.6 bits (70), Expect(2) = 2e-23 Identities = 13/34 (38%), Positives = 24/34 (70%) Frame = -2 Query: 139 CYLVHLAQKTRILVTHQIDVLSRADFVVVMEKGA 38 C +A KTRILVT +++ L +AD ++++ +G+ Sbjct: 590 CVCKLMANKTRILVTSKMEHLKKADKILILHEGS 623 >CFTR_RABIT (Q00554) Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) Length = 1450 Score = 96.3 bits (238), Expect(2) = 2e-23 Identities = 46/95 (48%), Positives = 62/95 (65%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S I++ SQ WIM T++EN++F DE+R + ++ CQLE D+ T +GE Sbjct: 455 SGRISFCSQFSWIMPGTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFTEKDNTVLGEG 514 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GI LSGGQ+AR+SLARAVY D ++YLLD P LD Sbjct: 515 GITLSGGQRARISLARAVYKDADLYLLDSPFGYLD 549 Score = 35.8 bits (81), Expect = 0.043 Identities = 24/107 (22%), Positives = 49/107 (45%), Gaps = 7/107 (6%) Frame = -1 Query: 470 GYAWAS-------QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRV 312 G +W S ++ + Q+ +I + T R+N+ + + + + L + + Sbjct: 1241 GVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLDPYEQWSDQEIWKVADEVGLRSVIEQ 1300 Query: 311 LAAGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + + + G LS G K + LAR+V + ++ LLD+P + LD Sbjct: 1301 FPGKLDFVLVDGGYVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLD 1347 Score = 30.8 bits (68), Expect(2) = 2e-23 Identities = 12/34 (35%), Positives = 24/34 (70%) Frame = -2 Query: 139 CYLVHLAQKTRILVTHQIDVLSRADFVVVMEKGA 38 C +A KTRI+VT +++ L +AD ++++ +G+ Sbjct: 560 CVCKLMANKTRIMVTSKMEHLKKADKILILHEGS 593 >YBT1_YEAST (P32386) ATP-dependent bile acid permease Length = 1661 Score = 106 bits (264), Expect = 3e-23 Identities = 55/109 (50%), Positives = 71/109 (65%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 + SIAY SQ W++N T++ N+LF SP +E R + V C L+ D +L AG TEIGE Sbjct: 772 TNSIAYCSQAAWLLNDTVKNNILFNSPFNEARYKAVVEACGLKRDFEILKAGDLTEIGEK 831 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 GI LSGGQK RVSLARA+Y++ LLDD LSA+D+H I + G Sbjct: 832 GITLSGGQKQRVSLARALYSNARHVLLDDCLSAVDSHTASWIYDNCITG 880 Score = 38.9 bits (89), Expect = 0.005 Identities = 25/115 (21%), Positives = 54/115 (46%), Gaps = 21/115 (18%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAG--------- 300 +SI + Q P + + T++ N+ + + ++ EA++ L ++ ++ Sbjct: 1456 RSITIIPQDPTLFSGTIKTNLDPYDEFSDRQIFEALKRVNLISEEQLQQGATRETSNEAS 1515 Query: 299 ------------MGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + +EI E G NLS GQ+ + LAR++ ++ LLD+ +++D Sbjct: 1516 STNSENVNKFLDLSSEISEGGSNLSQGQRQLMCLARSLLRSPKIILLDEATASID 1570 >CFTR_SQUAC (P26362) Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) Length = 1492 Score = 96.7 bits (239), Expect(2) = 5e-23 Identities = 47/95 (49%), Positives = 62/95 (65%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S I+Y Q PWIM T+++N++F DE+R V CQLE D+ V T +G+ Sbjct: 486 SGRISYSPQVPWIMPGTIKDNIIFGLSYDEYRYTSVVNACQLEEDITVFPNKDKTVLGDG 545 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GI LSGGQ+AR+SLARA+Y D ++YLLD P S LD Sbjct: 546 GITLSGGQRARISLARALYKDADLYLLDSPFSHLD 580 Score = 37.7 bits (86), Expect = 0.011 Identities = 23/107 (21%), Positives = 50/107 (46%), Gaps = 7/107 (6%) Frame = -1 Query: 470 GYAWASQSI-------AYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRV 312 G +W S S+ + Q+ ++ + T R+N+ + + + + L++ + Sbjct: 1281 GISWNSVSLQKWRKAFGVIPQKVFVFSGTFRKNLDPYEQWSDEEIWKVTEEVGLKSMIEQ 1340 Query: 311 LAAGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + + + G LS G K + LAR++ + ++ LLD+P + LD Sbjct: 1341 FPDKLNFVLVDGGYILSNGHKQLMCLARSILSKAKILLLDEPTAHLD 1387 Score = 29.3 bits (64), Expect(2) = 5e-23 Identities = 12/33 (36%), Positives = 22/33 (66%) Frame = -2 Query: 139 CYLVHLAQKTRILVTHQIDVLSRADFVVVMEKG 41 C + KTRILVT +++ L +AD ++++ +G Sbjct: 591 CLCKLMVNKTRILVTSKLEHLKKADKILLLHEG 623 >ACC9_RAT (Q63563) Sulfonylurea receptor 2 Length = 1545 Score = 105 bits (261), Expect = 6e-23 Identities = 47/103 (45%), Positives = 69/103 (66%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 S+AY +Q+PW++NAT+ EN+ F S + R + C L+ D+ +L G TEIGE GI Sbjct: 747 SVAYAAQKPWLLNATVEENITFGSSFNRQRYKAVTDACSLQPDIDLLPFGDQTEIGERGI 806 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTE 141 NLSGGQ+ R+ +ARA+Y + + LDDP SALD H+ + ++ E Sbjct: 807 NLSGGQRQRICVARALYQNTNIVFLDDPFSALDIHLSDHLMQE 849 Score = 46.6 bits (109), Expect = 2e-05 Identities = 28/107 (26%), Positives = 55/107 (51%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 ++ + Q P + + ++R N+ + RL EA+ + QL+ ++ L G+ + E G N Sbjct: 1385 LSIILQDPILFSGSIRFNLDPECKCTDDRLWEALEIAQLKNMVKSLPGGLDATVTEGGEN 1444 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGA 126 S GQ+ LARA + ++D+ +++D E I+ +V+ A Sbjct: 1445 FSVGQRQLFCLARAFVRKSSILIMDEATASIDM-ATENILQKVVMTA 1490 >ABC1_SCHPO (Q92337) ATP-binding cassette transporter abc1 Length = 1427 Score = 100 bits (250), Expect = 1e-21 Identities = 51/102 (50%), Positives = 66/102 (64%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 SQ IAYV Q W+ N T+R N+LF P DE R + ++ C L++DL + G T I N Sbjct: 644 SQRIAYVPQAAWLRNGTIRSNILFGEPYDEERYFQIIKACCLDSDLNSMNDGDLTYIHSN 703 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 G +LSGGQK RVSLARA+Y++ EVY+ DD SALD +I Sbjct: 704 GSSLSGGQKQRVSLARALYSNAEVYIFDDIFSALDVSTSRKI 745 Score = 48.1 bits (113), Expect = 8e-06 Identities = 28/109 (25%), Positives = 52/109 (47%), Gaps = 8/109 (7%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEA--------DLRVLAAGM 297 Q I+ + Q P +++ T+R N+ F + L E ++ E+ L A + Sbjct: 1255 QRISLIPQDPVLISGTVRSNLDPFEEYGDGELNEILKTASCESLVQASNKNSLDAFAIHL 1314 Query: 296 GTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 T + G+N S GQ+ ++LARA+ + +LD+ +++D RI Sbjct: 1315 DTPVDSGGVNFSSGQRQILALARALVRKSRIVILDESTASVDDTTDRRI 1363 >YHD5_YEAST (P38735) Probable ATP-dependent permease YHL035C Length = 1592 Score = 100 bits (248), Expect = 2e-21 Identities = 51/109 (46%), Positives = 70/109 (64%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 + S AY SQ W++N T++ N++F + +E R + + C L+ DL +L AG TEIGE Sbjct: 745 TNSFAYCSQSAWLLNDTVKNNIIFDNFYNEDRYNKVIDACGLKRDLEILPAGDLTEIGEK 804 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 GI LSGGQK R+SLARAVY+ + LLDD LSA+D+H I + G Sbjct: 805 GITLSGGQKQRISLARAVYSSAKHVLLDDCLSAVDSHTAVWIYENCITG 853 Score = 42.4 bits (98), Expect = 5e-04 Identities = 29/109 (26%), Positives = 55/109 (50%), Gaps = 15/109 (13%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLR---VLAA------- 303 +SI + Q P + T++ NV + DE ++ +A+ L + VL + Sbjct: 1398 RSITIIPQDPILFAGTIKSNVDPYDEYDEKKIFKALSQVNLISSHEFEEVLNSEERFNST 1457 Query: 302 -----GMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + TEI E G+NLS G++ + +AR++ + ++ LLD+ S++D Sbjct: 1458 HNKFLNLHTEIAEGGLNLSQGERQLLFIARSLLREPKIILLDEATSSID 1506 >YK83_YEAST (P36028) Probable ATP-dependent permease YKR103W/YKR104W Length = 1558 Score = 93.6 bits (231), Expect = 2e-19 Identities = 41/109 (37%), Positives = 72/109 (66%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 + S+AY SQ PW+++ T+++NV+F ++ + + ++ C L+ D++ + AG+ T++G+ Sbjct: 729 TNSMAYCSQTPWLISGTIKDNVVFGEIFNKQKFDDVMKSCCLDKDIKAMTAGIRTDVGDG 788 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 G +LSGGQ+ R++LARA+Y+ +LDD LSA+D I E L G Sbjct: 789 GFSLSGGQQQRIALARAIYSSSRYLILDDCLSAVDPETALYIYEECLCG 837 Score = 35.4 bits (80), Expect = 0.056 Identities = 27/115 (23%), Positives = 50/115 (43%), Gaps = 22/115 (19%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHR-------------LQEAVRVCQL------- 330 SI+ + Q P + + T+R N+ P D + ++E +C + Sbjct: 1361 SISCIPQDPTLFDGTVRSNL---DPFDRYSDVQIYGVLSKVGLIEECDELCLIFEQEQPN 1417 Query: 329 --EADLRVLAAGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LR + T + G NLS GQ+ + LAR++ R + L+D+ +++D Sbjct: 1418 FSSHKLRNRFIDLNTVVKSGGSNLSQGQRQLLCLARSMLGARNIMLIDEATASID 1472 >CFTR_XENLA (P26363) Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) Length = 1485 Score = 93.2 bits (230), Expect = 2e-19 Identities = 46/102 (45%), Positives = 63/102 (61%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 S I++ Q WIM T++EN++F D++R ++ CQLE D+ T +GE Sbjct: 486 SGRISFSPQVSWIMPGTIKENIVFGVSYDQYRYLSVIKACQLEEDISKFPEKDNTVLGEG 545 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 GI LSGGQ+AR+SLARAVY D ++YLLD P S LD + I Sbjct: 546 GITLSGGQRARISLARAVYKDADLYLLDSPFSYLDLFTEKEI 587 Score = 35.8 bits (81), Expect = 0.043 Identities = 22/94 (23%), Positives = 46/94 (48%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 ++ + Q+ +I + ++R+N+ + + L + L+ + + + + G Sbjct: 1287 KAFGVIPQKVFIFSGSIRKNLDPYGKWSDEELLKVTEEVGLKLIIDQFPGQLDFVLLDGG 1346 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LS G K V LAR+V + ++ LLD+P + LD Sbjct: 1347 CVLSHGHKQLVCLARSVLSKAKILLLDEPSAHLD 1380 >HEPA_ANASP (P22638) Heterocyst differentiation ATP-binding protein hepA Length = 607 Score = 74.7 bits (182), Expect(2) = 2e-16 Identities = 38/105 (36%), Positives = 66/105 (62%), Gaps = 1/105 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF-FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 + +A VSQ +I N ++R+N+ + S A E ++E R+ + + G T++G+ Sbjct: 438 RKMAVVSQDTFIFNTSIRDNIAYGTSGASEAEIREVARLANALQFIEEMPEGFDTKLGDR 497 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTE 141 G+ LSGGQ+ R+++ARA+ D E+ +LD+ SALD+ V ER++ E Sbjct: 498 GVRLSGGQRQRIAIARALLRDPEILILDEATSALDS-VSERLIQE 541 Score = 29.3 bits (64), Expect(2) = 2e-16 Identities = 11/27 (40%), Positives = 20/27 (74%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +T I + H++ +++AD VVVME+G + Sbjct: 550 RTVIAIAHRLSTIAKADKVVVMEQGRI 576 >PEDD_PEDAC (P36497) Pediocin PA-1 transport/processing ATP-binding protein pedD (EC 3.4.22.-) (Pediocin AcH transport ATP-binding protein papD) Length = 724 Score = 72.8 bits (177), Expect(2) = 5e-16 Identities = 38/109 (34%), Positives = 65/109 (59%), Gaps = 2/109 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSP--ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 Q I YV Q+P+I + ++ EN+L S + + +A +++ D+ L G T + E Sbjct: 562 QYINYVPQEPFIFSGSVLENLLLGSRPGVTQQMIDQACSFAEIKTDIENLPQGYHTRLSE 621 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLF 132 +G NLSGGQK R+S+ARA+ + + ++ D+ S LD +IV+++LF Sbjct: 622 SGFNLSGGQKQRLSIARALLSPAQCFIFDESTSNLDTITEHKIVSKLLF 670 Score = 29.6 bits (65), Expect(2) = 5e-16 Identities = 12/33 (36%), Positives = 22/33 (66%) Frame = -2 Query: 133 LVHLAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 L+ + KT I V H++++ S+ D VVV++ G + Sbjct: 668 LLFMKDKTIIFVAHRLNIASQTDKVVVLDHGKI 700 >MESD_LEUME (Q10418) Mesentericin Y105 transport/processing ATP-binding protein mesD (EC 3.4.22.-) Length = 722 Score = 71.6 bits (174), Expect(2) = 2e-15 Identities = 36/106 (33%), Positives = 66/106 (62%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP--ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 I Y+ Q+P+I + ++ EN+L + + + AV + +++ D+ ++ G GTE+ E+G Sbjct: 565 INYLPQEPFIFSGSIMENLLLGAKPGTTQEDIIRAVEIAEIKDDIEKMSQGFGTELAESG 624 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 N+SGGQK R++LARA+ D V +LD+ S LD ++I+ ++ Sbjct: 625 -NISGGQKQRIALARAILVDSPVLILDESTSNLDVLTEKKIIDNLM 669 Score = 28.9 bits (63), Expect(2) = 2e-15 Identities = 11/33 (33%), Positives = 20/33 (60%) Frame = -2 Query: 133 LVHLAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 L+ L +KT I V H++ + R D ++ M+ G + Sbjct: 668 LMKLTEKTIIFVAHRLTISQRVDRILTMQSGKI 700 >MDLA_ECOLI (P77265) Multidrug resistance-like ATP-binding protein mdlA Length = 590 Score = 78.2 bits (191), Expect = 7e-15 Identities = 40/107 (37%), Positives = 65/107 (60%), Gaps = 1/107 (0%) Frame = -1 Query: 464 AWASQSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTE 288 +W S+ +A VSQ P++ + T+ N+ P A + ++ R+ + D+ L G TE Sbjct: 407 SWRSR-LAVVSQTPFLFSDTVANNIALGCPNATQQEIEHVARLASVHDDILRLPQGYDTE 465 Query: 287 IGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 +GE G+ LSGGQK R+S+ARA+ + E+ +LDD LSA+D +I+ Sbjct: 466 VGERGVMLSGGQKQRISIARALLVNAEILILDDALSAVDGRTEHQIL 512 >MSBA_COXBU (Q83D84) Lipid A export ATP-binding/permease protein msbA Length = 589 Score = 67.8 bits (164), Expect(2) = 2e-14 Identities = 33/93 (35%), Positives = 55/93 (59%), Gaps = 2/93 (2%) Frame = -1 Query: 437 VSQQPWIMNATLRENVLFFSPA--DEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGINL 264 VSQ + N T+ N+ + D+ ++ EA R + L G+ T IGENG+ L Sbjct: 419 VSQHTTLFNDTILNNIAYGQAGSIDKRKIIEAARAAHAMEFIEQLPEGLDTVIGENGVRL 478 Query: 263 SGGQKARVSLARAVYADREVYLLDDPLSALDAH 165 SGGQ+ R+++ARA++ + +++LD+ S+LD H Sbjct: 479 SGGQRQRIAIARALFKNAPIHILDEATSSLDTH 511 Score = 28.9 bits (63), Expect(2) = 2e-14 Identities = 9/26 (34%), Positives = 20/26 (76%) Frame = -2 Query: 118 QKTRILVTHQIDVLSRADFVVVMEKG 41 Q T +++ H++ + RAD+++V+E+G Sbjct: 526 QCTTLVIAHRLSTIERADWIMVLEEG 551 >MSBA_NEIMA (Q9JW59) Lipid A export ATP-binding/permease protein msbA Length = 621 Score = 69.3 bits (168), Expect(2) = 4e-14 Identities = 42/104 (40%), Positives = 62/104 (59%), Gaps = 1/104 (0%) Frame = -1 Query: 443 AYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 A VSQ ++ + TL ENV + P A E + A++ L++ + G+ IG NG N Sbjct: 454 ALVSQDVFLFDDTLFENVRYSRPDAGEAEVLSALQAANLQSLIDASPLGLHQPIGSNGSN 513 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQ+ RV++ARA+ D + LLD+ SALD + ER+V + L Sbjct: 514 LSGGQRQRVAIARAILKDAPILLLDEATSALD-NESERLVQQAL 556 Score = 26.6 bits (57), Expect(2) = 4e-14 Identities = 9/30 (30%), Positives = 19/30 (63%) Frame = -2 Query: 124 LAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 + +T I+V H++ + AD ++VM+ G + Sbjct: 560 MENRTGIIVAHRLTTIEGADRIIVMDDGKI 589 >MSBA_NEIMB (Q9JXR3) Lipid A export ATP-binding/permease protein msbA Length = 621 Score = 67.4 bits (163), Expect(2) = 2e-13 Identities = 42/104 (40%), Positives = 62/104 (59%), Gaps = 1/104 (0%) Frame = -1 Query: 443 AYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 A VSQ ++ + TL ENV + P A E + A++ L++ + G+ IG NG N Sbjct: 454 ALVSQDVFLFDDTLFENVRYSRPDAGEAEVLFALQTANLQSLIDSSPLGLHQPIGSNGSN 513 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQ+ RV++ARA+ D + LLD+ SALD + ER+V + L Sbjct: 514 LSGGQRQRVAIARAILKDAPILLLDEATSALD-NESERLVQQAL 556 Score = 26.6 bits (57), Expect(2) = 2e-13 Identities = 9/30 (30%), Positives = 19/30 (63%) Frame = -2 Query: 124 LAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 + +T I+V H++ + AD ++VM+ G + Sbjct: 560 MENRTGIIVAHRLTTIEGADRIIVMDDGKI 589 >CYDC_ECOLI (P23886) Transport ATP-binding protein cydC Length = 573 Score = 64.7 bits (156), Expect(2) = 3e-13 Identities = 40/103 (38%), Positives = 62/103 (60%), Gaps = 1/103 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 Q+I+ V Q+ + +ATLR+N+L SP + + L E +R LE L AG+ + +GE Sbjct: 414 QTISVVPQRVHLFSATLRDNLLLASPGSSDEALSEILRRVGLEKLLE--DAGLNSWLGEG 471 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 G LSGG+ R+++ARA+ D + LLD+P LDA +I+ Sbjct: 472 GRQLSGGELRRLAIARALLHDAPLVLLDEPTEGLDATTESQIL 514 Score = 28.5 bits (62), Expect(2) = 3e-13 Identities = 11/30 (36%), Positives = 21/30 (70%) Frame = -2 Query: 124 LAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 + +KT ++VTH++ LSR ++VM+ G + Sbjct: 521 MREKTVLMVTHRLRGLSRFQQIIVMDNGQI 550 >MDR3_CAEEL (P34713) Multidrug resistance protein 3 (P-glycoprotein C) Length = 1268 Score = 72.8 bits (177), Expect = 3e-13 Identities = 44/124 (35%), Positives = 67/124 (54%), Gaps = 5/124 (4%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLF-FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 +IA V Q+P + N T+REN+ + + ++++A + + + L G T +G +G Sbjct: 1106 NIALVGQEPTLFNLTIRENITYGLENITQDQVEKAATLANIHTFVMGLPDGYDTSVGASG 1165 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL----FGAPCTKDTH 105 LSGGQK RV++ARA+ D ++ LLD+ SALD E+IV E L G C H Sbjct: 1166 GRLSGGQKQRVAIARAIVRDPKILLLDEATSALDTE-SEKIVQEALDKARLGRTCVVIAH 1224 Query: 104 PCHT 93 T Sbjct: 1225 RLST 1228 Score = 60.5 bits (145), Expect = 2e-09 Identities = 38/110 (34%), Positives = 57/110 (51%), Gaps = 1/110 (0%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA-DEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W +I V Q+P I AT+ EN+ + ++EA ++ + L+ T I Sbjct: 449 WLRSTIGIVQQEPIIFVATVAENIRMGDVLITDQDIEEACKMANAHEFICKLSDRYDTVI 508 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G + LSGGQK RV++ARA+ ++ LLD+ SALD ER+V L Sbjct: 509 GAGAVQLSGGQKQRVAIARAIVRKPQILLLDEATSALDTE-SERMVQTAL 557 >PMD1_SCHPO (P36619) Leptomycin B resistance protein pmd1 Length = 1362 Score = 72.8 bits (177), Expect = 3e-13 Identities = 42/111 (37%), Positives = 66/111 (59%), Gaps = 2/111 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPAD--EHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 + IA VSQ+P + T+REN++ + D E + EA + + + L G T G+ Sbjct: 1195 KQIALVSQEPTLYQGTVRENIVLGASKDVSEEEMIEACKKANIHEFILGLPNGYNTLCGQ 1254 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGA 126 G +LSGGQK R+++ARA+ + ++ LLD+ SALD+H E++V E L A Sbjct: 1255 KGSSLSGGQKQRIAIARALIRNPKILLLDEATSALDSH-SEKVVQEALNAA 1304 Score = 60.5 bits (145), Expect = 2e-09 Identities = 38/123 (30%), Positives = 64/123 (52%), Gaps = 10/123 (8%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPAD----------EHRLQEAVRVCQLEADLRVLAAGM 297 I+ V Q+P + T+ EN+ + P E R+ +A ++ + L Sbjct: 498 ISLVQQEPVLFATTVFENITYGLPDTIKGTLSKEELERRVYDAAKLANAYDFIMTLPEQF 557 Query: 296 GTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGAPCT 117 T +G+ G +SGGQK R+++ARAV +D ++ LLD+ SALD+ E +V + L A + Sbjct: 558 STNVGQRGFLMSGGQKQRIAIARAVISDPKILLLDEATSALDSK-SEVLVQKALDNASRS 616 Query: 116 KDT 108 + T Sbjct: 617 RTT 619 >COMA_STRPN (Q03727) Transport/processing ATP-binding protein comA (EC 3.4.22.-) Length = 717 Score = 71.6 bits (174), Expect = 7e-13 Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 4/110 (3%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQE----AVRVCQLEADLRVLAAGMGTEI 285 Q I Y+SQQP++ N T+ EN+L A E QE AV + ++ D+ + TE+ Sbjct: 558 QYINYLSQQPYVFNGTILENLLL--GAKEGTTQEDILRAVELAEIREDIERMPLNYQTEL 615 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +G +SGGQ+ R++LARA+ D V +LD+ S+LD +RIV ++ Sbjct: 616 TSDGAGISGGQRQRIALARALLTDAPVLILDEATSSLDILTEKRIVDNLI 665 >Y742_STRCO (Q9ZNB0) Hypothetical ABC transporter ATP-binding protein SCO0742 Length = 584 Score = 62.8 bits (151), Expect(2) = 7e-13 Identities = 35/95 (36%), Positives = 56/95 (58%), Gaps = 1/95 (1%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 SI YV Q +++ +LR+N+L +P DE L ++ +L+ + L G+ T +G G Sbjct: 418 SIGYVEQDAPVLSGSLRDNLLLGNPEGDEATLAAVLKTTRLDGLVERLPNGLETLVGHRG 477 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDA 168 LSGG++ RV++ARA+ + LLD+ S LDA Sbjct: 478 TKLSGGERQRVAIARALLRRPRLLLLDEATSQLDA 512 Score = 28.9 bits (63), Expect(2) = 7e-13 Identities = 15/43 (34%), Positives = 28/43 (65%), Gaps = 1/43 (2%) Frame = -2 Query: 157 NES*LKCYLVHLAQKTRILVT-HQIDVLSRADFVVVMEKGAVQ 32 NE+ L+ + +A+ T +LV H++ ++ AD +VVM+ G V+ Sbjct: 514 NEAALRDTVADVARTTTVLVVAHRLSTVTMADRIVVMDAGRVR 556 >YD49_MYCTU (Q11019) Hypothetical ABC transporter ATP-binding protein Rv1349/MT1392/Mb1384 Length = 579 Score = 67.0 bits (162), Expect(2) = 1e-12 Identities = 43/116 (37%), Positives = 67/116 (57%), Gaps = 2/116 (1%) Frame = -1 Query: 464 AWASQSI-AYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGT 291 A A Q++ + V Q P++ + T+R+NV P A + + +AVR+ +++ + L G T Sbjct: 402 ARAQQAVCSVVFQHPYLFHGTIRDNVFAADPGASDDQFAQAVRLARVDELIARLPDGANT 461 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGAP 123 +GE G LSGG++ RVS+ARA+ V L+D+ SALDA E V + L P Sbjct: 462 IVGEAGSALSGGERQRVSIARALLKAAPVLLVDEATSALDAE-NEAAVVDALAADP 516 Score = 24.3 bits (51), Expect(2) = 1e-12 Identities = 9/27 (33%), Positives = 18/27 (66%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +TR++V H++ + AD V+ ++ G V Sbjct: 519 RTRVIVAHRLASIRHADRVLFVDDGRV 545 >MDLA_BUCAP (Q8K985) Multidrug resistance-like ATP-binding protein mdlA Length = 581 Score = 70.5 bits (171), Expect = 2e-12 Identities = 35/106 (33%), Positives = 63/106 (59%), Gaps = 1/106 (0%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W S+ I V+Q ++ + ++ N+ P A + +++A ++ + D+ L G T++ Sbjct: 408 WRSK-IGVVNQTSFLFSDSISNNISLGKPKASQKEIEKAAKLADIHKDIVCLPQGYNTQV 466 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 GE G+ LSGGQK R+++ARA+ + E+ +LDD LSA+D I+ Sbjct: 467 GERGVMLSGGQKQRIAIARALLLNTEILILDDALSAVDGKTENNIL 512 >AB10_MOUSE (Q9JI39) ATP-binding cassette, sub-family B, member 10, mitochondrial precursor (ATP-binding cassette transporter 10) (ABC transporter 10 protein) (ABC-mitochondrial erythroid protein) (ABC-me protein) Length = 715 Score = 70.5 bits (171), Expect = 2e-12 Identities = 40/113 (35%), Positives = 61/113 (53%), Gaps = 4/113 (3%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLF----FSPADEHRLQEAVRVCQLEADLRVLAAGMG 294 W I VSQ+P + + ++ EN+ + S +++ A V +R G Sbjct: 530 WLRSKIGTVSQEPVLFSCSVAENIAYGADNLSSVTAQQVERAAEVANAAEFIRSFPQGFD 589 Query: 293 TEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 T +GE GI LSGGQK R+++ARA+ + ++ LLD+ SALDA E +V E L Sbjct: 590 TVVGEKGILLSGGQKQRIAIARALLKNPKILLLDEATSALDAE-NEHLVQEAL 641 >MDR1_CAEEL (P34712) Multidrug resistance protein 1 (P-glycoprotein A) Length = 1321 Score = 70.1 bits (170), Expect = 2e-12 Identities = 38/107 (35%), Positives = 64/107 (59%), Gaps = 3/107 (2%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFF---SPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 IA VSQ+P + + ++ EN+++ S +++EA R+ + + L G T +G+ Sbjct: 1155 IAIVSQEPTLFDCSIAENIIYGLDPSSVTMAQVEEAARLANIHNFIAELPEGFETRVGDR 1214 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G LSGGQK R+++ARA+ + ++ LLD+ SALD E++V E L Sbjct: 1215 GTQLSGGQKQRIAIARALVRNPKILLLDEATSALDTE-SEKVVQEAL 1260 Score = 68.2 bits (165), Expect = 8e-12 Identities = 39/107 (36%), Positives = 62/107 (57%), Gaps = 1/107 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENV-LFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 +++A VSQ+P + N T+ EN+ L + A ++ E ++ L G T +G+ Sbjct: 492 KNVAVVSQEPALFNCTIEENISLGKEGITREEMVAACKMANAEKFIKTLPNGYNTLVGDR 551 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G LSGGQK R+++ARA+ + ++ LLD+ SALDA E IV + L Sbjct: 552 GTQLSGGQKQRIAIARALVRNPKILLLDEATSALDAE-SEGIVQQAL 597 >COMA_STRR6 (P59653) Transport/processing ATP-binding protein comA (EC 3.4.22.-) Length = 717 Score = 69.7 bits (169), Expect = 3e-12 Identities = 40/110 (36%), Positives = 63/110 (57%), Gaps = 4/110 (3%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQE----AVRVCQLEADLRVLAAGMGTEI 285 Q I Y+ QQP++ N T+ EN+L A E QE AV + ++ D+ + TE+ Sbjct: 558 QYINYLPQQPYVFNGTILENLLL--GAKEGTTQEDILRAVELAEIREDIERMPLNYQTEL 615 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +G +SGGQ+ R++LARA+ D V +LD+ S+LD +RIV ++ Sbjct: 616 TSDGAGISGGQRQRIALARALLTDAPVLILDEATSSLDILTEKRIVDNLI 665 >MDLA_BUCAI (P57551) Multidrug resistance-like ATP-binding protein mdlA Length = 589 Score = 69.7 bits (169), Expect = 3e-12 Identities = 36/104 (34%), Positives = 60/104 (57%), Gaps = 1/104 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 IA V+Q ++ + T+ N+ P A + ++E ++ + D+ L T++GE G+ Sbjct: 412 IAVVNQTSFLFSDTISNNISLGKPNASQKEIEEVAKLADVHKDIIDLPERYETQVGERGV 471 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 LSGGQK RV +ARA+ + E+ +LDD LSA+DA I+ + Sbjct: 472 MLSGGQKQRVCIARALLLNAEILILDDALSAVDAQTENNILKNI 515 >AB10_HUMAN (Q9NRK6) ATP-binding cassette, sub-family B, member 10, mitochondrial precursor (ATP-binding cassette transporter 10) (ABC transporter 10 protein) (Mitochondrial ATP-binding cassette 2) (M-ABC2) Length = 738 Score = 69.7 bits (169), Expect = 3e-12 Identities = 40/113 (35%), Positives = 60/113 (53%), Gaps = 4/113 (3%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFF----SPADEHRLQEAVRVCQLEADLRVLAAGMG 294 W I VSQ+P + + ++ EN+ + S +Q V A +R G Sbjct: 565 WLRSKIGTVSQEPILFSCSIAENIAYGADDPSSVTAEEIQRVAEVANAVAFIRNFPQGFN 624 Query: 293 TEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 T +GE G+ LSGGQK R+++ARA+ + ++ LLD+ SALDA E +V E L Sbjct: 625 TVVGEKGVLLSGGQKQRIAIARALLKNPKILLLDEATSALDAE-NEYLVQEAL 676 >MSBA_VIBPA (Q87R16) Lipid A export ATP-binding/permease protein msbA Length = 582 Score = 62.8 bits (151), Expect(2) = 3e-12 Identities = 37/108 (34%), Positives = 58/108 (53%), Gaps = 2/108 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHR--LQEAVRVCQLEADLRVLAAGMGTEIGE 279 + A VSQ + N T+ N+ + + R ++ A ++ + + G+ T IGE Sbjct: 417 EQFALVSQNVHLFNDTIANNIAYATEDKYERSDIEHAAKLAHAMEFINKMENGLDTMIGE 476 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 NG +LSGGQ+ RV++ARA+ D V +LD+ SALD ER + L Sbjct: 477 NGASLSGGQRQRVAIARALLRDAPVLILDEATSALDTE-SERAIQAAL 523 Score = 26.9 bits (58), Expect(2) = 3e-12 Identities = 8/27 (29%), Positives = 20/27 (74%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 KT +++ H++ + +AD ++V++ GA+ Sbjct: 530 KTVLVIAHRLSTIEKADEILVVDDGAI 556 >MDL1_CANAL (P97998) ATP-dependent permease MDL1 Length = 685 Score = 68.9 bits (167), Expect = 5e-12 Identities = 41/102 (40%), Positives = 61/102 (59%), Gaps = 2/102 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIG-ENG 273 + YV Q+P + + T++EN+LF A + + A+ + +R L G+ T+IG N Sbjct: 518 LGYVQQEPLLFSGTIKENILFGKEDATDEEINNALNLSYASNFVRHLPDGLDTKIGASNS 577 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 LSGGQK RVSLAR + D ++ +LD+ SALD+ V E IV Sbjct: 578 TQLSGGQKQRVSLARTLIRDPKILILDEATSALDS-VSEEIV 618 >MSBA_SHEON (Q8EDF0) Lipid A export ATP-binding/permease protein msbA Length = 601 Score = 68.9 bits (167), Expect = 5e-12 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 2/94 (2%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQ--EAVRVCQLEADLRVLAAGMGTEIGENG 273 +A VSQQ + N T+ N+ + P + R Q EA + + L G+ T++GENG Sbjct: 438 VALVSQQVTLFNDTIANNIAYAYPGEVTREQIIEAATLAHAMEFIEQLPDGLDTQVGENG 497 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + LSGGQ+ R+++ARA+ D V +LD+ SALD Sbjct: 498 VLLSGGQRQRIAIARAMLRDAPVLILDEATSALD 531 >YFIB_BACSU (P54718) Hypothetical ABC transporter ATP-binding protein yfiB Length = 573 Score = 68.6 bits (166), Expect = 6e-12 Identities = 35/106 (33%), Positives = 60/106 (56%), Gaps = 1/106 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 + I YV Q+ + + T++EN+ + A + +A ++ Q+ + L G T +G+ Sbjct: 405 RQIGYVPQEVLLFSGTIKENIAWGKENASLDEIMDAAKLAQIHETILKLPNGYDTVLGQR 464 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 G+NLSGGQK R+S+ARA+ + LLDD SALD +++ + Sbjct: 465 GVNLSGGQKQRISIARALIRKPAILLLDDSTSALDLQTEAKLLEAI 510 >HLYB_PASHA (P16532) Leukotoxin secretion/processing ATP-binding protein (EC 3.4.22.-) Length = 708 Score = 58.2 bits (139), Expect(2) = 6e-12 Identities = 33/108 (30%), Positives = 57/108 (52%), Gaps = 1/108 (0%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA-DEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W + I V Q ++N ++REN+ P R+ A ++ + L G T + Sbjct: 541 WLRRQIGVVLQDNVLLNRSIRENIALSDPGMPMERVIYAAKLAGAHDFISELREGYNTIV 600 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTE 141 GE G LSGGQ+ R+++ARA+ + ++ + D+ SALD + E I+ + Sbjct: 601 GEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALD-YESEHIIMQ 647 Score = 30.4 bits (67), Expect(2) = 6e-12 Identities = 11/27 (40%), Positives = 19/27 (70%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +T IL+ H++ + AD ++VMEKG + Sbjct: 656 RTVILIAHRLSTVKNADRIIVMEKGEI 682 >ABC8_HUMAN (Q9NUT2) ATP-binding cassette, sub-family B, member 8, mitochondrial precursor (Mitochondrial ATP-binding cassette 1) (M-ABC1) Length = 735 Score = 68.2 bits (165), Expect = 8e-12 Identities = 39/107 (36%), Positives = 57/107 (53%), Gaps = 1/107 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFS-PADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 Q + ++SQ+P + T+ EN+ F A + + A R + G T +GE Sbjct: 549 QVVGFISQEPVLFGTTIMENIRFGKLEASDEEVYTAAREANAHEFITSFPEGYNTVVGER 608 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G LSGGQK R+++ARA+ V +LD+ SALDA ER+V E L Sbjct: 609 GTTLSGGQKQRLAIARALIKQPTVLILDEATSALDAE-SERVVQEAL 654 >CYDD_ECOLI (P29018) Transport ATP-binding protein cydD Length = 588 Score = 68.2 bits (165), Expect = 8e-12 Identities = 39/101 (38%), Positives = 60/101 (59%), Gaps = 1/101 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 +++V Q P + ATLR+NVL P A E LQ A+ + L +L G+ T +G+ Sbjct: 425 LSWVGQNPQLPAATLRDNVLLARPDASEQELQAALDNAWVSEFLPLLPQGVDTPVGDQAA 484 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 LS GQ RV++ARA+ + LLD+P ++LDAH +R++ Sbjct: 485 RLSVGQAQRVAVARALLNPCSLLLLDEPAASLDAHSEQRVM 525 >MSBA_RALSO (Q8XXB6) Lipid A export ATP-binding/permease protein msbA Length = 592 Score = 68.2 bits (165), Expect = 8e-12 Identities = 43/110 (39%), Positives = 62/110 (56%), Gaps = 4/110 (3%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF----FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 + IA+VSQ + N T+ NV + S D R++ A+ L + L G+ T I Sbjct: 424 RQIAFVSQDVVLFNDTIAANVAYGARDASEIDMARVRRALEAAYLTDVVDNLPDGVDTNI 483 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G+NG LSGGQ+ R+++ARAVY D + +LD+ SALD+ ER V L Sbjct: 484 GDNGSKLSGGQRQRLAIARAVYKDAPILILDEATSALDSE-SERQVQAAL 532 >MDR4_DROME (Q00449) Multidrug resistance protein homolog 49 (P-glycoprotein 49) Length = 1302 Score = 67.8 bits (164), Expect = 1e-11 Identities = 36/105 (34%), Positives = 57/105 (54%), Gaps = 1/105 (0%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W I V Q+P + T+ EN+ + P A + +++A R + L G T++ Sbjct: 475 WLRSQIGVVGQEPVLFATTIGENIRYGRPSATQADIEKAARAANCHDFITRLPKGYDTQV 534 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 GE G +SGGQK R+++ARA+ +V LLD+ SALD +R+ Sbjct: 535 GEKGAQISGGQKQRIAIARALVRQPQVLLLDEATSALDPTSEKRV 579 Score = 54.3 bits (129), Expect = 1e-07 Identities = 33/108 (30%), Positives = 57/108 (52%), Gaps = 4/108 (3%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVL----FFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 + VSQ+P + + T+ EN+ F + EA + + + L G T +G+ Sbjct: 1137 LGLVSQEPVLFDRTIAENIAYGNNFRDDVSMQEIIEAAKKSNIHNFISALPQGYDTRLGK 1196 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQK R+++ARA+ + ++ +LD+ SALD E++V + L Sbjct: 1197 TS-QLSGGQKQRIAIARALVRNPKILILDEATSALDLE-SEKVVQQAL 1242 >MDL1_YEAST (P33310) ATP-dependent permease MDL1 Length = 695 Score = 67.8 bits (164), Expect = 1e-11 Identities = 40/108 (37%), Positives = 59/108 (54%), Gaps = 4/108 (3%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPAD----EHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 I YV Q+P + N T+ +N+L+ P + + R++ A+ L G+ T +G Sbjct: 510 IGYVQQEPLLFNGTILDNILYCIPPEIAEQDDRIRRAIGKANCTKFLANFPDGLQTMVGA 569 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G LSGGQK R++LARA D V +LD+ SALD+ E IV + L Sbjct: 570 RGAQLSGGQKQRIALARAFLLDPAVLILDEATSALDSQ-SEEIVAKNL 616 >HLYB_PASSP (P55122) Leukotoxin secretion/processing ATP-binding protein (EC 3.4.22.-) Length = 708 Score = 57.0 bits (136), Expect(2) = 1e-11 Identities = 32/108 (29%), Positives = 57/108 (52%), Gaps = 1/108 (0%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA-DEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W + I V Q ++N ++REN+ P R+ A ++ + + G T + Sbjct: 541 WLRRQIGVVLQDNVLLNRSIRENIALSEPGMSMERVIYAAKLAGAHDFISDVREGYNTIV 600 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTE 141 GE G LSGGQ+ R+++ARA+ + ++ + D+ SALD + E I+ + Sbjct: 601 GEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALD-YESEHIIMQ 647 Score = 30.4 bits (67), Expect(2) = 1e-11 Identities = 11/27 (40%), Positives = 19/27 (70%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +T IL+ H++ + AD ++VMEKG + Sbjct: 656 RTVILIAHRLSTVKNADRIIVMEKGEI 682 >RT1B_ACTPL (P26760) Toxin RTX-I secretion/processing ATP-binding protein (EC 3.4.22.-) (RTX-I toxin determinant B) (APX-IB) (HLY-IB) (Cytolysin IB) (CLY-IB) Length = 707 Score = 57.0 bits (136), Expect(2) = 2e-11 Identities = 28/98 (28%), Positives = 52/98 (53%), Gaps = 1/98 (1%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA-DEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W + + V Q ++N ++R+N+ P ++ A ++ + L G T + Sbjct: 540 WLRRQVGVVLQDNVLLNRSIRDNIALADPGMPMEKIVHAAKLAGAHEFISELREGYNTIV 599 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GE G LSGGQ+ R+++ARA+ + ++ + D+ SALD Sbjct: 600 GEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALD 637 Score = 29.6 bits (65), Expect(2) = 2e-11 Identities = 10/27 (37%), Positives = 19/27 (70%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +T I++ H++ + AD ++VMEKG + Sbjct: 655 RTVIIIAHRLSTVKNADRIIVMEKGQI 681 >LCNC_LACLA (Q00564) Lactococcin A transport/processing ATP-binding protein lcnC (EC 3.4.22.-) Length = 715 Score = 66.6 bits (161), Expect = 2e-11 Identities = 34/106 (32%), Positives = 64/106 (60%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP--ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 I Y+ QQP+I ++ +N+L + A + + +AV + ++ AD+ + G TE+ + Sbjct: 558 INYLPQQPYIFTGSILDNLLLGANENASQEEILKAVELAEIRADIEQMQLGYQTELSSDA 617 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +LSGGQK R++LARA+ + ++ +LD+ S LD ++I+ +L Sbjct: 618 SSLSGGQKQRIALARALLSPAKILILDEATSNLDMITEKKILKNLL 663 >PRTD_ERWCH (P23596) Proteases secretion ATP-binding protein prtD Length = 575 Score = 66.6 bits (161), Expect = 2e-11 Identities = 33/105 (31%), Positives = 60/105 (57%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 +I Y+ Q + +L EN+ F AD ++ A ++ + + L G TE+G+ G Sbjct: 406 TIGYLPQDVQLFKGSLAENIARFGDADPEKVVAAAKLAGVHELILSLPNGYDTELGDGGG 465 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQ+ R+ LARA+Y D + +LD+P ++LD+ + ++ ++ Sbjct: 466 GLSGGQRQRIGLARAMYGDPCLLILDEPNASLDSEGDQALMQAIV 510 >MSBA_WIGBR (Q8D2U8) Lipid A export ATP-binding/permease protein msbA Length = 581 Score = 58.5 bits (140), Expect(2) = 3e-11 Identities = 32/94 (34%), Positives = 55/94 (58%), Gaps = 2/94 (2%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPA--DEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 IA VSQ ++ N T+ N+ + ++++++A + + + G+ T IGENG Sbjct: 418 IALVSQNIYLFNDTIANNIAYAKKKIYSKYQIEKAAYMAYAMDFIIKMKHGLNTIIGENG 477 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LSGGQ+ R+++ARA+ D + +LD+ SALD Sbjct: 478 TLLSGGQRQRIAIARALLRDCPILILDEATSALD 511 Score = 27.7 bits (60), Expect(2) = 3e-11 Identities = 7/27 (25%), Positives = 20/27 (74%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +T +++ H+I + ++D ++++EKG + Sbjct: 529 RTSLVIAHRISTIKKSDMILLVEKGKI 555 >RT3B_ACTPL (Q04473) Toxin RTX-III secretion/processing ATP-binding protein (EC 3.4.22.-) (RTX-III toxin determinant B) (APX-IIIB) (Cytolysin IIIB) (CLY-IIIB) Length = 711 Score = 56.2 bits (134), Expect(2) = 5e-11 Identities = 32/108 (29%), Positives = 57/108 (52%), Gaps = 1/108 (0%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA-DEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W + I V Q ++N ++R+N+ P+ R+ A ++ + L G T + Sbjct: 544 WLRRQIGVVLQDNVLLNRSIRDNIALTDPSMSMERVIYAAKLAGAHDFISELREGYNTIV 603 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTE 141 GE G LSGGQ+ R+++ARA+ + + + D+ SALD + E I+ + Sbjct: 604 GELGAGLSGGQRQRIAIARALVNNPRILIFDEATSALD-YESEHIIMQ 650 Score = 29.3 bits (64), Expect(2) = 5e-11 Identities = 10/27 (37%), Positives = 19/27 (70%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +T I++ H++ + AD ++VMEKG + Sbjct: 659 RTVIIIAHRLSTVKNADRIIVMEKGHI 685 >MDLA_BUCBP (Q89A97) Multidrug resistance-like ATP-binding protein mdlA Length = 579 Score = 65.5 bits (158), Expect = 5e-11 Identities = 32/95 (33%), Positives = 56/95 (58%), Gaps = 1/95 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 + ++ V+Q ++ + T+ N+ P A + +++A L D+ G T++GE Sbjct: 411 KKMSIVNQTTFLFSDTIANNIKLGKPYASQKEIEQATTFSDLHNDIMTFPQGYNTQVGER 470 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GI LSGGQK R+S+ARA+ E+ +LD+ LS++D Sbjct: 471 GIMLSGGQKQRISIARALLLKSEILILDNALSSVD 505 >LCCL_LACLA (Q9CJB8) Lactococcin transport/processing ATP-binding protein lcnC-like (EC 3.4.22.-) Length = 715 Score = 65.1 bits (157), Expect = 7e-11 Identities = 33/106 (31%), Positives = 62/106 (58%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP--ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 I Y+ QQP+I ++ +N+L + + + AV + ++ AD+ + G TE+ + Sbjct: 558 INYLPQQPYIFTGSIMDNLLLGASEATSQEEIIRAVELAEIRADIEQMQLGYQTELSSDA 617 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +LSGGQK R++LARA+ + ++ +LD+ S LD ++I+ +L Sbjct: 618 SSLSGGQKQRIALARALLSPAKILILDEATSNLDMITEKKILKNLL 663 >Y4GM_RHISN (P55469) Probable ABC transporter ATP-binding protein Y4GM Length = 586 Score = 65.1 bits (157), Expect = 7e-11 Identities = 33/94 (35%), Positives = 55/94 (58%), Gaps = 1/94 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENV-LFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I +V Q ++ + T++ N+ L A + + EA + + + G TE+GENGI Sbjct: 422 IGFVGQDTFLFSGTIKYNISLGREGASDEEIIEAAKTANAHDFIMKMPHGYDTEVGENGI 481 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDA 168 LSGGQK R+++ARA+ + E+ + D+ SALD+ Sbjct: 482 KLSGGQKQRITIARAMLRNAEILIFDEATSALDS 515 >HLYB_ACTAC (P23702) Leukotoxin secretion/processing ATP-binding protein (EC 3.4.22.-) Length = 707 Score = 57.0 bits (136), Expect(2) = 8e-11 Identities = 29/98 (29%), Positives = 52/98 (53%), Gaps = 1/98 (1%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA-DEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W + + V Q ++N ++REN+ +P ++ A ++ + L G T + Sbjct: 540 WLRRQVGVVLQDNVLLNRSIRENIALTNPGMPMEKVIAAAKLAGAHDFISELREGYNTVV 599 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GE G LSGGQ+ R+++ARA+ + + + D+ SALD Sbjct: 600 GEQGAGLSGGQRQRIAIARALVNNPRILIFDEATSALD 637 Score = 27.7 bits (60), Expect(2) = 8e-11 Identities = 8/27 (29%), Positives = 19/27 (70%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +T +++ H++ + AD ++VM+KG + Sbjct: 655 RTVLIIAHRLSTVKNADRIIVMDKGEI 681 >YWJA_BACSU (P45861) Hypothetical ABC transporter ATP-binding protein ywjA Length = 575 Score = 64.3 bits (155), Expect = 1e-10 Identities = 36/93 (38%), Positives = 54/93 (58%), Gaps = 1/93 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFS-PADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I V Q ++ + TLREN+ + A E + +AV+ LE + + G+ T IGE G+ Sbjct: 409 IGVVQQDVFLFSGTLRENIAYGRLGASEEDIWQAVKQAHLEELVHNMPDGLDTMIGERGV 468 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LSGGQK R+S+AR + + +LD+ SALD Sbjct: 469 KLSGGQKQRLSIARMFLKNPSILILDEATSALD 501 >MAM1_SCHPO (P78966) Mating factor M secretion protein mam1 (Multiple drug resistance protein homolog) (P-glycoprotein) Length = 1336 Score = 57.8 bits (138), Expect(2) = 1e-10 Identities = 35/94 (37%), Positives = 53/94 (56%), Gaps = 1/94 (1%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 +I V QQP I + T+REN++ + A E +E R+ ++ T E Sbjct: 511 TITLVCQQPVIFDMTIRENIIMRNENASESDFEEVCRLALVDEFALTFDQSYDTPCKE-- 568 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 +LSGGQ+ R++LARA+ D E+ +LD+P SALD Sbjct: 569 ASLSGGQQQRIALARALLRDTEILILDEPTSALD 602 Score = 53.9 bits (128), Expect(2) = 8e-10 Identities = 29/98 (29%), Positives = 56/98 (57%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIG 282 W + +A V Q+P ++ +T+ E++L+ D + + +A+ + ++ L G+ T + Sbjct: 1171 WLLKKVAIVDQKPHLLGSTILESLLYGVDRDINSVMDALDKTYMTEVIQNLPNGLDTPLL 1230 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDA 168 E N SGGQ R++ ARA+ + + +LD+ SALD+ Sbjct: 1231 EFSKNFSGGQIQRLAFARALLRNPRLLILDECTSALDS 1268 Score = 27.3 bits (59), Expect(2) = 8e-10 Identities = 10/27 (37%), Positives = 19/27 (70%) Frame = -2 Query: 112 TRILVTHQIDVLSRADFVVVMEKGAVQ 32 T +++THQ ++ AD ++VM+ G V+ Sbjct: 1284 TVLIITHQPSLMKLADRIIVMDSGIVK 1310 Score = 26.2 bits (56), Expect(2) = 1e-10 Identities = 9/29 (31%), Positives = 19/29 (65%) Frame = -2 Query: 127 HLAQKTRILVTHQIDVLSRADFVVVMEKG 41 H KT +++TH + ++ + V+V++KG Sbjct: 616 HRKGKTTLVITHDMSQINNDELVLVIDKG 644 >MSBA_VIBCH (Q9KQW9) Lipid A export ATP-binding/permease protein msbA Length = 582 Score = 63.9 bits (154), Expect = 1e-10 Identities = 38/105 (36%), Positives = 58/105 (55%), Gaps = 2/105 (1%) Frame = -1 Query: 443 AYVSQQPWIMNATLRENVLFFSPADEHR--LQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 A VSQ + N T+ N+ + + + R +++A R + + G+ T IGENG Sbjct: 420 ALVSQNVHLFNDTIANNIAYAAEGEYTREQIEQAARQAHAMEFIENMPQGLDTVIGENGT 479 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +LSGGQ+ RV++ARA+ D V +LD+ SALD ER + L Sbjct: 480 SLSGGQRQRVAIARALLRDAPVLILDEATSALDTE-SERAIQAAL 523 >MSBA_SALTY (Q8XFG5) Lipid A export ATP-binding/permease protein msbA Length = 582 Score = 63.9 bits (154), Expect = 1e-10 Identities = 37/106 (34%), Positives = 59/106 (55%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHR--LQEAVRVCQLEADLRVLAAGMGTEIGENG 273 +A VSQ + N T+ N+ + + R ++EA R+ + + G+ T IGENG Sbjct: 419 VALVSQNVHLFNDTVANNIAYARTEEYSREQIEEAARMAYAMDFINKMDNGLDTIIGENG 478 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 + LSGGQ+ R+++ARA+ D + +LD+ SALD ER + L Sbjct: 479 VLLSGGQRQRIAIARALLRDSPILILDEATSALDTE-SERAIQAAL 523 >MDR1_HUMAN (P08183) Multidrug resistance protein 1 (P-glycoprotein 1) (CD243 antigen) Length = 1280 Score = 63.5 bits (153), Expect = 2e-10 Identities = 36/112 (32%), Positives = 60/112 (53%), Gaps = 3/112 (2%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQ---LEADLRVLAAGMGT 291 W + VSQ+P + + ++ EN+ + + +E VR + + A + L T Sbjct: 1108 WLRAHLGIVSQEPILFDCSIAENIAYGDNSRVVSQEEIVRAAKEANIHAFIESLPNKYST 1167 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 ++G+ G LSGGQK R+++ARA+ + LLD+ SALD E++V E L Sbjct: 1168 KVGDKGTQLSGGQKQRIAIARALVRQPHILLLDEATSALDTE-SEKVVQEAL 1218 Score = 55.1 bits (131), Expect = 7e-08 Identities = 32/93 (34%), Positives = 51/93 (54%), Gaps = 1/93 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I VSQ+P + T+ EN+ + +++AV+ + L T +GE G Sbjct: 470 IGVVSQEPVLFATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGA 529 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LSGGQK R+++ARA+ + ++ LLD+ SALD Sbjct: 530 QLSGGQKQRIAIARALVRNPKILLLDEATSALD 562 >AARD_PROST (Q52402) Transport ATP-binding protein aarD Length = 588 Score = 63.5 bits (153), Expect = 2e-10 Identities = 35/101 (34%), Positives = 56/101 (55%), Gaps = 1/101 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I +V Q P + TL EN+ P A E +Q+A+ + L +L G+ T +G+ Sbjct: 425 IGWVGQNPHLPEQTLIENICLGKPTASEAEIQQAIDDAYVSEFLPMLPDGLNTRLGDYAA 484 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 LS GQ RV++AR + + LLD+P ++LDAH +R++ Sbjct: 485 RLSVGQAQRVAVARTLLKPSRILLLDEPAASLDAHSEKRVM 525 >YC73_MYCTU (Q11046) Hypothetical ABC transporter ATP-binding protein Rv1273c/MT1311/Mb1304c Length = 582 Score = 63.5 bits (153), Expect = 2e-10 Identities = 35/104 (33%), Positives = 58/104 (55%), Gaps = 4/104 (3%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPAD----EHRLQEAVRVCQLEADLRVLAAGMGTEIG 282 +I V Q+ ++ + T+ +N+ + D E + EA+RV AD V G+ T + Sbjct: 411 AIGLVPQRSYLFSGTVADNLRYGGGPDQVVTEQEMWEALRVAA--ADGFVQTDGLQTRVA 468 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 + G+N SGGQ+ R+++ARAV +Y+ DD SALD H ++ Sbjct: 469 QGGVNFSGGQRQRLAIARAVIRRPAIYVFDDAFSALDVHTDAKV 512 >MSBA_SHIFL (Q83LP0) Lipid A export ATP-binding/permease protein msbA Length = 582 Score = 63.5 bits (153), Expect = 2e-10 Identities = 37/106 (34%), Positives = 58/106 (54%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHR--LQEAVRVCQLEADLRVLAAGMGTEIGENG 273 +A VSQ + N T+ N+ + R ++EA R+ + + G+ T IGENG Sbjct: 419 VALVSQNVHLFNDTVANNIAYARTEQYSREQIEEAARMAYAMDFINKMDNGLDTVIGENG 478 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 + LSGGQ+ R+++ARA+ D + +LD+ SALD ER + L Sbjct: 479 VLLSGGQRQRIAIARALLRDSPILILDEATSALDTE-SERAIQAAL 523 >MSBA_ECOLI (P60752) Lipid A export ATP-binding/permease protein msbA Length = 582 Score = 63.5 bits (153), Expect = 2e-10 Identities = 37/106 (34%), Positives = 58/106 (54%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHR--LQEAVRVCQLEADLRVLAAGMGTEIGENG 273 +A VSQ + N T+ N+ + R ++EA R+ + + G+ T IGENG Sbjct: 419 VALVSQNVHLFNDTVANNIAYARTEQYSREQIEEAARMAYAMDFINKMDNGLDTVIGENG 478 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 + LSGGQ+ R+++ARA+ D + +LD+ SALD ER + L Sbjct: 479 VLLSGGQRQRIAIARALLRDSPILILDEATSALDTE-SERAIQAAL 523 >MSBA_ECOL6 (Q8FJB1) Lipid A export ATP-binding/permease protein msbA Length = 582 Score = 63.5 bits (153), Expect = 2e-10 Identities = 37/106 (34%), Positives = 58/106 (54%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHR--LQEAVRVCQLEADLRVLAAGMGTEIGENG 273 +A VSQ + N T+ N+ + R ++EA R+ + + G+ T IGENG Sbjct: 419 VALVSQNVHLFNDTVANNIAYARTEQYSREQIEEAARMAYAMDFINKMDNGLDTVIGENG 478 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 + LSGGQ+ R+++ARA+ D + +LD+ SALD ER + L Sbjct: 479 VLLSGGQRQRIAIARALLRDSPILILDEATSALDTE-SERAIQAAL 523 >MSBA_ECO57 (P60753) Lipid A export ATP-binding/permease protein msbA Length = 582 Score = 63.5 bits (153), Expect = 2e-10 Identities = 37/106 (34%), Positives = 58/106 (54%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHR--LQEAVRVCQLEADLRVLAAGMGTEIGENG 273 +A VSQ + N T+ N+ + R ++EA R+ + + G+ T IGENG Sbjct: 419 VALVSQNVHLFNDTVANNIAYARTEQYSREQIEEAARMAYAMDFINKMDNGLDTVIGENG 478 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 + LSGGQ+ R+++ARA+ D + +LD+ SALD ER + L Sbjct: 479 VLLSGGQRQRIAIARALLRDSPILILDEATSALDTE-SERAIQAAL 523 >CYDD_HAEIN (P45082) Transport ATP-binding protein cydD Length = 586 Score = 54.7 bits (130), Expect(2) = 2e-10 Identities = 34/105 (32%), Positives = 61/105 (58%), Gaps = 1/105 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFS-PADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 IA+V Q P ++ T++EN+L A++ + +A+ Q + L G+ EI + G+ Sbjct: 425 IAWVGQNPLLLQGTIKENLLLGDVQANDEEINQALMRSQAKEFTDKL--GLHHEIKDGGL 482 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +S GQ R+++ARA+ ++ LLD+P ++LDA E +V + L Sbjct: 483 GISVGQAQRLAIARALLRKGDLLLLDEPTASLDAQ-SENLVLQAL 526 Score = 28.5 bits (62), Expect(2) = 2e-10 Identities = 12/38 (31%), Positives = 23/38 (60%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAVQLL*PLGYLQH 2 +T +++TH+I+ L + D + VM++G + LQH Sbjct: 533 QTTLMITHRIEDLKQCDQIFVMQRGEIVQQGKFTELQH 570 >HMT1_SCHPO (Q02592) Heavy metal tolerance protein precursor Length = 830 Score = 63.2 bits (152), Expect = 2e-10 Identities = 34/101 (33%), Positives = 53/101 (52%), Gaps = 1/101 (0%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 SI V Q + N T+ N+ + P A + A + Q+ + G + +GE G Sbjct: 659 SIGVVPQDSTLFNDTILYNIKYAKPSATNEEIYAAAKAAQIHDRILQFPDGYNSRVGERG 718 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 + LSGG+K RV++ARA+ D + LLD+ SALD + +I Sbjct: 719 LKLSGGEKQRVAVARAILKDPSIILLDEATSALDTNTERQI 759 >MSBA_PSEAE (Q9HUG8) Lipid A export ATP-binding/permease protein msbA Length = 603 Score = 63.2 bits (152), Expect = 2e-10 Identities = 33/94 (35%), Positives = 55/94 (58%), Gaps = 2/94 (2%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLF--FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 IA V+QQ + N ++ N+ + + A ++ A + + + L G TE+GENG Sbjct: 433 IALVTQQVTLFNDSVANNIAYGDLAGAPREEIERAAKAANAKEFIDNLPQGFDTEVGENG 492 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + LSGGQ+ R+++ARA+ D + +LD+ SALD Sbjct: 493 VLLSGGQRQRLAIARALLKDAPLLILDEATSALD 526 >MDR2_MOUSE (P21440) Multidrug resistance protein 2 (P-glycoprotein 2) Length = 1276 Score = 63.2 bits (152), Expect = 2e-10 Identities = 37/114 (32%), Positives = 58/114 (50%), Gaps = 5/114 (4%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFS-----PADEHRLQEAVRVCQLEADLRVLAAGM 297 W + VSQ+P + + ++ EN+ + P DE + A + + + L Sbjct: 1104 WLRAQLGIVSQEPILFDCSIAENIAYGDNSRVVPHDE--IVRAAKEANIHPFIETLPQKY 1161 Query: 296 GTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 T +G+ G LSGGQK R+++ARA+ V LLD+ SALD E++V E L Sbjct: 1162 NTRVGDKGTQLSGGQKQRIAIARALIRQPRVLLLDEATSALDTE-SEKVVQEAL 1214 Score = 55.5 bits (132), Expect = 5e-08 Identities = 31/93 (33%), Positives = 52/93 (55%), Gaps = 1/93 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFF-SPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I VSQ+P + + T+ EN+ + +++AV+ + L T +G+ G Sbjct: 469 IGVVSQEPVLFSTTIAENIRYGRGNVTMDEIEKAVKEANAYDFIMKLPQKFDTLVGDRGA 528 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LSGGQK R+++ARA+ + ++ LLD+ SALD Sbjct: 529 QLSGGQKQRIAIARALVRNPKILLLDEATSALD 561 >MDR3_HUMAN (P21439) Multidrug resistance protein 3 (P-glycoprotein 3) Length = 1279 Score = 62.8 bits (151), Expect = 3e-10 Identities = 33/112 (29%), Positives = 58/112 (51%), Gaps = 3/112 (2%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA---DEHRLQEAVRVCQLEADLRVLAAGMGT 291 W + VSQ+P + + ++ EN+ + + + + A + + + L T Sbjct: 1107 WLRAQLGIVSQEPILFDCSIAENIAYGDNSRVVSQDEIVSAAKAANIHPFIETLPHKYET 1166 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +G+ G LSGGQK R+++ARA+ ++ LLD+ SALD E++V E L Sbjct: 1167 RVGDKGTQLSGGQKQRIAIARALIRQPQILLLDEATSALDTE-SEKVVQEAL 1217 Score = 57.0 bits (136), Expect = 2e-08 Identities = 32/93 (34%), Positives = 52/93 (55%), Gaps = 1/93 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFF-SPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I VSQ+P + + T+ EN+ + +++AV+ + L T +GE G Sbjct: 472 IGVVSQEPVLFSTTIAENICYGRGNVTMDEIKKAVKEANAYEFIMKLPQKFDTLVGERGA 531 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LSGGQK R+++ARA+ + ++ LLD+ SALD Sbjct: 532 QLSGGQKQRIAIARALVRNPKILLLDEATSALD 564 >MSBA_PASMU (Q9CMG7) Lipid A export ATP-binding/permease protein msbA Length = 582 Score = 62.8 bits (151), Expect = 3e-10 Identities = 35/97 (36%), Positives = 59/97 (60%), Gaps = 3/97 (3%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQ---LEADLRVLAAGMGTEIG 282 ++ A VSQQ + N T+ N+ + + D++ +E ++ + + L G+ T IG Sbjct: 417 KNCAVVSQQVHLFNDTIANNIAY-AAKDKYSREEIIKAAKDAYAMEFIEKLEHGLDTVIG 475 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 ENG+NLSGGQ+ R+++ARA+ + V +LD+ SALD Sbjct: 476 ENGVNLSGGQRQRLAIARALLRNSPVLILDEATSALD 512 >MSBA_VIBVU (Q8DAV2) Lipid A export ATP-binding/permease protein msbA Length = 583 Score = 62.8 bits (151), Expect = 3e-10 Identities = 37/106 (34%), Positives = 60/106 (56%), Gaps = 3/106 (2%) Frame = -1 Query: 443 AYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAA---GMGTEIGENG 273 A VSQ + N T+ N+ + + D++ ++ R +L + ++ G+ T +GENG Sbjct: 420 ALVSQNVHLFNDTIANNIAY-AAGDKYSREDIERAAELAHAMEFISKMENGLDTMVGENG 478 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +LSGGQ+ RV++ARA+ D V +LD+ SALD ER + L Sbjct: 479 ASLSGGQRQRVAIARALLRDAPVLILDEATSALDTE-SERAIQSAL 523 >HLYB_PROVU (P11599) Hemolysin secretion/processing ATP-binding protein (EC 3.4.22.-) Length = 707 Score = 52.8 bits (125), Expect(2) = 4e-10 Identities = 27/98 (27%), Positives = 51/98 (52%), Gaps = 1/98 (1%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA-DEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W + + V Q ++N ++ +N+ P ++ A ++ + L G T + Sbjct: 540 WLRRQVGVVLQDNVLLNRSIIDNIALADPGMPVEKVIHAAKLAGAHDFISELREGYNTIV 599 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GE G LSGGQ+ R+++ARA+ + ++ + D+ SALD Sbjct: 600 GEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALD 637 Score = 29.6 bits (65), Expect(2) = 4e-10 Identities = 10/27 (37%), Positives = 19/27 (70%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +T I++ H++ + AD ++VMEKG + Sbjct: 655 RTVIIIAHRLSTVKNADRIIVMEKGQI 681 >MDR2_CRIGR (P21449) Multidrug resistance protein 2 (P-glycoprotein 2) Length = 1276 Score = 62.4 bits (150), Expect = 4e-10 Identities = 33/112 (29%), Positives = 58/112 (51%), Gaps = 3/112 (2%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA---DEHRLQEAVRVCQLEADLRVLAAGMGT 291 W + VSQ+P + + ++ EN+ + + + ++ A + + + L T Sbjct: 1106 WLRAHLGIVSQEPILFDCSIAENIAYGDNSRVVSQDEIERAAKEANIHQFIESLPDKYNT 1165 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +G+ G LSGGQK R+++ARA+ + LLD+ SALD E++V E L Sbjct: 1166 RVGDKGTQLSGGQKQRIAIARALVRQPHILLLDEATSALDTE-SEKVVQEAL 1216 Score = 55.5 bits (132), Expect = 5e-08 Identities = 35/105 (33%), Positives = 55/105 (52%), Gaps = 1/105 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I VSQ+P + T+ EN+ + +++AV+ + L T +GE G Sbjct: 469 IGVVSQEPVLFATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGA 528 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQK R+++ARA+ + ++ LLD+ SALD E +V L Sbjct: 529 QLSGGQKQRIAIARALVRNPKILLLDEATSALDTE-SEAVVQAAL 572 >MDR1_CRIGR (P21448) Multidrug resistance protein 1 (P-glycoprotein 1) Length = 1276 Score = 62.4 bits (150), Expect = 4e-10 Identities = 33/112 (29%), Positives = 58/112 (51%), Gaps = 3/112 (2%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA---DEHRLQEAVRVCQLEADLRVLAAGMGT 291 W + VSQ+P + + ++ EN+ + + + ++ A + + + L T Sbjct: 1105 WLRAHLGIVSQEPILFDCSIAENIAYGDNSRVVSQDEIERAAKEANIHQFIESLPDKYNT 1164 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +G+ G LSGGQK R+++ARA+ + LLD+ SALD E++V E L Sbjct: 1165 RVGDKGTQLSGGQKQRIAIARALVRQPHILLLDEATSALDTE-SEKVVQEAL 1215 Score = 55.5 bits (132), Expect = 5e-08 Identities = 35/105 (33%), Positives = 55/105 (52%), Gaps = 1/105 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I VSQ+P + T+ EN+ + +++AV+ + L T +GE G Sbjct: 467 IGVVSQEPVLFATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGA 526 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQK R+++ARA+ + ++ LLD+ SALD E +V L Sbjct: 527 QLSGGQKQRIAIARALVRNPKILLLDEATSALDTE-SEAVVQAAL 570 >HLYB_ECOLI (P08716) Hemolysin secretion/processing ATP-binding protein (EC 3.4.22.-) Length = 707 Score = 52.4 bits (124), Expect(2) = 5e-10 Identities = 27/98 (27%), Positives = 52/98 (53%), Gaps = 1/98 (1%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA-DEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W + + V Q ++N ++ +N+ +P ++ A ++ + L G T + Sbjct: 540 WLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIV 599 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GE G LSGGQ+ R+++ARA+ + ++ + D+ SALD Sbjct: 600 GEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALD 637 Score = 29.6 bits (65), Expect(2) = 5e-10 Identities = 10/27 (37%), Positives = 19/27 (70%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +T I++ H++ + AD ++VMEKG + Sbjct: 655 RTVIIIAHRLSTVKNADRIIVMEKGKI 681 >HLY2_ECOLI (P10089) Hemolysin secretion/processing ATP-binding protein (EC 3.4.22.-) Length = 707 Score = 52.4 bits (124), Expect(2) = 5e-10 Identities = 27/98 (27%), Positives = 52/98 (53%), Gaps = 1/98 (1%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA-DEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W + + V Q ++N ++ +N+ +P ++ A ++ + L G T + Sbjct: 540 WLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIV 599 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GE G LSGGQ+ R+++ARA+ + ++ + D+ SALD Sbjct: 600 GEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALD 637 Score = 29.6 bits (65), Expect(2) = 5e-10 Identities = 10/27 (37%), Positives = 19/27 (70%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 +T I++ H++ + AD ++VMEKG + Sbjct: 655 RTVIIIAHRLSTVKNADRIIVMEKGKI 681 >MDR3_MOUSE (P21447) Multidrug resistance protein 3 (P-glycoprotein 3) (MDR1A) Length = 1276 Score = 62.0 bits (149), Expect = 6e-10 Identities = 36/113 (31%), Positives = 60/113 (53%), Gaps = 4/113 (3%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGM----G 294 W + VSQ+P + + ++ EN+ + + +E VR + EA++ + Sbjct: 1104 WLRAQLGIVSQEPILFDCSIAENIAYGDNSRVVSYEEIVRAAK-EANIHQFIDSLPDKYN 1162 Query: 293 TEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 T +G+ G LSGGQK R+++ARA+ + LLD+ SALD E++V E L Sbjct: 1163 TRVGDKGTQLSGGQKQRIAIARALVRQPHILLLDEATSALDTE-SEKVVQEAL 1214 Score = 55.8 bits (133), Expect = 4e-08 Identities = 35/105 (33%), Positives = 55/105 (52%), Gaps = 1/105 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFF-SPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I VSQ+P + T+ EN+ + +++AV+ + L T +GE G Sbjct: 466 IGVVSQEPVLFATTIAENIRYGREDVTMDEIEKAVKEANAYDFIMKLPHQFDTLVGERGA 525 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQK R+++ARA+ + ++ LLD+ SALD E +V L Sbjct: 526 QLSGGQKQRIAIARALVRNPKILLLDEATSALDTE-SEAVVQAAL 569 >CYAB_BORPE (P18770) Cyclolysin secretion/processing ATP-binding protein cyaB (EC 3.4.22.-) Length = 712 Score = 61.6 bits (148), Expect = 7e-10 Identities = 36/112 (32%), Positives = 60/112 (53%), Gaps = 4/112 (3%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 + + V Q+ + N ++R+N+ P A H + A R+ + L G T +GEN Sbjct: 546 RQLGVVLQESTLFNRSVRDNIALTRPGASMHEVVAAARLAGAHEFICQLPEGYDTMLGEN 605 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD---AHVGERIVTEVLFG 129 G+ LSGGQ+ R+ +ARA+ V +LD+ SALD H+ +R + ++ G Sbjct: 606 GVGLSGGQRQRIGIARALIHRPRVLILDEATSALDYESEHIIQRNMRDICDG 657 >MDR1_LEIEN (Q06034) Multidrug resistance protein 1 (P-glycoprotein 1) Length = 1280 Score = 61.6 bits (148), Expect = 7e-10 Identities = 33/96 (34%), Positives = 57/96 (59%), Gaps = 1/96 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 ++I+ V Q+P + + T+REN+ + A + ++EA R+ + ++ G TE+G Sbjct: 1112 RNISIVLQEPNLFSGTVRENIRYAREGATDEEVEEAARLAHIHHEIIKWTDGYDTEVGYK 1171 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDA 168 G LSGGQK R+++AR + + LLD+ SALD+ Sbjct: 1172 GRALSGGQKQRIAIARGLLRRPRLLLLDEATSALDS 1207 Score = 57.8 bits (138), Expect = 1e-08 Identities = 37/98 (37%), Positives = 51/98 (52%), Gaps = 1/98 (1%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W Q I VSQ+P + T+ ENV P A + + EA R + + L T + Sbjct: 465 WRDQ-IGIVSQEPNLFAGTMMENVRMGKPNATDEEVVEACRQANIHDTIMALPDRYDTPV 523 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 G G LSGGQK R+++ARA+ + LLD+ SALD Sbjct: 524 GPVGSLLSGGQKQRIAIARALVKRPPILLLDEATSALD 561 >MSBA_YERPE (Q8ZGA9) Lipid A export ATP-binding/permease protein msbA Length = 582 Score = 61.6 bits (148), Expect = 7e-10 Identities = 37/106 (34%), Positives = 58/106 (54%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHR--LQEAVRVCQLEADLRVLAAGMGTEIGENG 273 +A VSQ + N T+ N+ + R ++EA R+ + + G+ T IGENG Sbjct: 419 VALVSQNVHLFNDTVANNIAYARNEQYSRAEIEEAARMAYAMDFINKMEHGLDTVIGENG 478 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 I LSGGQ+ R+++ARA+ + + +LD+ SALD ER + L Sbjct: 479 IMLSGGQRQRIAIARALLRNCPILILDEATSALDTE-SERAIQAAL 523 >ABC9_RAT (Q9QYJ4) ATP-binding cassette, sub-family B, member 9 precursor (ATP-binding cassette transporter 9) (ABC transporter 9 protein) (TAP-like protein) (TAPL) Length = 762 Score = 61.2 bits (147), Expect = 9e-10 Identities = 37/107 (34%), Positives = 58/107 (54%), Gaps = 1/107 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQ-EAVRVCQLEADLRVLAAGMGTEIGENGI 270 I+ VSQ+P + ++ +N+ + P + EA + + L G TE GE G Sbjct: 578 ISLVSQEPVLFARSITDNISYGLPTVPFEMVVEAAQKANAHGFIMELQDGYSTETGEKGA 637 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 LSGGQK RV++ARA+ + V +LD+ SALDA E ++ + + G Sbjct: 638 QLSGGQKQRVAMARALVRNPPVLILDEATSALDAE-SEYLIQQAIHG 683 >ABC9_MOUSE (Q9JJ59) ATP-binding cassette, sub-family B, member 9 precursor (ATP-binding cassette transporter 9) (ABC transporter 9 protein) (TAP-like protein) (TAPL) (mABCB9) Length = 762 Score = 61.2 bits (147), Expect = 9e-10 Identities = 37/107 (34%), Positives = 58/107 (54%), Gaps = 1/107 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQ-EAVRVCQLEADLRVLAAGMGTEIGENGI 270 I+ VSQ+P + ++ +N+ + P + EA + + L G TE GE G Sbjct: 578 ISLVSQEPVLFARSITDNISYGLPTVPFEMVVEAAQKANAHGFIMELQDGYSTETGEKGA 637 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 LSGGQK RV++ARA+ + V +LD+ SALDA E ++ + + G Sbjct: 638 QLSGGQKQRVAMARALVRNPPVLILDEATSALDAE-SEYLIQQAIHG 683 >MDR1_MOUSE (P06795) Multidrug resistance protein 1 (P-glycoprotein 1) Length = 1276 Score = 61.2 bits (147), Expect = 9e-10 Identities = 36/113 (31%), Positives = 60/113 (53%), Gaps = 4/113 (3%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGM----G 294 W + VSQ+P + + ++ EN+ + + +E VR + EA++ + Sbjct: 1106 WLRAHLGIVSQEPILFDCSIAENIAYGDNSRAVSHEEIVRAAK-EANIHQFIDSLPDKYN 1164 Query: 293 TEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 T +G+ G LSGGQK R+++ARA+ + LLD+ SALD E++V E L Sbjct: 1165 TRVGDKGTQLSGGQKQRIAIARALVRQPHILLLDEATSALDTE-SEKVVQEAL 1216 Score = 55.8 bits (133), Expect = 4e-08 Identities = 35/105 (33%), Positives = 55/105 (52%), Gaps = 1/105 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFF-SPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I VSQ+P + T+ EN+ + +++AV+ + L T +GE G Sbjct: 469 IGVVSQEPVLFATTIAENIRYGREDVTMDEIEKAVKEANAYDFIMKLPHQFDTLVGERGA 528 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQK R+++ARA+ + ++ LLD+ SALD E +V L Sbjct: 529 QLSGGQKQRIAIARALVRNPKILLLDEATSALDTE-SEAVVQAAL 572 >CYDC_BACSU (P94366) Transport ATP-binding protein cydC Length = 567 Score = 61.2 bits (147), Expect = 9e-10 Identities = 36/95 (37%), Positives = 51/95 (53%), Gaps = 1/95 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 +++ Y+ Q P+I + TL N+ F+ P A A L + L G+ IGE Sbjct: 401 KNLLYIPQHPYIFDDTLGNNIRFYHPSASAEDTTRAAASAGLTELVNNLPDGLEGRIGEG 460 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 G LSGGQ RV+LARA +R + LLD+P + LD Sbjct: 461 GRALSGGQAQRVALARAFLGNRPILLLDEPTAHLD 495 >ABC9_HUMAN (Q9NP78) ATP-binding cassette, sub-family B, member 9 precursor (ATP-binding cassette transporter 9) (ABC transporter 9 protein) (TAP-like protein) (TAPL) (hABCB9) Length = 766 Score = 61.2 bits (147), Expect = 9e-10 Identities = 37/107 (34%), Positives = 58/107 (54%), Gaps = 1/107 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQ-EAVRVCQLEADLRVLAAGMGTEIGENGI 270 I+ VSQ+P + ++ +N+ + P + EA + + L G TE GE G Sbjct: 582 ISLVSQEPVLFARSITDNISYGLPTVPFEMVVEAAQKANAHGFIMELQDGYSTETGEKGA 641 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 LSGGQK RV++ARA+ + V +LD+ SALDA E ++ + + G Sbjct: 642 QLSGGQKQRVAMARALVRNPPVLILDEATSALDAE-SEYLIQQAIHG 687 >TAGB_DICDI (P54683) Prestalk-specific protein tagB precursor (EC 3.4.21.-) Length = 1905 Score = 58.5 bits (140), Expect(2) = 1e-09 Identities = 37/105 (35%), Positives = 59/105 (56%), Gaps = 2/105 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFF--SPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 + V Q P++ +AT+ EN+ + +P E + EA ++ + L T+IGE G Sbjct: 1599 VTNVHQHPFLFDATIGENIGYAIDNPTQEDII-EAAKLAYAHEFINDLPKKYDTQIGEAG 1657 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 NLSGGQK R+++ARA+ A R++ LLD+ + LD E I + Sbjct: 1658 -NLSGGQKKRIAVARAICAKRKIMLLDEITAELDPESEEAITQSI 1701 Score = 22.3 bits (46), Expect(2) = 1e-09 Identities = 8/24 (33%), Positives = 15/24 (62%) Frame = -2 Query: 112 TRILVTHQIDVLSRADFVVVMEKG 41 T ++V H++ + D + V+EKG Sbjct: 1709 TVVMVAHKVAAVRDCDKIFVLEKG 1732 >STE6_YEAST (P12866) Mating factor A secretion protein STE6 (Multiple drug resistance protein homolog) (P-glycoprotein) Length = 1290 Score = 60.8 bits (146), Expect = 1e-09 Identities = 36/105 (34%), Positives = 58/105 (55%), Gaps = 11/105 (10%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSP-----------ADEHRLQEAVRVCQLEADLRVLA 306 ++I V Q+ + N TLR+N+L S + H +++A ++ L+ + L Sbjct: 433 ENITVVEQRCTLFNDTLRKNILLGSTDSVRNADCSTNENRHLIKDACQMALLDRFILDLP 492 Query: 305 AGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 G+ T IG G+ LSGGQ+ RV++ARA D + LD+ +SALD Sbjct: 493 DGLETLIGTGGVTLSGGQQQRVAIARAFIRDTPILFLDEAVSALD 537 Score = 46.2 bits (108), Expect = 3e-05 Identities = 32/112 (28%), Positives = 59/112 (52%), Gaps = 2/112 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPAD--EHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 + I+ V Q+P + N T+R+N+ + + E + +A++ + + G+ T I Sbjct: 1128 KEISVVEQKPLLFNGTIRDNLTYGLQDEILEIEMYDALKYVGIHDFVISSPQGLDTRIDT 1187 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGAP 123 LSGGQ R+ +ARA+ ++ +LD+ SALD+ V I+ E++ P Sbjct: 1188 T--LLSGGQAQRLCIARALLRKSKILILDECTSALDS-VSSSIINEIVKKGP 1236 >MDR2_RAT (Q08201) Multidrug resistance protein 2 (P-glycoprotein 2) Length = 1278 Score = 60.5 bits (145), Expect = 2e-09 Identities = 33/112 (29%), Positives = 57/112 (50%), Gaps = 3/112 (2%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA---DEHRLQEAVRVCQLEADLRVLAAGMGT 291 W + VSQ+P + + ++ +N+ + + + + A + + + L T Sbjct: 1106 WLRAQLGIVSQEPILFDCSIAKNIAYGDNSRVVSQDEIVRAAKEANIHPFIETLPQKYET 1165 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +G+ G LSGGQK R+++ARA+ V LLD+ SALD E++V E L Sbjct: 1166 RVGDKGTQLSGGQKQRIAIARALIRQPRVLLLDEATSALDTE-SEKVVQEAL 1216 Score = 55.1 bits (131), Expect = 7e-08 Identities = 31/93 (33%), Positives = 52/93 (55%), Gaps = 1/93 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFF-SPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I VSQ+P + + T+ EN+ + +++AV+ + L T +G+ G Sbjct: 469 IGVVSQEPVLFSTTIAENIRYGRGNVTMDEIKKAVKEANAYDFIMKLPQKFDTLVGDRGA 528 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LSGGQK R+++ARA+ + ++ LLD+ SALD Sbjct: 529 QLSGGQKQRIAIARALVRNPKILLLDEATSALD 561 >SUNT_BACSU (O30671) Sublancin 168 processing and transport ATP-binding protein sunT (EC 3.4.22.-) Length = 705 Score = 60.5 bits (145), Expect = 2e-09 Identities = 33/109 (30%), Positives = 58/109 (53%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 I Y+ + P++ T++EN+ D++ ++ A + Q + L ++ ENG N Sbjct: 559 IVYIDENPFLFKGTIKENLCMGEIFDQNEIENACIMSQCHEFICNLDKQYSYKLSENGSN 618 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGAPC 120 LS GQK R++LARA+ +V +LD+ LS +D +++ E L C Sbjct: 619 LSTGQKQRLALARAILHQPQVLILDESLSNIDPD-NTKLIYETLHRMDC 666 >Y664_HAEIN (Q57538) Probable ABC transporter ATP-binding protein HI0664 Length = 552 Score = 60.5 bits (145), Expect = 2e-09 Identities = 37/113 (32%), Positives = 61/113 (53%), Gaps = 1/113 (0%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENV-LFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 ++AY++QQ +I N T+ EN+ L A + EA + + + L G T++ E G Sbjct: 414 NMAYITQQTYIFNETIEENIRLARRDATLEEIMEAAKKASIHDFILSLPQGYQTKMTELG 473 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGAPCTK 114 NLS G+K R+ +ARA + + LLD+P S LD+ + E ++ + L K Sbjct: 474 GNLSDGEKQRIGIARAFLHNAPIILLDEPTSNLDS-LNEAMILKSLLNVKAEK 525 >MDR5_DROME (Q00748) Multidrug resistance protein homolog 65 (P-glycoprotein 65) Length = 1302 Score = 60.1 bits (144), Expect = 2e-09 Identities = 36/110 (32%), Positives = 59/110 (53%), Gaps = 1/110 (0%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W +IA V Q+P + T+ +N+ + P A + ++ A + L + I Sbjct: 478 WLRSNIAVVGQEPVLFLGTIAQNISYGKPGATQKEIEAAATQAGAHEFITNLPESYRSMI 537 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 GE G LSGGQK R+++ARA+ + ++ LLD+ SALD + E+ V + L Sbjct: 538 GERGSQLSGGQKQRIAIARALIQNPKILLLDEATSALD-YQSEKQVQQAL 586 Score = 53.9 bits (128), Expect = 2e-07 Identities = 33/107 (30%), Positives = 56/107 (52%), Gaps = 3/107 (2%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQE---AVRVCQLEADLRVLAAGMGTEIGEN 276 + VSQ+P + ++ EN+ + + E A + + + L G T +G Sbjct: 1138 LGIVSQEPTLFERSIAENIAYGDNRRSVSMVEIIAAAKSANAHSFIISLPNGYDTRMGAR 1197 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G LSGGQK R+++ARA+ + ++ LLD+ SALD E++V + L Sbjct: 1198 GTQLSGGQKQRIAIARALVRNPKILLLDEATSALDLQ-SEQLVQQAL 1243 >MDR3_CRIGR (P23174) Multidrug resistance protein 3 (P-glycoprotein 3) Length = 1281 Score = 60.1 bits (144), Expect = 2e-09 Identities = 33/112 (29%), Positives = 56/112 (50%), Gaps = 3/112 (2%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPA---DEHRLQEAVRVCQLEADLRVLAAGMGT 291 W + VSQ+P + + ++ EN+ + + + + A + + + L T Sbjct: 1109 WLRAQLGIVSQEPVLFDCSIAENIAYGDNSRVVSQDEIVRAAKAANIHPFIETLPQKYKT 1168 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +G+ G LSGGQK R+++ RA+ V LLD+ SALD E++V E L Sbjct: 1169 RVGDKGTQLSGGQKQRLAIRRALIRQPRVLLLDEATSALDTE-SEKVVQEAL 1219 Score = 57.0 bits (136), Expect = 2e-08 Identities = 32/93 (34%), Positives = 52/93 (55%), Gaps = 1/93 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFF-SPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I VSQ+P + + T+ EN+ + +++AV+ + L T +GE G Sbjct: 472 IGVVSQEPVLFSTTIAENIRYGRGNVTMEEIKKAVKEANAYEFIMKLPQKFDTLVGERGA 531 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LSGGQK R+++ARA+ + ++ LLD+ SALD Sbjct: 532 QLSGGQKQRIAIARALVRNPKILLLDEATSALD 564 >TAP1_HUMAN (Q03518) Antigen peptide transporter 1 (APT1) (Peptide transporter TAP1) (Peptide transporter PSF1) (Peptide supply factor 1) (PSF-1) (Peptide transporter involved in antigen processing 1) Length = 748 Score = 55.8 bits (133), Expect(2) = 2e-09 Identities = 39/118 (33%), Positives = 63/118 (53%), Gaps = 3/118 (2%) Frame = -1 Query: 467 YAWASQSIAYVSQQPWIMNATLRENVLFF---SPADEHRLQEAVRVCQLEADLRVLAAGM 297 + + + +A V Q+P + +L+EN+ + P E AV+ + + L G Sbjct: 574 HRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVK-SGAHSFISGLPQGY 632 Query: 296 GTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGAP 123 TE+ E G LSGGQ+ V+LARA+ V +LDD SALDA+ + V ++L+ +P Sbjct: 633 DTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDAN-SQLQVEQLLYESP 689 Score = 23.9 bits (50), Expect(2) = 2e-09 Identities = 7/25 (28%), Positives = 18/25 (72%) Frame = -2 Query: 106 ILVTHQIDVLSRADFVVVMEKGAVQ 32 +L+T + ++ +AD ++ +E GA++ Sbjct: 697 LLITQHLSLVEQADHILFLEGGAIR 721 >LMRA_LACLA (Q9CHL8) Multidrug resistance ABC transporter ATP-binding and permease protein Length = 590 Score = 59.3 bits (142), Expect = 4e-09 Identities = 35/111 (31%), Positives = 64/111 (57%), Gaps = 2/111 (1%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPAD--EHRLQEAVRVCQLEADLRVLAAGMGTE 288 W SQ I +VSQ IM T+REN+ + D + L + + + + + + + TE Sbjct: 421 WRSQ-IGFVSQDSAIMAGTIRENLTYGLEGDYTDEDLWQVLDLAFARSFVENMPDQLNTE 479 Query: 287 IGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 +GE G+ +SGGQ+ R+++ARA + ++ +LD+ ++LD+ E +V + L Sbjct: 480 VGERGVKISGGQRQRLAIARAFLRNPKILMLDEATASLDSE-SESMVQKAL 529 >MDR1_RAT (P43245) Multidrug resistance protein 1 (P-glycoprotein 1) Length = 1277 Score = 59.3 bits (142), Expect = 4e-09 Identities = 33/109 (30%), Positives = 57/109 (52%), Gaps = 3/109 (2%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPA---DEHRLQEAVRVCQLEADLRVLAAGMGTEIG 282 +++ VSQ+P + + ++ EN+ + + + A R + + L T +G Sbjct: 1110 RALGIVSQEPILFDCSIAENIAYGDNSRVVSHEEIVRAAREANIHQFIDSLPEKYNTRVG 1169 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 + G LSGGQK R+++ARA+ + LLD+ SALD E++V E L Sbjct: 1170 DKGTQLSGGQKQRIAIARALVRQPHILLLDEATSALDTE-SEKVVQEAL 1217 Score = 55.5 bits (132), Expect = 5e-08 Identities = 35/105 (33%), Positives = 55/105 (52%), Gaps = 1/105 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I VSQ+P + T+ EN+ + +++AV+ + L T +GE G Sbjct: 469 IGVVSQEPVLFATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGA 528 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQK R+++ARA+ + ++ LLD+ SALD E +V L Sbjct: 529 QLSGGQKQRIAIARALVRNPKILLLDEATSALDTE-SEAVVQAAL 572 >MDR_PLAFF (P13568) Multidrug resistance protein (Chloroquine resistance protein) Length = 1419 Score = 55.8 bits (133), Expect(2) = 4e-09 Identities = 33/104 (31%), Positives = 62/104 (59%), Gaps = 3/104 (2%) Frame = -1 Query: 437 VSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEAD---LRVLAAGMGTEIGENGIN 267 VSQ+P + N ++ EN+ F ++ L++ RV + A + L T +G G + Sbjct: 1254 VSQEPMLFNMSIYENIKF--GREDATLEDVKRVSKFAAIDEFIESLPNKYDTNVGPYGKS 1311 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQK R+++ARA+ + ++ LLD+ S+LD++ E+++ + + Sbjct: 1312 LSGGQKQRIAIARALLREPKILLLDEATSSLDSN-SEKLIEKTI 1354 Score = 43.5 bits (101), Expect = 2e-04 Identities = 19/41 (46%), Positives = 29/41 (70%) Frame = -1 Query: 293 TEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 T +G N LSGGQK R+S+ARA+ + ++ +LD+ S+LD Sbjct: 554 TLVGSNASKLSGGQKQRISIARAIMRNPKILILDEATSSLD 594 Score = 23.1 bits (48), Expect(2) = 4e-09 Identities = 10/23 (43%), Positives = 15/23 (65%) Frame = -2 Query: 121 AQKTRILVTHQIDVLSRADFVVV 53 A KT I + H+I + R+D +VV Sbjct: 1361 ADKTIITIAHRIASIKRSDKIVV 1383 >YNT9_SCHPO (Q9Y7M7) Probable ATP-dependent permease C9B6.09c Length = 726 Score = 52.4 bits (124), Expect(2) = 4e-09 Identities = 31/100 (31%), Positives = 53/100 (53%), Gaps = 1/100 (1%) Frame = -1 Query: 467 YAWASQSIAYVSQQPWIMNATLRENVLFF-SPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 + W S V Q+P + + T+ EN+ + S A + +++A + L T Sbjct: 554 HQWRSH-FGLVGQEPVLFSGTIGENIAYGKSNASQEEIEDAAKRANCSFVLS-FPEKWST 611 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 ++G G+ LSGGQK R+++ARA+ + +LD+ SALD Sbjct: 612 QVGTRGLQLSGGQKQRIAIARALLRNPAFLILDEATSALD 651 Score = 26.6 bits (57), Expect(2) = 4e-09 Identities = 11/33 (33%), Positives = 19/33 (57%) Frame = -2 Query: 133 LVHLAQKTRILVTHQIDVLSRADFVVVMEKGAV 35 L+H T I + H++ + RAD ++V+ G V Sbjct: 665 LMHNRSMTTITIAHKLATIRRADQIIVVGDGKV 697 >MSBA_XANAC (Q8PKS5) Lipid A export ATP-binding/permease protein msbA Length = 589 Score = 58.9 bits (141), Expect = 5e-09 Identities = 36/108 (33%), Positives = 60/108 (55%), Gaps = 2/108 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF--FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 + IA V QQ + + ++ +NV F AD +L+ A+ + L G+ + +G Sbjct: 421 RQIALVGQQVMLFDGSIADNVAFGEMRNADAGKLERAILGANAMEFVAQLPEGLQSHVGT 480 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G LSGGQ+ R+++ARA+ D V +LD+ +ALD + ER+V + L Sbjct: 481 KGGRLSGGQRQRLAIARAMLKDAPVLILDEATAALD-NESERLVQDAL 527 >MSBA_XANCP (Q8P8W4) Lipid A export ATP-binding/permease protein msbA Length = 589 Score = 58.2 bits (139), Expect = 8e-09 Identities = 34/108 (31%), Positives = 60/108 (55%), Gaps = 2/108 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF--FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 + IA V QQ + + ++ ENV + D +L+ A++ + L G+ + +G Sbjct: 421 RQIALVGQQVMLFDGSIAENVAYGEMRQCDAGQLERAIQGANAMEFVAQLPEGLQSHVGT 480 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G LSGGQ+ R+++ARA+ D + +LD+ +ALD + ER+V + L Sbjct: 481 KGGRLSGGQRQRLAIARAMLKDAPILILDEATAALD-NESERLVQDAL 527 >TAP2_HUMAN (Q03519) Antigen peptide transporter 2 (APT2) (Peptide transporter TAP2) (Peptide transporter PSF2) (Peptide supply factor 2) (PSF-2) (Peptide transporter involved in antigen processing 2) Length = 686 Score = 58.2 bits (139), Expect = 8e-09 Identities = 27/100 (27%), Positives = 56/100 (56%), Gaps = 1/100 (1%) Frame = -1 Query: 467 YAWASQSIAYVSQQPWIMNATLRENVLF-FSPADEHRLQEAVRVCQLEADLRVLAAGMGT 291 + + + V Q+P + + ++R N+ + ++ ++ A + + ++ + G+ T Sbjct: 539 HCYLHSQVVSVGQEPVLFSGSVRNNIAYGLQSCEDDKVMAAAQAAHADDFIQEMEHGIYT 598 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 ++GE G L+ GQK R+++ARA+ D V +LD+ SALD Sbjct: 599 DVGEKGSQLAAGQKQRLAIARALVRDPRVLILDEATSALD 638 >MDLB_ECOLI (P75706) Multidrug resistance-like ATP-binding protein mdlB Length = 593 Score = 57.8 bits (138), Expect = 1e-08 Identities = 32/101 (31%), Positives = 54/101 (53%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 Q +A V Q P ++ T NV E R+ +A+ QL R ++ G+ T +GE G Sbjct: 415 QGVAMVQQDPVVLADTFLANVTLGRDISEERVWQALETVQLAELARSMSDGIYTPLGEQG 474 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 NLS GQK ++LAR + ++ +LD+ +++D+ + I Sbjct: 475 NNLSVGQKQLLALARVLVETPQILILDEATASIDSGTEQAI 515 >APRD_PSEAE (Q03024) Alkaline protease secretion ATP-binding protein aprD Length = 593 Score = 57.8 bits (138), Expect = 1e-08 Identities = 32/92 (34%), Positives = 49/92 (53%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN 267 I Y+ Q + T+ EN+ F ++ EA R+ + + L G T +G G Sbjct: 409 IGYLPQDIELFAGTVAENIARFGEVQADKVVEAARLAGVHELVLRLPQGYDTVLGVGGAG 468 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LSGGQ+ R++LARA+Y + +LD+P S LD Sbjct: 469 LSGGQRQRIALARALYGAPTLVVLDEPNSNLD 500 >CVAB_ECOLI (P22520) Colicin V secretion/processing ATP-binding protein cvaB (EC 3.4.22.-) Length = 698 Score = 57.4 bits (137), Expect = 1e-08 Identities = 34/94 (36%), Positives = 51/94 (54%), Gaps = 1/94 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPA-DEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 IA V Q + + ++REN+ F+ DE + E R + + + G T IGE G Sbjct: 569 IACVMQDDRLFSGSIRENICGFAEEMDEEWMVECARASHIHDVIMNMPMGYETLIGELGE 628 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDA 168 LSGGQK R+ +ARA+Y + +D+ SALD+ Sbjct: 629 GLSGGQKQRIFIARALYRKPGILFMDEATSALDS 662 >MSBA_HAEIN (P44407) Lipid A export ATP-binding/permease protein msbA Length = 587 Score = 57.4 bits (137), Expect = 1e-08 Identities = 37/109 (33%), Positives = 59/109 (54%), Gaps = 3/109 (2%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRV---LAAGMGTEIG 282 ++ A VSQQ + N T+ N+ + + D++ +E + + L L T IG Sbjct: 422 ENCAVVSQQVHLFNDTIANNIAY-AAQDKYSREEIIAAAKAAYALEFIEKLPQVFDTVIG 480 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 ENG +LSGGQ+ R+++ARA+ + V +LD+ SALD ER + L Sbjct: 481 ENGTSLSGGQRQRLAIARALLRNSPVLILDEATSALDTE-SERAIQSAL 528 >LMRA_LACLC (P97046) Multidrug resistance ABC transporter ATP-binding and permease protein Length = 590 Score = 57.0 bits (136), Expect = 2e-08 Identities = 31/100 (31%), Positives = 59/100 (59%), Gaps = 2/100 (2%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPAD--EHRLQEAVRVCQLEADLRVLAAGMGTE 288 W SQ I +VSQ IM T+REN+ + + + L + + + + + + + TE Sbjct: 421 WRSQ-IGFVSQDSAIMAGTIRENLTYGLEGNFTDEDLWQVLDLAFARSFVENMPDQLNTE 479 Query: 287 IGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDA 168 +GE G+ +SGGQ+ R+++ARA + ++ +LD+ ++LD+ Sbjct: 480 VGERGVKISGGQRQRLAIARAFLRNPKILMLDEATASLDS 519 >MCHF_ECOLI (Q9EXN5) Probable microcin H47 secretion/processing ATP-binding protein mchF (EC 3.4.22.-) Length = 698 Score = 57.0 bits (136), Expect = 2e-08 Identities = 35/105 (33%), Positives = 54/105 (51%), Gaps = 1/105 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 IA V Q + + ++REN+ F+ D+ + E R + + + G T IGE G Sbjct: 569 IACVMQDDRLFSGSIRENICGFAEETDDEWMTECARASHIHDVIMKMPMGYETLIGELGE 628 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQK R+ +ARA+Y + +D+ S+LD ER V + Sbjct: 629 GLSGGQKQRIFIARALYRKPGILFMDEATSSLDTE-SERFVNAAI 672 >MSBA_FRANO (Q47908) Lipid A export ATP-binding/permease protein msbA Length = 593 Score = 57.0 bits (136), Expect = 2e-08 Identities = 35/106 (33%), Positives = 59/106 (55%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLF--FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 ++ VSQ + + T+ N+ F E + +A++ ++ L+ G+ T IG NG Sbjct: 426 LSIVSQNVHLFDDTVYNNIAFGLSREVSEDEVIDALKRANAYEFVQELSDGIHTNIGNNG 485 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQ+ R+S+ARA+ + V + D+ SALD + ER+V + L Sbjct: 486 SKLSGGQRQRISIARALLKNAPVLIFDEATSALD-NESERVVQQAL 530 >TAP2_RAT (P36372) Antigen peptide transporter 2 (APT2) Length = 703 Score = 57.0 bits (136), Expect = 2e-08 Identities = 29/104 (27%), Positives = 59/104 (56%), Gaps = 1/104 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF-FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 + + V Q+P + + ++++N+ + ++ ++ A + + + + G+ TEIGE Sbjct: 544 RQVVLVGQEPVLFSGSVKDNIAYGLRDCEDAQVMAAAQAACADDFIGEMTNGINTEIGEK 603 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVT 144 G L+ GQK R+++ARA+ + V +LD+ SALDA + + T Sbjct: 604 GSQLAVGQKQRLAIARALVRNPRVLILDEATSALDAECEQALQT 647 >AB11_HUMAN (O95342) Bile salt export pump (ATP-binding cassette, sub-family B, member 11) Length = 1321 Score = 56.6 bits (135), Expect = 2e-08 Identities = 37/110 (33%), Positives = 57/110 (51%), Gaps = 1/110 (0%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFF-SPADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W I V Q+P + + T+ EN+ + A + +A + + L T + Sbjct: 493 WLRDQIGIVEQEPVLFSTTIAENIRYGREDATMEDIVQAAKEANAYNFIMDLPQQFDTLV 552 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 GE G +SGGQK RV++ARA+ + ++ LLD SALD + E +V EVL Sbjct: 553 GEGGGQMSGGQKQRVAIARALIRNPKILLLDMATSALD-NESEAMVQEVL 601 Score = 53.5 bits (127), Expect = 2e-07 Identities = 31/96 (32%), Positives = 51/96 (53%), Gaps = 3/96 (3%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADE---HRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 +I VSQ+P + ++ +N+ + E R+ A + QL + L T +G Sbjct: 1155 NIGIVSQEPVLFACSIMDNIKYGDNTKEIPMERVIAAAKQAQLHDFVMSLPEKYETNVGS 1214 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 G LS G+K R+++ARA+ D ++ LLD+ SALD Sbjct: 1215 QGSQLSRGEKQRIAIARAIVRDPKILLLDEATSALD 1250 >CHVA_AGRT5 (P18768) Beta-(1-->2)glucan export ATP-binding protein chvA (Attachment protein) Length = 588 Score = 56.2 bits (134), Expect = 3e-08 Identities = 34/105 (32%), Positives = 55/105 (52%), Gaps = 1/105 (0%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENV-LFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 SIA V Q ++N ++REN+ L A + + EA + G T++GE G Sbjct: 410 SIATVFQDAGLLNRSIRENIRLGRETATDAEVVEAAAAAAATDFIDSRINGYLTQVGERG 469 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 LSGG++ R+++ARA+ + + +LD+ SALD R+ V Sbjct: 470 NRLSGGERQRIAIARAILKNAPILVLDEATSALDVETEARVKAAV 514 >ATM1_YEAST (P40416) Transporter ATM1, mitochondrial precursor Length = 690 Score = 56.2 bits (134), Expect = 3e-08 Identities = 32/104 (30%), Positives = 53/104 (50%), Gaps = 1/104 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFS-PADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I V Q + N T+ ENV F A + + V QL ++ L G T +GE G+ Sbjct: 512 IGVVPQDTPLFNDTIWENVKFGRIDATDEEVITVVEKAQLAPLIKKLPQGFDTIVGERGL 571 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 +SGG+K R+++AR + + + D+ SALD H + ++ + Sbjct: 572 MISGGEKQRLAIARVLLKNARIMFFDEATSALDTHTEQALLRTI 615 >TAGC_DICDI (Q23868) Prestalk-specific protein tagC precursor (EC 3.4.21.-) Length = 1743 Score = 54.3 bits (129), Expect(2) = 4e-08 Identities = 32/105 (30%), Positives = 58/105 (55%), Gaps = 2/105 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFF--SPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 + V Q P++ +A++++N+ + +P E + EA ++ ++ L T +G G Sbjct: 1529 VTCVHQNPYLFDASIKDNIGYALDNPTIEEVI-EAAKLAYAHEFIKDLPQQYDTVLGSAG 1587 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 LSGGQK R+++ARA+ A R++ LLD+ + LD E I + Sbjct: 1588 SLLSGGQKKRIAIARAICAKRKIMLLDEITAELDPESEEAITQSI 1632 Score = 21.2 bits (43), Expect(2) = 4e-08 Identities = 7/24 (29%), Positives = 15/24 (62%) Frame = -2 Query: 112 TRILVTHQIDVLSRADFVVVMEKG 41 T ++V H++ + D + V++KG Sbjct: 1640 TVVMVAHKVAAVRDCDKIFVLDKG 1663 >AB11_RAT (O70127) Bile salt export pump (ATP-binding cassette, sub-family B, member 11) (Sister of P-glycoprotein) Length = 1321 Score = 55.8 bits (133), Expect = 4e-08 Identities = 34/105 (32%), Positives = 52/105 (49%), Gaps = 1/105 (0%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFF-SPADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W I V Q+P + + T+ EN+ F A + +A + + L T + Sbjct: 493 WLRDQIGIVEQEPVLFSTTIAENIRFGREDATMEDIVQAAKDANAYNFIMALPQQFDTLV 552 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 GE G +SGGQK RV++ARA+ + ++ LLD SALD R+ Sbjct: 553 GEGGGQMSGGQKQRVAIARALIRNPKILLLDMATSALDNESEARV 597 Score = 54.3 bits (129), Expect = 1e-07 Identities = 31/105 (29%), Positives = 56/105 (53%), Gaps = 3/105 (2%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAV---RVCQLEADLRVLAAGMGTEIGE 279 +I VSQ+P + + ++ +N+ + E ++ A+ + QL + L T +G Sbjct: 1155 NIGIVSQEPVLFDCSIMDNIKYGDNTKEISVERAIAAAKQAQLHDFVMSLPEKYETNVGI 1214 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVT 144 G LS G+K R+++ARA+ D ++ LLD+ SALD + + T Sbjct: 1215 QGSQLSRGEKQRIAIARAIVRDPKILLLDEATSALDTESEKTVQT 1259 >CYDD_BACSU (P94367) Transport ATP-binding protein cydD Length = 575 Score = 55.8 bits (133), Expect = 4e-08 Identities = 31/109 (28%), Positives = 60/109 (55%), Gaps = 1/109 (0%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENV-LFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 + ++A ++Q+P + + ++ N+ L A + ++ A + +L + L G T + E Sbjct: 409 ADAVAVLNQKPHLFDTSILNNIRLGNGEASDEDVRRAAKQVKLHDYIESLPDGYHTSVQE 468 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLF 132 GI SGG++ R++LAR + D + +LD+P LD + ER + E +F Sbjct: 469 TGIRFSGGERQRIALARILLQDTPIIILDEPTVGLDP-ITERELMETVF 516 >TAP2_MOUSE (P36371) Antigen peptide transporter 2 (APT2) (Histocompatibility antigen modifier 2) Length = 702 Score = 55.1 bits (131), Expect = 7e-08 Identities = 28/96 (29%), Positives = 56/96 (58%), Gaps = 1/96 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF-FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 + + V Q+P + + ++++N+ + ++ ++ A + + + + G+ TEIGE Sbjct: 543 RQVVLVGQEPVLFSGSVKDNIAYGLRDCEDAQVMAAAQAACADDFIGEMTNGINTEIGEK 602 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDA 168 G L+ GQK R+++ARA+ + V +LD+ SALDA Sbjct: 603 GGQLAVGQKQRLAIARALVRNPRVLILDEATSALDA 638 >ABC7_HUMAN (O75027) ATP-binding cassette, sub-family B, member 7, mitochondrial precursor (ATP-binding cassette transporter 7) (ABC transporter 7 protein) Length = 752 Score = 54.7 bits (130), Expect = 9e-08 Identities = 31/103 (30%), Positives = 56/103 (54%), Gaps = 1/103 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFS-PADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 +++ V Q + + T+ N+L+ + A + ++ L + + G T++GE Sbjct: 546 RAVGVVPQDAVLFHNTIYYNLLYGNISASPEEVYAVAKLAGLHDAILRMPHGYDTQVGER 605 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 G+ LSGG+K RV++ARA+ D V L D+ S+LD+ E I+ Sbjct: 606 GLKLSGGEKQRVAIARAILKDPPVILYDEATSSLDSITEETIL 648 >MSBA_PSEPK (Q88D92) Lipid A export ATP-binding/permease protein msbA Length = 602 Score = 54.7 bits (130), Expect = 9e-08 Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 2/94 (2%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHR--LQEAVRVCQLEADLRVLAAGMGTEIGENG 273 ++ V+Q + N T+ N+ + A R ++ A + + L G TE+GENG Sbjct: 432 VSQVTQHVTLFNDTVANNIAYGDLAGAPRADIEAAAADAYAKEFVDRLPKGFDTEVGENG 491 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + LSGGQ+ R+++ARA+ + + +LD+ SALD Sbjct: 492 VLLSGGQRQRLAIARALLKNAPLLILDEATSALD 525 >MSBA_PSESM (Q87VF3) Lipid A export ATP-binding/permease protein msbA Length = 600 Score = 54.7 bits (130), Expect = 9e-08 Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 2/94 (2%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHR--LQEAVRVCQLEADLRVLAAGMGTEIGENG 273 IA V+Q + N ++ N+ + A R ++ A + + L G T++GENG Sbjct: 430 IAQVNQNVTLFNDSIANNIAYGDLAGAPRADIEAAAADAYAKEFIDQLPQGFDTQVGENG 489 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + LSGGQ+ R+++ARA+ + + +LD+ SALD Sbjct: 490 VLLSGGQRQRLAIARALLKNAPLLILDEATSALD 523 >MDL2_YEAST (P33311) ATP-dependent permease MDL2 Length = 820 Score = 54.7 bits (130), Expect = 9e-08 Identities = 31/95 (32%), Positives = 52/95 (54%), Gaps = 3/95 (3%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLF---FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 I V Q+P +M+ T+R+N+ + ++P E ++ + C + T IG + Sbjct: 571 IGIVQQEPVLMSGTIRDNITYGLTYTPTKEE-IRSVAKQCFCHNFITKFPNTYDTVIGPH 629 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 G LSGGQK R+++ARA+ + +LD+ SALD Sbjct: 630 GTLLSGGQKQRIAIARALIKKPTILILDEATSALD 664 >AB11_RABIT (Q9N0V3) Bile salt export pump (ATP-binding cassette, sub-family B, member 11) (Sister of P-glycoprotein) Length = 1321 Score = 54.3 bits (129), Expect = 1e-07 Identities = 30/96 (31%), Positives = 52/96 (54%), Gaps = 3/96 (3%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADE---HRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 +I VSQ+P + ++++N+ + E R+ A + Q+ + L T +G Sbjct: 1155 NIGIVSQEPVLFACSIKDNIKYGDNTQEIPMERIIAAAKKAQVHDFVMSLPEKYETNVGS 1214 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 G LS G+K R+++ARA+ D ++ LLD+ SALD Sbjct: 1215 QGSQLSRGEKQRIAIARAIVRDPKILLLDEATSALD 1250 Score = 50.8 bits (120), Expect = 1e-06 Identities = 36/110 (32%), Positives = 54/110 (49%), Gaps = 1/110 (0%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFF-SPADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W I V Q+P + T+ E + + A L +A + + L T + Sbjct: 493 WLRNQIGIVEQEPVLFFHTIAEKIRYGREDATMEDLIQAAKEANAYNFIMDLPQQFDTLV 552 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 GE G +SGGQK RV++ARA+ + ++ LLD SALD + E +V E L Sbjct: 553 GEGGGQMSGGQKQRVAIARALIRNPKILLLDMATSALD-NESEAMVQEAL 601 >YA51_HAEIN (Q57180) Hypothetical ABC transporter ATP-binding protein HI1051 Length = 614 Score = 54.3 bits (129), Expect = 1e-07 Identities = 30/103 (29%), Positives = 57/103 (55%), Gaps = 6/103 (5%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTE---- 288 + I V+Q +++ ++R+N+++ P A + + A + + L+ G + Sbjct: 438 RQIGLVTQDTSLLHRSVRDNIIYGRPNATDEEMVLAAERAEAADFIPFLSDSQGRKGYDA 497 Query: 287 -IGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHV 162 +GE G+ LSGGQ+ R+++AR + D + LLD+ SALD+ V Sbjct: 498 HVGERGVKLSGGQRQRIAIARVMLKDAPILLLDEATSALDSEV 540 >Y663_HAEIN (P71355) Hypothetical ABC transporter ATP-binding protein HI0663 Length = 560 Score = 51.2 bits (121), Expect(2) = 1e-07 Identities = 32/105 (30%), Positives = 52/105 (49%), Gaps = 3/105 (2%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLA---AGMGTEIG 282 Q ++ VS ++ TLREN+ A E + C + +L G+ ++ Sbjct: 388 QKVSLVSHSSYVFKGTLRENMTM---AKIDATDEQIYACLEQVNLAQFVRDNGGLDMQLL 444 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 G NLSGGQ R++LARA+ + E+Y+ D+ S +D E I+ Sbjct: 445 SRGANLSGGQIQRLALARALLHNAELYIFDEATSNIDVESEEIIL 489 Score = 22.7 bits (47), Expect(2) = 1e-07 Identities = 8/26 (30%), Positives = 18/26 (69%) Frame = -2 Query: 118 QKTRILVTHQIDVLSRADFVVVMEKG 41 QKT ++++H++ AD + V+++G Sbjct: 498 QKTIVMISHRLANAVNADCINVLDQG 523 >TAP1_RAT (P36370) Antigen peptide transporter 1 (APT1) Length = 725 Score = 53.9 bits (128), Expect = 2e-07 Identities = 37/113 (32%), Positives = 58/113 (51%), Gaps = 5/113 (4%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGM----GTEIGE 279 +A V Q+P + + REN+ + E + +E+ +G TE+GE Sbjct: 558 VAAVGQEPLLFGRSFRENIAY--GLTRTPTMEEITAVAMESGAHDFISGFPQGYDTEVGE 615 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI-VTEVLFGAP 123 G LSGGQ+ V+LARA+ + +LDD SALDA G ++ V +L+ +P Sbjct: 616 TGNQLSGGQRQAVALARALIRKPRLLILDDATSALDA--GNQLRVQRLLYESP 666 >AB11_MOUSE (Q9QY30) Bile salt export pump (ATP-binding cassette, sub-family B, member 11) (Sister of P-glycoprotein) Length = 1321 Score = 53.5 bits (127), Expect = 2e-07 Identities = 30/96 (31%), Positives = 53/96 (55%), Gaps = 3/96 (3%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAV---RVCQLEADLRVLAAGMGTEIGE 279 +I VSQ+P + + ++ +N+ + E ++ A+ + QL + L T +G Sbjct: 1155 NIGIVSQEPVLFDCSIMDNIKYGDNTKEISVERAIAAAKQAQLHDFVMSLPEKYETNVGI 1214 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 G LS G+K R+++ARA+ D ++ LLD+ SALD Sbjct: 1215 QGSQLSRGEKQRIAIARAIVRDPKILLLDEATSALD 1250 Score = 53.5 bits (127), Expect = 2e-07 Identities = 33/98 (33%), Positives = 49/98 (50%), Gaps = 1/98 (1%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENV-LFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 W I V Q+P + + T+ EN+ L A + +A + + L T + Sbjct: 493 WLRDQIGIVEQEPVLFSTTIAENIRLGREEATMEDIVQAAKDANAYNFIMALPQQFDTLV 552 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 GE G +SGGQK RV++ARA+ ++ LLD SALD Sbjct: 553 GEGGGQMSGGQKQRVAIARALIRKPKILLLDMATSALD 590 >YFIC_BACSU (P54719) Hypothetical ABC transporter ATP-binding protein yfiC Length = 604 Score = 53.5 bits (127), Expect = 2e-07 Identities = 32/106 (30%), Positives = 56/106 (52%), Gaps = 1/106 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFS-PADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 +++ +V Q ++ T+REN+ + A + ++ A + + + L G T + +N Sbjct: 440 KNMGFVLQDSFLFQGTIRENIRYGRLDASDQEVEAAAKTANAHSFIERLPKGYDTVLTQN 499 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 G +S GQK +S+ARAV AD + +LD+ S +D VTEV Sbjct: 500 GSGISQGQKQLISIARAVLADPVLLILDEATSNIDT------VTEV 539 >NDVA_RHIME (P18767) Beta-(1-->2)glucan export ATP-binding protein ndvA Length = 616 Score = 53.1 bits (126), Expect = 3e-07 Identities = 33/102 (32%), Positives = 51/102 (50%), Gaps = 1/102 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENV-LFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 +SIA V Q +MN ++ EN+ L A + A + G T +GE Sbjct: 440 RSIATVFQDAGLMNRSIGENIRLGREDASLDEVMAAAEAAAASDFIEDRLNGYDTVVGER 499 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 G LSGG++ RV++ARA+ + + +LD+ SALD R+ Sbjct: 500 GNRLSGGERQRVAIARAILKNAPILVLDEATSALDVETEARV 541 >YC72_MYCTU (Q11047) Hypothetical ABC transporter ATP-binding protein Rv1272c/MT1310/Mb1303c Length = 631 Score = 53.1 bits (126), Expect = 3e-07 Identities = 28/93 (30%), Positives = 51/93 (54%), Gaps = 1/93 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I V Q W+ + T+ EN+ + P A + EA R ++ + L AG T + +G Sbjct: 473 IGMVLQDTWLYDGTIAENIAYGRPEATTDEIVEAARAAHVDRFVNTLPAGYQTRVSGDGG 532 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 ++S G+K +++ARA A ++ +LD+ S++D Sbjct: 533 SISVGEKQLITIARAFLARPQLLILDEATSSVD 565 >ABC6_HUMAN (Q9NP58) ATP-binding cassette, sub-family B, member 6, mitochondrial precursor (Mitochondrial ABC transporter 3) (Mt-ABC transporter 3) (ABC transporter umat) Length = 842 Score = 53.1 bits (126), Expect = 3e-07 Identities = 29/93 (31%), Positives = 48/93 (51%), Gaps = 1/93 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFS-PADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 I V Q + N T+ +N+ + A ++ A + + + G T++GE G+ Sbjct: 666 IGVVPQDTVLFNDTIADNIRYGRVTAGNDEVEAAAQAAGIHDAIMAFPEGYRTQVGERGL 725 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LSGG+K RV++AR + + LLD+ SALD Sbjct: 726 KLSGGEKQRVAIARTILKAPGIILLDEATSALD 758 >TAP1_MOUSE (P21958) Antigen peptide transporter 1 (APT1) (Histocompatibility antigen modifier 1) Length = 724 Score = 53.1 bits (126), Expect = 3e-07 Identities = 37/113 (32%), Positives = 59/113 (52%), Gaps = 5/113 (4%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGM----GTEIGE 279 +A V Q+P + + REN+ + + E + +E+ +G TE+GE Sbjct: 557 VAAVGQEPLLFGRSFRENIAY--GLNRTPTMEEITAVAVESGAHDFISGFPQGYDTEVGE 614 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI-VTEVLFGAP 123 G LSGGQ+ V+LARA+ + +LDD SALDA G ++ V +L+ +P Sbjct: 615 TGNQLSGGQRQAVALARALIRKPLLLILDDATSALDA--GNQLRVQRLLYESP 665 >CYS2_RHIME (Q92VJ2) Sulfate/thiosulfate import ATP-binding protein cysA 2 (EC 3.6.3.25) (Sulfate-transporting ATPase 2) Length = 367 Score = 43.5 bits (101), Expect(2) = 3e-07 Identities = 21/39 (53%), Positives = 28/39 (71%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQ+ RV+LARA+ + V LLD+P ALDA V + + Sbjct: 137 LSGGQRQRVALARAMAVEPNVLLLDEPFGALDAQVRKEL 175 Score = 28.9 bits (63), Expect(2) = 3e-07 Identities = 16/28 (57%), Positives = 19/28 (67%), Gaps = 1/28 (3%) Frame = -2 Query: 112 TRILVTH-QIDVLSRADFVVVMEKGAVQ 32 T I VTH Q + L AD VVVM KGA++ Sbjct: 189 TTIFVTHDQEEALELADRVVVMSKGAIE 216 >MSBA_XYLFA (Q9PEE7) Lipid A export ATP-binding/permease protein msbA Length = 589 Score = 52.4 bits (124), Expect = 4e-07 Identities = 31/108 (28%), Positives = 57/108 (52%), Gaps = 2/108 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF--FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 + IA V QQ + + ++ EN+ + ++ V + + L G+ ++G Sbjct: 421 RQIALVGQQVMLFDGSIAENIAYGEMRQVVSEEIERVVVDANAQDFVNQLPEGLQFQVGV 480 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G LSGGQ+ R+++ARA+ D + +LD+ +ALD + ER+V + L Sbjct: 481 KGGRLSGGQRQRLAIARAMLKDAPILILDEATAALD-NESERLVQDAL 527 >ABC7_MOUSE (Q61102) ATP-binding cassette, sub-family B, member 7, mitochondrial (ATP-binding cassette transporter 7) (ABC transporter 7 protein) (Fragment) Length = 694 Score = 52.4 bits (124), Expect = 4e-07 Identities = 30/103 (29%), Positives = 56/103 (54%), Gaps = 1/103 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFS-PADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 +++ V Q + + T+ N+L+ + A + ++ L + + G T++GE Sbjct: 488 RAVGVVPQDAVLFHNTIYYNLLYGNINASPEEVYAVAKLAGLHDAILRMPHGYDTQVGER 547 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 G+ LSGG+K RV++ARA+ + V L D+ S+LD+ E I+ Sbjct: 548 GLKLSGGEKQRVAIARAILKNPPVILYDEATSSLDSITEETIL 590 >YD01_SCHPO (O14286) Putative ABC transporter C15A10.01 in chromosome I Length = 693 Score = 52.4 bits (124), Expect = 4e-07 Identities = 27/106 (25%), Positives = 56/106 (52%), Gaps = 1/106 (0%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 ++I V Q + N T+ N+ + +P A + EA + ++ + G T++GE Sbjct: 517 KAIGVVPQDTPLFNDTILYNIGYGNPKASNDEIVEAAKKAKIHDIIESFPEGYQTKVGER 576 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 G+ +SGG+K R++++R + + E+ D+ SALD + ++ + Sbjct: 577 GLMISGGEKQRLAVSRLLLKNPEILFFDEATSALDTNTERALLRNI 622 >CYS1_RHIME (Q92XW1) Sulfate/thiosulfate import ATP-binding protein cysA 1 (EC 3.6.3.25) (Sulfate-transporting ATPase 1) Length = 347 Score = 43.5 bits (101), Expect(2) = 6e-07 Identities = 21/39 (53%), Positives = 28/39 (71%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQ+ RV+LARA+ + V LLD+P ALDA V + + Sbjct: 137 LSGGQRQRVALARAMAVEPSVLLLDEPFGALDAQVRKEL 175 Score = 28.1 bits (61), Expect(2) = 6e-07 Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 1/28 (3%) Frame = -2 Query: 112 TRILVTH-QIDVLSRADFVVVMEKGAVQ 32 T + VTH Q + L AD VVVM KGA++ Sbjct: 189 TTLFVTHDQEEALELADRVVVMSKGAIE 216 >LAGD_LACLA (P59852) Lactococcin G processing and transport ATP-binding protein lagD (EC 3.4.22.-) Length = 703 Score = 52.0 bits (123), Expect = 6e-07 Identities = 31/103 (30%), Positives = 54/103 (52%), Gaps = 3/103 (2%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQ---LEADLRVLAAGMGTEIGEN 276 + YV Q+ + N T+ +N L F + + ++ R C+ L + + + E Sbjct: 545 VTYVPQESFFFNGTIIDN-LTFGLSHQPEFEKIFRACKAACLVDFINQQPLRFDSVLEEG 603 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 G NLSGGQK R+++ARA+ D E+ + D+ S LD + + I+ Sbjct: 604 GNNLSGGQKQRLAIARAILNDSEIIIFDEATSGLDTLLEKEIL 646 >MSBA_XYLFT (Q87EF0) Lipid A export ATP-binding/permease protein msbA Length = 589 Score = 51.2 bits (121), Expect = 1e-06 Identities = 30/108 (27%), Positives = 57/108 (52%), Gaps = 2/108 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF--FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 + IA V QQ + + ++ +N+ + ++ V + + L G+ ++G Sbjct: 421 RQIALVGQQVMLFDGSIADNIAYGEMRQVVSEEIERVVVDANAQDFVNQLPEGLQFQVGV 480 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 G LSGGQ+ R+++ARA+ D + +LD+ +ALD + ER+V + L Sbjct: 481 KGGRLSGGQRQRLAIARAMLKDAPILILDEATAALD-NESERLVQDAL 527 >MDLB_BUCBP (Q89A96) Multidrug resistance-like ATP-binding protein mdlB Length = 578 Score = 50.8 bits (120), Expect = 1e-06 Identities = 29/94 (30%), Positives = 53/94 (56%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 ++I+ V Q P I+N T+ EN+ ++ + ++ +L + L G+ T +GENG Sbjct: 414 KNISIVQQDPIILNDTILENITLGRNISTKKVLKILKTIKLIQFVNSLPKGLKTLLGENG 473 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 LS GQK +S+AR + + ++ +LD+ S +D Sbjct: 474 NILSIGQKQLLSIARTLISCPKILILDEATSNVD 507 >CYDC_HAEIN (P45081) Transport ATP-binding protein cydC Length = 576 Score = 50.4 bits (119), Expect = 2e-06 Identities = 30/106 (28%), Positives = 55/106 (51%), Gaps = 2/106 (1%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP--ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 I +++Q+ + + TLR+N+ F S + ++ E + L L G+ +G+ G Sbjct: 415 ICFLTQRVHVFSDTLRQNLQFASADKISDEQMIEMLHQVGLSKLLEQEGKGLNLWLGDGG 474 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGG++ R+ LAR + + + LLD+P LD +I+ +L Sbjct: 475 RPLSGGEQRRLGLARILLNNASILLLDEPTEGLDRETERQILRLIL 520 >EXP8_STRPN (P35598) Putative ABC transporter ATP-binding protein exp8 (Exported protein 8) Length = 583 Score = 50.1 bits (118), Expect = 2e-06 Identities = 21/95 (22%), Positives = 52/95 (54%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 ++I V Q+P++ + T++ N+ + + ++Q A ++ ++ L G + + E G Sbjct: 415 KNIGLVLQEPFLYHGTIKSNIAMYQETSDEQVQAAAAFVDADSFIQELPQGYDSPVSERG 474 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDA 168 + S GQ+ ++ AR V + ++ +LD+ + +D+ Sbjct: 475 SSFSTGQRQLLAFARTVASQPKILILDEATANIDS 509 >Y288_THEMA (Q9WYC4) Hypothetical ABC transporter ATP-binding protein TM0288 Length = 598 Score = 49.7 bits (117), Expect = 3e-06 Identities = 28/101 (27%), Positives = 57/101 (56%), Gaps = 1/101 (0%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 SI V Q + + T++EN+ + +P A + ++EA ++ + ++ L G T + +NG Sbjct: 430 SIGIVLQDTILFSTTVKENLKYGNPGATDEEIKEAAKLTHSDHFIKHLPEGYETVLTDNG 489 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 +LS GQ+ +++ RA A+ ++ +LD+ S +D + I Sbjct: 490 EDLSQGQRQLLAITRAFLANPKILILDEATSNVDTKTEKSI 530 >Y015_MYCPN (P75094) Hypothetical ABC transporter ATP-binding protein MG015 homolog (D12_orf634) Length = 634 Score = 49.7 bits (117), Expect = 3e-06 Identities = 32/109 (29%), Positives = 58/109 (53%), Gaps = 1/109 (0%) Frame = -1 Query: 464 AWASQSIAYVSQQPWIMNATLRENV-LFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTE 288 AW + I+ V Q P++ + T++EN+ + A + + EA +V + L G T Sbjct: 468 AWR-EKISIVLQDPFLFSGTIKENIRMGRQDATDEEIIEACKVANAHDFIMRLPQGYNTF 526 Query: 287 IGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTE 141 I LS G++ +++ARAV + V LLD+ S++D H E+++ + Sbjct: 527 ISNKTDYLSVGERQLLTIARAVIRNAPVLLLDEATSSIDVH-SEKLIQQ 574 >PSTB_XANAC (Q8PM59) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 267 Score = 49.3 bits (116), Expect = 4e-06 Identities = 36/107 (33%), Positives = 59/107 (55%), Gaps = 8/107 (7%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLF-------FSPAD-EHRLQEAVRVCQLEADLRVLAAGMGT 291 + V Q+P T+ ENV + S AD ++R+++A+R L +++ Sbjct: 103 VGMVFQKPVPFPMTIFENVAYGIRHHEKLSKADMQNRVEQALRQGALWDEVK-------D 155 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 ++G++ + LSGGQ+ R+ +ARAV +V LLD+P SALD RI Sbjct: 156 KLGQSALGLSGGQQQRLCIARAVALRPDVLLLDEPTSALDPISTSRI 202 >YD48_MYCTU (Q11018) Hypothetical ABC transporter ATP-binding protein Rv1348/MT1390/Mb1383 Length = 859 Score = 49.3 bits (116), Expect = 4e-06 Identities = 32/105 (30%), Positives = 55/105 (52%), Gaps = 1/105 (0%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSP-ADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGI 270 + +V Q+ +++ T EN+ P A ++Q A R Q+ + L G T +G N Sbjct: 686 VGFVLQEAQLVHGTAAENIALAVPDAPAEQVQVAAREAQIHDRVLRLPDGYDTVLGANS- 744 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGG++ R+++ARA+ D V +LD+ + D E +V + L Sbjct: 745 GLSGGERQRLTIARAILGDTPVLILDEATAFADPE-SEYLVQQAL 788 >CYSA_BRAJA (Q89UD2) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 344 Score = 42.0 bits (97), Expect(2) = 4e-06 Identities = 19/39 (48%), Positives = 28/39 (71%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQ+ R++LARA+ + + LLD+P ALDA V + + Sbjct: 137 LSGGQRQRIALARALAIEPRILLLDEPFGALDAKVRKEL 175 Score = 26.6 bits (57), Expect(2) = 4e-06 Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 1/35 (2%) Frame = -2 Query: 133 LVHLAQKTRILVTH-QIDVLSRADFVVVMEKGAVQ 32 L H T I VTH Q + L A+ VVVM+KG ++ Sbjct: 182 LHHEINVTSIFVTHDQEEALEVANRVVVMDKGRIE 216 >FBC2_HAEIN (P44513) Ferric cations import ATP-binding protein fbpC 2 (EC 3.6.3.30) Length = 356 Score = 48.5 bits (114), Expect = 6e-06 Identities = 24/44 (54%), Positives = 34/44 (77%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 LSGGQ+ RV+LARA+ + E+ LLD+P SALD H+ ++I E+L Sbjct: 146 LSGGQQQRVALARALAPNPELILLDEPFSALDEHLRQQIRQEML 189 >PSTB_XANCP (Q8PAG0) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 267 Score = 48.5 bits (114), Expect = 6e-06 Identities = 36/107 (33%), Positives = 58/107 (54%), Gaps = 8/107 (7%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLF-------FSPAD-EHRLQEAVRVCQLEADLRVLAAGMGT 291 + V Q+P T+ ENV + S AD ++R++ A+R L +++ Sbjct: 103 VGMVFQKPVPFPMTIFENVAYGIRHHEKLSKADMQNRVEHALRQGALWDEVK-------D 155 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 ++G++ + LSGGQ+ R+ +ARAV +V LLD+P SALD RI Sbjct: 156 KLGQSALGLSGGQQQRLCIARAVALRPDVLLLDEPTSALDPISTSRI 202 >CYSA_SYNY3 (P74548) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 355 Score = 48.5 bits (114), Expect = 6e-06 Identities = 33/93 (35%), Positives = 49/93 (52%), Gaps = 7/93 (7%) Frame = -1 Query: 407 TLRENVLFFSPADEH-------RLQEAVRVCQLEADLRVLAAGMGTEIGENGINLSGGQK 249 T+R+N+ F +H R++E + + QLE G+G LSGGQ+ Sbjct: 90 TIRQNIAFGLEIRKHPPAKTKERVEELLSLIQLE--------GLGNRYPSQ---LSGGQR 138 Query: 248 ARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 RV+LARA+ +V LLD+P ALDA V + + Sbjct: 139 QRVALARALAVQPQVLLLDEPFGALDAKVRKEL 171 >SPAT_BACSU (P33116) Subtilin transport ATP-binding protein spaT Length = 614 Score = 43.1 bits (100), Expect(2) = 7e-06 Identities = 27/85 (31%), Positives = 47/85 (55%), Gaps = 6/85 (7%) Frame = -1 Query: 407 TLRENVLFFSPADEH---RLQEAVRVCQLEADLRVLAAGMGTEIG---ENGINLSGGQKA 246 TL+EN+ F H ++ E + + + + + T++G + G LSGGQ Sbjct: 443 TLKENIGFGQIDKLHQTNKMHEVLDIVRADFLKSHSSYQFDTQLGLWFDEGRQLSGGQWQ 502 Query: 245 RVSLARAVYADREVYLLDDPLSALD 171 +++LARA + + +Y+LD+P SALD Sbjct: 503 KIALARAYFREASLYILDEPSSALD 527 Score = 24.6 bits (52), Expect(2) = 7e-06 Identities = 9/27 (33%), Positives = 17/27 (62%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAV 35 K I ++H++ AD ++VM+KG + Sbjct: 545 KIGIFISHRLVAAKLADRIIVMDKGEI 571 >PSTB_THEMA (Q9X0Y8) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 251 Score = 48.1 bits (113), Expect = 8e-06 Identities = 34/103 (33%), Positives = 53/103 (51%), Gaps = 4/103 (3%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLF----FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 + V Q+P ++ +NV F +H L V +A L + +E+ + Sbjct: 87 VGMVFQKPTPFPMSIYDNVAFGPRIHGVKSKHILDRIVEESLKKA---ALWDEVKSELNK 143 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 +G LSGGQ+ R+ +ARA+ + EV LLD+P SALD +RI Sbjct: 144 SGTRLSGGQQQRLCIARALAVEPEVILLDEPTSALDPIATQRI 186 >PSB1_PSEPK (Q88JJ0) Phosphate import ATP-binding protein pstB 1 (EC 3.6.3.27) (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) Length = 279 Score = 47.8 bits (112), Expect = 1e-05 Identities = 35/109 (32%), Positives = 54/109 (49%), Gaps = 10/109 (9%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLF----------FSPADEHRLQEAVRVCQLEADLRVLAAGM 297 I V QQP + ++ +NV F +H LQ A +++ L+V Sbjct: 109 IGMVFQQPNPFSMSIFDNVAFGLRLNRYKGDLGDRVKHALQGAALWDEVKDKLKV----- 163 Query: 296 GTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 +G++LSGGQ+ R+ +ARA+ + EV LLD+P SALD R+ Sbjct: 164 ------SGLSLSGGQQQRLCIARAIATEPEVLLLDEPCSALDPIATRRV 206 >TROB_TREPA (P96117) Zinc transport system ATP-binding protein troB Length = 266 Score = 47.8 bits (112), Expect = 1e-05 Identities = 33/104 (31%), Positives = 50/104 (48%), Gaps = 3/104 (2%) Frame = -1 Query: 446 IAYVSQQP---WIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 +AYV Q+ W T+ + VL S + + + A + GMG + Sbjct: 81 VAYVPQRSAVDWDFPTTVFDVVLMGSYGSLGWILRPGKREKARAREAIEEVGMGAFLDRQ 140 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVT 144 LSGGQ+ RV LARA+ D ++Y +D+P +DA + IVT Sbjct: 141 ISELSGGQQQRVFLARALVQDADLYFMDEPFQGVDAATEQAIVT 184 >PSB2_LISMO (Q8Y4E9) Phosphate import ATP-binding protein pstB 2 (EC 3.6.3.27) (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) Length = 271 Score = 47.8 bits (112), Expect = 1e-05 Identities = 33/97 (34%), Positives = 54/97 (55%), Gaps = 3/97 (3%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQ-LEADLRVLAAG--MGTEIG 282 + I V Q+P ++ ENV F H ++ + + +E LR A + ++G Sbjct: 105 KEIGMVFQKPNPFTKSIYENVAF--GLKRHGMKNKKEIMERVEKSLRRAALWDEVKDDLG 162 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 ++ ++LSGGQ+ R+ +ARAV +V LLD+P SALD Sbjct: 163 KSALSLSGGQQQRLCIARAVAMQPKVLLLDEPASALD 199 >PSB2_LISIN (Q927Z7) Phosphate import ATP-binding protein pstB 2 (EC 3.6.3.27) (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) Length = 271 Score = 47.8 bits (112), Expect = 1e-05 Identities = 33/97 (34%), Positives = 54/97 (55%), Gaps = 3/97 (3%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQ-LEADLRVLAAG--MGTEIG 282 + I V Q+P ++ ENV F H ++ + + +E LR A + ++G Sbjct: 105 KEIGMVFQKPNPFTKSIYENVAF--GLKRHGMKNKKEIMERVEKSLRRAALWDEVKDDLG 162 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 ++ ++LSGGQ+ R+ +ARAV +V LLD+P SALD Sbjct: 163 KSALSLSGGQQQRLCIARAVAMQPKVLLLDEPASALD 199 >PSTB_RHILO (Q98FL5) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 267 Score = 47.4 bits (111), Expect = 1e-05 Identities = 33/98 (33%), Positives = 53/98 (54%), Gaps = 6/98 (6%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLR--VLAAGMGTEIGE-- 279 I V Q+P ++ EN+ F RL E + +++ + + A + TE+ + Sbjct: 103 IGMVFQKPTPFPMSIYENIAFGV-----RLYEKISKAEMDGRVEQALKRAALWTEVKDKL 157 Query: 278 --NGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 +G++LSGGQ+ R+ +AR V EV LLD+P SALD Sbjct: 158 NASGLSLSGGQQQRLCIARTVAVKPEVILLDEPASALD 195 >CMA2_SALTY (P61378) Cytochrome c biogenesis ATP-binding export protein ccmA 2 (EC 3.6.3.41) (Heme exporter protein A 2) Length = 205 Score = 47.4 bits (111), Expect = 1e-05 Identities = 38/121 (31%), Positives = 54/121 (44%), Gaps = 5/121 (4%) Frame = -1 Query: 452 QSIAYVSQQPWIMNA-TLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 +S+ ++ QP I T REN+ FF P D RL EA+ L V A Sbjct: 74 RSLLWIGHQPGIKTRLTARENLHFFHPGDGARLPEALAQAGLAGFEDVPVA--------- 124 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD----AHVGERIVTEVLFGAPCTKDT 108 LS GQ+ RV+LAR +++LD+P +A+D A + R+ G T Sbjct: 125 --QLSAGQQRRVALARLWLTRAALWVLDEPFTAIDVNGVARLTRRMAAHTAQGGMVILTT 182 Query: 107 H 105 H Sbjct: 183 H 183 >CMA1_SALTY (Q8ZKZ9) Cytochrome c biogenesis ATP-binding export protein ccmA 1 (EC 3.6.3.41) (Heme exporter protein A 1) Length = 205 Score = 47.4 bits (111), Expect = 1e-05 Identities = 38/121 (31%), Positives = 54/121 (44%), Gaps = 5/121 (4%) Frame = -1 Query: 452 QSIAYVSQQPWIMNA-TLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 +S+ ++ QP I T REN+ FF P D RL EA+ L V A Sbjct: 74 RSLLWIGHQPGIKTRLTARENLHFFHPGDGARLPEALAQAGLAGFEDVPVA--------- 124 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD----AHVGERIVTEVLFGAPCTKDT 108 LS GQ+ RV+LAR +++LD+P +A+D A + R+ G T Sbjct: 125 --QLSAGQQRRVALARLWLTRAALWVLDEPFTAIDVNGVARLTRRMAAHTAQGGMVILTT 182 Query: 107 H 105 H Sbjct: 183 H 183 >CCMA_SALTI (P61377) Cytochrome c biogenesis ATP-binding export protein ccmA (EC 3.6.3.41) (Heme exporter protein A) Length = 205 Score = 47.4 bits (111), Expect = 1e-05 Identities = 38/121 (31%), Positives = 54/121 (44%), Gaps = 5/121 (4%) Frame = -1 Query: 452 QSIAYVSQQPWIMNA-TLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN 276 +S+ ++ QP I T REN+ FF P D RL EA+ L V A Sbjct: 74 RSLLWIGHQPGIKTRLTARENLHFFHPGDGARLPEALAQAGLAGFEDVPVA--------- 124 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD----AHVGERIVTEVLFGAPCTKDT 108 LS GQ+ RV+LAR +++LD+P +A+D A + R+ G T Sbjct: 125 --QLSAGQQRRVALARLWLTRAALWVLDEPFTAIDVNGVARLTRRMAAHTAQGGMVILTT 182 Query: 107 H 105 H Sbjct: 183 H 183 >MDLB_BUCAP (Q8K984) Multidrug resistance-like ATP-binding protein mdlB Length = 580 Score = 47.4 bits (111), Expect = 1e-05 Identities = 25/103 (24%), Positives = 54/103 (52%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 ++I V Q P ++ T N+ E ++ ++ L + ++ + G+ + +GE G Sbjct: 416 KNILMVQQDPIVLADTFSSNITLGKKISEEKIWNVLKTVHLSSLVQSMPKGIYSILGEEG 475 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVT 144 NLS GQK +++AR + + ++ +LD+ + +D+ + I T Sbjct: 476 NNLSLGQKQLLAIARILVRNPKILILDEATANIDSGTEKLIQT 518 >POTA_MYCGE (P47288) Spermidine/putrescine transport ATP-binding protein potA homolog Length = 559 Score = 47.4 bits (111), Expect = 1e-05 Identities = 23/43 (53%), Positives = 32/43 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 LSGG K RV+LAR++ + E+ LLD+PLSALDA V + + E+ Sbjct: 348 LSGGMKQRVALARSLVVEPEILLLDEPLSALDAKVRKNLQKEL 390 >MSMX_BACSU (P94360) Probable multiple sugar-binding transport ATP-binding protein msmX Length = 365 Score = 47.4 bits (111), Expect = 1e-05 Identities = 28/81 (34%), Positives = 45/81 (55%) Frame = -1 Query: 377 PADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGINLSGGQKARVSLARAVYADREVYL 198 P + R++EA ++ LE L LSGGQ+ RV+L RA+ D +V+L Sbjct: 109 PEIKKRVEEAAKILGLEEYLHRKPKA-----------LSGGQRQRVALGRAIVRDAKVFL 157 Query: 197 LDDPLSALDAHVGERIVTEVL 135 +D+PLS LDA + ++ E++ Sbjct: 158 MDEPLSNLDAKLRVQMRAEII 178 >LCN3_LACLA (P37608) Lacticin 481/lactococcin transport/processing ATP-binding protein lcnDR3 (EC 3.4.22.-) Length = 691 Score = 43.5 bits (101), Expect(2) = 2e-05 Identities = 28/103 (27%), Positives = 55/103 (53%), Gaps = 3/103 (2%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIMNATLRENVLFFSPADE---HRLQEAVRVCQLEADLRVLAAG 300 GY Q I VSQ + +L EN++ + ++E ++ + ++ + + L Sbjct: 523 GYENLRQIIGVVSQNMNLRKGSLIENIVSNNNSEELDIQKINDVLKDVNMLELVDSLPQK 582 Query: 299 MGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + +++ ENG NLSGGQ R+ +A+++ + + D+P S+LD Sbjct: 583 IFSQLFENGKNLSGGQIQRLLIAKSLLNNNKFIFWDEPFSSLD 625 Score = 23.1 bits (48), Expect(2) = 2e-05 Identities = 8/29 (27%), Positives = 18/29 (62%) Frame = -2 Query: 115 KTRILVTHQIDVLSRADFVVVMEKGAVQL 29 +T I+++H +DVL D V+ ++ + + Sbjct: 645 QTIIMISHHLDVLKYVDRVIYIDDKKIMI 673 >CYSA_SYNP7 (P14788) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 344 Score = 47.0 bits (110), Expect = 2e-05 Identities = 33/82 (40%), Positives = 44/82 (53%) Frame = -1 Query: 407 TLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGINLSGGQKARVSLAR 228 T+R+N+ F +H +E VR E V G+G LSGGQ+ RV+LAR Sbjct: 96 TVRKNIAFGLELRKHT-KEKVRARVEELLELVQLTGLGDRYPSQ---LSGGQRQRVALAR 151 Query: 227 AVYADREVYLLDDPLSALDAHV 162 A+ +V LLD+P ALDA V Sbjct: 152 ALAVQPQVLLLDEPFGALDAKV 173 >CYS2_AGRT5 (Q8UA73) Sulfate/thiosulfate import ATP-binding protein cysA 2 (EC 3.6.3.25) (Sulfate-transporting ATPase 2) Length = 341 Score = 47.0 bits (110), Expect = 2e-05 Identities = 30/83 (36%), Positives = 47/83 (56%), Gaps = 1/83 (1%) Frame = -1 Query: 407 TLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAA-GMGTEIGENGINLSGGQKARVSLA 231 TL EN+ F + + +A +++ L ++ G+G +SGGQ+ RV+LA Sbjct: 90 TLHENIAFGMKVSKVKRDKAAIDARVKELLNLVKLDGLGDRFPAQ---ISGGQRQRVALA 146 Query: 230 RAVYADREVYLLDDPLSALDAHV 162 RA+ D +V LLD+P ALDA+V Sbjct: 147 RALSVDPKVLLLDEPFGALDANV 169 >CYSA_MYCTU (P71747) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 353 Score = 47.0 bits (110), Expect = 2e-05 Identities = 23/39 (58%), Positives = 29/39 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQ+ R++LARA+ D EV LLD+P ALDA V E + Sbjct: 137 LSGGQRQRMALARALAVDPEVLLLDEPFGALDAKVREEL 175 >PSTB_TROW8 (Q83HT1) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 257 Score = 46.6 bits (109), Expect = 2e-05 Identities = 33/100 (33%), Positives = 51/100 (51%), Gaps = 3/100 (3%) Frame = -1 Query: 461 WASQSIAYVSQQPW-IMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRV--LAAGMGT 291 + Q + +SQ+P ++RENVL + R+ + +E LR L + Sbjct: 80 YVRQEVGMISQRPNPFPTMSIRENVLAGIKLNRKRIHRIQQNELMERCLRSVNLWDEVHN 139 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 +G G LSGGQ+ R+ +ARA+ V L+D+P SALD Sbjct: 140 RLGRPGGELSGGQQQRLCIARAIAVSPRVILMDEPCSALD 179 >PSTB_BIFLO (Q8G7F4) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 259 Score = 46.6 bits (109), Expect = 2e-05 Identities = 32/83 (38%), Positives = 47/83 (56%), Gaps = 4/83 (4%) Frame = -1 Query: 407 TLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN----GINLSGGQKARV 240 ++RENVL + H L ++ +E LR A + E+ + GI LSGGQ+ R+ Sbjct: 101 SIRENVLAGVRLNNHHLAKSDADDLVEWALR--GANLWEEVKDRLDNPGIGLSGGQQQRL 158 Query: 239 SLARAVYADREVYLLDDPLSALD 171 +ARAV +V L+D+P SALD Sbjct: 159 CIARAVAVHPQVLLMDEPCSALD 181 >PSTB_NITEU (Q82VR4) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 266 Score = 46.6 bits (109), Expect = 2e-05 Identities = 25/66 (37%), Positives = 39/66 (59%) Frame = -1 Query: 368 EHRLQEAVRVCQLEADLRVLAAGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDD 189 E R++ A+R L +++ +G+ NLSGGQ+ R+ +ARA+ D E+ L D+ Sbjct: 136 EERVENALRNAALWEEVK-------DRLGDLAFNLSGGQQQRLCIARALATDPEILLFDE 188 Query: 188 PLSALD 171 P SALD Sbjct: 189 PTSALD 194 >Y4FO_RHISN (P55453) Putative ABC transporter ATP-binding protein y4fO Length = 339 Score = 46.6 bits (109), Expect = 2e-05 Identities = 23/56 (41%), Positives = 35/56 (62%) Frame = -1 Query: 305 AGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 AG+ ++ + N+SGGQ+ RV++ARA+ V L D+PLS LDA V + E+ Sbjct: 130 AGISDQLDKKPANMSGGQQQRVAIARALVTGSRVLLFDEPLSNLDAKVRAAMRKEI 185 >HST6_CANAL (P53706) ATP-dependent permease HST6 (STE6 homolog) Length = 1323 Score = 46.2 bits (108), Expect = 3e-05 Identities = 30/107 (28%), Positives = 56/107 (52%), Gaps = 2/107 (1%) Frame = -1 Query: 452 QSIAYVSQQPWIMN-ATLRENVLFFSPADEHRLQEAVRVCQLEADLR-VLAAGMGTEIGE 279 Q+I + Q P I + T+ EN+ + D++ +A+ +E L + + + Sbjct: 449 QNITLLEQNPVIFDDKTIAENIAI-AIVDDYDSLQAIPYYLIEQSAHFALLSDLDLNMKV 507 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 N + LSGGQ+ R+S+ARA + V ++D+ SALD + ++ +V Sbjct: 508 NHLTLSGGQQQRISIARAYLKNSPVLIMDESFSALDTETKQGLIEKV 554 >PSB2_SHEON (Q8E9I8) Phosphate import ATP-binding protein pstB 2 (EC 3.6.3.27) (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) Length = 249 Score = 45.8 bits (107), Expect = 4e-05 Identities = 36/109 (33%), Positives = 56/109 (51%), Gaps = 5/109 (4%) Frame = -1 Query: 449 SIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLR--VLAAGMGTEIGEN 276 S+ V Q+P ++ EN+ F A + +AV +E LR L + T + Sbjct: 84 SVGMVFQKPNPFPMSIYENIAFGLKAQGVK-DKAVLDAVVENSLRGAALWEEVKTRLHTP 142 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALD---AHVGERIVTEV 138 LSGGQ+ R+ +ARA+ + EV L+D+P SALD H E ++ E+ Sbjct: 143 AFGLSGGQQQRLCIARAIAMEPEVILMDEPTSALDPIATHKIEELMDEL 191 >POTA_MYCPN (P75059) Spermidine/putrescine transport ATP-binding protein potA homolog Length = 560 Score = 45.8 bits (107), Expect = 4e-05 Identities = 22/43 (51%), Positives = 32/43 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 LSGG K RV+LAR++ + ++ LLD+PLSALDA V + + E+ Sbjct: 349 LSGGMKQRVALARSLVIEPDILLLDEPLSALDAKVRKNLQKEL 391 >PSB1_ENTFA (Q834B4) Phosphate import ATP-binding protein pstB 1 (EC 3.6.3.27) (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) Length = 252 Score = 45.8 bits (107), Expect = 4e-05 Identities = 33/100 (33%), Positives = 54/100 (54%), Gaps = 6/100 (6%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFF----SPADEHRLQEAVRVCQLEADLRVLAA--GMGT 291 + I V QQP ++ ENV++ D+ L EAV E L+ A + Sbjct: 86 KEIGMVFQQPNPFPFSVYENVIYGLRLKGVKDKQVLDEAV-----ETSLKAAAVWEDVKD 140 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 ++ ++ ++LSGGQ+ RV +AR + + ++ LLD+P SALD Sbjct: 141 KLHKSALSLSGGQQQRVCIARVLAVEPDIILLDEPTSALD 180 >PSB2_LACPL (Q88YK7) Phosphate import ATP-binding protein pstB 2 (EC 3.6.3.27) (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) Length = 251 Score = 45.8 bits (107), Expect = 4e-05 Identities = 34/110 (30%), Positives = 56/110 (50%), Gaps = 4/110 (3%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF----FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 + I V QQP ++ ENV++ D+ RL AV +A + + + Sbjct: 85 KEIGMVFQQPNPFPFSIYENVIYGLRLAGVHDKERLDAAVEKSLKQA---AIWDEVKDRL 141 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 N ++LSGGQ+ RV +AR + + ++ LLD+ SALD + R++ E L Sbjct: 142 HANALSLSGGQQQRVCIARVLAVEPDIILLDEATSALDP-ISSRMIEETL 190 >SSUB_ECOLI (P38053) Putative aliphatic sulfonates transport ATP-binding protein ssuB Length = 255 Score = 45.8 bits (107), Expect = 4e-05 Identities = 29/55 (52%), Positives = 35/55 (63%), Gaps = 1/55 (1%) Frame = -1 Query: 329 EADLRVLAA-GMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDA 168 +A R LAA G+ GE LSGGQK RV+LARA+ + LLD+PL ALDA Sbjct: 111 DAARRALAAVGLENRAGEWPAALSGGQKQRVALARALIHRPGLLLLDEPLGALDA 165 >THIQ_HAEIN (P44986) Thiamine transport ATP-binding protein thiQ Length = 229 Score = 45.4 bits (106), Expect = 5e-05 Identities = 22/46 (47%), Positives = 31/46 (67%) Frame = -1 Query: 308 AAGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + G+G + +LSGGQK RV+LAR + D+ + LLD+P SALD Sbjct: 130 SVGLGDYLERLPNSLSGGQKQRVALARCLLRDKPILLLDEPFSALD 175 >PSB1_HALN1 (Q9HS13) Phosphate import ATP-binding protein pstB 1 (EC 3.6.3.27) (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) Length = 281 Score = 45.4 bits (106), Expect = 5e-05 Identities = 20/40 (50%), Positives = 30/40 (75%) Frame = -1 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 ++ +G+ LSGGQ+ R+ +ARA+ D EV L+D+P SALD Sbjct: 169 QLDSSGVALSGGQQQRLCIARAIAPDPEVLLMDEPASALD 208 >MACB_ECOLI (P75831) Macrolide-specific ABC-type efflux carrier Length = 648 Score = 45.4 bits (106), Expect = 5e-05 Identities = 21/40 (52%), Positives = 29/40 (72%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIV 147 LSGGQ+ RVS+ARA+ +V L D+P ALD+H GE ++ Sbjct: 145 LSGGQQQRVSIARALMNGGQVILADEPTGALDSHSGEEVM 184 >YTMN_BACSU (O34900) Probable amino-acid ABC transporter ATP-binding protein ytmN Length = 259 Score = 45.4 bits (106), Expect = 5e-05 Identities = 40/112 (35%), Positives = 59/112 (52%), Gaps = 3/112 (2%) Frame = -1 Query: 461 WASQSIAYVSQQPWIM-NATLRENVLF-FSPADEHRLQEAVRVCQLEADLRVLAAGMGTE 288 W + A V QQ + + T+ ENV+ + A + R Q+A V + E + G+ + Sbjct: 77 WLRKQTAMVFQQYHLFAHKTVIENVMEGLTIARKMRKQDAYAVAENE----LRKVGLQDK 132 Query: 287 IGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAH-VGERIVTEVL 135 + LSGGQK RV +ARA+ +V L D+P +ALD VGE V EV+ Sbjct: 133 LNAYPSQLSGGQKQRVGIARALAIHPDVLLFDEPTAALDPELVGE--VLEVM 182 >NODI_RHIGA (P50332) Nod factor export ATP-binding protein I (Nodulation ATP-binding protein I) Length = 347 Score = 45.4 bits (106), Expect = 5e-05 Identities = 41/130 (31%), Positives = 62/130 (47%), Gaps = 12/130 (9%) Frame = -1 Query: 458 ASQSIAYVSQQPWI-MNATLRENVLFF-------SPADEHRLQEAVRVCQLEADLRVLAA 303 A SI VSQ + M T+REN+L F + A E + + QLEA V + Sbjct: 119 ARASIGVVSQFDNLDMEFTVRENLLVFGRYFQMSTRAIEKLIPSLLEFAQLEAKADVRVS 178 Query: 302 GMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDA----HVGERIVTEVL 135 +LSGG K R++LARA+ D ++ +LD+P + LD + ER+ + ++ Sbjct: 179 -----------DLSGGMKRRLTLARALVNDPQLLILDEPTTGLDPPARHQIWERLRSLLI 227 Query: 134 FGAPCTKDTH 105 G TH Sbjct: 228 RGKTILLTTH 237 >PSTB_BRAJA (Q89VF2) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 273 Score = 45.4 bits (106), Expect = 5e-05 Identities = 35/100 (35%), Positives = 51/100 (51%), Gaps = 8/100 (8%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMG--------T 291 + V Q+P T+ EN+ F RL E ++ + E D RV A G Sbjct: 109 VGMVFQKPTPFPMTIYENIAFGI-----RLYE--KISKSEMDDRVEKALRGGALWNEVKD 161 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 ++ +G++LSGGQ+ R+ +AR V EV L D+P SALD Sbjct: 162 KLNASGLSLSGGQQQRLCIARTVAVRPEVILFDEPCSALD 201 >PSB2_VIBCH (Q9KU04) Phosphate import ATP-binding protein pstB 2 (EC 3.6.3.27) (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) Length = 273 Score = 45.4 bits (106), Expect = 5e-05 Identities = 35/98 (35%), Positives = 52/98 (53%), Gaps = 6/98 (6%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQ--EAVRVCQLEADLRVLAAGMGTEIG--- 282 + V Q+P ++ ENV++ RLQ + R A+ + AA + E+ Sbjct: 109 VGMVFQRPNPFPKSIYENVVYGL-----RLQGIKNSRALDDAAEQSLRAAALWDEVKHRL 163 Query: 281 -ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 EN LSGGQ+ R+ +ARA+ + EV LLD+P SALD Sbjct: 164 HENAFGLSGGQQQRLVIARAIAIEPEVLLLDEPTSALD 201 >CYSA_CHLVU (P56344) Probable sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 236 Score = 45.4 bits (106), Expect = 5e-05 Identities = 33/94 (35%), Positives = 53/94 (56%), Gaps = 8/94 (8%) Frame = -1 Query: 407 TLRENVLFF-------SPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGIN-LSGGQ 252 T+ ENV F S + R+ E +++ QLE + G++ N LSGGQ Sbjct: 90 TVSENVAFGLEIQKIDSLLKKKRVNELLKLMQLE------------KFGDSYPNQLSGGQ 137 Query: 251 KARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 + RV+LARA+ + +V LLD+P +ALDA + +++ Sbjct: 138 RQRVALARALAMEPKVLLLDEPFAALDAKIRKQL 171 >PSB1_THETN (Q8RCU0) Phosphate import ATP-binding protein pstB 1 (EC 3.6.3.27) (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) Length = 239 Score = 45.1 bits (105), Expect = 7e-05 Identities = 32/96 (33%), Positives = 54/96 (56%), Gaps = 2/96 (2%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVR-VCQLEADLRVLAAGMGTE-IGE 279 + I V Q+P++ T++EN+ L ++R ++A + A G+ + + + Sbjct: 76 RKIGMVFQRPFLFEGTVKENI---------ELGPSLRGEKNIDALFYLEAVGLSKDYLFK 126 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + NLSGG+ RVS+ARA+ EV LLD+P S+LD Sbjct: 127 DVNNLSGGEAQRVSIARALANSPEVLLLDEPTSSLD 162 >CYSA_SALTY (P40860) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 365 Score = 45.1 bits (105), Expect = 7e-05 Identities = 21/39 (53%), Positives = 29/39 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQK RV+LARA+ + ++ LLD+P ALDA V + + Sbjct: 137 LSGGQKQRVALARALAVEPQILLLDEPFGALDAQVRKEL 175 >CYSA_SALTI (Q8Z4V6) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 364 Score = 45.1 bits (105), Expect = 7e-05 Identities = 21/39 (53%), Positives = 29/39 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQK RV+LARA+ + ++ LLD+P ALDA V + + Sbjct: 137 LSGGQKQRVALARALAVEPQILLLDEPFGALDAQVRKEL 175 >CYSA_ECOLI (P16676) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 365 Score = 45.1 bits (105), Expect = 7e-05 Identities = 21/39 (53%), Positives = 29/39 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQK RV+LARA+ + ++ LLD+P ALDA V + + Sbjct: 137 LSGGQKQRVALARALAVEPQILLLDEPFGALDAQVRKEL 175 >CYSA_ECOL6 (Q8FFB3) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 365 Score = 45.1 bits (105), Expect = 7e-05 Identities = 21/39 (53%), Positives = 29/39 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQK RV+LARA+ + ++ LLD+P ALDA V + + Sbjct: 137 LSGGQKQRVALARALAVEPQILLLDEPFGALDAQVRKEL 175 >CYSA_ECO57 (Q8XBJ8) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 365 Score = 45.1 bits (105), Expect = 7e-05 Identities = 21/39 (53%), Positives = 29/39 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQK RV+LARA+ + ++ LLD+P ALDA V + + Sbjct: 137 LSGGQKQRVALARALAVEPQILLLDEPFGALDAQVRKEL 175 >MCJD_ECOLI (Q9X2W0) Microcin J25 export ATP-binding/permease protein mcjD (Microcin J25 secretion ATP-binding protein mcjD) (Microcin J25 immunity protein) Length = 580 Score = 45.1 bits (105), Expect = 7e-05 Identities = 29/96 (30%), Positives = 50/96 (52%), Gaps = 1/96 (1%) Frame = -1 Query: 455 SQSIAYVSQQPWIMNATLRENVLFFS-PADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 + +I Y++Q +I TLR N+ + A E+ + + +++ L + + T + Sbjct: 418 NDAIYYLTQDDYIFMDTLRFNLRLANYDASENEIFKVLKLANLSV-VNNEPVSLDTHLIN 476 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 G N SGGQK R+SLAR + ++D+ SALD Sbjct: 477 RGNNYSGGQKQRISLARLFLRKPAIIIIDEATSALD 512 >PSB2_ENTFA (Q834B3) Phosphate import ATP-binding protein pstB 2 (EC 3.6.3.27) (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) Length = 269 Score = 45.1 bits (105), Expect = 7e-05 Identities = 30/96 (31%), Positives = 50/96 (52%), Gaps = 4/96 (4%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLF----FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 I V Q+P + ++ EN+ F D+ +L E V +A L + + + Sbjct: 105 IGMVFQRPNPFSKSIYENITFALKQHGEKDKKKLDEIVETSLKQA---ALWDQVKDNLNK 161 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + + LSGGQ+ R+ +ARA+ ++ LLD+P SALD Sbjct: 162 SALALSGGQQQRLCIARAIAMKPDILLLDEPASALD 197 >CYSA_YERPE (Q8D0W8) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 363 Score = 45.1 bits (105), Expect = 7e-05 Identities = 21/39 (53%), Positives = 29/39 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQK RV+LARA+ + ++ LLD+P ALDA V + + Sbjct: 137 LSGGQKQRVALARALAVEPQILLLDEPFGALDAQVRKEL 175 >Y014_MYCPN (P75095) Hypothetical ABC transporter ATP-binding protein MG014 homolog (D12_orf623) Length = 623 Score = 45.1 bits (105), Expect = 7e-05 Identities = 23/53 (43%), Positives = 33/53 (62%) Frame = -1 Query: 275 GINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFGAPCT 117 G NLSGGQK RV++AR V ++ +LDD +SALDA +++ + P T Sbjct: 511 GKNLSGGQKQRVAIARTVITKPQILVLDDSMSALDALTEKKVRENIANELPGT 563 >PSB2_HALN1 (Q9HML8) Phosphate import ATP-binding protein pstB 2 (EC 3.6.3.27) (Phosphate-transporting ATPase 2) (ABC phosphate transporter 2) Length = 345 Score = 45.1 bits (105), Expect = 7e-05 Identities = 19/39 (48%), Positives = 29/39 (74%) Frame = -1 Query: 287 IGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 +G+N + LSGGQ+ R+ +AR + D +V L+D+P SALD Sbjct: 234 LGDNALGLSGGQQQRLCIARCLAVDPDVILMDEPASALD 272 >PSTB_CAUCR (Q9ABD6) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 274 Score = 45.1 bits (105), Expect = 7e-05 Identities = 32/96 (33%), Positives = 49/96 (51%), Gaps = 4/96 (4%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGEN--- 276 + V Q+P T+ ENV + +A +E+ L+ AG+ E+ + Sbjct: 109 VGMVFQKPNPFPKTIFENVAYGPRIHGLATGKAELEAIVESSLK--KAGLWNEVADRLHQ 166 Query: 275 -GINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 G LSGGQ+ R+ +ARA+ EV L+D+P SALD Sbjct: 167 PGTGLSGGQQQRLVIARAIAVSPEVILMDEPCSALD 202 >PSB1_YERPE (Q8ZCX5) Phosphate import ATP-binding protein pstB 1 (EC 3.6.3.27) (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) (Phosphate-specific transport component 1) Length = 270 Score = 45.1 bits (105), Expect = 7e-05 Identities = 35/98 (35%), Positives = 49/98 (50%), Gaps = 6/98 (6%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFF----SPADEHRLQEAVRVCQLEADLRVLAAG--MGTEI 285 + V Q+P ++ ENV++ D L EAV E LR A + + Sbjct: 106 VGMVFQRPNPFPKSIYENVVYGLRLQGVRDRRVLDEAV-----ERSLRAAALWHEVKDRL 160 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 EN LS GQ+ R+ +ARA+ + EV LLD+P SALD Sbjct: 161 RENAFRLSSGQQQRLVIARAIAIEPEVLLLDEPTSALD 198 >PSB1_STRMU (Q8DU24) Phosphate import ATP-binding protein pstB 1 (EC 3.6.3.27) (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) Length = 252 Score = 45.1 bits (105), Expect = 7e-05 Identities = 35/112 (31%), Positives = 56/112 (50%), Gaps = 4/112 (3%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFF----SPADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 + I V QQP T+ ENV++ D+ L EAV + A + + + Sbjct: 86 KEIGMVFQQPNPFPMTIYENVVYGLRLKGVKDKKILDEAVEKSLVGASIW---DEVKDRL 142 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 ++ I LSGGQ+ RV +AR + ++ LLD+P SALD + + + L+G Sbjct: 143 HDSAIGLSGGQQQRVCIARVLATSPKIILLDEPTSALDP-ISAGKIEDTLYG 193 >CYSA_VIBCH (Q9KUI0) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 376 Score = 45.1 bits (105), Expect = 7e-05 Identities = 22/39 (56%), Positives = 28/39 (71%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQK R++LARA+ EV LLD+P ALDA V + + Sbjct: 137 LSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKEL 175 >CYS1_SHEON (Q8EBC3) Sulfate/thiosulfate import ATP-binding protein cysA 1 (EC 3.6.3.25) (Sulfate-transporting ATPase 1) Length = 376 Score = 45.1 bits (105), Expect = 7e-05 Identities = 22/39 (56%), Positives = 28/39 (71%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQK R++LARA+ EV LLD+P ALDA V + + Sbjct: 137 LSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKEL 175 >Y4OS_RHISN (P55604) Probable ABC transporter ATP-binding protein y4oS Length = 371 Score = 45.1 bits (105), Expect = 7e-05 Identities = 22/55 (40%), Positives = 35/55 (63%) Frame = -1 Query: 302 GMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 G+G + LSGGQ+ RV++ RA+ D +V+L D+PLS LDA + ++ E+ Sbjct: 138 GLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEI 192 >PSTB_CHLTE (Q8KDZ5) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 286 Score = 45.1 bits (105), Expect = 7e-05 Identities = 33/107 (30%), Positives = 54/107 (50%), Gaps = 6/107 (5%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF----FSPADEHRLQEAVRVCQLEADLRVLAAG--MGT 291 + I V Q+P ++ +N+ + D+ +L E V E LR A + Sbjct: 120 KKIGMVFQKPNPFPKSIFDNIAYGPKLHGIKDKKKLSEIV-----EKSLRKAALWDEVSD 174 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 + +N + LSGGQ+ R+ +ARA+ + E+ LLD+P SALD +I Sbjct: 175 RLDKNALGLSGGQQQRLCVARALAVEPEILLLDEPTSALDPKATAKI 221 >Y015_MYCGE (P47261) Hypothetical ABC transporter ATP-binding protein MG015 Length = 589 Score = 44.7 bits (104), Expect = 9e-05 Identities = 31/109 (28%), Positives = 55/109 (50%), Gaps = 1/109 (0%) Frame = -1 Query: 464 AWASQSIAYVSQQPWIMNATLRENV-LFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTE 288 AW + I+ V Q ++ + T++EN+ L A + + A + + L G T Sbjct: 423 AWR-EKISIVLQDSFLFSGTIKENIRLGRQDATDDEIIAACKTANAHDFIMRLPKGYDTY 481 Query: 287 IGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTE 141 I LS G++ +++ARAV + V LLD+ S++D H E+++ E Sbjct: 482 ISNKADYLSVGERQLLTIARAVIRNAPVLLLDEATSSVDVH-SEKLIQE 529 >PSB1_VIBVU (Q8DEW5) Phosphate import ATP-binding protein pstB 1 (EC 3.6.3.27) (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) Length = 272 Score = 44.7 bits (104), Expect = 9e-05 Identities = 22/37 (59%), Positives = 27/37 (72%) Frame = -1 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 EN LSGGQ+ R+ +ARAV + EV LLD+P SALD Sbjct: 164 ENAFGLSGGQQQRLVIARAVAIEPEVLLLDEPTSALD 200 >PSB1_VIBPA (Q87S48) Phosphate import ATP-binding protein pstB 1 (EC 3.6.3.27) (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) Length = 272 Score = 44.7 bits (104), Expect = 9e-05 Identities = 22/37 (59%), Positives = 27/37 (72%) Frame = -1 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 EN LSGGQ+ R+ +ARAV + EV LLD+P SALD Sbjct: 164 ENAFGLSGGQQQRLVIARAVAIEPEVLLLDEPTSALD 200 >HISP_ECOLI (P07109) Histidine transport ATP-binding protein hisP Length = 257 Score = 44.7 bits (104), Expect = 9e-05 Identities = 24/44 (54%), Positives = 32/44 (72%), Gaps = 1/44 (2%) Frame = -1 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAH-VGE 156 G+ ++LSGGQ+ RVS+ARA+ + EV L D+P SALD VGE Sbjct: 147 GKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDPELVGE 190 >PSTB_METJA (Q58418) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 252 Score = 44.7 bits (104), Expect = 9e-05 Identities = 20/40 (50%), Positives = 30/40 (75%) Frame = -1 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 E+ +N ++LSGGQ+ R+ +ARA+ EV L+D+P SALD Sbjct: 141 ELHKNALSLSGGQQQRLCIARAIAVKPEVLLMDEPTSALD 180 >PSB1_STRPN (Q97Q35) Phosphate import ATP-binding protein pstB 1 (EC 3.6.3.27) (Phosphate-transporting ATPase 1) (ABC phosphate transporter 1) Length = 252 Score = 44.7 bits (104), Expect = 9e-05 Identities = 36/112 (32%), Positives = 55/112 (49%), Gaps = 4/112 (3%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFF----SPADEHRLQEAVRVCQLEADLRVLAAGMGTEI 285 + I V QQP T+ ENV++ D+ L EAV A + + + Sbjct: 86 KEIGMVFQQPNPFPMTIYENVVYGLRINGIKDKQVLDEAVEKALQGASIW---DEVKDRL 142 Query: 284 GENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVLFG 129 ++ I LSGGQ+ RV +AR + ++ LLD+P SALD + + E L+G Sbjct: 143 YDSAIGLSGGQQQRVCVARVLATSPKIILLDEPTSALDP-ISAGKIEETLYG 193 >PSTB_AGRT5 (Q8UI76) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 271 Score = 44.7 bits (104), Expect = 9e-05 Identities = 32/96 (33%), Positives = 50/96 (52%), Gaps = 4/96 (4%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIG----E 279 + V Q+P T+ EN+ + P + + Q+ + + AG+ E+ E Sbjct: 106 VGMVFQKPNPFPKTIYENIAY-GPRIHGLARNKADMDQI-VEHSLQKAGLWNEVKDRLLE 163 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 +G LSGGQ+ R+ +ARAV EV L+D+P SALD Sbjct: 164 SGTGLSGGQQQRLCIARAVAVSPEVILMDEPCSALD 199 >MSMK_STRMU (Q00752) Multiple sugar-binding transport ATP-binding protein msmK Length = 377 Score = 44.7 bits (104), Expect = 9e-05 Identities = 20/44 (45%), Positives = 32/44 (72%) Frame = -1 Query: 269 NLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 +LSGGQ+ RV++ RA+ D +V+L+D+PLS LDA + + E+ Sbjct: 135 DLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEI 178 >PSTB_METTH (O27764) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 253 Score = 44.7 bits (104), Expect = 9e-05 Identities = 29/102 (28%), Positives = 55/102 (53%), Gaps = 8/102 (7%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLF------FSPAD--EHRLQEAVRVCQLEADLRVLAAGM 297 + + V Q+P ++ ENV + + D E R++E++R L +++ Sbjct: 87 KKVGMVFQKPNPFPKSIFENVAYGLRVHGYDDRDFIEERVEESLRAAALWDEVK------ 140 Query: 296 GTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 ++ ++ + LSGGQ+ R+ +AR + + EV L+D+P SALD Sbjct: 141 -DKLDKSALGLSGGQQQRLCIARTIAIEPEVILMDEPCSALD 181 >YD67_METJA (Q58762) Hypothetical ABC transporter ATP-binding protein MJ1367 Length = 297 Score = 44.3 bits (103), Expect = 1e-04 Identities = 20/43 (46%), Positives = 32/43 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEV 138 LSGG++ RV+LARA+ + + LLD+P SA+D + E I++E+ Sbjct: 130 LSGGEQQRVALARALILNPSILLLDEPTSAVDIKIKESIISEL 172 >PSTB_XYLFT (Q87C88) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 269 Score = 44.3 bits (103), Expect = 1e-04 Identities = 33/107 (30%), Positives = 53/107 (49%), Gaps = 8/107 (7%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADE--------HRLQEAVRVCQLEADLRVLAAGMGT 291 + V Q+P T+ ENV + E R+++A++ L +++ Sbjct: 105 VGMVFQKPVPFPMTIYENVAYGIRHHEVMCKSQMNDRVEQALQQSALWEEVK-------D 157 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 ++ +N + LSGGQ+ R+ +ARAV V LLD+P SALD RI Sbjct: 158 KLNQNALGLSGGQQQRLCIARAVALTPSVLLLDEPTSALDPISTSRI 204 >CYSA_ANASP (Q8Z0H0) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 338 Score = 44.3 bits (103), Expect = 1e-04 Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 7/89 (7%) Frame = -1 Query: 407 TLRENVLFF-----SPADE--HRLQEAVRVCQLEADLRVLAAGMGTEIGENGINLSGGQK 249 T+R+N+ F +PA++ R+++ + + QL +G+G LSGGQ+ Sbjct: 90 TVRQNIAFGLEIRKAPANKVKGRVEQLLELVQL--------SGLGDRYPSQ---LSGGQR 138 Query: 248 ARVSLARAVYADREVYLLDDPLSALDAHV 162 RV+LARA+ + V LLD+P ALDA V Sbjct: 139 QRVALARALAVEPSVLLLDEPFGALDAKV 167 >PSTB_TROWT (Q83GE8) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 257 Score = 44.3 bits (103), Expect = 1e-04 Identities = 32/100 (32%), Positives = 50/100 (50%), Gaps = 3/100 (3%) Frame = -1 Query: 461 WASQSIAYVSQQPW-IMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRV--LAAGMGT 291 + Q + + Q+P ++RENVL + R+ + +E LR L + Sbjct: 80 YVRQEVGMIFQRPNPFPTMSIRENVLAGIKLNRKRIHRIQQNELMERCLRSVNLWDEVHN 139 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 +G G LSGGQ+ R+ +ARA+ V L+D+P SALD Sbjct: 140 RLGRPGGELSGGQQQRLCIARAIAVSPRVILMDEPCSALD 179 >PSTB_AQUAE (O67154) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 257 Score = 44.3 bits (103), Expect = 1e-04 Identities = 20/37 (54%), Positives = 28/37 (75%) Frame = -1 Query: 281 ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 EN +LSGGQ+ R+ +ARA+ + EV L+D+P SALD Sbjct: 149 ENAYSLSGGQQQRLCIARAIAVEPEVLLMDEPTSALD 185 >CYSA_NITEU (Q82WT5) Sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 362 Score = 44.3 bits (103), Expect = 1e-04 Identities = 34/101 (33%), Positives = 49/101 (48%), Gaps = 13/101 (12%) Frame = -1 Query: 413 NATLRENVLFF-----------SPADEHRLQEAVRVCQLE--ADLRVLAAGMGTEIGENG 273 N T+ ENV F +P HR+ E +++ QL+ AD Sbjct: 88 NMTIFENVAFGLRVRPRKQRPNAPEINHRVTELLQLVQLDWLAD-------------RYP 134 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQ+ R++LARA+ + V LLD+P ALDA V + + Sbjct: 135 HQLSGGQRQRIALARALAVEPSVLLLDEPFGALDAKVRKEL 175 >MDR1_ENTHI (P16875) Multidrug resistance protein 1 (P-glycoprotein) (Fragment) Length = 114 Score = 44.3 bits (103), Expect = 1e-04 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 4/78 (5%) Frame = -1 Query: 461 WASQSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEAD----LRVLAAGMG 294 W I V Q+P + T+REN++ + E ++ + C A+ + LA G Sbjct: 37 WLRNQIGLVGQEPVLFAGTIRENIMLGAKEGETLSKDEMIECAKMANAHEFVSKLAEGYD 96 Query: 293 TEIGENGINLSGGQKARV 240 T IGE G LSGGQ+ R+ Sbjct: 97 TLIGEKGALLSGGQRQRI 114 >CYS1_AGRT5 (Q8UH62) Sulfate/thiosulfate import ATP-binding protein cysA 1 (EC 3.6.3.25) (Sulfate-transporting ATPase 1) Length = 346 Score = 44.3 bits (103), Expect = 1e-04 Identities = 22/39 (56%), Positives = 29/39 (74%) Frame = -1 Query: 266 LSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQ+ RV+LARAV + +V LLD+P ALDA V + + Sbjct: 137 LSGGQRQRVALARAVAIEPKVLLLDEPFGALDAKVRKEL 175 >UGPC_ECOLI (P10907) SN-glycerol-3-phosphate transport ATP-binding protein ugpC Length = 356 Score = 44.3 bits (103), Expect = 1e-04 Identities = 25/65 (38%), Positives = 37/65 (56%) Frame = -1 Query: 362 RLQEAVRVCQLEADLRVLAAGMGTEIGENGINLSGGQKARVSLARAVYADREVYLLDDPL 183 R++EA R+ +L+ L+ LSGGQ+ RV++ RA+ D V+L D+PL Sbjct: 114 RVKEAARILELDGLLK-----------RRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPL 162 Query: 182 SALDA 168 S LDA Sbjct: 163 SNLDA 167 >YQIZ_BACSU (P54537) Probable amino-acid ABC transporter ATP-binding protein yqiZ Length = 240 Score = 44.3 bits (103), Expect = 1e-04 Identities = 26/87 (29%), Positives = 51/87 (58%) Frame = -1 Query: 407 TLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENGINLSGGQKARVSLAR 228 T+ EN+++ A + +E+ + Q +A+ + G+ + + LSGGQK RV++AR Sbjct: 93 TVLENIMY---APVNVKKESKQAAQEKAEDLLRKVGLFEKRNDYPNRLSGGQKQRVAIAR 149 Query: 227 AVYADREVYLLDDPLSALDAHVGERIV 147 A+ + ++ L D+P SALD + + ++ Sbjct: 150 ALAMNPDIMLFDEPTSALDPEMVKEVL 176 >CYSA_MESVI (Q9MUN1) Probable sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATPase) Length = 348 Score = 44.3 bits (103), Expect = 1e-04 Identities = 34/108 (31%), Positives = 54/108 (50%), Gaps = 1/108 (0%) Frame = -1 Query: 470 GYAWASQSIAYVSQQPWIM-NATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMG 294 GY+ S++I +V Q + N T+ +N+ F + R +L V +G Sbjct: 68 GYSIQSRNIGFVFQNYALFKNMTVYDNIAFGLELRRISFNDISRKVNKLLEL-VQLQNLG 126 Query: 293 TEIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 LSGGQ+ R++LARA+ + +V LLD+P ALDA V + + Sbjct: 127 HRYPAQ---LSGGQRQRIALARALAIEPKVLLLDEPFGALDARVRKNL 171 >NIST_LACLA (Q03203) Nisin transport ATP-binding protein nisT Length = 600 Score = 39.3 bits (90), Expect(2) = 1e-04 Identities = 18/46 (39%), Positives = 30/46 (65%), Gaps = 3/46 (6%) Frame = -1 Query: 299 MGTEIG---ENGINLSGGQKARVSLARAVYADREVYLLDDPLSALD 171 + T++G + G LSGGQ +++LAR + +Y+LD+P +ALD Sbjct: 481 LDTQLGNWFQEGHQLSGGQWQKIALARTFFKKASIYILDEPSAALD 526 Score = 24.3 bits (51), Expect(2) = 1e-04 Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 1/36 (2%) Frame = -2 Query: 136 YLVHLAQKT-RILVTHQIDVLSRADFVVVMEKGAVQ 32 Y V L++ I ++H ++ +A+ +VVM+ G V+ Sbjct: 536 YFVALSENNISIFISHSLNAARKANKIVVMKDGQVE 571 >PSTB_XYLFA (Q9PBK0) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 267 Score = 43.9 bits (102), Expect = 2e-04 Identities = 32/107 (29%), Positives = 53/107 (49%), Gaps = 8/107 (7%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLFFSPADE--------HRLQEAVRVCQLEADLRVLAAGMGT 291 + V Q+P T+ ENV + E R+++A++ L +++ Sbjct: 103 VGMVFQKPVPFPMTIYENVAYGIRHHEVMSKSQMNDRVEQALQQSALWEEVK-------D 155 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 ++ +N + LSGGQ+ R+ +ARA+ V LLD+P SALD RI Sbjct: 156 KLNQNALGLSGGQQQRLCIARAIALTPSVLLLDEPTSALDPISTSRI 202 >MDLB_BUCAI (P57552) Multidrug resistance-like ATP-binding protein mdlB Length = 580 Score = 43.9 bits (102), Expect = 2e-04 Identities = 26/106 (24%), Positives = 56/106 (52%) Frame = -1 Query: 452 QSIAYVSQQPWIMNATLRENVLFFSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGENG 273 +++ V Q P +++ T N+ E ++ + L ++ + G+ + +GE G Sbjct: 416 RNVLMVQQDPIVLSDTFFYNITLGRKIPEEKVWNILDTVHLSDLVKSMPKGIYSLLGEEG 475 Query: 272 INLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERIVTEVL 135 NLS GQK +++AR + A +V +LD+ + +D+ E+++ + L Sbjct: 476 NNLSVGQKQLLAIARVLVAYPKVLILDEATANIDSGT-EQLIQKTL 520 >PSTB_EDWTA (Q9AML4) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) (Peripheral membrane protein B) Length = 259 Score = 43.9 bits (102), Expect = 2e-04 Identities = 39/134 (29%), Positives = 64/134 (47%), Gaps = 11/134 (8%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLF-------FSPAD-EHRLQEAVRVCQLEADLRVLAAGMGT 291 + V Q+P ++ +N+ F S AD + R+Q A+ L ++ + Sbjct: 95 VGMVFQKPTPFPMSIYDNIAFGVRLFEKLSRADMDERVQWALTKAALWSETK-------D 147 Query: 290 EIGENGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI---VTEVLFGAPC 120 ++ ++G +LSGGQ+ R+ +AR + EV LLD+P SALD RI +TE+ Sbjct: 148 KLHQSGYSLSGGQQQRLCIARGIAIRPEVLLLDEPCSALDPISTSRIEELITELKQDYTV 207 Query: 119 TKDTHPCHTSD*CS 78 TH + CS Sbjct: 208 VIVTHNMQQAARCS 221 >PSTB_ARCFU (O28912) Phosphate import ATP-binding protein pstB (EC 3.6.3.27) (Phosphate-transporting ATPase) (ABC phosphate transporter) Length = 251 Score = 43.9 bits (102), Expect = 2e-04 Identities = 32/103 (31%), Positives = 51/103 (49%), Gaps = 4/103 (3%) Frame = -1 Query: 446 IAYVSQQPWIMNATLRENVLF----FSPADEHRLQEAVRVCQLEADLRVLAAGMGTEIGE 279 I V Q P ++ +NV + D+ RL+E V +A L + + + Sbjct: 87 IGMVFQHPNPFPKSIFDNVAYGPRVHGIKDKERLKEIVEESLKKA---ALWDEVKDRLSD 143 Query: 278 NGINLSGGQKARVSLARAVYADREVYLLDDPLSALDAHVGERI 150 + + LSGGQ+ R+ +ARA+ + EV L D+P SALD +I Sbjct: 144 SALGLSGGQQQRLCIARAIATNPEVILFDEPTSALDPIAAAKI 186 Database: uniprot_sprot.fasta Posted date: Jul 7, 2004 11:51 AM Number of letters in database: 56,608,159 Number of sequences in database: 153,871 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 49,868,283 Number of Sequences: 153871 Number of extensions: 994713 Number of successful extensions: 3836 Number of sequences better than 1.0e-01: 500 Number of HSP's better than 0.1 without gapping: 3485 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 3751 length of database: 56,608,159 effective HSP length: 100 effective length of database: 41,221,059 effective search space used: 2308379304 frameshift window, decay const: 50, 0.1 T: 12 A: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) From M.Q.Lewis at exeter.ac.uk Wed Aug 4 16:25:08 2004 From: M.Q.Lewis at exeter.ac.uk (mql201) Date: Wed Aug 4 16:31:50 2004 Subject: [Bioperl-l] Bio::Graphics::Panel->add_track problem Message-ID: <41159627@minerva2.ex.ac.uk> Hello I want to print out a number of glyphs of different colours on the same track, but with this code there doesn't seem to be a way round having more than 1 colour per track: ## start with an array of colours # @colours = qw(white red green blue black yellow ...); # 190 colours in all ## specify new panel once, background white # $panel = Bio::Graphics::Panel->new(-length => 700, # length of panel in nt -width => 700, # physical width of img -pad_top => 10, # padding -pad_bottom => 10, -pad_left => 10, -pad_right => 10, -bgcolor => 'white', # colour of panel -key_color => 'white', -key_style => 'bottom'); ## the following code should create a 28 track panel (down) with 6 glyphs on ## each track (across), with each glyph a different colour got out of the array ## @colours. # my($start) = 10; my($end) = 60; for($x = 0; $x <=28; $x++) { # 28 tracks to make ## define glyph track # $track = $panel->add_track(-glyph => 'graded_segments', -linewidth => 2, -height => 8, -fontcolor => '#1d4305', # -bgcolor => 'some color', -label => 1, -bump => 1, -description => 1); ## but instead i want to use -bgcolor in the for loop below # for ($i = 0; $i <= 6; $i++) { my($feature) = Bio::SeqFeature::Generic->new(-display_name=>$key, -score=>2000, -start=>$start, ERROR, THIS SHOULD BE IN ADD_TRACK ABOVE -> -bgcolor => shift(@colours), ALTHOUGH I WANT IT IN HERE -> -end=>$end); $track->add_feature($feature); $start += 90; $end += 90; } $start = 10; $end = 60; } As you can see, its a std way of adding tracks, and glyphs to tracks, except i can't work out how to add glyphs without them having the same colour as the glyphs on the same track because i'd have specified the colour of the glyphs on that track, rather than the colour of the individual glyph. i've a feeling its a simple solution. Anybody have any idea? Many ta IA Mark From crabtree at tigr.org Wed Aug 4 17:03:49 2004 From: crabtree at tigr.org (Crabtree, Jonathan) Date: Wed Aug 4 17:05:59 2004 Subject: [Bioperl-l] Bio::Graphics::Panel->add_track problem Message-ID: Mark- The -bgcolor option of add_track will accept a coderef instead of a scalar. This is covered in the documentation (see 'perldoc Bio::Graphics::Panel'). Here's the relevant part: =head2 Options and Callbacks Instead of providing a constant value to an option, you may subsitute a code reference. This code reference will be called every time the panel needs to configure a glyph. The callback will be called with three arguments like this: sub callback { my ($feature,$option_name,$part_no,$total_parts,$glyph) = @_; # do something which results in $option_value being set return $option_value; } The five arguments are C<$feature>, a reference to the IO::SeqFeatureI object, C<$option_name>, the name of the option to configure, C<$part_no>, an integer index indicating which subpart of the feature is being drawn, C<$total_parts>, an integer indicating the total number of subfeatures in the feature, and finally C<$glyph>, the Glyph object itself. The latter fields are useful in the case of treating the first or last subfeature differently, such as using a different color for the terminal exon of a gene. Usually you will only need to examine the first argument. This example shows a callback examining the score() attribute of a feature (possibly a BLAST hit) and return the color "red" for high-scoring features, and "green" for low-scoring features: sub callback { my $feature = shift; if ($feature->score > 90) { return 'red'; else { return 'green'; } } The callback should return a string indicating the desired value of the option. To tell the panel to use the default value for this option, return the string "*default*". When you install a callback for a feature that contains subparts, the callback will be invoked first for the top-level feature, and then for each of its subparts (recursively). You should make sure to examine the feature's type to determine whether the option is appropriate. Some glyphs deliberately disable this recursive feature. The "track", "group", "transcript", "transcript2" and "segments" glyphs selectively disable the -bump, -label and -description options. This is to avoid, for example, a label being attached to each exon in a transcript, or the various segments of a gapped alignment bumping each other. You can override this behavior and force your callback to be invoked by providing add_track() with a true B<-all_callbacks> argument. In this case, you must be prepared to handle configuring options for the "group" and "track" glyphs. In particular, this means that in order to control the -bump option with a callback, you should specify -all_callbacks=E1, and turn on bumping when the callback is in the track or group glyphs. > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of mql201 > Sent: Wednesday, August 04, 2004 4:25 PM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] Bio::Graphics::Panel->add_track problem > > > Hello > > I want to print out a number of glyphs of different colours > on the same track, > but with this code there doesn't seem to be a way round > having more than 1 > colour per track: > > ## start with an array of colours > # > @colours = qw(white red green blue black yellow ...); # 190 > colours in all > > ## specify new panel once, background white > # > $panel = Bio::Graphics::Panel->new(-length => 700, # > length of panel in > nt > -width => 700, # > physical width of img > -pad_top => 10, # padding > -pad_bottom => 10, > -pad_left => 10, > -pad_right => 10, > -bgcolor => 'white', # > colour of panel > -key_color => 'white', > -key_style => 'bottom'); > > ## the following code should create a 28 track panel (down) > with 6 glyphs on > ## each track (across), with each glyph a different colour > got out of the > array > ## @colours. > # > my($start) = 10; > my($end) = 60; > for($x = 0; $x <=28; $x++) { # 28 tracks to make > ## define glyph track > # > $track = $panel->add_track(-glyph => 'graded_segments', > -linewidth => 2, > -height => 8, > -fontcolor => '#1d4305', > # -bgcolor => 'some color', > -label => 1, > -bump => 1, > -description => 1); > > ## but instead i want to use -bgcolor in the for loop below > # > for ($i = 0; $i <= 6; $i++) { > my($feature) = Bio::SeqFeature::Generic->new(-display_name=>$key, > -score=>2000, > -start=>$start, > ERROR, THIS SHOULD BE IN ADD_TRACK ABOVE -> -bgcolor => > shift(@colours), > ALTHOUGH I WANT IT IN HERE -> -end=>$end); > > $track->add_feature($feature); > $start += 90; > $end += 90; > } > $start = 10; > $end = 60; > } > > > As you can see, its a std way of adding tracks, and glyphs to > tracks, except i > can't work out how to add glyphs without them having the same > colour as the > glyphs on the same track because i'd have specified the > colour of the glyphs > on that track, rather than the colour of the individual glyph. > > i've a feeling its a simple solution. Anybody have any idea? > > Many ta IA > Mark > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-> bio.org/mailman/listinfo/bioperl-l > From lstein at cshl.edu Wed Aug 4 17:08:01 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed Aug 4 17:09:25 2004 Subject: [Bioperl-l] Seeking someone who likes XML for DAS2 project Message-ID: <200408041708.01626.lstein@cshl.edu> Hi, I've now got funding for the DAS/2 project and am looking for someone to work with me on the specification and server implementation. The job lasts two years and is compatible with telecommuting from home. I need someone who enjoys writing XML schema and technical documentation, is familiar with the HTTP protocol, and is comfortable with Bioperl. If interested, please send me an e-mail. Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From lstein at cshl.edu Wed Aug 4 17:11:24 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed Aug 4 17:13:43 2004 Subject: [Bioperl-l] Bio::Graphics::Panel->add_track problem In-Reply-To: <41159627@minerva2.ex.ac.uk> References: <41159627@minerva2.ex.ac.uk> Message-ID: <200408041711.24849.lstein@cshl.edu> Use a callback for the track -bgcolor. The callback can assign colors to individual glyphs. Lincoln On Wednesday 04 August 2004 04:25 pm, mql201 wrote: > Hello > > I want to print out a number of glyphs of different colours on the > same track, but with this code there doesn't seem to be a way round > having more than 1 colour per track: > > ## start with an array of colours > # > @colours = qw(white red green blue black yellow ...); # 190 > colours in all > > ## specify new panel once, background white > # > $panel = Bio::Graphics::Panel->new(-length => 700, # length of > panel in nt > -width => 700, # physical > width of img -pad_top => 10, # padding -pad_bottom => 10, > -pad_left => 10, > -pad_right => 10, > -bgcolor => 'white', # colour > of panel -key_color => 'white', > -key_style => 'bottom'); > > ## the following code should create a 28 track panel (down) with 6 > glyphs on ## each track (across), with each glyph a different > colour got out of the array > ## @colours. > # > my($start) = 10; > my($end) = 60; > for($x = 0; $x <=28; $x++) { # 28 tracks to make > ## define glyph track > # > $track = $panel->add_track(-glyph => 'graded_segments', > -linewidth => 2, > -height => 8, > -fontcolor => '#1d4305', > # -bgcolor => 'some color', > -label => 1, > -bump => 1, > -description => 1); > > ## but instead i want to use -bgcolor in the for loop below > # > for ($i = 0; $i <= 6; $i++) { > my($feature) = > Bio::SeqFeature::Generic->new(-display_name=>$key, -score=>2000, > -start=>$start, ERROR, THIS SHOULD BE IN ADD_TRACK ABOVE -> > -bgcolor => shift(@colours), ALTHOUGH I WANT IT IN HERE > -> -end=>$end); > > $track->add_feature($feature); > $start += 90; > $end += 90; > } > $start = 10; > $end = 60; > } > > > As you can see, its a std way of adding tracks, and glyphs to > tracks, except i can't work out how to add glyphs without them > having the same colour as the glyphs on the same track because i'd > have specified the colour of the glyphs on that track, rather than > the colour of the individual glyph. > > i've a feeling its a simple solution. Anybody have any idea? > > Many ta IA > Mark > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From Csaba.Ortutay at uta.fi Thu Aug 5 05:29:42 2004 From: Csaba.Ortutay at uta.fi (Csaba Ortutay) Date: Thu Aug 5 05:30:23 2004 Subject: [Bioperl-l] Trees and networks: ask for features Message-ID: <200408051229.42564.Csaba.Ortutay@uta.fi> Hello, I am using Bioperl to handle trees. My first question is that is it possible to write a TreeIO module, which can write trees in the Graph Description Language (gdl) format? The description is here: http://www.aisee.com/gdl/nutshell/ and shorter here: http://www.program-transformation.org/Transform/GraphDescriptionLanguage I wrote a short script, which can convert a nexus file to a dgl graph, but it lacks much of the functionality. (I included the script at the end of the mail. I am not a professional programmer, so don't look for an expert code.) Is there anybody who can (and wants) help me to develop this, and integrate to Bioperl? The another topic is the networks. A network (from my point of view) is very similar to trees except it is allowed to have more than 1 ancestor for a node. Or more, the relations is not strictly distinguished as ancestor or siblings, but in another way. GDL format is a valid file format to store networks too. It would be nice if someone could help to develop a module which can handle network objects, such as signaling networks, metabolic networks or pedigrees; similar to tree handling. I have seen that others also looked for solutions for network handling. Thanks for help: Csaba -- Csaba Ortutay PhD University of Tampere Institute of Medical Technology Bioinformatics Group Finland Csaba.Ortutay@uta.fi >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> nexus2gdl.pl: #!/usr/bin/perl -w use strict; use Bio::TreeIO; my $treeio=new Bio::TreeIO (-format=>'nexus', -file=>'mytree.tre' ); my $tree=$treeio->next_tree; my @nodes=$tree->get_nodes; my $i=0; my %gdlnodes; # Parsing the nodes of the tree into the %gdlnodes, # where hash key is the id of the node, value is a hash of siblings # The keys of sibling hash are the ids of siblings, and the value is simply 1 # which can be used in a more useful way later foreach (@nodes){ if (! $_->id){ $_->id('internal_'.$i++); } my @siblings=$_->each_Descendent; $gdlnodes{$_->id}->{1}=1; foreach my $son (@siblings){ if (! $son->id){ $son->id('internal_'.$i++); } $gdlnodes{$_->id}->{$son->id}=1; } } # Print out the gdl to the STDOUT print " // Tree in GDL format // graph: {title : \"Testtree\" layoutalgorithm: tree orientation: left_to_right arrowmode: free portsharing: yes "; foreach my $gnode (sort keys %gdlnodes){ print " node: {title : \"",$gnode,"\" } "; foreach my $son (sort keys %{$gdlnodes{$gnode}}){ if ($son eq '1'){next} print " edge: {source : \"",$gnode,"\" target : \"",$son,"\" } "; } } print "}\n"; exit; <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< From sdavis2 at mail.nih.gov Thu Aug 5 08:42:51 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu Aug 5 08:43:00 2004 Subject: [Bioperl-l] Das version Message-ID: A quick question: I was just trying out a script (make_das_conf.pl) from the Gbrowse distribution that asks for Das version 0.96, but CVS from bioperl-live has only 0.94. Is there another branch from CVS that I should be using? Thanks, Sean From hlapp at gmx.net Thu Aug 5 08:57:13 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu Aug 5 08:58:06 2004 Subject: [Bioperl-l] GO path and GO relationships In-Reply-To: Message-ID: I'm assuming you have looked at the Bio::Ontology::OntologyI API? Also, for GO the underlying engine is SimpleGOEngine.pm which basically delegates most functionality to a Graph::Directed instance (see Graph.pm from CPAN). Given the use cases though as you describe them, the GO API is probably indeed your best choice. At least what I can say is that none of the OntologyI or Graph.pm methods provides a straightforward solution to your problems. -hilmar On Wednesday, August 4, 2004, at 04:25 PM, Jason Stajich wrote: > The GO API is pretty powerful developed by Chris Mungall and others. > > http://www.godatabase.org/dev/ > Click on go-perl and go-db-perl to see SYNOPSIS information. > > > -jason > On Wed, 4 Aug 2004, Law, Annie wrote: > >> Hi, >> >> I would like to know if there are modules in bioperl that will help >> me find >> the go path, hierarchy corresponding to An input GO id. Also, I would >> like >> to know if there is something in bioperl if given as input a group of >> GO >> identifiers will indicate the >> Relationship between the GO identifiers ie. Parent or child of or is >> a. >> >> I am open to using resources available in bioperl db or separate >> modules. >> >> Thanks very much, >> Annie. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From pvh at egenetics.com Thu Aug 5 09:04:20 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Thu Aug 5 09:05:38 2004 Subject: [Bioperl-l] SeqIO fixing: detecting if a filehandle is open for writing Message-ID: <41123054.7000105@egenetics.com> I'm busy preparing patches to catch the different failure modes of SeqIO's constructor, but I'm stuck with one particular case. What if I open a filehandle for reading, and then pass that filehandle to SeqIO's constructor, and then call write_seq() on the SeqIO object. I.e. like this: use IO::File; use Bio::SeqIO; use Bio::PrimarySeq; my $fh = IO::File->new("myfile.fasta") || die "open failed: $!\n"; my $seqio = Bio::SeqIO->new(-fh => $fh, -format => 'fasta'); my $seq = new Bio::PrimarySeq(id => 'MYID', seq => 'GATTACCA'); $seqio->write_seq($seq); The current result is that write_seq() silently fails. I'm trying to deal with all misleading error messages & late failures at the moment, but I feel we're going to be left with some cases that can't be avoided in the end. Peter From miroslavac at health.nb.ca Thu Aug 5 08:52:20 2004 From: miroslavac at health.nb.ca (Miroslava Cuperlovic-Culf) Date: Thu Aug 5 09:13:20 2004 Subject: [Bioperl-l] Bio::Graphics::Panel Message-ID: <41122D84.8050607@health.nb.ca> Dear All, I would like to use Bio::Graphics to present exons mapped to dna in a gff file. I get nice figure for exact lengths of exons and introns. But as exons are much shorter than introns it is impossible to see their lengths. Thus I would like to either present exons in correct lengths and introns only as "..." or as a number of bases or alternatively as several figures, one for each exon. Is either of these possible? From perldoc for Bio::Graphics I understood that it is possible to open several pictures from one program so I tried to use: ... my $panel = Bio::Graphics::Panel->new( ... ... print $panel->gd->gif; $panel ->finished;... my $panel1 = Bio::Graphics::Panel->new( ... ... print $panel1->gd->gif; $panel1 ->finished; but in this way I only got the first panel opened. What am I doing wrong? Thanks very much for the ongoing help Mira - From reche at research.dfci.harvard.edu Wed Aug 4 19:37:38 2004 From: reche at research.dfci.harvard.edu (Pedro Antonio Reche) Date: Thu Aug 5 09:13:26 2004 Subject: [Bioperl-l] organism restricted blast search Message-ID: <45192F52-E66F-11D8-A804-000393BC20D0@research.dfci.harvard.edu> Hi, I am interested in carrying out a blast (or parse a blast search) in a way that only hits from a given organism will show. This is similar to what the NCBI blast site does currently I wonder if someone knows how to do it using bioperl. Thanks in advance for any help. Cheers ======================================================================== ===================== Dr. Pedro A Reche, Instructor of Medicine Dana-Farber Cancer Institute, Harvard Medical School TL: 617 632 3824 HIM Building, Room 401 FX: 617 632 3351 77 Avenue Louis Pasteur EM: reche@research.dfci.harvard.edu Boston, MA 02115, USA W3: www.mifoundation.org -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 982 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040804/c083a069/attachment.bin From crabtree at tigr.org Thu Aug 5 09:24:35 2004 From: crabtree at tigr.org (Crabtree, Jonathan) Date: Thu Aug 5 09:26:26 2004 Subject: [Bioperl-l] Bio::Graphics::Panel Message-ID: Mira- If you want to generate two images you'll need to direct $panel->gd->gif to one file, and $panel1->gd->gif to a second file. At the moment you're printing both to STDOUT, so it's not surprising that a subsequent display of that data shows only the first of the two images (since the program you're using to display the image probably gets to the end of the first GIF and thinks that it's done.) If you're rendering images for display on the web you could add a parameter to your script that tells it whether to generate the first of the two images or the second of the two. The HTML page that displays the images (which could itself be generated by a script) would then contain two tags, one for the first image, and the other for the second. If you want to render multiple Bio::Graphics::Panel images into a single GIF/PNG, this can be done, although there are some caveats. I posted some suggestions about this a while ago, so a search of the list archive should turn them up. Jonathan > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of > Miroslava Cuperlovic-Culf > Sent: Thursday, August 05, 2004 8:52 AM > To: BioPerl > Subject: [Bioperl-l] Bio::Graphics::Panel > > > Dear All, > I would like to use Bio::Graphics to present exons mapped to > dna in a > gff file. I get nice figure for exact lengths of exons and > introns. But > as exons are much shorter than introns it is impossible to see their > lengths. Thus I would like to either present exons in correct lengths > and introns only as "..." or as a number of bases or > alternatively as > several figures, one for each exon. Is either of these > possible? From perldoc for Bio::Graphics I understood that > it is possible to open > several pictures from one program so I tried to use: > ... > my $panel = Bio::Graphics::Panel->new( ... > ... > print $panel->gd->gif; > $panel ->finished;... > my $panel1 = Bio::Graphics::Panel->new( ... > ... > print $panel1->gd->gif; > $panel1 ->finished; > > but in this way I only got the first panel opened. > What am I doing wrong? > Thanks very much for the ongoing help > Mira > > - > From paulo.david at netvisao.pt Thu Aug 5 09:54:51 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Thu Aug 5 09:53:25 2004 Subject: [Bioperl-l] organism restricted blast search In-Reply-To: <45192F52-E66F-11D8-A804-000393BC20D0@research.dfci.harvard.edu> References: <45192F52-E66F-11D8-A804-000393BC20D0@research.dfci.harvard.edu> Message-ID: <41123C2B.70400@netvisao.pt> Pedro, You need to add a parameter like this: $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]'; For more information, read the synopsis here: http://search.cpan.org/~birney/bioperl/Bio/Tools/Run/RemoteBlast.pm -Paulo Pedro Antonio Reche wrote: > Hi, > I am interested in carrying out a blast (or parse a blast search) in a > way that only hits from a given organism will show. This is similar to > what the NCBI blast site does currently I wonder if someone knows how > to do it using bioperl. Thanks in advance for any help. > Cheers From fernan at iib.unsam.edu.ar Thu Aug 5 09:47:20 2004 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Thu Aug 5 09:53:44 2004 Subject: [Bioperl-l] organism restricted blast search In-Reply-To: <45192F52-E66F-11D8-A804-000393BC20D0@research.dfci.harvard.edu> References: <45192F52-E66F-11D8-A804-000393BC20D0@research.dfci.harvard.edu> Message-ID: <20040805134720.GD72520@iib.unsam.edu.ar> +----[ Pedro Antonio Reche (05.Aug.2004 10:28): | | Hi, | I am interested in carrying out a blast (or parse a blast search) in a | way that only hits from a given organism will show. This is similar to | what the NCBI blast site does currently I wonder if someone knows how | to do it using bioperl. Thanks in advance for any help. | Cheers | +----] If you use Bio::Tools:Run::RemoteBlast to run your searches remotely at the NCBI, you can do something along the lines of: #change a parameter $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]'; this was taken from the synopsis of the mentioned module. You can of course replace your entrez query with whatever you like. If you're doing local blast searches, I guess it's not possible. If anyone has a way of doing it, please enlighten me. Fernan -- Fernan Aguero - fernan at iib.unsam.edu.ar Phone: +54 11 4580-7255/7 ext 310, Fax: +54 11 4752-9639 Check http://genoma.unsam.edu.ar/~fernan for more info. From hlapp at gmx.net Thu Aug 5 09:55:05 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu Aug 5 09:56:00 2004 Subject: [Bioperl-l] SeqIO fixing: detecting if a filehandle is open for writing In-Reply-To: <41123054.7000105@egenetics.com> Message-ID: <0E4E5C88-E6E7-11D8-84A8-000A959EB4C4@gmx.net> Quite frankly IMNSHO if you open a file for reading and then - unsuccessfully - try to write to the file this is not a bioperl error, or perl error for that matter, but a programming error. Perl will be no more verbose if you do this ... at least as far as I'm aware. I.e., the documentation should be that if you do an operation to a file or SeqIO handle for which you did not open it in the first place then the behavior is undefined. -hilmar On Thursday, August 5, 2004, at 02:04 PM, Peter van Heusden wrote: > I'm busy preparing patches to catch the different failure modes of > SeqIO's constructor, but I'm stuck with one particular case. What if I > open a filehandle for reading, and then pass that filehandle to > SeqIO's constructor, and then call write_seq() on the SeqIO object. > I.e. like this: > > use IO::File; > use Bio::SeqIO; > use Bio::PrimarySeq; > > my $fh = IO::File->new("myfile.fasta") || die "open failed: $!\n"; > > my $seqio = Bio::SeqIO->new(-fh => $fh, -format => 'fasta'); > > my $seq = new Bio::PrimarySeq(id => 'MYID', seq => 'GATTACCA'); > > $seqio->write_seq($seq); > > The current result is that write_seq() silently fails. I'm trying to > deal with all misleading error messages & late failures at the moment, > but I feel we're going to be left with some cases that can't be > avoided in the end. > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From Richard.Adams at ed.ac.uk Thu Aug 5 10:11:53 2004 From: Richard.Adams at ed.ac.uk (Richard Adams) Date: Thu Aug 5 10:13:35 2004 Subject: [Bioperl-l] remote access to web services Message-ID: <41124029.7040200@ed.ac.uk> Hi, I was wondering if anyone had an opinion on the utility of the Bio:Tools::Analysis::Protein/DNA modules (described in the SimpleWebAnalysis HOWTO docs) which wrap various remote sequence analysis programs. Given the serious effort into long term, heavy duty solutions like Pise and Soaplab I'm weighing up if it's worth the effort to maintain and develop these modules. Richard -- Dr Richard Adams Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk From pvh at egenetics.com Thu Aug 5 10:13:38 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Thu Aug 5 10:14:59 2004 Subject: [Bioperl-l] SeqIO fixing: detecting if a filehandle is open for writing In-Reply-To: <0E4E5C88-E6E7-11D8-84A8-000A959EB4C4@gmx.net> References: <0E4E5C88-E6E7-11D8-84A8-000A959EB4C4@gmx.net> Message-ID: <41124092.5060208@egenetics.com> Hilmar Lapp wrote: > Quite frankly IMNSHO if you open a file for reading and then - > unsuccessfully - try to write to the file this is not a bioperl error, > or perl error for that matter, but a programming error. Perl will be > no more verbose if you do this ... at least as far as I'm aware. > > I.e., the documentation should be that if you do an operation to a > file or SeqIO handle for which you did not open it in the first place > then the behavior is undefined. > Yep, as I said in my documentation, the options are fix the documentation or fix the code. I acknowledge that this is programming error - but the implication is that a single typo (no '>' when opening the file) results in silent failure - i.e. it appears to work, but doesn't. The Perl behaviour is slightly different (not that I think anyone checks these things): if you do 'print $fh "FOO\n"' and $fh is open for reading only, the return value of print is undef (otherwise it is 1). There might not be anything do-able about this case, but as far as possible I think that reasonable programmer errors should be caught. Peter From Richard.Adams at ed.ac.uk Thu Aug 5 11:57:56 2004 From: Richard.Adams at ed.ac.uk (Richard Adams) Date: Thu Aug 5 11:59:09 2004 Subject: [Bioperl-l] Secondary structure prediction Message-ID: <41125904.3070503@ed.ac.uk> Hi Jon, One way is to use the Bio::Tools::Analysis::Protein::HNN/Gor4/Sopma module e.g., e.g., if you have a Bio::Seq object, $seq my $sopma = Bio::Tools::Analysis::Protein::Sopma->new (-seq=>$seq, states=>4); $sopma->run; print $sopma->result;# #raw text to standard error my @fts = $tool->result('Bio::SeqFeatureI'); $seq->add_SeqFeature(@fts); will submit the sequence to the analysis, run remotely, and return the results as sequence features. This is described more fully in the SimpleWebAnalysis HOWTO document. There is also an EMBOSS program garnier which can be wrapped using the Bio::Tools::EMBOSS module. HTH Richard -- Dr Richard Adams Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk From jason at cgt.duhs.duke.edu Thu Aug 5 11:58:40 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Aug 5 11:59:56 2004 Subject: [Bioperl-l] SeqIO fixing: detecting if a filehandle is open for writing In-Reply-To: <41123054.7000105@egenetics.com> References: <41123054.7000105@egenetics.com> Message-ID: On Thu, 5 Aug 2004, Peter van Heusden wrote: > I'm busy preparing patches to catch the different failure modes of > SeqIO's constructor, but I'm stuck with one particular case. What if I > open a filehandle for reading, and then pass that filehandle to SeqIO's > constructor, and then call write_seq() on the SeqIO object. I.e. like this: > > use IO::File; > use Bio::SeqIO; > use Bio::PrimarySeq; > > my $fh = IO::File->new("myfile.fasta") || die "open failed: $!\n"; > > my $seqio = Bio::SeqIO->new(-fh => $fh, -format => 'fasta'); > > my $seq = new Bio::PrimarySeq(id => 'MYID', seq => 'GATTACCA'); > > $seqio->write_seq($seq); > > The current result is that write_seq() silently fails. I'm trying to > deal with all misleading error messages & late failures at the moment, > but I feel we're going to be left with some cases that can't be avoided > in the end. My feeling is that any logic here should be pushed up to Bio::Root::IO anyays. If we had a way to test if a filehandle was read/write we would use this in a number of places in Bioperl. The removal of automagic use of \*ARGV from Bio::Root::IO was due to a problem with this as well in Bio::Tools::GFF. AFAIK there is no way to test if a handle is for reading or writing or both... -jason > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Thu Aug 5 12:03:58 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Aug 5 12:05:29 2004 Subject: [Bioperl-l] organism restricted blast search In-Reply-To: <20040805134720.GD72520@iib.unsam.edu.ar> References: <45192F52-E66F-11D8-A804-000393BC20D0@research.dfci.harvard.edu> <20040805134720.GD72520@iib.unsam.edu.ar> Message-ID: I believe there are ways of building virtual subsets of the databases locally with some tricks with formatdb but I don't really know them. You can also parse your reports and lookup the GI number using the tools in Bio::Taxonomy and Bio::DB::Taxonomy to get the species name and or restrict hits to a particular subset of the taxonomy hierarchy. There were some posts in the last few months about this. You can re-write your report with Bio::SearchIO::Writer::TextResultWriter or HTMLResultWriter and feed in a function which will only output a hit if it falls in a particular domain of the taxonomy. That is a lot of shorthand as to how program it up - if you really need something like this can point you to more working code. -jason On Thu, 5 Aug 2004, Fernan Aguero wrote: > +----[ Pedro Antonio Reche (05.Aug.2004 10:28): > | > | Hi, > | I am interested in carrying out a blast (or parse a blast search) in a > | way that only hits from a given organism will show. This is similar to > | what the NCBI blast site does currently I wonder if someone knows how > | to do it using bioperl. Thanks in advance for any help. > | Cheers > | > +----] > > If you use Bio::Tools:Run::RemoteBlast to run your searches > remotely at the NCBI, you can do something along the lines of: > > #change a parameter > $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]'; > > this was taken from the synopsis of the mentioned module. > You can of course replace your entrez query with whatever > you like. > > If you're doing local blast searches, I guess it's not > possible. If anyone has a way of doing it, please enlighten > me. > > Fernan > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From Anthony.Underwood at hpa.org.uk Thu Aug 5 12:05:05 2004 From: Anthony.Underwood at hpa.org.uk (SRMD, Col - Underwood, Anthony) Date: Thu Aug 5 12:10:53 2004 Subject: [Bioperl-l] EMBOSS tools and bioperl Message-ID: <427DA33A6101484BA7A72934AF90DF73051AAA39@exchange1.phls.org.uk> Hi bioperlers I have a perl program using bioperl and the EMBOSS factory module. The program works fine from the command line but not as cgi which is obviously running as a different user. I have a suspicion it's something to do with paths. Is there an environmental variable I need to set to run emboss programs as there is with local blast and bioperl e.g BEGIN {$ENV{BLASTDIR} = '/usr/local/blast';$ENV{BLASTDATADIR} = '/usr/local/blast/data/databases'; } When I run these two lines within the script $factory = Bio::Factory::EMBOSS -> new(); $needle = $factory->program('needle') || die "needle_factory $!"; <----------line 23 the error message is needle_factory No such file or directory at /usr/local/apache/cgi-bin/needle_test.cgi line 23. Please can anybody advise. Many thanks Anthony ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ************************************************************************** From amackey at pcbi.upenn.edu Thu Aug 5 12:20:31 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Thu Aug 5 12:21:47 2004 Subject: [Bioperl-l] organism restricted blast search In-Reply-To: References: <45192F52-E66F-11D8-A804-000393BC20D0@research.dfci.harvard.edu> <20040805134720.GD72520@iib.unsam.edu.ar> Message-ID: <5EE2E100-E6FB-11D8-A48E-000A9577009E@pcbi.upenn.edu> On Aug 5, 2004, at 12:03 PM, Jason Stajich wrote: > I believe there are ways of building virtual subsets of the databases > locally with some tricks with formatdb but I don't really know them. You can make a file that has the GI numbers of the sequences you want to search against (say, a GI number dump from the Taxonomy DB), and then use "-l gilist" with NCBI blast tools > You can also parse your reports and lookup the GI number using the > tools > in Bio::Taxonomy and Bio::DB::Taxonomy to get the species name and or > restrict hits to a particular subset of the taxonomy hierarchy. This also works, but your expectation values will be artificially conservative (as you actually searched a potentially much larger database). -Aaron From hz5 at njit.edu Thu Aug 5 12:29:01 2004 From: hz5 at njit.edu (hz5@njit.edu) Date: Thu Aug 5 12:30:13 2004 Subject: [Bioperl-l] flip Bio::Graphics::Panel In-Reply-To: References: Message-ID: <1091723341.4112604dd6e0c@webmail.njit.edu> Hello, I flip the panel when a transcript is on minus strand, but the problems is that the key panel doesn't display well, flipped to the right side and not randering well. Anybody know how to deal with this? Thanks! haibo From hlapp at gmx.net Thu Aug 5 13:24:44 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu Aug 5 13:48:35 2004 Subject: [Bioperl-l] SeqIO fixing: detecting if a filehandle is open for writing In-Reply-To: <41124092.5060208@egenetics.com> Message-ID: <57DFDD16-E704-11D8-B3BB-000A959EB4C4@gmx.net> On Thursday, August 5, 2004, at 03:13 PM, Peter van Heusden wrote: > The Perl behaviour is slightly different (not that I think anyone > checks these things): if you do 'print $fh "FOO\n"' and $fh is open > for reading only, the return value of print is undef (otherwise it is > 1). > > There might not be anything do-able about this case, but as far as > possible I think that reasonable programmer errors should be caught. Well if that's the case since $seqio->write_seq() doesn't need to return anything really other than an indicator for success or failure why don't we do exactly that. I.e., why don't you fix $seqio->write_seq() to return success or failure as much as perl itself does it. In fact, if the first, or any for that matter, print statement in SeqIO fails according to the return value from perl, one could argue that another print attempt does not need to be made or is even harmful if it succeeds b/c partial but seemingly complete output would be the result. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From lstein at cshl.edu Thu Aug 5 16:40:11 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Thu Aug 5 16:41:35 2004 Subject: [Bioperl-l] flip Bio::Graphics::Panel In-Reply-To: <1091723341.4112604dd6e0c@webmail.njit.edu> References: <1091723341.4112604dd6e0c@webmail.njit.edu> Message-ID: <200408051640.11761.lstein@cshl.edu> This is fixed in recent versions of bioperl-live on CVS Lincoln On Thursday 05 August 2004 12:29 pm, hz5@njit.edu wrote: > Hello, > I flip the panel when a transcript is on minus strand, but the > problems is that the key panel doesn't display well, flipped to the > right side and not randering well. > > Anybody know how to deal with this? > Thanks! > haibo > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From wgh8089 at earthlink.net Thu Aug 5 21:56:04 2004 From: wgh8089 at earthlink.net (Bill Herbert) Date: Thu Aug 5 21:57:16 2004 Subject: [Bioperl-l] Problems using a pers\l script to connect to GenBank Message-ID: <29092046.1091757365252.JavaMail.root@dewey.psp.pas.earthlink.net> Hi All, This may be an elementary problem but it's giving me fits! I'm trying to connect to GenBank using the following script: use Bio::Perl; use Bio::DB::GenBank; $gb = new Bio::DB::GenBank(); $seq = $gb->get_seq_by_id('MUSIGBa1'); Bioperl and Bundle are installed, and the file GenBank.pm is installed at perl\lib\Bio\DB, but when I execute this script I get the message: Can't locate object method "get_seq_by_id" via package "Bio::DB::GenBank." Any suggestions? Thanks a million for any help. Bill From jason at cgt.duhs.duke.edu Thu Aug 5 23:10:15 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Aug 5 23:11:43 2004 Subject: [Bioperl-l] Problems using a pers\l script to connect to GenBank In-Reply-To: <29092046.1091757365252.JavaMail.root@dewey.psp.pas.earthlink.net> References: <29092046.1091757365252.JavaMail.root@dewey.psp.pas.earthlink.net> Message-ID: Case MatTers... Try: get_Seq_by_id() -jason On Thu, 5 Aug 2004, Bill Herbert wrote: > Hi All, > > This may be an elementary problem but it's giving me fits! > > I'm trying to connect to GenBank using the following script: > > use Bio::Perl; > use Bio::DB::GenBank; > $gb = new Bio::DB::GenBank(); > $seq = $gb->get_seq_by_id('MUSIGBa1'); > > Bioperl and Bundle are installed, and the file GenBank.pm is installed at perl\lib\Bio\DB, but when I execute this script I get the message: > Can't locate object method "get_seq_by_id" via package "Bio::DB::GenBank." > > Any suggestions? > > Thanks a million for any help. > Bill > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From maria at cbm.bio.uniroma2.it Fri Aug 6 06:50:17 2004 From: maria at cbm.bio.uniroma2.it (Maria Persico) Date: Fri Aug 6 06:52:22 2004 Subject: [Bioperl-l] retrieving by acc from a local multifasta file In-Reply-To: <29092046.1091757365252.JavaMail.root@dewey.psp.pas.earthlink.net> Message-ID: Hi All, This may be a stupid problem but for me it's something difficult: I have a list of swissprot accessions(my_acc) and I want to extract from uniprot_sprot.fasta only sequences of my list. How can do this with bioperl? thanks, Maria Maria Persico MINT database, Cesareni Group Universita' di Tor Vergata, via della Ricerca Scientifica 00133 Roma, Italy Tel: +39 0672594315 FAX: +39 0672594766 e-mail: maria@cbm.bio.uniroma2.it From sanges at biogem.it Fri Aug 6 07:06:45 2004 From: sanges at biogem.it (Remo Sanges) Date: Fri Aug 6 07:08:00 2004 Subject: [Bioperl-l] retrieving by acc from a local multifasta file In-Reply-To: References: Message-ID: On Aug 6, 2004, at 12:50 PM, Maria Persico wrote: > Hi All, > > This may be a stupid problem but for me it's something difficult: > I have a list of swissprot accessions(my_acc) and I want to extract > from > uniprot_sprot.fasta only sequences of my list. > How can do this with bioperl? Hi Maria, you could create an index of your fasta file and then retrieve sequences from it. Read the tutorial section 'III.1.2 Indexing and accessing local databases' http://bioperl.org/Core/Latest/bptutorial.html and the documentation of Bio::Index::Fasta module http://doc.bioperl.org/releases/bioperl-1.4/Bio/Index/Fasta.html HTH Remo From paulo.david at netvisao.pt Fri Aug 6 07:47:42 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Fri Aug 6 07:46:09 2004 Subject: [Bioperl-l] retrieving by acc from a local multifasta file In-Reply-To: References: Message-ID: <41136FDE.3070004@netvisao.pt> Maria, If your fasta file is in a format that can be parsed by Bioperl, I think you just need to load the sequences into a Bio::Seq object, using Bio::SeqIO. ( for details check http://search.cpan.org/~birney/bioperl-1.4/Bio/SeqIO.pm ) Then you can get the accesion number of each sequence with $seq->accesion_number and only retrieve those that match your list. ( for details check http://search.cpan.org/~birney/bioperl-1.4/Bio/Seq.pm ) Good luck, Paulo Maria Persico wrote: >I have a list of swissprot accessions(my_acc) and I want to extract from >uniprot_sprot.fasta only sequences of my list. >How can do this with bioperl? > From Anthony.Underwood at hpa.org.uk Thu Aug 5 12:31:19 2004 From: Anthony.Underwood at hpa.org.uk (SRMD, Col - Underwood, Anthony) Date: Fri Aug 6 07:53:48 2004 Subject: [Bioperl-l] EMBOSS tools and bioperl Message-ID: <427DA33A6101484BA7A72934AF90DF73051AAA3A@exchange1.phls.org.uk> Thank you Joshua that was the trick- the apache user didn't have anything defined for the $PATH variable. Specifying /usr/local/bin in a statement like BEGIN {$ENV{PATH}='/usr/local/bin/';} at the beginning of the script did he trick. Thanks for your quick reply, Anthony -----Original Message----- From: Orvis, Joshua D. (HSC) [mailto:Joshua-Orvis@ouhsc.edu] Sent: 05 August 2004 17:26 To: SRMD, Col - Underwood, Anthony; bioperl-l@bioperl.org Cc: SRMD, Col - Chandra, Manosree Subject: RE: [Bioperl-l] EMBOSS tools and bioperl my "needle" is in /usr/local/bin, and if that isn't in apache's path you could do something like this at the top of your CGI script: $ENV{'PATH'} = "/usr/local/bin"; or $ENV{'PATH'} .= ":/usr/local/bin"; ## if you want to keep the existing PATH as well Joshua -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org on behalf of SRMD, Col - Underwood, Anthony Sent: Thu 2004-08-05 11:05 AM To: bioperl-l@bioperl.org Cc: SRMD, Col - Chandra, Manosree Subject: [Bioperl-l] EMBOSS tools and bioperl Hi bioperlers I have a perl program using bioperl and the EMBOSS factory module. The program works fine from the command line but not as cgi which is obviously running as a different user. I have a suspicion it's something to do with paths. Is there an environmental variable I need to set to run emboss programs as there is with local blast and bioperl e.g BEGIN {$ENV{BLASTDIR} = '/usr/local/blast';$ENV{BLASTDATADIR} = '/usr/local/blast/data/databases'; } When I run these two lines within the script $factory = Bio::Factory::EMBOSS -> new(); $needle = $factory->program('needle') || die "needle_factory $!"; <----------line 23 the error message is needle_factory No such file or directory at /usr/local/apache/cgi-bin/needle_test.cgi line 23. Please can anybody advise. Many thanks Anthony ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ************************************************************************** _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ************************************************************************** From Joshua-Orvis at ouhsc.edu Thu Aug 5 12:25:39 2004 From: Joshua-Orvis at ouhsc.edu (Orvis, Joshua D. (HSC)) Date: Fri Aug 6 07:54:16 2004 Subject: [Bioperl-l] EMBOSS tools and bioperl Message-ID: my "needle" is in /usr/local/bin, and if that isn't in apache's path you could do something like this at the top of your CGI script: $ENV{'PATH'} = "/usr/local/bin"; or $ENV{'PATH'} .= ":/usr/local/bin"; ## if you want to keep the existing PATH as well Joshua -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org on behalf of SRMD, Col - Underwood, Anthony Sent: Thu 2004-08-05 11:05 AM To: bioperl-l@bioperl.org Cc: SRMD, Col - Chandra, Manosree Subject: [Bioperl-l] EMBOSS tools and bioperl Hi bioperlers I have a perl program using bioperl and the EMBOSS factory module. The program works fine from the command line but not as cgi which is obviously running as a different user. I have a suspicion it's something to do with paths. Is there an environmental variable I need to set to run emboss programs as there is with local blast and bioperl e.g BEGIN {$ENV{BLASTDIR} = '/usr/local/blast';$ENV{BLASTDATADIR} = '/usr/local/blast/data/databases'; } When I run these two lines within the script $factory = Bio::Factory::EMBOSS -> new(); $needle = $factory->program('needle') || die "needle_factory $!"; <----------line 23 the error message is needle_factory No such file or directory at /usr/local/apache/cgi-bin/needle_test.cgi line 23. Please can anybody advise. Many thanks Anthony ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ************************************************************************** _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From barry.moore at genetics.utah.edu Fri Aug 6 08:45:33 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri Aug 6 08:46:52 2004 Subject: [Bioperl-l] retrieving by acc from a local multifasta file In-Reply-To: References: Message-ID: <41137D6D.5070501@genetics.utah.edu> Maria, If this is a one off script, and you are doing something simple with your sequences once you extract them, then you may not need to use BioPerl at all. You could read the complete uniprot_sprot.fasta file into a hash keyed off of the accession to create a simple database in memory. Then you can retrieve the sequences you need by accession. It will take a while to build that hash even on a fairly good computer, so it's not an approach that you would want to use for a script that you will run alot. Try the following code. Barry ----------------------------------------------------------------------------------- #!/usr/bin/perl use strict; use warnings; #Your list of SwissProt accessions. my @accs = ('Q43495', 'P13813', 'P15455'); #Open and read your uniprot file. open (IN, "uniprot_sprot.fasta"); my $uniprot_data = join "", (); #Extract fasta sequences into a hash keyed on the accession. my %seq_db; while($uniprot_data =~ /^>.*?\(([\d\w]{6})\).*?\n(^(?!>).*\n)+/gm) { $seq_db{$1} = $&; } #Loop over your accessions, and do something with the sequence. for my $acc (@accs) { print "$seq_db{$acc}\n\n"; } --------------------------------------------------------------------------------------- Maria Persico wrote: >Hi All, > >This may be a stupid problem but for me it's something difficult: >I have a list of swissprot accessions(my_acc) and I want to extract from >uniprot_sprot.fasta only sequences of my list. >How can do this with bioperl? > >thanks, > >Maria > > > >Maria Persico >MINT database, Cesareni Group >Universita' di Tor Vergata, via della Ricerca Scientifica >00133 Roma, Italy >Tel: +39 0672594315 >FAX: +39 0672594766 >e-mail: maria@cbm.bio.uniroma2.it > > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From michael.watson at bbsrc.ac.uk Fri Aug 6 09:44:58 2004 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Fri Aug 6 09:46:33 2004 Subject: [Bioperl-l] Queries differ Message-ID: <8975119BCD0AC5419D61A9CF1A923E951746A3@iahce2knas1.iah.bbsrc.reserved> Hi Why when querying GenBank through bioperl do I get 740 records returned, yet when I query GenBank through the NCBI website it tells me there are 822 sequences in GenBank for the same query string? Mick Michael Watson Head of Informatics Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire RG20 7NN UK Phone : +44 (0)1635 578411 ext. 2535 Mobile: +44 (0)7990 827831 E-mail: michael.watson@bbsrc.ac.uk From Steven.Roels at mpi.com Fri Aug 6 13:48:53 2004 From: Steven.Roels at mpi.com (Roels, Steven) Date: Fri Aug 6 13:50:59 2004 Subject: [Bioperl-l] identifying objects in Bio::Graphics SVG Message-ID: Hello, I'd like to take the nice SVG output I can generate with the Bio::Graphics modules, and add javascript to (for example) alter/hide elements based on a slider or other user-controlled input. Is there a way to map various panel items to the resulting svg components? e.g transcript3, exon4 == Given that the "" grouping element doesn't seem to be used (which would facilitate this for non-simple elements), I'm guessing not, but thought I would ask. Thanks, -Steve ***************************************************************** Steve Roels, Ph.D. Senior Scientist I Computational Biology Millennium Pharmaceuticals, Inc. Phone: 617.761.6820 640 Memorial Drive FAX: 617.577.3555 Cambridge, MA 02139-4815 Email: steven.roels@mpi.com ***************************************************************** This e-mail, including any attachments, is a confidential business communication, and may contain information that is confidential, proprietary and/or privileged. This e-mail is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone else. If you are not the(an) intended recipient, please immediately delete this e-mail from your computer system and notify the sender. Thank you. From crabtree at tigr.org Fri Aug 6 14:20:07 2004 From: crabtree at tigr.org (Crabtree, Jonathan) Date: Fri Aug 6 14:23:00 2004 Subject: [Bioperl-l] identifying objects in Bio::Graphics SVG Message-ID: Hi Steve- I looked into this briefly and I'm pretty sure that the answer is "no". The way that the Bio::Graphics module generates SVG output is by using GD::SVG, which is more or less a drop-in replacement for GD. Since the GD API doesn't require (or permit, AFAIK) the association of logical identifiers with graphics primitives (e.g., these four lines are part of exon #1234), this information isn't included in the GD API calls and therefore isn't available to GD::SVG. So even if GD::SVG wanted to group the various elements within an SVG roup, it doesn't have any way of gleaning the necessary information without going beyond the GD API. Now of course this isn't to say that it wouldn't be possible to implement this type of functionality, but it would require making Bio::Graphics somewhat more SVG-aware than it is now, and would probably entail delving into the workings of GD::SVG a little bit. I can also imagine taking a somewhat heavyweight approach that would be relatively inefficient but might be easier to implement. One could conceivably make a fresh GD::SVG object for each glyph to be rendered, and then add some code to Bio::Graphics to strip out the essential SVG rendered by each glyph, wrap it in a element, and place it into a dummy top-level GD::SVG object that serves only to collect the text of the SVG document. I don't know...at some point it's going to be easier to just go ahead and add direct SVG support into Bio::Graphics. Jonathan p.s. Re-reading your original message, it might be possible to do something using the bounding box of the feature of interest (which can be obtained from the Bio::Graphics panel) to search through the SVG text for the relevant section. It would be messy, though, and rather indirect. > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of > Roels, Steven > Sent: Friday, August 06, 2004 1:49 PM > To: bioperl-l@bioperl.org > Subject: [Bioperl-l] identifying objects in Bio::Graphics SVG > > > > Hello, > > I'd like to take the nice SVG output I can generate with the > Bio::Graphics modules, and add javascript to (for example) > alter/hide elements based on a slider or other user-controlled input. > > Is there a way to map various panel items to the resulting > svg components? > > e.g transcript3, exon4 == > > Given that the "" grouping element doesn't seem to be used > (which would facilitate this for non-simple elements), I'm > guessing not, but thought I would ask. > > Thanks, > > -Steve > > ***************************************************************** > Steve Roels, Ph.D. > Senior Scientist I > Computational Biology > Millennium Pharmaceuticals, Inc. Phone: 617.761.6820 > 640 Memorial Drive FAX: 617.577.3555 > Cambridge, MA 02139-4815 Email: steven.roels@mpi.com > ***************************************************************** > > > > > This e-mail, including any attachments, is a confidential > business communication, and may contain information that is > confidential, proprietary and/or privileged. This e-mail is > intended only for the individual(s) to whom it is addressed, > and may not be saved, copied, printed, disclosed or used by > anyone else. If you are not the(an) intended recipient, > please immediately delete this e-mail from your computer > system and notify the sender. Thank you. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-> bio.org/mailman/listinfo/bioperl-l > From harris at cshl.edu Fri Aug 6 15:16:58 2004 From: harris at cshl.edu (Todd Harris) Date: Fri Aug 6 15:18:09 2004 Subject: [Bioperl-l] identifying objects in Bio::Graphics SVG In-Reply-To: Message-ID: Jonathon pretty much beat me to the answer. GD::SVG is really just intended as proxy for GD.pm to get SVG output from GD scripts. It doesn't take advantage of much of the richness of SVG since these elements reside outside the scope of GD. That said, I have experimented with minor things like adding descriptive IDs to SVG objects. I'd be interested to see if boxes() will work with GD::SVG rendered panels. I suspect it will choke - please let me know. It shouldn't be too hard to add this support which might allow greater SVG flexibility from Bio::Graphics for the short term. For the longer term, I'd rather see generic Bio::Graphics objects that contain no format-specific graphic generation. These would in turn use Bio::Graphics::SVG, Bio::Graphics::Postscript, to draw/calculate the actual primitives as necessary. Given the duct-tape approach of GD::SVG, overloading it to handle the additional options of SVG could get messy - fast. Duck and cover. Todd > On 8/6/04 1:20 PM, Crabtree, Jonathan wrote: > > Hi Steve- > > I looked into this briefly and I'm pretty sure that the answer is "no". > The way that the Bio::Graphics module generates SVG output is by using > GD::SVG, which is more or less a drop-in replacement for GD. Since the > GD API doesn't require (or permit, AFAIK) the association of logical > identifiers with graphics primitives (e.g., these four lines are part of > exon #1234), this information isn't included in the GD API calls and > therefore isn't available to GD::SVG. So even if GD::SVG wanted to > group the various elements within an SVG roup, it doesn't have any > way of gleaning the necessary information without going beyond the GD > API. > > Now of course this isn't to say that it wouldn't be possible to > implement this type of functionality, but it would require making > Bio::Graphics somewhat more SVG-aware than it is now, and would probably > entail delving into the workings of GD::SVG a little bit. I can also > imagine taking a somewhat heavyweight approach that would be relatively > inefficient but might be easier to implement. One could conceivably > make a fresh GD::SVG object for each glyph to be rendered, and then add > some code to Bio::Graphics to strip out the essential SVG rendered by > each glyph, wrap it in a element, and place it into a dummy > top-level GD::SVG object that serves only to collect the text of the SVG > document. I don't know...at some point it's going to be easier to just > go ahead and add direct SVG support into Bio::Graphics. > > Jonathan > > p.s. Re-reading your original message, it might be possible to do > something using the bounding box of the feature of interest (which can > be obtained from the Bio::Graphics panel) to search through the SVG text > for the relevant section. It would be messy, though, and rather > indirect. > >> -----Original Message----- >> From: bioperl-l-bounces@portal.open-bio.org >> [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of >> Roels, Steven >> Sent: Friday, August 06, 2004 1:49 PM >> To: bioperl-l@bioperl.org >> Subject: [Bioperl-l] identifying objects in Bio::Graphics SVG >> >> >> >> Hello, >> >> I'd like to take the nice SVG output I can generate with the >> Bio::Graphics modules, and add javascript to (for example) >> alter/hide elements based on a slider or other user-controlled input. >> >> Is there a way to map various panel items to the resulting >> svg components? >> >> e.g transcript3, exon4 == >> >> Given that the "" grouping element doesn't seem to be used >> (which would facilitate this for non-simple elements), I'm >> guessing not, but thought I would ask. >> >> Thanks, >> >> -Steve >> >> ***************************************************************** >> Steve Roels, Ph.D. >> Senior Scientist I >> Computational Biology >> Millennium Pharmaceuticals, Inc. Phone: 617.761.6820 >> 640 Memorial Drive FAX: 617.577.3555 >> Cambridge, MA 02139-4815 Email: steven.roels@mpi.com >> ***************************************************************** >> >> >> >> >> This e-mail, including any attachments, is a confidential >> business communication, and may contain information that is >> confidential, proprietary and/or privileged. This e-mail is >> intended only for the individual(s) to whom it is addressed, >> and may not be saved, copied, printed, disclosed or used by >> anyone else. If you are not the(an) intended recipient, >> please immediately delete this e-mail from your computer >> system and notify the sender. Thank you. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-> bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From ls_work at covad.net Fri Aug 6 15:21:48 2004 From: ls_work at covad.net (Lee Sam) Date: Fri Aug 6 15:23:09 2004 Subject: [Bioperl-l] Lining Up Glyphs on Bio::Panel Message-ID: <004601c47bea$a6a436c0$e200a8c0@apartment.leesam.net> When I use Bio::Graphics to render a number of adjacent genes, I can't get them to line up (they always render on two lines). Is there a way to force them to render on a single line? From Nathan.Agrin at umassmed.edu Fri Aug 6 16:13:14 2004 From: Nathan.Agrin at umassmed.edu (Agrin, Nathan) Date: Fri Aug 6 16:14:53 2004 Subject: [Bioperl-l] Lining Up Glyphs on Bio::Panel Message-ID: <89AA811FD79DC94788093B23DA79E71F0184D6DB@edunivmail02.ad.umassmed.edu> put -bump => 0, in your $panel->add_track{} line -nate -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of Lee Sam Sent: Friday, August 06, 2004 3:22 PM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Lining Up Glyphs on Bio::Panel When I use Bio::Graphics to render a number of adjacent genes, I can't get them to line up (they always render on two lines). Is there a way to force them to render on a single line? _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From todd.harris at cshl.edu Fri Aug 6 15:09:54 2004 From: todd.harris at cshl.edu (Todd Harris) Date: Fri Aug 6 21:37:06 2004 Subject: [Bioperl-l] identifying objects in Bio::Graphics SVG In-Reply-To: Message-ID: Jonathon pretty much beat me to the answer. GD::SVG is really just intended as proxy for GD.pm to get SVG output from GD scripts. It doesn't take advantage of much of the richness of SVG since these elements reside outside the scope of GD. That said, I have experimented with minor things like adding descriptive IDs to SVG objects. I'd be interested to see if boxes() will work with GD::SVG rendered panels. I suspect it will choke - please let me know. It shouldn't be too hard to add this support which might allow greater SVG flexibility from Bio::Graphics for the short term. For the longer term, I'd rather see generic Bio::Graphics objects that contain no format-specific graphic generation. These would in turn use Bio::Graphics::SVG, Bio::Graphics::Postscript, to draw/calculate the actual primitives as necessary. Given the duct-tape approach of GD::SVG, overloading it to handle the additional options of SVG could get messy - fast. Duck and cover. Todd > On 8/6/04 1:20 PM, Crabtree, Jonathan wrote: > > Hi Steve- > > I looked into this briefly and I'm pretty sure that the answer is "no". > The way that the Bio::Graphics module generates SVG output is by using > GD::SVG, which is more or less a drop-in replacement for GD. Since the > GD API doesn't require (or permit, AFAIK) the association of logical > identifiers with graphics primitives (e.g., these four lines are part of > exon #1234), this information isn't included in the GD API calls and > therefore isn't available to GD::SVG. So even if GD::SVG wanted to > group the various elements within an SVG roup, it doesn't have any > way of gleaning the necessary information without going beyond the GD > API. > > Now of course this isn't to say that it wouldn't be possible to > implement this type of functionality, but it would require making > Bio::Graphics somewhat more SVG-aware than it is now, and would probably > entail delving into the workings of GD::SVG a little bit. I can also > imagine taking a somewhat heavyweight approach that would be relatively > inefficient but might be easier to implement. One could conceivably > make a fresh GD::SVG object for each glyph to be rendered, and then add > some code to Bio::Graphics to strip out the essential SVG rendered by > each glyph, wrap it in a element, and place it into a dummy > top-level GD::SVG object that serves only to collect the text of the SVG > document. I don't know...at some point it's going to be easier to just > go ahead and add direct SVG support into Bio::Graphics. > > Jonathan > > p.s. Re-reading your original message, it might be possible to do > something using the bounding box of the feature of interest (which can > be obtained from the Bio::Graphics panel) to search through the SVG text > for the relevant section. It would be messy, though, and rather > indirect. > >> -----Original Message----- >> From: bioperl-l-bounces@portal.open-bio.org >> [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of >> Roels, Steven >> Sent: Friday, August 06, 2004 1:49 PM >> To: bioperl-l@bioperl.org >> Subject: [Bioperl-l] identifying objects in Bio::Graphics SVG >> >> >> >> Hello, >> >> I'd like to take the nice SVG output I can generate with the >> Bio::Graphics modules, and add javascript to (for example) >> alter/hide elements based on a slider or other user-controlled input. >> >> Is there a way to map various panel items to the resulting >> svg components? >> >> e.g transcript3, exon4 == >> >> Given that the "" grouping element doesn't seem to be used >> (which would facilitate this for non-simple elements), I'm >> guessing not, but thought I would ask. >> >> Thanks, >> >> -Steve >> >> ***************************************************************** >> Steve Roels, Ph.D. >> Senior Scientist I >> Computational Biology >> Millennium Pharmaceuticals, Inc. Phone: 617.761.6820 >> 640 Memorial Drive FAX: 617.577.3555 >> Cambridge, MA 02139-4815 Email: steven.roels@mpi.com >> ***************************************************************** >> >> >> >> >> This e-mail, including any attachments, is a confidential >> business communication, and may contain information that is >> confidential, proprietary and/or privileged. This e-mail is >> intended only for the individual(s) to whom it is addressed, >> and may not be saved, copied, printed, disclosed or used by >> anyone else. If you are not the(an) intended recipient, >> please immediately delete this e-mail from your computer >> system and notify the sender. Thank you. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-> bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From allenday at ucla.edu Sun Aug 8 03:28:08 2004 From: allenday at ucla.edu (Allen Day) Date: Sun Aug 8 03:30:06 2004 Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file Message-ID: just commited this to cvs. if you pass a -file arg to a Root::IO subclass, the following happens: if(the file exists){ do as before } elsif(the file doesn't exist, and the name looks like a url) { try a few times to { download the url to a local tempfile, and update -file to point to the tempfile } if(couldn't download the file){ throw an error } } i'm open to moving urls to a special -url argument instead of overloading -file. what do people think? -allen From jason at cgt.duhs.duke.edu Sun Aug 8 10:30:16 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Sun Aug 8 10:31:38 2004 Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file In-Reply-To: References: Message-ID: I'm sort of against putting too much in Root::IO only because it means one more thing that can go wrong in an essential component. I'd rather make the logic explicit so maybe going the -url route would be safer? The 'longway' for doing this is, below, is this still too much work? I guess you want to have the retry in place. my $bp = Bio::SeqIO->new(-format => 'fasta', -fh => Bio::Root::HTTPget->getFH($url) ); -j On Sun, 8 Aug 2004, Allen Day wrote: > just commited this to cvs. if you pass a -file arg to a Root::IO > subclass, the following happens: > > if(the file exists){ > do as before > } > elsif(the file doesn't exist, and the name looks like a url) { > try a few times to { > download the url to a local tempfile, and update -file to point > to the tempfile > } > if(couldn't download the file){ > throw an error > } > } > > i'm open to moving urls to a special -url argument instead of overloading > -file. what do people think? > > -allen > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From birney at ebi.ac.uk Sun Aug 8 10:53:47 2004 From: birney at ebi.ac.uk (Ewan Birney) Date: Sun Aug 8 10:54:54 2004 Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file In-Reply-To: Message-ID: On Sun, 8 Aug 2004, Allen Day wrote: > just commited this to cvs. if you pass a -file arg to a Root::IO > subclass, the following happens: > > if(the file exists){ > do as before > } > elsif(the file doesn't exist, and the name looks like a url) { > try a few times to { > download the url to a local tempfile, and update -file to point > to the tempfile > } > if(couldn't download the file){ > throw an error > } > } > > i'm open to moving urls to a special -url argument instead of overloading > -file. what do people think? I think this sounds safer ---- but then again this sort of magic is much appreciated by newbies/lazy coders. I don't have a strong opinion I guess... > > -allen > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From michael.watson at bbsrc.ac.uk Mon Aug 9 04:52:42 2004 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Mon Aug 9 04:53:53 2004 Subject: [Bioperl-l] Problems retrieving sequences with Bio::DB::Query::GenBank Message-ID: <8975119BCD0AC5419D61A9CF1A923E957C289A@iahce2knas1.iah.bbsrc.reserved> Hi I am having a few problems with Bio::DB::Query::GenBank (Bioperl 1.4, Suse Linux). Here is my script: #!/usr/bin/perl use Bio::DB::Query::GenBank; use Bio::SeqIO; use Bio::DB::GenBank; my $query_string = 'Avian infectious bronchitis virus [Organism]'; my $query = Bio::DB::Query::GenBank->new(-db => 'nucleotide', -query => $query_string, -verbose => 0); my $count = $query->count; print "Query has $count sequences\n"; my $db = new Bio::DB::GenBank; my $stream = $db->get_Stream_by_query($query); my $out = Bio::SeqIO->new(-format => 'Fasta' , -file => '>out.fasta'); while (my($seq) = $stream->next_seq()) { $out->write_seq($seq); } So this is all "by the book" code, mostly taken directly from the docs. What happens is that out.fasta fills up with 500 sequences (there should be 810) and then I get an error: ------------- EXCEPTION ------------- MSG: Did not provide a valid Bio::PrimarySeqI object STACK Bio::SeqIO::fasta::write_seq /usr/local/bioperl-1.4/Bio/SeqIO/fasta.pm:178 STACK toplevel scripts/get_seqs.pl:26 -------------------------------------- Speaking from personal experience, I have never been able to get the "get_stream_by..." methods to work. Does anyone have a clue what might be going wrong? Thanks Mick From birney at ebi.ac.uk Mon Aug 9 05:09:57 2004 From: birney at ebi.ac.uk (Ewan Birney) Date: Mon Aug 9 05:11:53 2004 Subject: [Bioperl-l] Problems retrieving sequences with Bio::DB::Query::GenBank In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E957C289A@iahce2knas1.iah.bbsrc.reserved> Message-ID: Mike I suspect one of the IDs is bad and GenBank is giving back an error message that Bioperl is not skipping/querying. If you look at the next ID after the last successful ID and query it by hand is it really there? IF this is the case, then it is definitely a bioperl bug- it should do something more elegant than this... ----------------------------------------------------------------- Ewan Birney. Work: +44 1223 494420 Email: birney "at" ebi.ac.uk Clerical Assistant: shelley "at" ebi.ac.uk Please cc shelley for urgent or diary-dependent requests ----------------------------------------------------------------- From benb at fruitfly.org Mon Aug 9 01:47:02 2004 From: benb at fruitfly.org (ben berman) Date: Mon Aug 9 09:56:17 2004 Subject: [Bioperl-l] is Bio::Graphics::Glyph::line supposed to draw description? Message-ID: <898EB90C-E9C7-11D8-9BDB-000D93AF7910@fruitfly.org> I was trying to draw a description string with the Bio::Graphics::Glyph::line glyph, but it doesn't seem to work. I checked the latest version (1.5) , and the draw() function is as follows: > sub draw { > my $self = shift; > my $gd = shift; > my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_); > > my $fg = $self->fgcolor; > my $a2 = $self->SUPER::height/2; > my $center = $y1+$a2; > > $gd->line($x1,$center,$x2,$center,$fg); > # add a label if requested > $self->draw_label($gd,@_) if $self->option('label'); > > } The arrow glyph, which does seem to implement the description string correctly, has the following: > # add a label if requested > $self->draw_label($gd,$dx,$dy) if $self->option('label'); > $self->draw_description($gd,$dx,$dy) if $self->option('description'); > } > Is this omission by design? Based on the documentation for Panel::add_track, i kind of expected all glyphs to implement this if possible. i would commit the change myself, but i want to be cautious since i'm not an active contributor. thanks, ben. From hlapp at gmx.net Mon Aug 9 11:42:19 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon Aug 9 11:43:07 2004 Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file In-Reply-To: Message-ID: I lean with Ewan to -url as I like explicit commands better than possibly dubious magic behind the scenes ... imagine someone stores files by names that match their url ... There's one thing though that's important IMO that Jason brings up: I don't know how you implemented this but I think Bio::Root::IO must not be dependent on LWP or any such beast that doesn't come with perl. -hilmar On Sunday, August 8, 2004, at 12:28 AM, Allen Day wrote: > just commited this to cvs. if you pass a -file arg to a Root::IO > subclass, the following happens: > > if(the file exists){ > do as before > } > elsif(the file doesn't exist, and the name looks like a url) { > try a few times to { > download the url to a local tempfile, and update -file to point > to the tempfile > } > if(couldn't download the file){ > throw an error > } > } > > i'm open to moving urls to a special -url argument instead of > overloading > -file. what do people think? > > -allen > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From sutripa at vbi.vt.edu Mon Aug 9 22:12:03 2004 From: sutripa at vbi.vt.edu (Sucheta Tripathy) Date: Mon Aug 9 22:13:15 2004 Subject: [Bioperl-l] (no subject) Message-ID: <5.1.0.14.0.20040809220754.02f42ea8@mail.vbi.vt.edu> Hello, I am trying to retrieve sequences from a genbank index file which I created using the script bp_index.pl The scripts are obtained from the distribution. It created the index file in the desirable location, however, when I try to fetch the sequence with the script bp_fetch.pl using: perl bp_fetch.pl -acc genbank:BT015122 don't get the sequence. It says : Sequence BT015122 in Database genbank is not present. The sequence is there in the genbank data that I indexed. Can anyone pl. specify where I might be going wrong. Thanks Sucheta From yinyb at mail.cbi.pku.edu.cn Mon Aug 9 23:23:47 2004 From: yinyb at mail.cbi.pku.edu.cn (Yin Yanbin) Date: Mon Aug 9 23:22:01 2004 Subject: [Bioperl-l] parsing FASTA output References: <5.1.0.14.0.20040809220754.02f42ea8@mail.vbi.vt.edu> Message-ID: <001e01c47e89$72cc56b0$cefa69a2@cbiyinyb> Hello, I wrote a script to parse several tFASTY search results. For some input files, it works well, but for others it crashed and gave out the following warnings: -------------------- WARNING --------------------- MSG: Unrecognized alignment line (3) ' statistics sampled from 60000 to 665286 sequences' --------------------------------------------------- Modification of non-creatable array value attempted, subscript -3 at /usr/local/lib/perl5/site_perl/5.6.1/Bio/SearchIO/fasta.pm line 348, line 229825. I updated my bioperl system, but it still compained. Did anyone could help me with this? Thanks in advance! Yanbin From pvh at egenetics.com Tue Aug 10 04:38:59 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Tue Aug 10 04:40:05 2004 Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file In-Reply-To: References: Message-ID: <411889A3.10209@egenetics.com> Hilmar Lapp wrote: > I lean with Ewan to -url as I like explicit commands better than > possibly dubious magic behind the scenes ... imagine someone stores > files by names that match their url ... > > There's one thing though that's important IMO that Jason brings up: I > don't know how you implemented this but I think Bio::Root::IO must not > be dependent on LWP or any such beast that doesn't come with perl. > I'm with the majority in that 'magic' creates possible confusion and more room for error. As to Hilmar's idea of not depending on LWP, I think this is also a good idea, and maybe the URL code can be a kind of 'mixin' - i.e. implement it in another module and then have Bio::Root::IO optionally add it as a plugin. What do you intend to do with this capability? Is there going to be another module that depends on the -url ability? Peter From jurgen.pletinckx at algonomics.com Tue Aug 10 05:53:29 2004 From: jurgen.pletinckx at algonomics.com (Jurgen Pletinckx) Date: Tue Aug 10 05:37:39 2004 Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file In-Reply-To: <411889A3.10209@egenetics.com> Message-ID: # ... As to Hilmar's idea of not depending on LWP, I # think this is also a good idea, and maybe the URL code can be a kind of # 'mixin' - i.e. implement it in another module and then have # Bio::Root::IO optionally add it as a plugin. Except that we already depend on LWP::UserAgent. We might as well use it if we've got it, right? The usual motivation: there's a lot of hard work in LWP. Sure, we could copy it, or recreate it, but why bother? (I would vote for an explicit -url param, if this were a democracy) -- Jurgen Pletinckx AlgoNomics NV From amackey at pcbi.upenn.edu Tue Aug 10 07:00:27 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Tue Aug 10 07:01:34 2004 Subject: [Bioperl-l] parsing FASTA output In-Reply-To: <001e01c47e89$72cc56b0$cefa69a2@cbiyinyb> References: <5.1.0.14.0.20040809220754.02f42ea8@mail.vbi.vt.edu> <001e01c47e89$72cc56b0$cefa69a2@cbiyinyb> Message-ID: <7C7717F0-EABC-11D8-B816-000A9577009E@pcbi.upenn.edu> If you send me a file that fails, I should be able to fix it. -Aaron On Aug 9, 2004, at 11:23 PM, Yin Yanbin wrote: > Hello, > > I wrote a script to parse several tFASTY search results. For some > input files, it works well, but for others it crashed and gave out the > following warnings: > > > -------------------- WARNING --------------------- > MSG: Unrecognized alignment line (3) ' statistics sampled from 60000 > to 665286 sequences' > --------------------------------------------------- > Modification of non-creatable array value attempted, subscript -3 at > /usr/local/lib/perl5/site_perl/5.6.1/Bio/SearchIO/fasta.pm line 348, > line 229825. > > > I updated my bioperl system, but it still compained. > > Did anyone could help me with this? Thanks in advance! From iain.wallace at ucd.ie Tue Aug 10 07:52:55 2004 From: iain.wallace at ucd.ie (Iain Wallace) Date: Tue Aug 10 08:07:27 2004 Subject: [Bioperl-l] Displaying an alignment using Bio::Graphics Message-ID: Hi all, I was wondering if any one knows how to display a multiple sequence alignment using the Bio::Graphics modules. Ideally I would like to colour in certain columns depending on a mask that I have created ? (FYI The particular project is to colour in the columns of a test alignment which have corresponing columns in a reference alignment). thanks Iain Wallace ____________ Virus checked by G DATA AntiVirusKit Version: AVK 12.0.594 from 19.09.2003 Virus news: www.antiviruslab.com From sutripa at vbi.vt.edu Tue Aug 10 08:15:03 2004 From: sutripa at vbi.vt.edu (Sucheta Tripathy) Date: Tue Aug 10 08:16:16 2004 Subject: [Bioperl-l] Bio::Index sequence fetching Message-ID: <3376.204.212.236.88.1092140103.squirrel@webmail.vbi.vt.edu> I am sorry for posting it again.. I did it yesterday without a subject line. I am trying to retrieve records from a genbank index file that I had created using bp_index.pl. I have set the environment variables as desired. While fetching records I use the following syntax: bp_fetch.pl -fmt genbank genbank:50355994 where 50355994 is the GI number of one of the sequences. But I don't get any results. It says sequence 50355994 in database genbank not present. Can anyone please comment where I may be going wrong. Thanks Sucheta -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 From jason at cgt.duhs.duke.edu Tue Aug 10 09:34:30 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Aug 10 09:35:38 2004 Subject: [Bioperl-l] Displaying an alignment using Bio::Graphics In-Reply-To: References: Message-ID: I think Lincoln wrote something recently - I don't remember where he put it though. I do it with HTML - this produces LARGE files though since every base gets an html tag. The number matching is for intron mapping stuff so wouldn't be necessary for you. $aln is an alignment #consed colors %COLOR = ('A' => 'green', 'T' => 'red','G'=> 'orange', 'C' => 'blue'); my $str = IO::String->new(); my $out = Bio::AlignIO->new(-format => 'clustalw', -linelength => 100, -fh => $str); $out->write_aln($aln); $out->close(); my $str2 = IO::String->new(${$str->string_ref}); print $outfh "
\n";
        while(<$str2>) {
            if( /^CLUSTAL|MUSCLE/ ) {
            } elsif( /^(\s*\S+\s+)(\S+)(\s*\d*\s*)$/ox ) {
                my ($pre,$seq,$post) = ($1,$2,$3);
                # add 'bold' tags
                $seq =~ s/(\d+)/$1<\/b>/g;
                $seq =~ s/(A+)/$1<\/font>/g;
                $seq =~ s/(C+)/$1<\/font>/g;
                $seq =~ s/(G+)/$1<\/font>/g;
                $seq =~ s/(T+)/$1<\/font>/g;
                $_ = join('',$pre,$seq,$post);
            }
            print $outfh $_;
        }
        print $outfh "<\/pre>\n<\/html>\n";

Or for AA
# shapely color table from
#http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/SHAPELY.HTM
my %SHAPELYPEPCOLOR = ('D'    => 'A00042',  # dark red
                       'T'    => 'A00042',  # dark red
                       'E'    => '660000',  # red-brown
                       'C'    => 'FFFF70',  # bright yellow
                       'M'    => 'B8A042',  # dark yellow
                       'Y'    => 'B8A042',  # dark yellow
                       'K'    => '4747B8',  # blue
                       'R'    => '00007C',  # dark blue
                       'S'    => 'FF4C4C',  # orange
                       'Q'    => 'FF4C4C',  # orange
                       'F'    => '534C42',  # dark grey
                       'P'    => '534C42',  # dark grey
                       'W'    => '534C42',  # dark grey
                       'N'    => 'FF7C70',  # peach
                       'G'    => 'C8C8C8',  # grey
                       'V'    => 'C8C8C8',  # grey
                       'I'    => '004C00',  # dark green
                       'L'    => '455E45',  # grey-green
                       'A'    => '8CFF8C',  # light green
                       'H'    => '7070FF',  # pale blue
                       );
my %PEPCOLOR = %AMINOPEPCOLOR;
       # pep seqs
       $str = IO::String->new();
       $out = Bio::AlignIO->new(-format => 'clustalw',
                                 -linelength => 100,
                                 -fh     => $str);
        $out->write_aln($aln);
        $out->close();
        $str2 = IO::String->new(${$str->string_ref});
        print $outfhp "
\n";
        $out->close();
        while(<$str2>) {
            if( /^CLUSTAL|MUSCLE/ ) {
            } elsif( /^(\s*\S+\s+)(\S+)(\s*\d*\s*)$/ox ) {
                my ($pre,$seq,$post) = ($1,$2,$3);
                # add 'bold' tags for intron phase
                $seq =~ s/(\d+)/$1<\/b>/g;
                # base becomes base with font color tag
                $seq =~ s/([DTECMYKRSQFPWNGVILAH])/$1<\/font>/g;
                $_ = join('',$pre,$seq,$post);
            }
            print $outfhp $_;
        }
        print $outfhp "<\/pre>\n<\/html>\n";



On Tue, 10 Aug 2004, Iain Wallace wrote:

> Hi all,
>
> I was wondering if any one knows how to display a multiple sequence
> alignment using the Bio::Graphics modules.
> Ideally I would like to colour in certain columns depending on a mask that I
> have created ?
> (FYI The particular project is to colour in the columns of a test alignment
> which have corresponing columns in a reference alignment).
>
> thanks
>
> Iain Wallace
>
>
>
> ____________
> Virus checked by G DATA AntiVirusKit
> Version: AVK 12.0.594 from 19.09.2003
> Virus news: www.antiviruslab.com
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From avilella at ub.edu  Tue Aug 10 08:03:33 2004
From: avilella at ub.edu (Albert Vilella)
Date: Tue Aug 10 09:45:39 2004
Subject: [Bioperl-l] orthologous genes extracting
In-Reply-To: <1356.10.10.120.61.1091596127.squirrel@webmail.sibs.ac.cn>
References: <1356.10.10.120.61.1091596127.squirrel@webmail.sibs.ac.cn>
Message-ID: <1092139413.11425.24.camel@localhost.localdomain>

> >
> Is there a way of extracting orthologous genes from homologene database?>
> > Is there a perl module to do it?

I remember a post in the ensembl-dev mailing list about this: there is
something done on the Ensembl API for the Ensembl DB orthology
relations,

Hope it helps,

    Albert.

> 
> Thanks.
> 
> 
> Songmin Xie
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
Albert J Vilella -- avilella_at_ub_dot_edu
------------------------------------------------
Dept Genetica - Universitat de Barcelona
Diagonal 645, Barcelona, Catalunya
08028, SPAIN
Phone +34 (0) 93 403 70 82
Fax   +34 (0) 93 411 09 69
------------------------------------------------
avilella_at_ebi_dot_ac_dot_uk
EMBL Outstation, European Bioinformatics Inst.
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
------------------------------------------------

From QLiu at genelogic.com  Mon Aug  9 14:50:52 2004
From: QLiu at genelogic.com (QLiu@genelogic.com)
Date: Tue Aug 10 09:46:44 2004
Subject: [Bioperl-l] Makefile.PL
Message-ID: 

Hi,

I am a beginner for Bioperl.  I just downloaded the core distribution. 
When I tried to install it at the step of perl Makefile.PL, I encountered 
the following error.  Do you know what the problem might be?

Not enough arguments for mkdir at Makefile.PL line 119, near "$dest_dir) "
BEGIN not safe after errors--compilation aborted at Makefile.PL line 273.

Thanks very much!

Qing

Qing Liu, Ph. D.
Product Development Manager, Product Development
Gene Logic Inc.
708 Quince Orchard Road
Gaithersburg, MD 20878
Phone: 240-364-6260
Fax: 240-364-6262
Email: qliu@genelogic.com

Mailing Address/Corporate Headquarters
610 Professional Drive
Gaithersburg, MD 20879






==========================================================================
==  The information contained in this email message is intended only for 
use by the      ==
==  recipient(s) to which it is addressed.  This message may be privileged 
and            ==
==  confidential and protected from disclosure.  If the reader of this 
message is not        ==
==  the intended recipient or an agent responsible for delivering it to 
the intended           ==
==  recipient,  you are hereby notified that you have received this 
document in error       ==
==  and that any review, retransmission, dissemination, distribution, 
copying or other     ==
==  use of, or taking of any action in reliance upon this information, is 
strictly                       ==
==  prohibited.  If you have received this communication in error, please 
contact the       ==
==  sender and delete the material from your computer.    ==
========================================================================== 

From jburdick at gradient.cis.upenn.edu  Tue Aug 10 10:27:49 2004
From: jburdick at gradient.cis.upenn.edu (Josh Burdick)
Date: Tue Aug 10 10:32:55 2004
Subject: [Bioperl-l] Displaying an alignment using Bio::Graphics
In-Reply-To: 
References: 
	
Message-ID: <4118DB65.8030000@gradient.cis.upenn.edu>

Jason Stajich wrote:

>I think Lincoln wrote something recently - I don't remember where he put
>it though.
>  
>
    I wrote a Perl module to write out DNA (or an arbitrary string), 
with HTML tags around some regions.
    Don't know if this is useful in your case, since it's only for one 
string.  If anyone wants to adapt it for use in bioperl, feel free.  
It's attached at the end of this message.

>I do it with HTML - this produces LARGE files though since every base gets
>an html tag.  The number matching is for intron mapping stuff so wouldn't
>be necessary for you.
>  
>

    This code is a bit more efficient, since it only adds tags at the 
beginning and end of where things are colored, or otherwise tagged.  It 
has some weird bugs, though, if you add non-nested regions.  Browsers 
typically won't complain, but exactly which tag will have precedence 
where is unpredictable.
    I'd guess HTML is still fewer bytes/base than a readable image file, 
though if the image is compressed, that's less certain.
    Josh

-- 
Josh Burdick
jburdick@gradient.cis.upenn.edu
http://www.cis.upenn.edu/~jburdick

cut here
--------------

# Write a sequence, with bits of it colored as HTML.

package local::Bio::ColoredSeq;

# Constructor.
# Args:
#   Seq object containing the Seq in question
sub new {
    my($type, $seq) = @_;
    my $self = ();

    $self->{'seq'} = $seq;
    my %h = ();
    $self->{'tags'} = \%h;
    return bless $self, $type;
}

# Add a tag around a certain region of the sequence text.
# Args:
#   opening_tag, closing_tag - the HTML tags to put around
#     that chunk of sequence.
#   loc - ref. to list of things implementing RangeI
# Note that currently, later tags override earlier tags.
sub add_tag {
    my($self, $opening_tag, $closing_tag, $locs) = @_;

    foreach (@$locs) {
	my $a = $_->start + 1;
	my $b = $_->end + 1;
#	print "$a $b $opening_tag $closing_tag\n";
	next if ($a == $b);
	$self->{'tags'}->{$a} = $self->{'tags'}->{$a} . $opening_tag;
	$self->{'tags'}->{$b} = $closing_tag . $self->{'tags'}->{$b};
    }
}

# HTML, showing bits of the sequence in various colors.
sub as_html {
    my($self) = @_;
    my $line_length = 50;
    my $s = "";

    my $seq = $self->{'seq'};
    my %tags = %{$self->{'tags'}};

    foreach my $i (1..($seq->length)) {
	if (defined $tags{$i}) {
	    $s = $s . $tags{$i};
	}
	if ($i % $line_length == 1) {
	    $s = $s . "
\n";
	}
	$s = $s . $seq->subseq($i, $i);
    }
    
    return $s;
}

1;


From tex at biosysadmin.com  Mon Aug  9 20:48:03 2004
From: tex at biosysadmin.com (James Thompson)
Date: Tue Aug 10 13:01:57 2004
Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file
In-Reply-To: 
Message-ID: 

As a newbie/lazy coder, it may be a bit more polite to try and open things
that look like URLs, but I can't imagine many situations in which having a url
masquerading as a file would be that useful.

It seems more correct to just throw a helpful exception saying "Error: Can't
open file, is it a URL?" if the -file arg looks URLish. It really makes more
sense to me to keep -file's and -url's as separate concepts.

Tex Thompson
RIT Bioinformatics


On Sun, 8 Aug 2004, Allen Day wrote:

> just commited this to cvs.  if you pass a -file arg to a Root::IO 
> subclass, the following happens:
> 
> if(the file exists){
>   do as before
> }
> elsif(the file doesn't exist, and the name looks like a url) {
>   try a few times to {
>     download the url to a local tempfile, and update -file to point
>     to the tempfile
>   }
>   if(couldn't download the file){
>     throw an error
>   }
> }
> 
> i'm open to moving urls to a special -url argument instead of overloading 
> -file.  what do people think?
> 
> -allen
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 

From hlapp at gnf.org  Tue Aug 10 14:21:28 2004
From: hlapp at gnf.org (Hilmar Lapp)
Date: Tue Aug 10 14:22:38 2004
Subject: [Bioperl-l] Makefile.PL
In-Reply-To: 
References: 
Message-ID: <18F96B0C-EAFA-11D8-B2DF-000A95AE92B0@gnf.org>

Bioperl version? OS? OS version? Version of Perl?

On Aug 9, 2004, at 11:50 AM, QLiu@genelogic.com wrote:

> Hi,
>
> I am a beginner for Bioperl.  I just downloaded the core distribution.
> When I tried to install it at the step of perl Makefile.PL, I  
> encountered
> the following error.  Do you know what the problem might be?
>
> Not enough arguments for mkdir at Makefile.PL line 119, near  
> "$dest_dir) "
> BEGIN not safe after errors--compilation aborted at Makefile.PL line  
> 273.
>
> Thanks very much!
>
> Qing
>
> Qing Liu, Ph. D.
> Product Development Manager, Product Development
> Gene Logic Inc.
> 708 Quince Orchard Road
> Gaithersburg, MD 20878
> Phone: 240-364-6260
> Fax: 240-364-6262
> Email: qliu@genelogic.com
>
> Mailing Address/Corporate Headquarters
> 610 Professional Drive
> Gaithersburg, MD 20879
>
>
>
>
>
>
> ======================================================================= 
> ===
> ==  The information contained in this email message is intended only  
> for
> use by the      ==
> ==  recipient(s) to which it is addressed.  This message may be  
> privileged
> and            ==
> ==  confidential and protected from disclosure.  If the reader of this
> message is not        ==
> ==  the intended recipient or an agent responsible for delivering it to
> the intended           ==
> ==  recipient,  you are hereby notified that you have received this
> document in error       ==
> ==  and that any review, retransmission, dissemination, distribution,
> copying or other     ==
> ==  use of, or taking of any action in reliance upon this information,  
> is
> strictly                       ==
> ==  prohibited.  If you have received this communication in error,  
> please
> contact the       ==
> ==  sender and delete the material from your computer.    ==
> ======================================================================= 
> ===
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

From hlapp at gnf.org  Tue Aug 10 14:22:56 2004
From: hlapp at gnf.org (Hilmar Lapp)
Date: Tue Aug 10 14:24:06 2004
Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file
In-Reply-To: 
References: 
Message-ID: <4D60B9E6-EAFA-11D8-B2DF-000A95AE92B0@gnf.org>


On Aug 10, 2004, at 2:53 AM, Jurgen Pletinckx wrote:

> Except that we already depend on LWP::UserAgent. We might
> as well use it if we've got it, right?
>

The core doesn't depend on it. In fact, unless you want to use Bio::DB 
modules or remote BLAST or other remote tools you could as well live 
w/o it.

	-hilmar
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

From allenday at ucla.edu  Tue Aug 10 15:29:37 2004
From: allenday at ucla.edu (Allen Day)
Date: Tue Aug 10 15:32:10 2004
Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file
In-Reply-To: <411889A3.10209@egenetics.com>
References: 
	<411889A3.10209@egenetics.com>
Message-ID: 

On Tue, 10 Aug 2004, Peter van Heusden wrote:

> Hilmar Lapp wrote:
> 
> > I lean with Ewan to -url as I like explicit commands better than 
> > possibly dubious magic behind the scenes ... imagine someone stores 
> > files by names that match their url ...
> >
> > There's one thing though that's important IMO that Jason brings up: I 
> > don't know how you implemented this but I think Bio::Root::IO must not 
> > be dependent on LWP or any such beast that doesn't come with perl.
> >
> I'm with the majority in that 'magic' creates possible confusion and 
> more room for error. As to Hilmar's idea of not depending on LWP, I 
> think this is also a good idea, and maybe the URL code can be a kind of 
> 'mixin' - i.e. implement it in another module and then have 
> Bio::Root::IO optionally add it as a plugin. What do you intend to do 
> with this capability? Is there going to be another module that depends 
> on the -url ability?

Bio::Root::IO::_initialize_io() now accepts a '-url' argument.

If present, and if LWP is loadable, _initialize_io() attempts to use
LWP::Simple::getstore() to download the url to a local tempfile, and
assigns that tempfile to the equivalent of _initialize_io()'s '-file'
argument.  This works for HTTP, HTTPS, FTP, and all other protocols
supported by LWP.  If a file request fails, there is a retry loop in place
to retry a few times to fetch the file.

If LWP is not loadable, _initialze_io() uses Bio::Root::HTTPget to open a
socket to the file's host and sets '-fh' to read from this socket.  This
only works for HTTP.  There is no retry loop in place here, as
Bio::Root::HTTPget throws an error if it can't open the socket.  It's
possible to modify Bio::Root::HTTPget to do retries, but I didn't feel
like poking around in there.

Still remaining to be done:

  [1] add -url to the documentation
  [2] checking for existance of clashing '-file' or '-fh' arguments
  [3] add additional tests to t/RootIO.t for testing https and ftp 
      retrievals.

Regarding another module depending on this, yes, there will be one, that's
the only reason I added this :).  I have a new FeatureIO subsystem.  One
format it can parse is GFF v3.  Valid GFF v3 requires features to be typed
according to the Sequence Ontology or an extension thereof.  As part of
the parse it downloads the Sequence Ontology DAG-Edit files, parses them
into a Bio::Ontology, and returns Bio::SeqFeatureI objects with
Annotation::OntologyTerms attached.

I will commit the FeatureIO code soon.

-Allen


> 
> Peter
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
From jason at cgt.duhs.duke.edu  Tue Aug 10 15:43:13 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Aug 10 15:44:24 2004
Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file
In-Reply-To: 
References: 
	<411889A3.10209@egenetics.com>
	
Message-ID: 

On Tue, 10 Aug 2004, Allen Day wrote:

> On Tue, 10 Aug 2004, Peter van Heusden wrote:
>
> > Hilmar Lapp wrote:
> >
> > > I lean with Ewan to -url as I like explicit commands better than
> > > possibly dubious magic behind the scenes ... imagine someone stores
> > > files by names that match their url ...
> > >
> > > There's one thing though that's important IMO that Jason brings up: I
> > > don't know how you implemented this but I think Bio::Root::IO must not
> > > be dependent on LWP or any such beast that doesn't come with perl.
> > >
> > I'm with the majority in that 'magic' creates possible confusion and
> > more room for error. As to Hilmar's idea of not depending on LWP, I
> > think this is also a good idea, and maybe the URL code can be a kind of
> > 'mixin' - i.e. implement it in another module and then have
> > Bio::Root::IO optionally add it as a plugin. What do you intend to do
> > with this capability? Is there going to be another module that depends
> > on the -url ability?
>
> Bio::Root::IO::_initialize_io() now accepts a '-url' argument.
>
> If present, and if LWP is loadable, _initialize_io() attempts to use
> LWP::Simple::getstore() to download the url to a local tempfile, and
> assigns that tempfile to the equivalent of _initialize_io()'s '-file'
> argument.  This works for HTTP, HTTPS, FTP, and all other protocols
> supported by LWP.  If a file request fails, there is a retry loop in place
> to retry a few times to fetch the file.

The tempfile gets cleaned up by LWP?  We do this sort of thing in
Bio::Tools::Run::RemoteBlast and within Bio::DB::NCBIHelper,et al perhaps
we can localize some of that code to a -url param where it is a GET
request...

>
> If LWP is not loadable, _initialze_io() uses Bio::Root::HTTPget to open a
> socket to the file's host and sets '-fh' to read from this socket.  This
> only works for HTTP.  There is no retry loop in place here, as
> Bio::Root::HTTPget throws an error if it can't open the socket.  It's
> possible to modify Bio::Root::HTTPget to do retries, but I didn't feel
> like poking around in there.
>
> Still remaining to be done:
>
>   [1] add -url to the documentation
>   [2] checking for existance of clashing '-file' or '-fh' arguments
>   [3] add additional tests to t/RootIO.t for testing https and ftp
>       retrievals.
>
> Regarding another module depending on this, yes, there will be one, that's
> the only reason I added this :).  I have a new FeatureIO subsystem.  One
> format it can parse is GFF v3.  Valid GFF v3 requires features to be typed
> according to the Sequence Ontology or an extension thereof.  As part of
> the parse it downloads the Sequence Ontology DAG-Edit files, parses them
> into a Bio::Ontology, and returns Bio::SeqFeatureI objects with
> Annotation::OntologyTerms attached.
>
> I will commit the FeatureIO code soon.
>

Cool! Will it also support some sort of caching of SO too?  Maybe we can
change Tools::GFF to delegate to FeatureIO for GFF3 files instead of
having 2 modules doing the same thing.

Also, have you worked on the alignment <-> GFF3 at all either?  It is an
almost-doable thing with HSP->cigar_line but I am not sure we have a
cigar2HSP factory yet.


-jason



> -Allen
>
>
> >
> > Peter
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From allenday at ucla.edu  Tue Aug 10 15:57:22 2004
From: allenday at ucla.edu (Allen Day)
Date: Tue Aug 10 16:00:01 2004
Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file
In-Reply-To: 
References: 
	<411889A3.10209@egenetics.com>
	
	
Message-ID: 

On Tue, 10 Aug 2004, Jason Stajich wrote:

> On Tue, 10 Aug 2004, Allen Day wrote:
> 
> > On Tue, 10 Aug 2004, Peter van Heusden wrote:
> >
> > > Hilmar Lapp wrote:
> > >
> > > > I lean with Ewan to -url as I like explicit commands better than
> > > > possibly dubious magic behind the scenes ... imagine someone stores
> > > > files by names that match their url ...
> > > >
> > > > There's one thing though that's important IMO that Jason brings up: I
> > > > don't know how you implemented this but I think Bio::Root::IO must not
> > > > be dependent on LWP or any such beast that doesn't come with perl.
> > > >
> > > I'm with the majority in that 'magic' creates possible confusion and
> > > more room for error. As to Hilmar's idea of not depending on LWP, I
> > > think this is also a good idea, and maybe the URL code can be a kind of
> > > 'mixin' - i.e. implement it in another module and then have
> > > Bio::Root::IO optionally add it as a plugin. What do you intend to do
> > > with this capability? Is there going to be another module that depends
> > > on the -url ability?
> >
> > Bio::Root::IO::_initialize_io() now accepts a '-url' argument.
> >
> > If present, and if LWP is loadable, _initialize_io() attempts to use
> > LWP::Simple::getstore() to download the url to a local tempfile, and
> > assigns that tempfile to the equivalent of _initialize_io()'s '-file'
> > argument.  This works for HTTP, HTTPS, FTP, and all other protocols
> > supported by LWP.  If a file request fails, there is a retry loop in place
> > to retry a few times to fetch the file.
> 
> The tempfile gets cleaned up by LWP?  We do this sort of thing in
> Bio::Tools::Run::RemoteBlast and within Bio::DB::NCBIHelper,et al perhaps
> we can localize some of that code to a -url param where it is a GET
> request...

no, i use Bio::Root::IO::tempfile() to generate the tempfile, and use LWP
to write into that.  LWP doesn't know how to clean up after itself, as far
as i can tell.

> 
> >
> > If LWP is not loadable, _initialze_io() uses Bio::Root::HTTPget to open a
> > socket to the file's host and sets '-fh' to read from this socket.  This
> > only works for HTTP.  There is no retry loop in place here, as
> > Bio::Root::HTTPget throws an error if it can't open the socket.  It's
> > possible to modify Bio::Root::HTTPget to do retries, but I didn't feel
> > like poking around in there.
> >
> > Still remaining to be done:
> >
> >   [1] add -url to the documentation
> >   [2] checking for existance of clashing '-file' or '-fh' arguments
> >   [3] add additional tests to t/RootIO.t for testing https and ftp
> >       retrievals.
> >
> > Regarding another module depending on this, yes, there will be one, that's
> > the only reason I added this :).  I have a new FeatureIO subsystem.  One
> > format it can parse is GFF v3.  Valid GFF v3 requires features to be typed
> > according to the Sequence Ontology or an extension thereof.  As part of
> > the parse it downloads the Sequence Ontology DAG-Edit files, parses them
> > into a Bio::Ontology, and returns Bio::SeqFeatureI objects with
> > Annotation::OntologyTerms attached.
> >
> > I will commit the FeatureIO code soon.
> >
> 
> Cool! Will it also support some sort of caching of SO too?  Maybe we can
> change Tools::GFF to delegate to FeatureIO for GFF3 files instead of
> having 2 modules doing the same thing.

well, it just caches to the tempfile right now and deletes on program
termination, but if you want to add functionality for -url to store the
file somewhere (perhaps in a filename in $TEMPDIR that is the md5 sum of
the URL?), be my guest.

my idea is to do away with Bio::Tools::GFF entirely.

> Also, have you worked on the alignment <-> GFF3 at all either?  It is an
> almost-doable thing with HSP->cigar_line but I am not sure we have a
> cigar2HSP factory yet.

nope, haven't looked at this.  i don't really do alignments so i don't
need this functionality.

-allen


> 
> 
> -jason
> 
> 
> 
> > -Allen
> >
> >
> > >
> > > Peter
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
From jsun at utdallas.edu  Tue Aug 10 16:52:05 2004
From: jsun at utdallas.edu (Sun, Jian)
Date: Tue Aug 10 16:53:10 2004
Subject: [Bioperl-l] How to display a Text file using web browser under CGI 
Message-ID: 

Dear all;
    Could anybody help me to figure out How to display a Text file using the web browser in a CGI program?
 
Thanks in advance
Jian

From amackey at pcbi.upenn.edu  Wed Aug 11 07:51:40 2004
From: amackey at pcbi.upenn.edu (Aaron J. Mackey)
Date: Wed Aug 11 07:52:45 2004
Subject: [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit
In-Reply-To: <200408110727.i7B7RTSO019714@pub.open-bio.org>
References: <200408110727.i7B7RTSO019714@pub.open-bio.org>
Message-ID: 


On Aug 11, 2004, at 3:27 AM, Hilmar Lapp wrote:

> Log Message:
> Made primary_id() to delegate. Yes, always. Also, added a Seq test to 
> make
> sure glaring inconsistencies don't happen again.

I'm not going to argue vociferously, but I imagine that the issue might 
be Seq.pm's that don't actually have underlying PrimarySeq's associated 
with them ... perhaps your delegation can check to see whether there's 
actually something to delegate to?

-Aaron

From barry.moore at genetics.utah.edu  Tue Aug 10 18:06:44 2004
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Wed Aug 11 08:05:44 2004
Subject: [Bioperl-l] orthologous genes extracting
In-Reply-To: <1092139413.11425.24.camel@localhost.localdomain>
References: <1356.10.10.120.61.1091596127.squirrel@webmail.sibs.ac.cn>
	<1092139413.11425.24.camel@localhost.localdomain>
Message-ID: <411946F4.9030509@genetics.utah.edu>

Just download the homologene file from 
ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current and read it into a hash.

Barry

Albert Vilella wrote:

>>Is there a way of extracting orthologous genes from homologene database?>
>>    
>>
>>>Is there a perl module to do it?
>>>      
>>>
>
>I remember a post in the ensembl-dev mailing list about this: there is
>something done on the Ensembl API for the Ensembl DB orthology
>relations,
>
>Hope it helps,
>
>    Albert.
>
>  
>
>>Thanks.
>>
>>
>>Songmin Xie
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l@portal.open-bio.org
>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>    
>>

-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

From hlapp at gmx.net  Wed Aug 11 12:02:06 2004
From: hlapp at gmx.net (Hilmar Lapp)
Date: Wed Aug 11 12:02:49 2004
Subject: [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit
In-Reply-To: 
Message-ID: 

Well the thing is by definition they always have an underlying 
PrimarySeq. And, almost all flat attributes do delegate to the 
PrimarySeq. See the constructor.

If there is to be a Seq w/o an underlying PrimarySeq we'll have to do 
some serious re-thinking of how we do things. Just as an example, when 
you attach features to a Seq object, the method will attach the 
PrimarySeq to the feature.

	-hilmar

On Wednesday, August 11, 2004, at 04:51  AM, Aaron J. Mackey wrote:

>
> On Aug 11, 2004, at 3:27 AM, Hilmar Lapp wrote:
>
>> Log Message:
>> Made primary_id() to delegate. Yes, always. Also, added a Seq test to 
>> make
>> sure glaring inconsistencies don't happen again.
>
> I'm not going to argue vociferously, but I imagine that the issue 
> might be Seq.pm's that don't actually have underlying PrimarySeq's 
> associated with them ... perhaps your delegation can check to see 
> whether there's actually something to delegate to?
>
> -Aaron
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


From hlapp at gnf.org  Wed Aug 11 12:18:25 2004
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Aug 11 12:19:09 2004
Subject: [Bioperl-l] Re: sequences > 4000 chars getting truncated on update
	on Oracle
In-Reply-To: 
Message-ID: <1278E0A4-EBB2-11D8-B4F5-000A959EB4C4@gnf.org>

Marc,

I believe I found a fix that doesn't hit performance (i.e., it doesn't 
force a load and re-serialization when the sequence actually has not 
changed). I just committed the fixes to bioperl-db, and I also added 
extensive testing of potentially problematic situations to simpleseq.t. 
The tests all pass ...

If you get a chance, give it a try.

	-hilmar
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


From muratem at eng.uah.edu  Wed Aug 11 13:29:15 2004
From: muratem at eng.uah.edu (Mike Muratet)
Date: Wed Aug 11 13:30:18 2004
Subject: [Bioperl-l] Performance of Bio::Index methods
Message-ID: 

Greetings

I'm working on a task in which I need to index Genbank files. (Alas,
putting them in mysql is not a option at the moment.) The indexing option
out of the box (SDBM?) is slow. Spreading the index across several files
speeds it up significantly which suprises me. Can anyone tell me the
algorithm used? I would expect it to be linear in the number of records,
but it seems to be otherwise. 

The documentation recommends Berkeley DB as being faster. Does anyone have
any experience with how much faster? I've used Berkeley in the past, but
never tried to compare the two.

Cheers

Mike


From allenday at ucla.edu  Wed Aug 11 21:41:39 2004
From: allenday at ucla.edu (Allen Day)
Date: Wed Aug 11 21:43:59 2004
Subject: [Bioperl-l] existing obo parser in perl?
Message-ID: 

is there a perl implementation of OBO format parsing? described here:

http://www.geneontology.org/GO.format.html#oboflat

-allen
From rich at thevillas.eclipse.co.uk  Thu Aug 12 11:20:54 2004
From: rich at thevillas.eclipse.co.uk (rich)
Date: Thu Aug 12 11:26:41 2004
Subject: [Bioperl-l] parsing bl2seq alignment with Bio::AlignIO
Message-ID: <411B8AD6.1040606@thevillas.eclipse.co.uk>

Hi,

i'm using Bio::AlignIO and specifically $aln = $report_align->next_aln() 
to read the 2 alignments from the bl2seq formatted file at the bottom of 
this mail.

Does anyone know why it only reads in the first alignment? ie

Query: 299  GEVDVKDVTFTYQGKEKPALSHVSFSIPQGKTVALVGRSGSGKSTIANLFTRFYDVDSGS 
358
           G++ VKD+T  Y       L ++SFSI  G+ V L+GR+GSGKST+ + F R  + + G
Sbjct: 1226 GQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRLLNTE-GE 
1284

Query: 359  ICLDGHDVRDYKLTNLRRHFALVSQNVHLFNDTIANNIAYAAEGEYTREQIEQAARQAHA 
418
           I +DG       L   R+ F ++ Q V +F+ T   N+      +++ ++I + A +
Sbjct: 1285 IQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLD--PYEQWSDQEIWKVADEVGL 
1342

Query: 419  MEFIENMPQGLDTVIGENGTSLSGGQRQRVAIARALLRDAPVLILDEATSALDTESERAI 
478
              IE  P  LD V+ + G  LS G +Q + +AR++L  A +L+LDE ++ LD  + + I
Sbjct: 1343 RSVIEQFPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPVTYQII 
1402

Query: 479  QAALDELQKNKTVLVIAHRLSTIEQADEILVVDEGEI 515
           +  L +   + TV++  HR+  + +  + LV++E ++
Sbjct: 1403 RRTLKQAFADCTVILCEHRIEAMLECQQFLVIEENKV 1439

Any help appreciated,
thanks
Rich



use Bio::AlignIO;
use Bio::Align::AlignI;

my $report_align  = Bio::AlignIO->new(-file => '/tmp/align' ,
                                              '-format' => 'bl2seq');

my $loop_num=1;

while(my $aln = $report_align->next_aln()){
                   print $loop_num++,"\n";
  }


Query=
        (523 letters)

 >, 1498 aa.
         Length = 1498

Score =  117 bits (292), Expect = 4e-30
Identities = 68/217 (31%), Positives = 120/217 (55%), Gaps = 3/217 (1%)

Query: 299  GEVDVKDVTFTYQGKEKPALSHVSFSIPQGKTVALVGRSGSGKSTIANLFTRFYDVDSGS 
358
           G++ VKD+T  Y       L ++SFSI  G+ V L+GR+GSGKST+ + F R  + + G
Sbjct: 1226 GQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRLLNTE-GE 
1284

Query: 359  ICLDGHDVRDYKLTNLRRHFALVSQNVHLFNDTIANNIAYAAEGEYTREQIEQAARQAHA 
418
           I +DG       L   R+ F ++ Q V +F+ T   N+      +++ ++I + A +
Sbjct: 1285 IQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLD--PYEQWSDQEIWKVADEVGL 
1342

Query: 419  MEFIENMPQGLDTVIGENGTSLSGGQRQRVAIARALLRDAPVLILDEATSALDTESERAI 
478
              IE  P  LD V+ + G  LS G +Q + +AR++L  A +L+LDE ++ LD  + + I
Sbjct: 1343 RSVIEQFPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPVTYQII 
1402

Query: 479  QAALDELQKNKTVLVIAHRLSTIEQADEILVVDEGEI 515
           +  L +   + TV++  HR+  + +  + LV++E ++
Sbjct: 1403 RRTLKQAFADCTVILCEHRIEAMLECQQFLVIEENKV 1439



Score = 87.0 bits (214), Expect = 4e-21
Identities = 61/237 (25%), Positives = 116/237 (48%), Gaps = 20/237 (8%)

Query: 278 FGLMDLETERDNGKYEAERVNGEVDVKDVTFTYQGKEKPALSHVSFSIPQGKTVALVGRS 337
          FG +  + +++N   +    NG+  +    F+  G   P L  ++F I +G+ +A+ G +
Sbjct: 423 FGELFEKAKQNNNNRKTS--NGDDSLFFSNFSLLGT--PVLKDINFKIERGQLLAVAGST 478

Query: 338 GSGKSTIANLFTRFYDVDSGSICLDGHDVRDYKLTNLRRHFALVSQNVHLFNDTIANNIA 397
          G+GK+++  +     +   G I   G               +  SQ   +   TI  NI
Sbjct: 479 GAGKTSLLMVIMGELEPSEGKIKHSGR-------------ISFCSQFSWIMPGTIKENII 525

Query: 398 YAAEGEYTREQIEQAARQAHAMEFIENMPQGLDTVIGENGTSLSGGQRQRVAIARALLRD 457
          +     Y   +     +     E I    +  + V+GE G +LSGGQR R+++ARA+ +D
Sbjct: 526 FGVS--YDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLSGGQRARISLARAVYKD 583

Query: 458 APVLILDEATSALDTESERAI-QAALDELQKNKTVLVIAHRLSTIEQADEILVVDEG 513
          A + +LD     LD  +E+ I ++ + +L  NKT +++  ++  +++AD+IL++ EG
Sbjct: 584 ADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKMEHLKKADKILILHEG 640


Lambda     K      H
  0.322    0.136    0.384

Gapped
Lambda     K      H
  0.267   0.0410    0.140


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1908
Number of Sequences: 0
Number of extensions: 52
Number of successful extensions: 6
Number of sequences better than 10.0: 1
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 2
length of query: 523
length of database: 1498
effective HSP length: 43
effective length of query: 480
effective length of database: 1455
effective search space:   698400
effective search space used:   698400
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 30 (16.8 bits)
S2: 30 (16.2 bits)

From pvh at egenetics.com  Thu Aug 12 07:04:50 2004
From: pvh at egenetics.com (Peter van Heusden)
Date: Thu Aug 12 11:56:53 2004
Subject: [Bioperl-l] I'm 'breaking' write_seq in bsml
Message-ID: <411B4ED2.2040004@egenetics.com>

As per the discussion on making SeqIO 'safe' to use, I'm going through 
the code in Bio/SeqIO/*.pm and ensuring that write_seq() returns 1 if it 
succeeds, and undef if it fails. At the moment the bsml module returns 
the XML object from write_seq, so making this module consistent with all 
the others breaks backwards compatibility.

Is this a problem for anyone?

Peter
From hlapp at gmx.net  Thu Aug 12 12:16:02 2004
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu Aug 12 12:16:40 2004
Subject: [Bioperl-l] existing obo parser in perl?
In-Reply-To: 
Message-ID: 

Nope, not yet. Both Chris and I were contemplating to write it but 
obviously have had other obligations ... Go ahead if you need it.

	-hilmar

On Wednesday, August 11, 2004, at 06:41  PM, Allen Day wrote:

> is there a perl implementation of OBO format parsing? described here:
>
> http://www.geneontology.org/GO.format.html#oboflat
>
> -allen
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


From hlapp at gmx.net  Thu Aug 12 12:19:22 2004
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu Aug 12 12:19:55 2004
Subject: [Bioperl-l] I'm 'breaking' write_seq in bsml
In-Reply-To: <411B4ED2.2040004@egenetics.com>
Message-ID: <5EE999F0-EC7B-11D8-BBB8-000A959EB4C4@gmx.net>

Note that returning TRUE or FALSE is what counts. Returning the XML 
object upon success is equivalent to returning TRUE I would suppose, 
and otherwise return undef.

	-hilmar

On Thursday, August 12, 2004, at 04:04  AM, Peter van Heusden wrote:

> As per the discussion on making SeqIO 'safe' to use, I'm going through 
> the code in Bio/SeqIO/*.pm and ensuring that write_seq() returns 1 if 
> it succeeds, and undef if it fails. At the moment the bsml module 
> returns the XML object from write_seq, so making this module 
> consistent with all the others breaks backwards compatibility.
>
> Is this a problem for anyone?
>
> Peter
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


From muratem at eng.uah.edu  Thu Aug 12 14:44:26 2004
From: muratem at eng.uah.edu (Mike Muratet)
Date: Thu Aug 12 14:45:27 2004
Subject: [Bioperl-l] Comparing DB_FILE and SDBM
Message-ID: 

Greetings

I did a comparison myself of Bio::Index::GenBank between DB_FILE and SDBM
on the latest version of the files from the Genbank primate division using
a Compaq with 376K of memory and a 2.4GHz Pentium 4 Xeon. I used the
environment variable to control the indexer. I got the latest release of
Berkeley from SleepyCat. 

Using DB_FILE

real    38m32.751s
user    6m36.070s
sys     1m16.650s

Using SDBM

real    46m13.856s
user    6m34.400s
sys     1m15.010s

A negligible difference. Has anyone tried to compare the libraries (or
knows where someone has?)

Thanks

Mike 

From cjm at fruitfly.org  Thu Aug 12 03:37:28 2004
From: cjm at fruitfly.org (Chris Mungall)
Date: Thu Aug 12 16:39:45 2004
Subject: [Bioperl-l] Re: [SO-devel] existing obo parser in perl?
In-Reply-To: 
Message-ID: 


Yes, you need to download the go-perl library (get it from sf cvs)

www.godatabase.org/dev

the parser throws xml events which you can catch, or you can use the
default handler which builds graphy objects

i recall promising hilmar i'd look at adding a parser to bioperl but i
haven't managed to do this yet

On Wed, 11 Aug 2004, Allen Day wrote:

> is there a perl implementation of OBO format parsing? described here:
>
> http://www.geneontology.org/GO.format.html#oboflat
>
> -allen
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media
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From laurichj at bioinfo.ucr.edu  Thu Aug 12 17:10:48 2004
From: laurichj at bioinfo.ucr.edu (Josh Lauricha)
Date: Thu Aug 12 17:12:01 2004
Subject: [Bioperl-l] Comparing DB_FILE and SDBM
In-Reply-To: 
References: 
Message-ID: <20040812211048.GA1961@bioinfo.ucr.edu>

On Thu 08/12/04 13:44, Mike Muratet wrote:
> Greetings
> 
> I did a comparison myself of Bio::Index::GenBank between DB_FILE and SDBM
> on the latest version of the files from the Genbank primate division using
> a Compaq with 376K of memory and a 2.4GHz Pentium 4 Xeon. I used the

Wow, now thats a machine in desprate need of a memory upgrade.

> environment variable to control the indexer. I got the latest release of
> Berkeley from SleepyCat. 
> 
> Using DB_FILE
> 
> real    38m32.751s
> user    6m36.070s
> sys     1m16.650s
> 
> Using SDBM
> 
> real    46m13.856s
> user    6m34.400s
> sys     1m15.010s

How loaded was that machine? (I'm assuming just the tests.)

> 
> A negligible difference. Has anyone tried to compare the libraries (or
> knows where someone has?)

I never compared the DB libraries, but I did some comparison between
regexp and XML::SAX for tigr.pm, and found that using the XML::SAX
module on top of Expat was horribly slow. The start to finish times for
regexp were <5m while XML::SAX was >25m, even though the regexp were
parsing considerably more data out at the time. And regexp took 4-5m of
CPU time, XML::SAX would do 5-8m meaning that XML::SAX would idle for
quite a while during its run.

I have a feeling that perl yeilds its timeslice for whatever reason when
switching from a library to perl-code, making libraries that do a lot of
function calls (such as XML parser and DBs) very slow in terms of
latency.

Can anyone confirm or deny this?

Thanks,

-- 

------------------------------------------------------
| Josh Lauricha            | Ford, you're turning    |
| laurichj@bioinfo.ucr.edu | into a penguin. Stop    |
| Bioinformatics, UCR      | it                      |
|----------------------------------------------------|
| OpenPG:                                            |
|  4E7D 0FC0 DB6C E91D 4D7B C7F3 9BE9 8740 E4DC 6184 |
|----------------------------------------------------|
From pvh at egenetics.com  Thu Aug 12 17:17:14 2004
From: pvh at egenetics.com (Peter van Heusden)
Date: Thu Aug 12 17:18:15 2004
Subject: [Bioperl-l] I'm 'breaking' write_seq in bsml
In-Reply-To: <5EE999F0-EC7B-11D8-BBB8-000A959EB4C4@gmx.net>
References: <5EE999F0-EC7B-11D8-BBB8-000A959EB4C4@gmx.net>
Message-ID: <411BDE5A.5060407@egenetics.com>

Hilmar Lapp wrote:

> Note that returning TRUE or FALSE is what counts. Returning the XML 
> object upon success is equivalent to returning TRUE I would suppose, 
> and otherwise return undef.
>
Ah! Good point, I'll do it that way.

Peter

From lstein at cshl.edu  Thu Aug 12 18:08:40 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Thu Aug 12 18:08:52 2004
Subject: [Bioperl-l] Bio::Root::IO reads URLs from -file
In-Reply-To: 
References: 
	
	
Message-ID: <200408121808.40654.lstein@cshl.edu>

The "perlish" way to do this is:

	-file => "GET http://foobar.com/index.html |"

This will, in fact, work using the current codebase (without Allen's patches), 
provided that the GET command from LWP is installed.  If you don't have GET 
installed, you can do the same thing with "wget" or any of a large number of 
URL fetcher commands.

Lincoln

On Tuesday 10 August 2004 03:57 pm, Allen Day wrote:
> On Tue, 10 Aug 2004, Jason Stajich wrote:
> > On Tue, 10 Aug 2004, Allen Day wrote:
> > > On Tue, 10 Aug 2004, Peter van Heusden wrote:
> > > > Hilmar Lapp wrote:
> > > > > I lean with Ewan to -url as I like explicit commands better than
> > > > > possibly dubious magic behind the scenes ... imagine someone stores
> > > > > files by names that match their url ...
> > > > >
> > > > > There's one thing though that's important IMO that Jason brings up:
> > > > > I don't know how you implemented this but I think Bio::Root::IO
> > > > > must not be dependent on LWP or any such beast that doesn't come
> > > > > with perl.
> > > >
> > > > I'm with the majority in that 'magic' creates possible confusion and
> > > > more room for error. As to Hilmar's idea of not depending on LWP, I
> > > > think this is also a good idea, and maybe the URL code can be a kind
> > > > of 'mixin' - i.e. implement it in another module and then have
> > > > Bio::Root::IO optionally add it as a plugin. What do you intend to do
> > > > with this capability? Is there going to be another module that
> > > > depends on the -url ability?
> > >
> > > Bio::Root::IO::_initialize_io() now accepts a '-url' argument.
> > >
> > > If present, and if LWP is loadable, _initialize_io() attempts to use
> > > LWP::Simple::getstore() to download the url to a local tempfile, and
> > > assigns that tempfile to the equivalent of _initialize_io()'s '-file'
> > > argument.  This works for HTTP, HTTPS, FTP, and all other protocols
> > > supported by LWP.  If a file request fails, there is a retry loop in
> > > place to retry a few times to fetch the file.
> >
> > The tempfile gets cleaned up by LWP?  We do this sort of thing in
> > Bio::Tools::Run::RemoteBlast and within Bio::DB::NCBIHelper,et al perhaps
> > we can localize some of that code to a -url param where it is a GET
> > request...
>
> no, i use Bio::Root::IO::tempfile() to generate the tempfile, and use LWP
> to write into that.  LWP doesn't know how to clean up after itself, as far
> as i can tell.
>
> > > If LWP is not loadable, _initialze_io() uses Bio::Root::HTTPget to open
> > > a socket to the file's host and sets '-fh' to read from this socket. 
> > > This only works for HTTP.  There is no retry loop in place here, as
> > > Bio::Root::HTTPget throws an error if it can't open the socket.  It's
> > > possible to modify Bio::Root::HTTPget to do retries, but I didn't feel
> > > like poking around in there.
> > >
> > > Still remaining to be done:
> > >
> > >   [1] add -url to the documentation
> > >   [2] checking for existance of clashing '-file' or '-fh' arguments
> > >   [3] add additional tests to t/RootIO.t for testing https and ftp
> > >       retrievals.
> > >
> > > Regarding another module depending on this, yes, there will be one,
> > > that's the only reason I added this :).  I have a new FeatureIO
> > > subsystem.  One format it can parse is GFF v3.  Valid GFF v3 requires
> > > features to be typed according to the Sequence Ontology or an extension
> > > thereof.  As part of the parse it downloads the Sequence Ontology
> > > DAG-Edit files, parses them into a Bio::Ontology, and returns
> > > Bio::SeqFeatureI objects with Annotation::OntologyTerms attached.
> > >
> > > I will commit the FeatureIO code soon.
> >
> > Cool! Will it also support some sort of caching of SO too?  Maybe we can
> > change Tools::GFF to delegate to FeatureIO for GFF3 files instead of
> > having 2 modules doing the same thing.
>
> well, it just caches to the tempfile right now and deletes on program
> termination, but if you want to add functionality for -url to store the
> file somewhere (perhaps in a filename in $TEMPDIR that is the md5 sum of
> the URL?), be my guest.
>
> my idea is to do away with Bio::Tools::GFF entirely.
>
> > Also, have you worked on the alignment <-> GFF3 at all either?  It is an
> > almost-doable thing with HSP->cigar_line but I am not sure we have a
> > cigar2HSP factory yet.
>
> nope, haven't looked at this.  i don't really do alignments so i don't
> need this functionality.
>
> -allen
>
> > -jason
> >
> > > -Allen
> > >
> > > > Peter
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l@portal.open-bio.org
> > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
From chenn at cshl.edu  Thu Aug 12 22:47:43 2004
From: chenn at cshl.edu (Jack Chen)
Date: Thu Aug 12 23:13:18 2004
Subject: [Bioperl-l] seq() method of Bio::Seq module 
Message-ID: 

Hi,

Is there a way to preserve the original sequence format we seq() is used
to print the string of sequence? Say, 

#original sequence
>ABC
aaaaaaaaaaaaaaaaaa
cccccccccccccccccc
gggggggggggggggggg
tttttttttttttttttt

When I print the string of this sequence using seq() method in Bio::Seq
module, I get:
>ABC
aaaaaaaaaaaaaaaaaaccccccccccccccccccggggggggggggggggggggtttttttttttttttt
tt
(all spaces and newlines are removed)

How can I get the original sequence back:
>ABC
aaaaaaaaaaaaaaaaaa
cccccccccccccccccc
gggggggggggggggggg
tttttttttttttttttt

?

Thanks,

Jack





From allenday at ucla.edu  Fri Aug 13 01:21:13 2004
From: allenday at ucla.edu (Allen Day)
Date: Fri Aug 13 01:23:28 2004
Subject: [Bioperl-l] seq() method of Bio::Seq module 
In-Reply-To: 
References: 
Message-ID: 

you can't, the formatting isn't preserved.  you can try using Text::Wrap 
to reformat it back to the original.

-allen


On Thu, 12 Aug 2004, Jack Chen wrote:

> Hi,
> 
> Is there a way to preserve the original sequence format we seq() is used
> to print the string of sequence? Say, 
> 
> #original sequence
> >ABC
> aaaaaaaaaaaaaaaaaa
> cccccccccccccccccc
> gggggggggggggggggg
> tttttttttttttttttt
> 
> When I print the string of this sequence using seq() method in Bio::Seq
> module, I get:
> >ABC
> aaaaaaaaaaaaaaaaaaccccccccccccccccccggggggggggggggggggggtttttttttttttttt
> tt
> (all spaces and newlines are removed)
> 
> How can I get the original sequence back:
> >ABC
> aaaaaaaaaaaaaaaaaa
> cccccccccccccccccc
> gggggggggggggggggg
> tttttttttttttttttt
> 
> ?
> 
> Thanks,
> 
> Jack
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
From sdavis2 at mail.nih.gov  Fri Aug 13 09:35:37 2004
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Fri Aug 13 09:34:52 2004
Subject: [Bioperl-l] Bundle::Bioperl issue
Message-ID: 

Dear all,

I have been working on installing bioperl on another machine (I have it 
on several).  There seems to be a circular dependency in File::Spec and 
Cwd.  I wondered if anyone else had noticed this.  I wrote to the 
package maintainer, but have not heard back yet.

Any insights?

Thanks,
Sean

From nathanhaigh at ukonline.co.uk  Fri Aug 13 07:27:31 2004
From: nathanhaigh at ukonline.co.uk (Nathan Haigh)
Date: Fri Aug 13 09:50:53 2004
Subject: [Bioperl-l] mega next_aln unmatch
Message-ID: 

I've been playing with some of the alignment file formats and I've noticed
that when a mega file is read in it returns an alignment object that
contains the the sequences as represented in the mega file (i.e. with dots
for matched chars etc).

I'm not sure how all the other alignment format objects return their
sequences, but wouldn't it make more sense to return the object with the
chars converted back to sequence chars? i.e. make a call to $aln->unmatch()
prior to returning the alignment object at the end of mega.pm? I've just
seen that nexus.pm also makes the same call, so mega.pm should probably also
be brought into line with this also.

Regards
Nathan


From jason at cgt.duhs.duke.edu  Fri Aug 13 10:28:22 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Aug 13 10:29:27 2004
Subject: [Bioperl-l] mega next_aln unmatch
In-Reply-To: 
References: 
Message-ID: 

Good call.  Done.

Is anyone even using the mega format parser/writer?  I have not spent much
time making sure it is up to spec once the intial implementation was
written.

-jason
On Fri, 13 Aug 2004, Nathan Haigh wrote:

> I've been playing with some of the alignment file formats and I've noticed
> that when a mega file is read in it returns an alignment object that
> contains the the sequences as represented in the mega file (i.e. with dots
> for matched chars etc).
>
> I'm not sure how all the other alignment format objects return their
> sequences, but wouldn't it make more sense to return the object with the
> chars converted back to sequence chars? i.e. make a call to $aln->unmatch()
> prior to returning the alignment object at the end of mega.pm? I've just
> seen that nexus.pm also makes the same call, so mega.pm should probably also
> be brought into line with this also.
>
> Regards
> Nathan
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From dag at sonsorol.org  Fri Aug 13 10:46:51 2004
From: dag at sonsorol.org (Chris Dagdigian)
Date: Fri Aug 13 10:49:21 2004
Subject: [Bioperl-l] Bundle::Bioperl issue
In-Reply-To: 
References: 
Message-ID: <411CD45B.7000009@sonsorol.org>


I'm the maintainer and don't recall the email :) I did not notice this 
the last time I updated/ran the Bundle but perhaps something changed 
with File::Spec or Cwd. I'll download and see if I can replicate the issue.

-Chris


Sean Davis wrote:

> Dear all,
> 
> I have been working on installing bioperl on another machine (I have it 
> on several).  There seems to be a circular dependency in File::Spec and 
> Cwd.  I wondered if anyone else had noticed this.  I wrote to the 
> package maintainer, but have not heard back yet.
> 
> Any insights?
> 
> Thanks,
> Sean
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Chris Dagdigian, 
BioTeam  - Independent life science IT & informatics consulting
Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E iChat/AIM: bioteamdag  Web: http://bioteam.net
From nathanhaigh at ukonline.co.uk  Fri Aug 13 11:11:48 2004
From: nathanhaigh at ukonline.co.uk (Nathan Haigh)
Date: Fri Aug 13 11:13:12 2004
Subject: [Bioperl-l] require/use BioPerl version 1.4
Message-ID: 

Since the release of Bioperl 1.4, BioPerl has been split into separate
packages e.g. Core and Run components. I want to be able to request version
>=1.4 of the Core component and the Run Component - is this possible?

Thanks
Nathan


From jason at cgt.duhs.duke.edu  Fri Aug 13 11:36:19 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Aug 13 11:37:22 2004
Subject: [Bioperl-l] require/use BioPerl version 1.4
In-Reply-To: 
References: 
Message-ID: 

Bio::Root::Version holds the version.

We don't really have such a thing for the run component though.

You can get the installed version via $Object::VERSON, i.e.

% perl -I ~/bioperl/branch-1-4 -MBio::SeqIO -e 'print "$Bio::SeqIO::VERSION\n";'
1.4
% perl -I ~/bioperl/bioperl-live -MBio::SeqIO -e 'print "$Bio::SeqIO::VERSION\n";'
1.5

-jason
On Fri, 13 Aug 2004, Nathan Haigh wrote:

> Since the release of Bioperl 1.4, BioPerl has been split into separate
> packages e.g. Core and Run components. I want to be able to request version
> >=1.4 of the Core component and the Run Component - is this possible?
>
> Thanks
> Nathan
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From muratem at eng.uah.edu  Fri Aug 13 13:38:47 2004
From: muratem at eng.uah.edu (Mike Muratet)
Date: Fri Aug 13 13:39:53 2004
Subject: [Bioperl-l] Comparing DB_FILE and SDBM
In-Reply-To: <20040812211048.GA1961@bioinfo.ucr.edu>
Message-ID: 



On Thu, 12 Aug 2004, Josh Lauricha wrote:

> On Thu 08/12/04 13:44, Mike Muratet wrote:
> > Greetings
> > 
> > I did a comparison myself of Bio::Index::GenBank between DB_FILE and SDBM
> > on the latest version of the files from the Genbank primate division using
> > a Compaq with 376K of memory and a 2.4GHz Pentium 4 Xeon. I used the
> 
> Wow, now thats a machine in desprate need of a memory upgrade.
>

Well, yes. But it's all I've got.
 
> 
> How loaded was that machine? (I'm assuming just the tests.)
> 

I had some X sessions going to other (larger ;-) ) machines, but nothing
intensive.

> > 
> > A negligible difference. Has anyone tried to compare the libraries (or
> > knows where someone has?)
> 
> 
> I have a feeling that perl yeilds its timeslice for whatever reason when
> switching from a library to perl-code, making libraries that do a lot of
> function calls (such as XML parser and DBs) very slow in terms of
> latency.
> 
> Can anyone confirm or deny this?
> 

If anyone has any experience(s) to relate regarding the indexing of big
portions of Genbank, I'd like to hear how they did it. Should it really
take days?

Thanks

Mike

From jason at cgt.duhs.duke.edu  Fri Aug 13 13:59:09 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Aug 13 14:02:48 2004
Subject: [Bioperl-l] Comparing DB_FILE and SDBM
In-Reply-To: 
References: 
Message-ID: 

You could just write a little script which timed how long it takes just to
read through the whole primate division without doing any DB stuff - just
see how long it takes to go through the whole file, maybe see how many
records there are in it.

If you time this you'll get a baseline of how long it will take to index
.... Those files are pretty large from the primate div so I don't know if
that is the problem or the memory/disk requirements when the index file
gets really big.

If you run top when you are doing the indexing are you seeing mostly perl
CPU or system CPU - is it disk I/O that is killing you or is it running
full tilt in perl?

-jason
On Fri, 13 Aug 2004, Mike Muratet wrote:

>
>
> On Thu, 12 Aug 2004, Josh Lauricha wrote:
>
> > On Thu 08/12/04 13:44, Mike Muratet wrote:
> > > Greetings
> > >
> > > I did a comparison myself of Bio::Index::GenBank between DB_FILE and SDBM
> > > on the latest version of the files from the Genbank primate division using
> > > a Compaq with 376K of memory and a 2.4GHz Pentium 4 Xeon. I used the
> >
> > Wow, now thats a machine in desprate need of a memory upgrade.
> >
>
> Well, yes. But it's all I've got.
>
> >
> > How loaded was that machine? (I'm assuming just the tests.)
> >
>
> I had some X sessions going to other (larger ;-) ) machines, but nothing
> intensive.
>
> > >
> > > A negligible difference. Has anyone tried to compare the libraries (or
> > > knows where someone has?)
> >
> >
> > I have a feeling that perl yeilds its timeslice for whatever reason when
> > switching from a library to perl-code, making libraries that do a lot of
> > function calls (such as XML parser and DBs) very slow in terms of
> > latency.
> >
> > Can anyone confirm or deny this?
> >
>
> If anyone has any experience(s) to relate regarding the indexing of big
> portions of Genbank, I'd like to hear how they did it. Should it really
> take days?
>
> Thanks
>
> Mike
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From laurichj at bioinfo.ucr.edu  Fri Aug 13 14:00:35 2004
From: laurichj at bioinfo.ucr.edu (Josh Lauricha)
Date: Fri Aug 13 14:43:53 2004
Subject: [Bioperl-l] Comparing DB_FILE and SDBM
In-Reply-To: 
References: <20040812211048.GA1961@bioinfo.ucr.edu>
	
Message-ID: <20040813180035.GA4314@batch107a>

On Fri 08/13/04 12:38, Mike Muratet wrote:
> 
> 
> On Thu, 12 Aug 2004, Josh Lauricha wrote:
> 
> > On Thu 08/12/04 13:44, Mike Muratet wrote:
> > > Greetings
> > > 
> > > I did a comparison myself of Bio::Index::GenBank between DB_FILE and SDBM
> > > on the latest version of the files from the Genbank primate division using
> > > a Compaq with 376K of memory and a 2.4GHz Pentium 4 Xeon. I used the
> > 
> > Wow, now thats a machine in desprate need of a memory upgrade.
> >
> 
> Well, yes. But it's all I've got.

I was jokeing about the K vs M mix up ;) If the machine really does have
only 376K of memory, thats your problem... 

> If anyone has any experience(s) to relate regarding the indexing of big
> portions of Genbank, I'd like to hear how they did it. Should it really
> take days?

I've got the ests of genbank indexed... around 60G:

$ time gbfetch -i est.index BI509189 > /dev/null 

real    0m0.361s
user    0m0.300s
sys     0m0.050s

Don't want to go through the full indexing but that took quite some
time.. several hours I think. But, just reading the data takes at least
25 minutes, and this on a set of disks that will do ~60MB/s sustained
(hdparm -t) an normal IDE drive will do around 20.

The indexing doesn't do a full parse, just enough to get the ID numbers.

I don't think it should take days.... but if you've got a slow disk( as
root do: hdparm -t /dev/hda ), that could be it. The scripts I use are
basically just the synopsis, with the default DB.

-- 

------------------------------------------------------
| Josh Lauricha            | Ford, you're turning    |
| laurichj@bioinfo.ucr.edu | into a penguin. Stop    |
| Bioinformatics, UCR      | it                      |
|----------------------------------------------------|
| OpenPG:                                            |
|  4E7D 0FC0 DB6C E91D 4D7B C7F3 9BE9 8740 E4DC 6184 |
|----------------------------------------------------|
From laurichj at bioinfo.ucr.edu  Fri Aug 13 14:11:26 2004
From: laurichj at bioinfo.ucr.edu (Josh Lauricha)
Date: Fri Aug 13 14:43:55 2004
Subject: [Bioperl-l] Comparing DB_FILE and SDBM
In-Reply-To: 
References: 
	
Message-ID: <20040813181125.GA5110@batch107a>

On Fri 08/13/04 13:59, Jason Stajich wrote:
> If you run top when you are doing the indexing are you seeing mostly perl
> CPU or system CPU - is it disk I/O that is killing you or is it running
> full tilt in perl?

I forgot to mention this in my previous mail, but going by his `time`
output, I'm pretty sure the delay is not due to the perl stuff. There
was only a few minutes of CPU time used, but quite a bit of time from
start to finush. That leads me to think its a slow disk (or lotsa data,
depending on your viewpoint), or the same wierdness I got with XML::SAX.

-- 

------------------------------------------------------
| Josh Lauricha            | Ford, you're turning    |
| laurichj@bioinfo.ucr.edu | into a penguin. Stop    |
| Bioinformatics, UCR      | it                      |
|----------------------------------------------------|
| OpenPG:                                            |
|  4E7D 0FC0 DB6C E91D 4D7B C7F3 9BE9 8740 E4DC 6184 |
|----------------------------------------------------|
From kvddrift at earthlink.net  Sat Aug 14 15:32:51 2004
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Sat Aug 14 15:33:53 2004
Subject: [Bioperl-l] bioperl-run install problem
Message-ID: 

Hi,

When I install bioperl-run using fink on Mac OSX, I get an error that 
the file 
/sw/lib/perl5/5.8.1/darwin-thread-multi-2level/auto/Bio/.packlist 
already exists from bioperl itself. I haven't seen this error before, 
maybe something changed in the way fink installs stuff, I am not sure.  
I can easily remove the file packlist from the installation, but don't 
know if that will will give a problem when using bioperl and/or 
bioperl-run.

Is it ok to remove that file, or should I report this to the fink 
mailinglist, because that's what causing the error?

thanks,

- Koen.

From gyang at plantbio.uga.edu  Fri Aug 13 13:24:50 2004
From: gyang at plantbio.uga.edu (Guojun Yang)
Date: Mon Aug 16 08:27:08 2004
Subject: [Bioperl-l] Urgent: get_Stream_by_query difficulty or problem?
Message-ID: <20040813132450.da94e6ff@dogwood.plantbio.uga.edu>

Hi, everybody,
I am trying to get DNA seq from GenBank using bioperl method get_Stream_by_query. When the accession numbers and seqs were retrieved from a seq project, I found out that not all the query results are retrieved. i.e. the $count and @ids returned the same number (150756) of items as that using the NCBI Entrez page, but there are only 500 items were retrieved from the Seq object. Can anybody give me a hint on this? Is this possibly something internal to the method? Thank you! Guojun


From natg at shore.net  Mon Aug 16 12:15:18 2004
From: natg at shore.net (Nathan (Nat) Goodman)
Date: Mon Aug 16 12:15:01 2004
Subject: [Bioperl-l] orthologous genes extracting
Message-ID: 

Albert Vilella wrote:
>>Is there a way of extracting orthologous genes from homologene database?>
Barry Moore responded:
> Just download the homologene file from...

A word of caution:  HomoloGene includes many paralogs in its homology
groups.

I, too, am looking for a data source somewhere that provides orthologs (for
human, mouse, rat).  If anyone knows of one, please let me know!  If anyone
wants to work on this, let me know also!

Best,
Nat Goodman


From paulo.david at netvisao.pt  Mon Aug 16 12:47:19 2004
From: paulo.david at netvisao.pt (Paulo Almeida)
Date: Mon Aug 16 12:44:37 2004
Subject: [Bioperl-l] orthologous genes extracting
In-Reply-To: 
References: 
Message-ID: <4120E517.80508@netvisao.pt>

I have been using Ensmart, Ensembl's web interface for batch retrieval, 
at http://www.ensembl.org/Multi/martview
I think their orthologues are based on reciprocal BLASTs and sometimes 
also on synteny and whole genome alignment data.

-Paulo

Nathan (Nat) Goodman wrote:

>A word of caution:  HomoloGene includes many paralogs in its homology
>groups.
>
>I, too, am looking for a data source somewhere that provides orthologs (for
>human, mouse, rat).  If anyone knows of one, please let me know!  If anyone
>wants to work on this, let me know also!
>
>Best,
>Nat Goodman
>
From natg at shore.net  Mon Aug 16 13:42:51 2004
From: natg at shore.net (Nathan (Nat) Goodman)
Date: Mon Aug 16 13:42:31 2004
Subject: [Bioperl-l] orthologous genes extracting
In-Reply-To: <4120E517.80508@netvisao.pt>
Message-ID: 

Paulo said:
> I have been using Ensmart, Ensembl's web interface for batch retrieval,
> at http://www.ensembl.org/Multi/martview
> I think their orthologues are based on reciprocal BLASTs and sometimes
> also on synteny and whole genome alignment data.

Thanks.  I've seen problems with Ensembl similar to those with HomoloGene,
but as I look through my notes, these may have been pathological cases.  For
example, mouse Casp1 points to two human othologs, CASP1 and COP.  CASP1 is
a biologically validated ortholog, but COP is pretty similar and adjacent to
CASP1.

I'm wondering if anyone has combined a curated data source, eg, MGD, with
computed results to avoid cases like this.

Looking at the bigger picture, I see a need for "orthology" maps at various
levels of stringency.  What I'm discussing here is the most stringent case
in which we try hard to assign 1 ortholog per species to each gene.  (I
realize the issue is biologically complex and this simple notion will fail
for biological reasons in many cases, which is why I'm hoping someone else
has already solved the problem :)  It would be nice to also offer more
permissive maps including ones based entirely on sequence similarity.

Best,
Nat

From rwcitek at alum.calberkeley.org  Mon Aug 16 15:00:47 2004
From: rwcitek at alum.calberkeley.org (Robert Citek)
Date: Mon Aug 16 15:02:33 2004
Subject: [Bioperl-l] on-line collaboration
In-Reply-To: 
Message-ID: <9556D6E6-EFB6-11D8-BA66-000A95880F88@alum.calberkeley.org>


On Tuesday, Aug 3, 2004, at 10:57 US/Central, Jason Stajich wrote:
> On Tue, 3 Aug 2004, Robert Citek wrote:
>> Is there an IRC channel?
>
> nope - if someone wants to set it up that's great but I think most of 
> the
> devs prefer to do the question answering via email.

Apparently, there is one at irc://irc.freenode.net/bioinformatics.  If 
you use Mozilla, just type in the URI and Chatzilla should open to the 
channel.  If you use some other Internet Relay Chat client, then type 
in these commands:

/server irc.freenode.net
/join #bioinformatics

I've created a simple tips page on using Mozilla's Chatzilla here:

   http://www.cwelug.org/cgi-bin/wiki.cgi?InternetRelayChat

Regards,
- Robert

From lstein at cshl.edu  Mon Aug 16 17:39:32 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon Aug 16 17:41:14 2004
Subject: [Bioperl-l] Re: blast2gff.pl
In-Reply-To: <20040816064206.56153.qmail@web51706.mail.yahoo.com>
References: <20040816064206.56153.qmail@web51706.mail.yahoo.com>
Message-ID: <200408161739.32124.lstein@cshl.edu>

Hi Justin,

You know, I was absolutely sure that bioperl had a blast2gff script, 
but I can't find it.  So please send me your script and I will add it 
in.  Just make sure that the script has some POD documentation so 
that I don't have to write it!

Lincoln


On Monday 16 August 2004 02:42 am, you wrote:
> Hi Lincoln,
> Don't know if you remember me, I interviewed up at
> CSHL last year.
>
> I've been helping out with the Honey Bee Genome
> Project, and found it necessary to write a perl hack
> to turn BLAST result files into .gff files. Not sure
> if bioperl already has such a script, but I thought I
> would pass along mine in case it might be useful to
> others who use GBROWSE. It's beta code, and probably
> has a bug or two lurking. If you think it might be
> useful, I could go through it more thoroughly and
> refine it.
>
> Best regards,
> Justin Reese
>
>
>
> __________________________________
> Do you Yahoo!?
> Yahoo! Mail is new and improved - Check it out!
> http://promotions.yahoo.com/new_mail

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
From lstein at cshl.edu  Mon Aug 16 17:50:12 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon Aug 16 17:51:18 2004
Subject: [Bioperl-l] Re: blast2gff.pl
In-Reply-To: 
References: 
Message-ID: <200408161750.12372.lstein@cshl.edu>

Ah, that was it!  In any case, Justin, please send your script - I'm 
sure it will find use.

Lincoln

On Monday 16 August 2004 05:45 pm, Jack Chen wrote:
> There is a script bp_search2gff.pl by Jason.
>
> Jack
>
> On Mon, 16 Aug 2004, Lincoln Stein wrote:
> > Hi Justin,
> >
> > You know, I was absolutely sure that bioperl had a blast2gff
> > script, but I can't find it.  So please send me your script and I
> > will add it in.  Just make sure that the script has some POD
> > documentation so that I don't have to write it!
> >
> > Lincoln
> >
> > On Monday 16 August 2004 02:42 am, you wrote:
> > > Hi Lincoln,
> > > Don't know if you remember me, I interviewed up at
> > > CSHL last year.
> > >
> > > I've been helping out with the Honey Bee Genome
> > > Project, and found it necessary to write a perl hack
> > > to turn BLAST result files into .gff files. Not sure
> > > if bioperl already has such a script, but I thought I
> > > would pass along mine in case it might be useful to
> > > others who use GBROWSE. It's beta code, and probably
> > > has a bug or two lurking. If you think it might be
> > > useful, I could go through it more thoroughly and
> > > refine it.
> > >
> > > Best regards,
> > > Justin Reese
> > >
> > >
> > >
> > > __________________________________
> > > Do you Yahoo!?
> > > Yahoo! Mail is new and improved - Check it out!
> > > http://promotions.yahoo.com/new_mail
> >
> > --
> > Lincoln D. Stein
> > Cold Spring Harbor Laboratory
> > 1 Bungtown Road
> > Cold Spring Harbor, NY 11724
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
From lstein at cshl.edu  Tue Aug 17 13:49:48 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Tue Aug 17 13:52:07 2004
Subject: [Bioperl-l] Comparing DB_FILE and SDBM
In-Reply-To: <20040813181125.GA5110@batch107a>
References: 
	
	<20040813181125.GA5110@batch107a>
Message-ID: <200408171349.49188.lstein@cshl.edu>

There's been lots of benchmarking of the various DB implementations, 
including some reported in the perl PODs.  I suggest you look them 
up.

Lincoln

On Friday 13 August 2004 02:11 pm, Josh Lauricha wrote:
> On Fri 08/13/04 13:59, Jason Stajich wrote:
> > If you run top when you are doing the indexing are you seeing
> > mostly perl CPU or system CPU - is it disk I/O that is killing
> > you or is it running full tilt in perl?
>
> I forgot to mention this in my previous mail, but going by his
> `time` output, I'm pretty sure the delay is not due to the perl
> stuff. There was only a few minutes of CPU time used, but quite a
> bit of time from start to finush. That leads me to think its a slow
> disk (or lotsa data, depending on your viewpoint), or the same
> wierdness I got with XML::SAX.

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
From lstein at cshl.edu  Tue Aug 17 13:49:48 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Tue Aug 17 13:52:09 2004
Subject: [Bioperl-l] Comparing DB_FILE and SDBM
In-Reply-To: <20040813181125.GA5110@batch107a>
References: 
	
	<20040813181125.GA5110@batch107a>
Message-ID: <200408171349.49188.lstein@cshl.edu>

There's been lots of benchmarking of the various DB implementations, 
including some reported in the perl PODs.  I suggest you look them 
up.

Lincoln

On Friday 13 August 2004 02:11 pm, Josh Lauricha wrote:
> On Fri 08/13/04 13:59, Jason Stajich wrote:
> > If you run top when you are doing the indexing are you seeing
> > mostly perl CPU or system CPU - is it disk I/O that is killing
> > you or is it running full tilt in perl?
>
> I forgot to mention this in my previous mail, but going by his
> `time` output, I'm pretty sure the delay is not due to the perl
> stuff. There was only a few minutes of CPU time used, but quite a
> bit of time from start to finush. That leads me to think its a slow
> disk (or lotsa data, depending on your viewpoint), or the same
> wierdness I got with XML::SAX.

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
From brian_osborne at cognia.com  Wed Aug 18 09:26:12 2004
From: brian_osborne at cognia.com (Brian Osborne)
Date: Wed Aug 18 09:27:09 2004
Subject: [Bioperl-l] Re: blast2gff.pl
In-Reply-To: <200408161739.32124.lstein@cshl.edu>
Message-ID: 

Lincoln,

scripts/utilities/search2gff.PLS?

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Lincoln Stein
Sent: Monday, August 16, 2004 5:40 PM
To: jtr4v@alumni.virginia.edu
Cc: bioperl-l@bioperl.org
Subject: [Bioperl-l] Re: blast2gff.pl

Hi Justin,

You know, I was absolutely sure that bioperl had a blast2gff script,
but I can't find it.  So please send me your script and I will add it
in.  Just make sure that the script has some POD documentation so
that I don't have to write it!

Lincoln


On Monday 16 August 2004 02:42 am, you wrote:
> Hi Lincoln,
> Don't know if you remember me, I interviewed up at
> CSHL last year.
>
> I've been helping out with the Honey Bee Genome
> Project, and found it necessary to write a perl hack
> to turn BLAST result files into .gff files. Not sure
> if bioperl already has such a script, but I thought I
> would pass along mine in case it might be useful to
> others who use GBROWSE. It's beta code, and probably
> has a bug or two lurking. If you think it might be
> useful, I could go through it more thoroughly and
> refine it.
>
> Best regards,
> Justin Reese
>
>
>
> __________________________________
> Do you Yahoo!?
> Yahoo! Mail is new and improved - Check it out!
> http://promotions.yahoo.com/new_mail

--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
_______________________________________________
Bioperl-l mailing list
Bioperl-l@portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l


From chenn at cshl.edu  Mon Aug 16 17:45:26 2004
From: chenn at cshl.edu (Jack Chen)
Date: Wed Aug 18 09:47:50 2004
Subject: [Bioperl-l] Re: blast2gff.pl
In-Reply-To: <200408161739.32124.lstein@cshl.edu>
Message-ID: 

There is a script bp_search2gff.pl by Jason.

Jack        


On Mon, 16 Aug 2004, Lincoln Stein wrote:

> Hi Justin,
> 
> You know, I was absolutely sure that bioperl had a blast2gff script, 
> but I can't find it.  So please send me your script and I will add it 
> in.  Just make sure that the script has some POD documentation so 
> that I don't have to write it!
> 
> Lincoln
> 
> 
> On Monday 16 August 2004 02:42 am, you wrote:
> > Hi Lincoln,
> > Don't know if you remember me, I interviewed up at
> > CSHL last year.
> >
> > I've been helping out with the Honey Bee Genome
> > Project, and found it necessary to write a perl hack
> > to turn BLAST result files into .gff files. Not sure
> > if bioperl already has such a script, but I thought I
> > would pass along mine in case it might be useful to
> > others who use GBROWSE. It's beta code, and probably
> > has a bug or two lurking. If you think it might be
> > useful, I could go through it more thoroughly and
> > refine it.
> >
> > Best regards,
> > Justin Reese
> >
> >
> >
> > __________________________________
> > Do you Yahoo!?
> > Yahoo! Mail is new and improved - Check it out!
> > http://promotions.yahoo.com/new_mail
> 
> -- 
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 

From reche at research.dfci.harvard.edu  Mon Aug 16 18:30:44 2004
From: reche at research.dfci.harvard.edu (Pedro Antonio Reche)
Date: Wed Aug 18 09:47:56 2004
Subject: [Bioperl-l] help converting seq objects.
In-Reply-To: 
References: <45192F52-E66F-11D8-A804-000393BC20D0@research.dfci.harvard.edu>
	<20040805134720.GD72520@iib.unsam.edu.ar>
	
Message-ID: 

Hi all,
I have combined two scripts kindly provided by Jason Stajich to 1)  
Retrieve a list of seq records from genbank saving them in GenBank  
format; and 2)  get the translation feature from the file previously  
saved. The program -shown below- is works nicely, but I will nicer if I  
could parse the sequence object obtained from the GenBank database  
without printing  it. Does anyone knows how to do this? Thanks in  
advance for any help.
#!/usr/sbin/perl -w
# How to retrieve GenBank entries over the Web
# by Jason Stajich

use Bio::DB::GenBank;
use Bio::SeqIO;
use Bio::Seq;

$in = shift @ARGV;

###### acc numbes from file an array ##########
open (F, "$in") || die;
while(){
         next unless /(NM_\d+)\s/;
         $acc = $1;
         chomp($acc);
         push @AC, $acc;
}
close(F);
$list = join " ", @AC;
print "$list\n";

##### get genbank records into a file  
#######################################################
my $gb = new Bio::DB::GenBank;
my $seqio = $gb->get_Stream_by_acc(\@AC);
my $seqout = new Bio::SeqIO(-file => ">$in.gb", -format => 'GenBank');
#my $seqout = new Bio::SeqIO(-file => ">$ARGV[0].gb", -format =>  
'GenBank');
while( defined ($seq = $seqio->next_seq )) {
         $seqout->write_seq($seq);
}
###########get translation from file just created  
############################################
my $tmp  = "$in.gb";
my $temp = "$in.tfa";

my $in = new Bio::SeqIO(-file => "<$tmp", -format => 'genbank');
my $out = new Bio::SeqIO(-file => ">$temp", -format => 'fasta');
while ($seq = $in->next_seq ) {
         foreach my $f ( grep { $_->primary_tag eq 'CDS' }  
$seq->top_SeqFeatures ) {
                 my ($gname);
                 if ( $f->has_tag('gene') ) {
                         ($gname) = $f->each_tag_value('gene');
                 } elsif ( $f->has_tag('product') ) {
                         ($gname) = $f->each_tag_value('product');
                 }
                 ($gname) =~ s/\s+/_/g;
                 my ($ref) = $f->has_tag('protein_id') &&  
$f->each_tag_value('protein_id');
                 my ($gi)  = $f->has_tag('db_xref') &&  
$f->each_tag_value('db_xref');
                 my ($translation) = $f->has_tag('translation') &&  
$f->each_tag_value('translation');
                 unless( $gi && $ref && $gname && $translation ) {
                         print STDERR "not fully annotated CDS  
($gi,$ref,$gname), skipping...\n";
                         next;
                 }
                 my $tfa = Bio::PrimarySeq->new (-seq => $translation,  
-display_id =>
                                 sprintf("%s|%s|%s",$gi,$ref,$gname));
                         $out->write_seq($tfa);
     }
}
======================================================================== 
=====================
Dr. Pedro A Reche, Instructor of Medicine
Dana-Farber Cancer Institute, Harvard Medical School                     
      TL: 617 632 3824
HIM Building, Room 401                                                   
      FX: 617 632 3351
77 Avenue Louis Pasteur                                   EM:  
reche@research.dfci.harvard.edu
Boston, MA 02115, USA                                                 
W3: www.mifoundation.org

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From brian_osborne at cognia.com  Wed Aug 18 10:16:23 2004
From: brian_osborne at cognia.com (Brian Osborne)
Date: Wed Aug 18 10:17:17 2004
Subject: [Bioperl-l] Bio::Index sequence fetching
In-Reply-To: <3376.204.212.236.88.1092140103.squirrel@webmail.vbi.vt.edu>
Message-ID: 

Sucheta,

You need to use the "net::" suffix, the default is local, not remote.

Brian O.


-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Sucheta Tripathy
Sent: Tuesday, August 10, 2004 8:15 AM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] Bio::Index sequence fetching

I am sorry for posting it again.. I did it yesterday without a subject line.

I am trying to retrieve records from a genbank index file that I had
created using bp_index.pl. I have set the environment variables as
desired.

While fetching records I use the following syntax:

bp_fetch.pl -fmt genbank genbank:50355994 where 50355994 is the GI number
of one of the sequences.

But I don't get any results.

It says sequence 50355994 in database genbank not present.

Can anyone please comment where I may be going wrong.

Thanks

Sucheta


--
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606
_______________________________________________
Bioperl-l mailing list
Bioperl-l@portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l


From M.Q.Lewis at exeter.ac.uk  Wed Aug 18 11:03:23 2004
From: M.Q.Lewis at exeter.ac.uk (mql201)
Date: Wed Aug 18 11:10:15 2004
Subject: [Bioperl-l] Bio::Tools::IUPAC inconsistency
Message-ID: <4129129D@minerva2.ex.ac.uk>

Hello

I'm using the mod above.  I'm getting inconsistent output.  This fn, which 
takes an ambiguous DNA 
sequence and returns an array of all the possible variants expanded from IUPAC 
meta symbols:

sub expandMeta {
  my($uniqueseq);               # unique sequence object
  my(@rAr) = ();                # return array
  my($seqstr) = "";             # sequence attr of a sequence object

  my($ure) = $_[0];           # upstream regulatory element (sequence to 
check)

  my($ambiseq) = new Bio::Seq (-seq => $ure, -type => 'Dna');
  my($stream) = new Bio::Tools::IUPAC(-seq => $ambiseq);

  while($uniqueseq = $stream->next_seq()) {
    $seqstr = $uniqueseq->seq();
    print("$ure -> |$seqstr|
");
    ## process the unique Seq object.
    #
    @rAr = (@rAr, $seqstr);
  }
  return(@rAr);
}

when i feed it these two sequences, for example,
ANTTW
GGWAGGT

the print statement in the while loop outputs this:

ANTTW -> |ANTTW|
GGWAGGT -> |GGAAGGT|
GGWAGGT -> |GGTAGGT|

the fact that both strings go through the loop means they're being picked up, 
but i'd expect this 
kind of output:

ANTTW -> |AATTA|
ANTTW -> |ATTTA|
ANTTW -> |ACTTA|
ANTTW -> |AGTTA|
ANTTW -> |AATTT|
ANTTW -> |ATTTT|
ANTTW -> |ACTTT|
ANTTW -> |AGTTT|
GGWAGGT -> |GGAAGGT|
GGWAGGT -> |GGTAGGT|

I suspect this is an easy one, but i can't see where its going wrong.

many thanks IA
mark

From amackey at pcbi.upenn.edu  Wed Aug 18 11:33:56 2004
From: amackey at pcbi.upenn.edu (Aaron J. Mackey)
Date: Wed Aug 18 11:35:10 2004
Subject: [Bioperl-l] Bio::Tools::IUPAC inconsistency
Message-ID: <13AF62D4-F12C-11D8-9C37-000A9577009E@pcbi.upenn.edu>


The problem is that Bio::Tools::IUPAC doesn't know that your first 
sequence is DNA (it tries to guess, but guesses wrong).  Try setting 
-alphabet => "dna" in your Bio::Seq->new() call.

-Aaron

On Aug 18, 2004, at 11:03 AM, mql201 wrote:

> Hello
>
> I'm using the mod above.  I'm getting inconsistent output.  This fn, 
> which
> takes an ambiguous DNA
> sequence and returns an array of all the possible variants expanded 
> from IUPAC
> meta symbols:
>
> sub expandMeta {
>   my($uniqueseq);               # unique sequence object
>   my(@rAr) = ();                # return array
>   my($seqstr) = "";             # sequence attr of a sequence object
>
>   my($ure) = $_[0];           # upstream regulatory element (sequence 
> to
> check)
>
>   my($ambiseq) = new Bio::Seq (-seq => $ure, -type => 'Dna');
>   my($stream) = new Bio::Tools::IUPAC(-seq => $ambiseq);
>
>   while($uniqueseq = $stream->next_seq()) {
>     $seqstr = $uniqueseq->seq();
>     print("$ure -> |$seqstr|
");
>     ## process the unique Seq object.
>     #
>     @rAr = (@rAr, $seqstr);
>   }
>   return(@rAr);
> }
>
> when i feed it these two sequences, for example,
> ANTTW
> GGWAGGT
>
> the print statement in the while loop outputs this:
>
> ANTTW -> |ANTTW|
> GGWAGGT -> |GGAAGGT|
> GGWAGGT -> |GGTAGGT|
>
> the fact that both strings go through the loop means they're being 
> picked up,
> but i'd expect this
> kind of output:
>
> ANTTW -> |AATTA|
> ANTTW -> |ATTTA|
> ANTTW -> |ACTTA|
> ANTTW -> |AGTTA|
> ANTTW -> |AATTT|
> ANTTW -> |ATTTT|
> ANTTW -> |ACTTT|
> ANTTW -> |AGTTT|
> GGWAGGT -> |GGAAGGT|
> GGWAGGT -> |GGTAGGT|
>
> I suspect this is an easy one, but i can't see where its going wrong.
>
> many thanks IA
> mark
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  amackey@pcbi.upenn.edu
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697

From lstein at cshl.edu  Wed Aug 18 15:45:23 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Wed Aug 18 15:46:28 2004
Subject: [Bioperl-l] Re: Loading gff files into a MySQL database
In-Reply-To: <412362D8.1080707@irisa.fr>
References: <412362D8.1080707@irisa.fr>
Message-ID: <200408181545.23105.lstein@cshl.edu>

Hi Esther,

It sounds as though the version of bp_bulk_load_gff.pl that you are 
using is out of synch with the bioperl libraries.  Make sure that the 
Perl include path that you are using (as set with PERL5LIB 
environment variable) is pointing to the library files in 
bioperl-1.4.

Lincoln

On Wednesday 18 August 2004 10:08 am, Esther Kabore wrote:
> Hello,
> I have troubles when trying to load some gff files into my MySQL
> database via bp_bulk_load_gff or bp_fast_load_gff. Here is my
> command line:
> /db/gcgadmin/bioperl-1.4/scripts_temp/bp_bulk_load_gff.pl -d human
> XXI/NC_000021.gff
> And here is the error message I get back:
> Can't locate object method "split_group" via package "Bio::DB::GFF"
> at /db/gcgadmin/bioperl-1.4/scripts_temp/bp_bulk_load_gff.pl line
> 256, <> line 2
>
> Thank you for any help.
> Sincerely yours,
> Esther.

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
From barry.moore at genetics.utah.edu  Wed Aug 18 10:45:11 2004
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu Aug 19 09:07:06 2004
Subject: [Bioperl-l] help converting seq objects.
In-Reply-To: 
References: <45192F52-E66F-11D8-A804-000393BC20D0@research.dfci.harvard.edu>	<20040805134720.GD72520@iib.unsam.edu.ar>	
	
Message-ID: <41236B77.6090801@genetics.utah.edu>

Pedro,

If I understand you correctly you just want the entire script to run 
without the redundancy of writing the GB sequences to a file only to 
promptly reopen the file and read the sequences back in.  If so, you 
just need to delete a few lines of code and adjust your loops like this:

#!/usr/sbin/perl -w
# How to retrieve GenBank entries over the Web
# by Jason Stajich

use Bio::DB::GenBank;
use Bio::SeqIO;
use Bio::Seq;
use strict;

my $in = shift;
my @AC;

###### acc numbers from file to an array ##########
open (F, "$in") || die;
while(){
  next unless /(NM_\d+)\s/;
  my $acc = $1;
  chomp($acc);
  push @AC, $acc;
}
close(F);
my $list = join " ", @AC;
print "$list\n";

##### get genbank records  
#######################################################
my $gb = new Bio::DB::GenBank;
my $seqio = $gb->get_Stream_by_acc(\@AC);

###########get translation ############################################
my $temp = "$in.tfa";
my $out = new Bio::SeqIO(-file => ">$temp", -format => 'fasta');
while (my $seq = $seqio->next_seq ) {
  foreach my $f ( grep { $_->primary_tag eq 'CDS' } 
$seq->top_SeqFeatures ) {
    my ($gname);
    if ( $f->has_tag('gene') ) {
      ($gname) = $f->each_tag_value('gene');
    } elsif ( $f->has_tag('product') ) {
      ($gname) = $f->each_tag_value('product');
    }
    ($gname) =~ s/\s+/_/g;
    my ($ref) = $f->has_tag('protein_id') && 
$f->each_tag_value('protein_id');
    my ($gi) = $f->has_tag('db_xref') && $f->each_tag_value('db_xref');
    my ($translation) = $f->has_tag('translation') && 
$f->each_tag_value('translation');
    unless( $gi && $ref && $gname && $translation ) {
      print STDERR "not fully annotated CDS ($gi,$ref,$gname), 
skipping...\n";
      next;
    }
    my $tfa = Bio::PrimarySeq->new (-seq => $translation, -display_id =>
    sprintf("%s|%s|%s",$gi,$ref,$gname));
    $out->write_seq($tfa);
  }
}

From nathanhaigh at ukonline.co.uk  Wed Aug 18 12:22:07 2004
From: nathanhaigh at ukonline.co.uk (Nathan Haigh)
Date: Thu Aug 19 09:07:09 2004
Subject: [Bioperl-l] remote blast updates since BioPerl v1.4
Message-ID: 

Hi,



I've been using the modules in version 1.4 of BioPerl and noticed there
has been quite a few updates to SearchIO and remoteBlast. I was wondering
if they provide any additional functionality to those I'm using?



Also; this may be a trivial question but, is it possible to submit a
remoteBlast and retieve and print the results in a similar text format to
that used at NCBI?



Thanks

Nath



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From reche at research.dfci.harvard.edu  Wed Aug 18 09:49:44 2004
From: reche at research.dfci.harvard.edu (Pedro Antonio Reche)
Date: Thu Aug 19 09:07:14 2004
Subject: [Bioperl-l] help converting seq objects
Message-ID: <75EAFE94-F11D-11D8-B863-000393BC20D0@research.dfci.harvard.edu>

Hi all,
I have combined two scripts kindly provided by Jason Stajich to 1)  
Retrieve a list of seq records from genbank saving them in GenBank  
format; and 2)  get the translation feature from the file previously  
saved. The program -shown below- is works nicely, but I will nicer if I  
could parse the sequence object obtained from the GenBank database  
without printing  it. Does anyone knows how to do this? Thanks in  
advance for any help.

use Bio::DB::GenBank;
use Bio::SeqIO;
use Bio::Seq;

$in = shift @ARGV;

###### acc numbes from file an array ##########
open (F, "$in") || die;
while(){
         next unless /(NM_\d+)\s/;
         $acc = $1;
         chomp($acc);
         push @AC, $acc;
}
close(F);
$list = join " ", @AC;
print "$list\n";

##### get genbank records into a file  
#######################################################
my $gb = new Bio::DB::GenBank;
my $seqio = $gb->get_Stream_by_acc(\@AC);
my $seqout = new Bio::SeqIO(-file => ">$in.gb", -format => 'GenBank');
#my $seqout = new Bio::SeqIO(-file => ">$ARGV[0].gb", -format =>  
'GenBank');
while( defined ($seq = $seqio->next_seq )) {
         $seqout->write_seq($seq);
}
###########get translation from file just created  
############################################
my $tmp  = "$in.gb";
my $temp = "$in.tfa";

my $in = new Bio::SeqIO(-file => "<$tmp", -format => 'genbank');
my $out = new Bio::SeqIO(-file => ">$temp", -format => 'fasta');
while ($seq = $in->next_seq ) {
         foreach my $f ( grep { $_->primary_tag eq 'CDS' }  
$seq->top_SeqFeatures ) {
                 my ($gname);
                 if ( $f->has_tag('gene') ) {
                         ($gname) = $f->each_tag_value('gene');
                 } elsif ( $f->has_tag('product') ) {
                         ($gname) = $f->each_tag_value('product');
                 }
                 ($gname) =~ s/\s+/_/g;
                 my ($ref) = $f->has_tag('protein_id') &&  
$f->each_tag_value('protein_id');
                 my ($gi)  = $f->has_tag('db_xref') &&  
$f->each_tag_value('db_xref');
                 my ($translation) = $f->has_tag('translation') &&  
$f->each_tag_value('translation');
                 unless( $gi && $ref && $gname && $translation ) {
                         print STDERR "not fully annotated CDS  
($gi,$ref,$gname), skipping...\n";
                         next;
                 }
                 my $tfa = Bio::PrimarySeq->new (-seq => $translation,  
-display_id =>
                                 sprintf("%s|%s|%s",$gi,$ref,$gname));
                         $out->write_seq($tfa);
     }
}

======================================================================== 
=====================
Dr. Pedro A Reche, Instructor of Medicine
Dana-Farber Cancer Institute, Harvard Medical School                     
      TL: 617 632 3824
HIM Building, Room 401                                                   
      FX: 617 632 3351
77 Avenue Louis Pasteur                                   EM:  
reche@research.dfci.harvard.edu
Boston, MA 02115, USA                                                 
W3: www.mifoundation.org
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From shachar at compugen.co.il  Thu Aug 19 11:00:44 2004
From: shachar at compugen.co.il (Shachar Zehavi)
Date: Thu Aug 19 15:50:01 2004
Subject: [Bioperl-l] Implementing standalone Smith Waterman analysis using
	BioPerl interfaces.
Message-ID: 

Hello.

This is a newbie question...

I would like to implement a local Smith Waterman service and I don't really know which interfaces to use.

I saw that both Bio::Tools::Run::StandAloneBlast  and Bio::Tools::Run::Alignment::StandAloneFasta
inherit from Bio::Tools::Run::WrapperBase, but as far as I can understand some of the analysis running interface (parameters definition etc.) is defined in 
Bio::AnalysisI interface.

Is there a good example I can look at and learn from?

Thanks in advance,
Shachar.

Shachar Zehavi
Computational Medicine Infrastructure Team leader,
Compugen Ltd.
72 Pinchas Rosen, Tel Aviv 69512, Israel
------------------------------------
Tel: +972-3-765-8585
Direct: +44-(115)-877-0971 or +972-3-765-8543
Mobile: +44-(786)-791-2048
Fax: +972-3-765-8555
E-mail: shachar@compugen.co.il
Website: http://www.cgen.com

 
 <> 
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From hlapp at gnf.org  Thu Aug 19 15:51:19 2004
From: hlapp at gnf.org (Hilmar Lapp)
Date: Thu Aug 19 15:52:17 2004
Subject: [Bioperl-l] Re: [BioSQL-l] Swissprot Problems
In-Reply-To: <41246723.6080708@mrc-lmb.cam.ac.uk>
References: <41230ADB.60707@informatik.hu-berlin.de>
	<41246723.6080708@mrc-lmb.cam.ac.uk>
Message-ID: <239FAD60-F219-11D8-AD45-000A95AE92B0@gnf.org>

Thanks, this is helpful. So it appears we need to add recognition of  
the RG line to the swissprot SeqIO parser. I just committed a fix to  
the main trunk. There should be a test as well, didn't have the time  
yet - everybody feel free to step in. I also added code to deal with  
this on writing out and therefore also to Bio::Annotation::Reference.

I was being lazy and didn't check the manual myself, and sure enough  
paid the price ...

	-hilmar

On Aug 19, 2004, at 1:38 AM, Dave Howorth wrote:

> Raphael A. Bauer wrote:
>> just an interesting thing from Swiss-Prot:
>> If we want to load the latest Swiss-Prot flatfile with
>> load_seqdatabase.pl we get the following error (normally our
>> load_seqdatabase.pl works fine):
>> -------------------- WARNING ---------------------
>> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
>> values
>> were
>> ("",""A multicenter comparison of methods for typing strains of  
>> Pseudomonas
>> aeruginosa predominantly from patients with cystic fibrosis."","J.  
>> Infect.
>> Dis. 169:134-142(1994).","CRC-237261AF859664D3","","") FKs (613823)
>> ERROR:  null value in column "authors" violates not-null constraint
>> ---------------------------------------------------
>> Could not store Q53391:
>> ------------- EXCEPTION  -------------
>> ...
>> And that is what I would expect, because Q53391 has no RA line.
>> The Swiss-Prot manual says:
>> RG    Reference group    Once or more (Optional if RA line)   RA     
>> Reference authors    Once or more (Optional if RG line)
>> ...
>> ...
>> so I don't know how one can deal with this, because it is a clear
>> violation of the Swiss-Prot manual statements and therefore a  
>> violation
>> of the BioSQL schema definition (authors NOT NULL)...
>> We will remove the NOT NULL statements from the authors line in the
>> BioSQL schema to deal with this..
>
> Hilmar Lapp replied:
> >> We will remove the NOT NULL statements from the authors line in the
> >> BioSQL schema to deal with this..
> > Yep, I'll do this in the repository too.
>
>
> I'm a little confused by this. I'm interested in learning a bit about  
> these entries so I went to browse the entry  
>  proteinId=FMK7_PSEAE&pager.offset=0>
> The relevant section seems to be:
>
> RN   [1]
> RP   SEQUENCE FROM N.A.
> RC   STRAIN=KB7;
> RX   MEDLINE=94103636; PubMed=7903973;
> RG   INTERNATIONAL PSEUDOMONAS AERUGINOSA TYPING STUDY GROUP;
> RT   "A multicenter comparison of methods for typing strains of  
> Pseudomonas
> RT   aeruginosa predominantly from patients with cystic fibrosis.";
> RL   J. Infect. Dis. 169:134-142(1994).
>
> Then I went to the user manual  
>  where the relevant  
> text seems to be:
>
>     3.10.5. The RG line
>
> The Reference Group (RG) line lists the consortium name associated  
> with a given citation. The RG line is mainly used in submission  
> reference blocks, but can also be used in paper references, if the  
> working group is cited as an author in the paper. RG line and RA line  
> (Reference Author) can be present in the same reference block; at  
> least one RG or RA line is mandatory per reference block. An example  
> of the use of RG lines is shown below:
>
> RG   The mouse genome sequencing consortium;
>
>     3.10.6. The RA line
>
> The RA (Reference Author) lines list the authors of the paper (or  
> other work) cited. The RA line is present in most references, but  
> might be missing in references that cite a reference group (see RG  
> line). At least one RG or RA line is mandatory per reference block.
> --------------------
>
> So it seems to me that the record is valid according to the spec and  
> records do not need to have an RA line if they do have an RG line. It  
> is probably appropriate to use the value of the RG field as the  
> authors field in the database. Or am I missing something?
>
>
> >> Any better ideas?
> > No. There's not much you can do if people violate their own specs.
>
> There is another possible way to deal with errant records that violate  
> the spec. That is to maintain an exception dictionary. That is, for  
> each record that would fail validation, make a curated patch that can  
> be applied to the record before validation. Clearly this can be a lot  
> of work unless the initial record quality is already high. Submitting  
> the exceptions back to the originating institution is good to do as  
> well :)
>
> Cheers, Dave
> -- 
> Dave Howorth
> MRC Centre for Protein Engineering
> Hills Road, Cambridge, CB2 2QH
> 01223 252960
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l@open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

From barry.moore at genetics.utah.edu  Thu Aug 19 16:47:42 2004
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu Aug 19 16:48:25 2004
Subject: [Bioperl-l] Mapping related accession numbers
Message-ID: <412511EE.5080901@genetics.utah.edu>

I guess this is a bit off topic since the solution likely won't involve 
BioPerl, but hopefully you'll let me slide this time.  Given a RefSeq 
protein sequence (NP_ or XP_) I want to get the associated nucleotide 
sequence (NM_ or XM_).  Does anyone know of a file I can download that 
already has that mapped?

Barry

-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT



From barry.moore at genetics.utah.edu  Thu Aug 19 17:21:59 2004
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Thu Aug 19 17:22:46 2004
Subject: [Bioperl-l] Implementing standalone Smith Waterman analysis using
	BioPerl interfaces.
In-Reply-To: 
References: 
Message-ID: <412519F7.5090206@genetics.utah.edu>

Shachar-

The Bio::Factory::EMBOSS module has some documentation and happily for 
you the example they give is the for the program water which is a 
Smith-Waterman local alignment tool.

http://doc.bioperl.org/bioperl-run/Bio/Factory/EMBOSS.html

Barry

Shachar Zehavi wrote:

>Hello.
>
>This is a newbie question...
>
>I would like to implement a local Smith Waterman service and I don't really know which interfaces to use.
>
>I saw that both Bio::Tools::Run::StandAloneBlast  and Bio::Tools::Run::Alignment::StandAloneFasta
>inherit from Bio::Tools::Run::WrapperBase, but as far as I can understand some of the analysis running interface (parameters definition etc.) is defined in 
>Bio::AnalysisI interface.
>
>Is there a good example I can look at and learn from?
>
>Thanks in advance,
>Shachar.
>
>Shachar Zehavi
>Computational Medicine Infrastructure Team leader,
>Compugen Ltd.
>72 Pinchas Rosen, Tel Aviv 69512, Israel
>------------------------------------
>Tel: +972-3-765-8585
>Direct: +44-(115)-877-0971 or +972-3-765-8543
>Mobile: +44-(786)-791-2048
>Fax: +972-3-765-8555
>E-mail: shachar@compugen.co.il
>Website: http://www.cgen.com
>
> 
> <> 
>  
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT



From birney at ebi.ac.uk  Thu Aug 19 19:11:40 2004
From: birney at ebi.ac.uk (Ewan Birney)
Date: Thu Aug 19 19:12:19 2004
Subject: [Bioperl-l] orthologous genes extracting
In-Reply-To: 
Message-ID: 



On Mon, 16 Aug 2004, Nathan (Nat) Goodman wrote:

> Paulo said:
> > I have been using Ensmart, Ensembl's web interface for batch retrieval,
> > at http://www.ensembl.org/Multi/martview
> > I think their orthologues are based on reciprocal BLASTs and sometimes
> > also on synteny and whole genome alignment data.
>
> Thanks.  I've seen problems with Ensembl similar to those with HomoloGene,
> but as I look through my notes, these may have been pathological cases.  For
> example, mouse Casp1 points to two human othologs, CASP1 and COP.  CASP1 is
> a biologically validated ortholog, but COP is pretty similar and adjacent to
> CASP1.
>
> I'm wondering if anyone has combined a curated data source, eg, MGD, with
> computed results to avoid cases like this.

We would like to do this Nat in the future, and looking into improving our
automated procedures as well.



>
> Looking at the bigger picture, I see a need for "orthology" maps at various
> levels of stringency.  What I'm discussing here is the most stringent case
> in which we try hard to assign 1 ortholog per species to each gene.  (I
> realize the issue is biologically complex and this simple notion will fail
> for biological reasons in many cases, which is why I'm hoping someone else
> has already solved the problem :)  It would be nice to also offer more
> permissive maps including ones based entirely on sequence similarity.
>
> Best,
> Nat
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

From smarkel at scitegic.com  Thu Aug 19 21:28:38 2004
From: smarkel at scitegic.com (Scott Markel)
Date: Thu Aug 19 21:30:30 2004
Subject: [Bioperl-l] problem setting -find option for EMBOSS getorf
Message-ID: <412553C6.5030700@scitegic.com>

I'm using BioPerl 1.4 on a Windows XP box, with EMBOSS version
2.7.1-Win-0.6.  I think my problem is with run() in
Bio::Tools::Run::EMBOSSApplication.  When I set the -find
option to 1 in the anonymous hash for $application->run()'s
argument list using

   "-find"       => $::findOptionID,

everything is fine, i.e., the command line looks like

   ... -find 1 -circular Yes ...

When the -find option is set to 0, the value never makes
it to the command line and I get

   ... -find -circular Yes ...

which clearly upsets getorf.

A quick work-around is to prepend a space to -find's value.

I checked the Open-Bio Bug Database and didn't find this
problem.  Anyone seen this before?

Scott

-- 
Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel@scitegic.com
SciTegic Inc.                       mobile: +1 858 205 3653
9665 Chesapeake Drive, Suite 401    voice:  +1 858 279 8800, ext. 253
San Diego, CA 92123                 fax:    +1 858 279 8804
USA                                 web:    http://www.scitegic.com

From ls_work at covad.net  Fri Aug 20 18:22:48 2004
From: ls_work at covad.net (Lee Sam)
Date: Fri Aug 20 18:23:38 2004
Subject: [Bioperl-l] Bio::Graphics : Switching Glyph Colors On One Track
Message-ID: <000d01c48704$3b554740$e200a8c0@apartment.leesam.net>

Is there a way to change the glyph fillcolor and the bump option once the
track has been added? I'm trying to draw glyphs one top of other glyphs
(HSPs on top of genes in my case).

From tex at biosysadmin.com  Fri Aug 20 03:08:38 2004
From: tex at biosysadmin.com (James Thompson)
Date: Fri Aug 20 19:21:50 2004
Subject: [Bioperl-l] Trans-Splicing Coding Sequences
Message-ID: 

Dear Bioperlers,

I'm currently working on a project involving some trans-spliced coding sequences
from Arabidopsis, and I was wondering if BioPerl provided an easy way of taking a
trans-spliced CDS feature and correctly splicing it into a Bio::Seq object.

Here's my naive stab at doing this using the Bioperl methods that I know:

use strict;
use Bio::SeqIO;

my $seqio = Bio::SeqIO->new( -file => 'NC_001284.gbk', -format => 'genbank' );
my $genome = $seqio->next_seq;

foreach my $cds (grep { $_->primary_tag =~ /CDS/i } $genome->get_SeqFeatures) {
   print $cds->start, " -> ", $cds->end, "\n";
   print $cds->spliced_seq->translate->seq, "\n";

   last;
}

This just tries to use the spliced_seq method to splice the CDS into a sequence,
and here's the output:

79740 -> 333105
LFHDLWVYWSYPLRSISQDFDRIRNHWCSI*WYFYGDSVYRCRIPIQDHCSSFSYVGTRYL*GFTHPGYSIPFYCA*NLYFC
*YFTCFYLWFLWSYIATNLLFLQHCFYDLRSTGRHGPNESQKTSSS*FNWTCRLYSYWFLMWNHRRNSITTNWYLYLCINDD
GCIRHSFSITANPCQIYSGFGRSSQNESYFGYYLLHYYVLIRRNTPVSRLL*QILFVLRRFGLWGLLSSPSGSSD*RYRSFL
LYTLSEKNVF*YT*DMDSI*TNGS**VVTTSNDFLFHYFILAIPLSFVLSYSSNGTQFISLNESRIRSDPPTHVQSFFSGFP
RDLYH*CNLHFAHSWSCI*YL*EI*LSAVSQ*CGLAWIT*CSNNLASARRWRTSPNYCPFILE*SF*EGQFYIFLPNLSIIK
YGWYHFDVFRFFRPREV*CF*IHCINSTSYSRYALYDLGS*FNCHVFSY*ASKFMFLCNRSIKKKV*IFHGSRLEIFDLRCI
FLWNIIVW

The translated sequence for this coding sequence should look like this:

MKAEFVRILPHMFNLFLAVSPEIFIINATSILLIHGVVFSTSKK
YDYPPLASNVGWLGLLSVLITLLLLAAGAPLLTIAHLFWNNLFRRDNFTYFCQIFLLL
STAGTISMCFDSSDQERFDAFEFIVLIPLPTRGMLFMISAHDLIAMYLAIEPQSLCFY
VIAASKRKSEFSTEAGSKYLILGAFSSGILLFGCSMIYGSTGATHFDQLAKILTGYEI
TGARSSGIFMGILSIAVGFLFKITAVPFHMWAPDIYEGSPTPVTAFLSIAPKISISAN
ILRVSIYGSYGATLQQIFFFCSIASMILGALAAMAQTKVKRPLAHSSIGHVGYIRTGF
SCGTIEGIQSLLIGIFIYALMTMDAFAIVSALRQTRVKYIADLGALAKTNPISAITFS
ITMFSYAGIPPLAGFCSKFYLFFAALGCGAYFLAPVGVVTSVIGRFYYIRLVKRMFFD
TPRTWILYEPMDRNKSLLLAMTSFFITSSLLYPSPLFSVTHQMALSSYL

I'm guessing that the spliced_seq method in Bio::SeqFeatureI isn't correctly
recognizing the Location definition for this coding sequence, which looks like this:
CDS             complement(join(327890..328078,329735..330306,
                332945..333105,79740..80132,81113..81297))

Could anyone help me shed any light on this? Ideally I'd like to translate all
of these CDS features into individual Bio::Seq objects for further analysis,
and I thought I'd ask for a bit of help before I wrote my own parser. Should I
try sub-classing Bio::SeqFeature to overwrite the spliced_seq method, or has
someone else already figured out this problem? Any suggestions would be very
helpful.

Thanks, 

James Thompson

From lstein at cshl.edu  Sat Aug 21 13:45:58 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Sat Aug 21 13:46:42 2004
Subject: [Bioperl-l] Bio::Graphics : Switching Glyph Colors On One Track
In-Reply-To: <000d01c48704$3b554740$e200a8c0@apartment.leesam.net>
References: <000d01c48704$3b554740$e200a8c0@apartment.leesam.net>
Message-ID: <200408211345.58383.lstein@cshl.edu>

Yes, you can change any of the options up to the time that you render 
the image or its imagemap using the track configure() method:

	$track->configure(-bgcolor=>'blue');

The documentation for this is a mite hard to find.  It's in the 
Bio::Graphics::Glyph manual page, and it's there because the tracks 
are actually glyphs themselves.

Lincoln


On Friday 20 August 2004 06:22 pm, Lee Sam wrote:
> Is there a way to change the glyph fillcolor and the bump option
> once the track has been added? I'm trying to draw glyphs one top of
> other glyphs (HSPs on top of genes in my case).
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
From yousef at cs.haifa.ac.il  Sat Aug 21 22:50:14 2004
From: yousef at cs.haifa.ac.il (Yousef Malik)
Date: Sat Aug 21 22:50:56 2004
Subject: [Bioperl-l] (RNAfold)Convert bracktes structure to aligned like
	tructure
In-Reply-To: 
References: 
Message-ID: 


  Hi
  I would like to get your help on the following problem:
  How could one convert the output of RNAfold within the brackets structure
  GGCCAGUGUUGAGAGGCGGAGACUUGGGCAAUUGCUGGACGCUGCCCUGGGCAUUGCACUUGUCUCGGUCUGACAGUGCCGGCC
  ((((.((..((..((((.(((((..(((((((.(((((.......))..)))))))).)).))))).))))..))..)).))))
  (-36.00)

  To aligned like structure:
     A UG   AG    G     UU G     U   --  AC
  GGCC G  UUG  AGGC GAGAC  G GCAAU GCU  GG  G
  |||| |  |||  |||| |||||  | ||||| |||  ||  C
  CCGG C  GAC  UCUG CUCUG  C CGUUA CGG  CC  U
     C GU   AG    G     UU A     -   GU  CG

  Please reply to yousef@cs.haifa.ac.il
  Reagrds
  Malik

From lstein at cshl.edu  Fri Aug 20 10:18:31 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Sun Aug 22 03:38:29 2004
Subject: [Bioperl-l] New glyphs in bio::graphics
Message-ID: <200408201018.31703.lstein@cshl.edu>

Hi All,

This is a quick note to let everyone know that "Vsevolod (Simon) 
Ilyushchenko"  has just contributed a whole set of 
new Bio::Graphics glyphs that could be useful for high-magnification 
images.  The design for these glyphs comes from Mari Watanabe of HGC 
Japan.

The glyphs are available in the CVS version of bioperl.

Have fun!

Lincoln

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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From neilc at cmu.edu  Fri Aug 20 15:42:10 2004
From: neilc at cmu.edu (Neil C. Christopher)
Date: Sun Aug 22 03:38:52 2004
Subject: [Bioperl-l] Bioperl Blast
Message-ID: <32952.128.237.244.179.1093030930.squirrel@128.237.244.179>

I was wondering if the Blast API is up to date?  Does it work with the current blast?

Please let me know ASAP.

Thanks,

Neil Christopher

From rfsouza at citri.iq.usp.br  Fri Aug 20 11:06:04 2004
From: rfsouza at citri.iq.usp.br (Robson Francisco de Souza {S})
Date: Sun Aug 22 03:39:20 2004
Subject: [Bioperl-l] Mapping related accession numbers
In-Reply-To: <412511EE.5080901@genetics.utah.edu>
References: <412511EE.5080901@genetics.utah.edu>
Message-ID: <20040820150604.GB32138@cecm.usp.br>

Hi Barry,

On Thu, Aug 19, 2004 at 02:47:42PM -0600, Barry Moore wrote:
> I guess this is a bit off topic since the solution likely won't involve 
> BioPerl, but hopefully you'll let me slide this time.  Given a RefSeq 
> protein sequence (NP_ or XP_) I want to get the associated nucleotide 
> sequence (NM_ or XM_).  Does anyone know of a file I can download that 
> already has that mapped?

To my knowledge, The most complete source for such data is the NCBI Gene
database, accessible both through the Entrez interface and ftp. The file
you are interested in is

ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz

Robson

> Barry
> 
> -- 
> Barry Moore
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
From yousef at cs.haifa.ac.il  Sat Aug 21 19:22:10 2004
From: yousef at cs.haifa.ac.il (Yousef Malik)
Date: Sun Aug 22 03:39:42 2004
Subject: [Bioperl-l] (RNAfold)Convert bracktes structure to aligned like
	tructure
Message-ID: 

Hi
I would like to get your help on the following problem:
How could one convert the output of RNAfold within the brackets structure 
GGCCAGUGUUGAGAGGCGGAGACUUGGGCAAUUGCUGGACGCUGCCCUGGGCAUUGCACUUGUCUCGGUCUGACAGUGCCGGCC
((((.((..((..((((.(((((..(((((((.(((((.......))..)))))))).)).))))).))))..))..)).)))) 
(-36.00)

To aligned like structure:
     A UG   AG    G     UU G     U   --  AC
GGCC G  UUG  AGGC GAGAC  G GCAAU GCU  GG  G
|||| |  |||  |||| |||||  | ||||| |||  ||  C
CCGG C  GAC  UCUG CUCUG  C CGUUA CGG  CC  U
     C GU   AG    G     UU A     -   GU  CG

Please reply to yousef@cs.haifa.ac.il
Reagrds
Malik

From jason at cgt.duhs.duke.edu  Sun Aug 22 03:46:35 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Sun Aug 22 03:47:55 2004
Subject: [Bioperl-l] remote blast updates since BioPerl v1.4
In-Reply-To: 
References: 
Message-ID: 

I guess newer is better - I don't remember what was added to be honest but
you can look at the code changes via CVS diffs.  I don't remember when we
had to fix the change in NCBI API for the name of the UID but that might
be new.

-jason
On Wed, 18 Aug 2004, Nathan Haigh wrote:

> Hi,
>
>
>
> I've been using the modules in version 1.4 of BioPerl and noticed there
> has been quite a few updates to SearchIO and remoteBlast. I was wondering
> if they provide any additional functionality to those I'm using?
>
>
>
> Also; this may be a trivial question but, is it possible to submit a
> remoteBlast and retieve and print the results in a similar text format to
> that used at NCBI?
>
>
>
> Thanks
>
> Nath
>
>
>
> ---
> avast! Antivirus: Outbound message clean.
> Virus Database (VPS): 0434-1, 17/08/2004
> Tested on: 18/08/2004 17:21:29
> avast! is copyright (c) 2000-2003 ALWIL Software.
> http://www.avast.com
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From jason at cgt.duhs.duke.edu  Sun Aug 22 03:46:53 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Sun Aug 22 03:48:17 2004
Subject: [Bioperl-l] Trans-Splicing Coding Sequences
In-Reply-To: 
References: 
Message-ID: 

The problem is that we sort the order of the locations in the calling of
spliced_seq at around line 697 in Bio::SeqFeatureI so all you need to do
remove the sorting - if you want to add an optional 3rd argument to this
method which when true does not try and sort the sub locations.  Make
sense?  If it works, post a patch and we'll incorporate it.

-jason

 On Fri, 20 Aug 2004, James Thompson wrote:

> Dear Bioperlers,
>
> I'm currently working on a project involving some trans-spliced coding sequences
> from Arabidopsis, and I was wondering if BioPerl provided an easy way of taking a
> trans-spliced CDS feature and correctly splicing it into a Bio::Seq object.
>
> Here's my naive stab at doing this using the Bioperl methods that I know:
>
> use strict;
> use Bio::SeqIO;
>
> my $seqio = Bio::SeqIO->new( -file => 'NC_001284.gbk', -format => 'genbank' );
> my $genome = $seqio->next_seq;
>
> foreach my $cds (grep { $_->primary_tag =~ /CDS/i } $genome->get_SeqFeatures) {
>    print $cds->start, " -> ", $cds->end, "\n";
>    print $cds->spliced_seq->translate->seq, "\n";
>
>    last;
> }
>
> This just tries to use the spliced_seq method to splice the CDS into a sequence,
> and here's the output:
>
> 79740 -> 333105
> LFHDLWVYWSYPLRSISQDFDRIRNHWCSI*WYFYGDSVYRCRIPIQDHCSSFSYVGTRYL*GFTHPGYSIPFYCA*NLYFC
> *YFTCFYLWFLWSYIATNLLFLQHCFYDLRSTGRHGPNESQKTSSS*FNWTCRLYSYWFLMWNHRRNSITTNWYLYLCINDD
> GCIRHSFSITANPCQIYSGFGRSSQNESYFGYYLLHYYVLIRRNTPVSRLL*QILFVLRRFGLWGLLSSPSGSSD*RYRSFL
> LYTLSEKNVF*YT*DMDSI*TNGS**VVTTSNDFLFHYFILAIPLSFVLSYSSNGTQFISLNESRIRSDPPTHVQSFFSGFP
> RDLYH*CNLHFAHSWSCI*YL*EI*LSAVSQ*CGLAWIT*CSNNLASARRWRTSPNYCPFILE*SF*EGQFYIFLPNLSIIK
> YGWYHFDVFRFFRPREV*CF*IHCINSTSYSRYALYDLGS*FNCHVFSY*ASKFMFLCNRSIKKKV*IFHGSRLEIFDLRCI
> FLWNIIVW
>
> The translated sequence for this coding sequence should look like this:
>
> MKAEFVRILPHMFNLFLAVSPEIFIINATSILLIHGVVFSTSKK
> YDYPPLASNVGWLGLLSVLITLLLLAAGAPLLTIAHLFWNNLFRRDNFTYFCQIFLLL
> STAGTISMCFDSSDQERFDAFEFIVLIPLPTRGMLFMISAHDLIAMYLAIEPQSLCFY
> VIAASKRKSEFSTEAGSKYLILGAFSSGILLFGCSMIYGSTGATHFDQLAKILTGYEI
> TGARSSGIFMGILSIAVGFLFKITAVPFHMWAPDIYEGSPTPVTAFLSIAPKISISAN
> ILRVSIYGSYGATLQQIFFFCSIASMILGALAAMAQTKVKRPLAHSSIGHVGYIRTGF
> SCGTIEGIQSLLIGIFIYALMTMDAFAIVSALRQTRVKYIADLGALAKTNPISAITFS
> ITMFSYAGIPPLAGFCSKFYLFFAALGCGAYFLAPVGVVTSVIGRFYYIRLVKRMFFD
> TPRTWILYEPMDRNKSLLLAMTSFFITSSLLYPSPLFSVTHQMALSSYL
>
> I'm guessing that the spliced_seq method in Bio::SeqFeatureI isn't correctly
> recognizing the Location definition for this coding sequence, which looks like this:
> CDS             complement(join(327890..328078,329735..330306,
>                 332945..333105,79740..80132,81113..81297))
>
> Could anyone help me shed any light on this? Ideally I'd like to translate all
> of these CDS features into individual Bio::Seq objects for further analysis,
> and I thought I'd ask for a bit of help before I wrote my own parser. Should I
> try sub-classing Bio::SeqFeature to overwrite the spliced_seq method, or has
> someone else already figured out this problem? Any suggestions would be very
> helpful.
>
> Thanks,
>
> James Thompson
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From jason at cgt.duhs.duke.edu  Sun Aug 22 03:47:06 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Sun Aug 22 03:48:26 2004
Subject: [Bioperl-l] problem setting -find option for EMBOSS getorf
In-Reply-To: <412553C6.5030700@scitegic.com>
References: <412553C6.5030700@scitegic.com>
Message-ID: 

I seem to think we already fixed this post 1.4 for you -- are you using
code from bioperl-run which is the most recent from CVS?
I don't seem to have a problem.

$ perl test_getorf.pl
Command line: getorf  -sequence /tmp/9ZnCEdDyL3/gid4fZXSrb -find 0 -auto

code:
 my $app = $f->program('getorf');
 $app->run({'-find' => 0,
	   '-sequence' => $seq});



-jason


On Thu, 19 Aug 2004, Scott Markel wrote:

> I'm using BioPerl 1.4 on a Windows XP box, with EMBOSS version
> 2.7.1-Win-0.6.  I think my problem is with run() in
> Bio::Tools::Run::EMBOSSApplication.  When I set the -find
> option to 1 in the anonymous hash for $application->run()'s
> argument list using
>
>    "-find"       => $::findOptionID,
>
> everything is fine, i.e., the command line looks like
>
>    ... -find 1 -circular Yes ...
>
> When the -find option is set to 0, the value never makes
> it to the command line and I get
>
>    ... -find -circular Yes ...
>
> which clearly upsets getorf.
>
> A quick work-around is to prepend a space to -find's value.
>
> I checked the Open-Bio Bug Database and didn't find this
> problem.  Anyone seen this before?
>
> Scott
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From yinyb at mail.cbi.pku.edu.cn  Sun Aug 22 09:26:17 2004
From: yinyb at mail.cbi.pku.edu.cn (Yin Yanbin)
Date: Sun Aug 22 09:24:24 2004
Subject: [Bioperl-l] ensembl modules
References: <412553C6.5030700@scitegic.com>
	
Message-ID: <000f01c4884b$9b7690a0$cefa69a2@cbiyinyb>

Hello,

How can I use Refseq protein IDs or UniProt IDs or GenBank IDs to extract the corresponding Ensembl genes? 

Thanks!

Yanbin

From birney at ebi.ac.uk  Sun Aug 22 09:45:53 2004
From: birney at ebi.ac.uk (Ewan Birney)
Date: Sun Aug 22 09:46:24 2004
Subject: [Bioperl-l] ensembl modules
In-Reply-To: <000f01c4884b$9b7690a0$cefa69a2@cbiyinyb>
Message-ID: 



On Sun, 22 Aug 2004, Yin Yanbin wrote:

> Hello,
>
> How can I use Refseq protein IDs or UniProt IDs or GenBank IDs to
> extract the corresponding Ensembl genes?

the best thing is to check on Mart at

http://www.ensembl.org/Multi/martview

Then select "human, Ensembl genes" as a focus, unselect the genome
restriction on the filter (so it is genome wide) and select the ID-filter,
using RefSeq IDs. Then in output you can get all manner of outputs.


If you want to write a program, then using either the Ensembl APIs - for a
starting point look

http://www.ensembl.org/Docs/

in either Java or Perl will work or try out the Mart Java API and
command-line "shell"

http://www.ebi.ac.uk/biomart/index.html

Finally you can you MySQL drivers directly against ensembldb.ensembl.org
if these APIs are not to your taste.


If you get stuck, do get in touch with our helpdesk at:

http://www.ensembl.org/helpdesk/







>
> Thanks!
>
> Yanbin
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

From lstein at cshl.edu  Mon Aug 23 11:21:27 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon Aug 23 11:22:15 2004
Subject: [Bioperl-l] is Bio::Graphics::Glyph::line supposed to draw
	description?
In-Reply-To: <898EB90C-E9C7-11D8-9BDB-000D93AF7910@fruitfly.org>
References: <898EB90C-E9C7-11D8-9BDB-000D93AF7910@fruitfly.org>
Message-ID: <200408231121.27949.lstein@cshl.edu>

Sorry it took so long for me to respond to this.  This seems to be an 
oversight.  Please go ahead and commit the obvious fix if someone 
hasn't done so already.

Lincoln

On Monday 09 August 2004 01:47 am, ben berman wrote:
> I was trying to draw a description string with the
> Bio::Graphics::Glyph::line glyph, but it doesn't seem to work.  I
> checked the latest version (1.5) , and the draw() function is as
>
> follows:
> > sub draw {
> >   my $self = shift;
> >   my $gd = shift;
> >   my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_);
> >
> >   my $fg = $self->fgcolor;
> >   my $a2 = $self->SUPER::height/2;
> >   my $center = $y1+$a2;
> >
> >   $gd->line($x1,$center,$x2,$center,$fg);
> >   # add a label if requested
> >   $self->draw_label($gd,@_) if $self->option('label');
> >
> > }
>
> The arrow glyph, which does seem to implement the description
> string
>
> correctly, has the following:
> >   # add a label if requested
> >   $self->draw_label($gd,$dx,$dy)       if $self->option('label');
> >   $self->draw_description($gd,$dx,$dy) if
> > $self->option('description'); }
>
> Is this omission by design?  Based on the documentation for
> Panel::add_track, i kind of expected all glyphs to implement this
> if possible.
>
> i would commit the change myself, but i want to be cautious since
> i'm not an active contributor.
>
> thanks,
> ben.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
From lstein at cshl.edu  Mon Aug 23 11:37:55 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon Aug 23 11:38:47 2004
Subject: [Bioperl-l] identifying objects in Bio::Graphics SVG
In-Reply-To: 
References: 
Message-ID: <200408231137.55954.lstein@cshl.edu>

Following up on this old email message, I've placed this on the TODO 
list.

Lincoln

On Friday 06 August 2004 02:20 pm, Crabtree, Jonathan wrote:
> Hi Steve-
>
> I looked into this briefly and I'm pretty sure that the answer is
> "no". The way that the Bio::Graphics module generates SVG output is
> by using GD::SVG, which is more or less a drop-in replacement for
> GD.  Since the GD API doesn't require (or permit, AFAIK) the
> association of logical identifiers with graphics primitives (e.g.,
> these four lines are part of exon #1234), this information isn't
> included in the GD API calls and therefore isn't available to
> GD::SVG.  So even if GD::SVG wanted to group the various elements
> within an SVG roup, it doesn't have any way of gleaning the
> necessary information without going beyond the GD API.
>
> Now of course this isn't to say that it wouldn't be possible to
> implement this type of functionality, but it would require making
> Bio::Graphics somewhat more SVG-aware than it is now, and would
> probably entail delving into the workings of GD::SVG a little bit. 
> I can also imagine taking a somewhat heavyweight approach that
> would be relatively inefficient but might be easier to implement. 
> One could conceivably make a fresh GD::SVG object for each glyph to
> be rendered, and then add some code to Bio::Graphics to strip out
> the essential SVG rendered by each glyph, wrap it in a  element,
> and place it into a dummy top-level GD::SVG object that serves only
> to collect the text of the SVG document.  I don't know...at some
> point it's going to be easier to just go ahead and add direct SVG
> support into Bio::Graphics.
>
> Jonathan
>
> p.s. Re-reading your original message, it might be possible to do
> something using the bounding box of the feature of interest (which
> can be obtained from the Bio::Graphics panel) to search through the
> SVG text for the relevant section.  It would be messy, though, and
> rather indirect.
>
> > -----Original Message-----
> > From: bioperl-l-bounces@portal.open-bio.org
> > [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of
> > Roels, Steven
> > Sent: Friday, August 06, 2004 1:49 PM
> > To: bioperl-l@bioperl.org
> > Subject: [Bioperl-l] identifying objects in Bio::Graphics SVG
> >
> >
> >
> > Hello,
> >
> > I'd like to take the nice SVG output I can generate with the
> > Bio::Graphics modules, and add javascript to (for example)
> > alter/hide elements based on a slider or other user-controlled
> > input.
> >
> > Is there a way to map various panel items to the resulting
> > svg components?
> >
> > e.g transcript3, exon4 == 
> >
> > Given that the "" grouping element doesn't seem to be used
> > (which would facilitate this for non-simple elements), I'm
> > guessing not, but thought I would ask.
> >
> > Thanks,
> >
> > -Steve
> >
> > *****************************************************************
> > Steve Roels, Ph.D.
> > Senior Scientist I
> > Computational Biology
> > Millennium Pharmaceuticals, Inc.   Phone: 617.761.6820
> > 640 Memorial Drive                 FAX:   617.577.3555
> > Cambridge, MA 02139-4815           Email: steven.roels@mpi.com
> > *****************************************************************
> >
> >
> >
> >
> > This e-mail, including any attachments, is a confidential
> > business communication, and may contain information that is
> > confidential, proprietary and/or privileged.  This e-mail is
> > intended only for the individual(s) to whom it is addressed,
> > and may not be saved, copied, printed, disclosed or used by
> > anyone else.  If you are not the(an) intended recipient,
> > please immediately delete this e-mail from your computer
> > system and notify the sender.  Thank you.
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-> bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
From lstein at cshl.edu  Mon Aug 23 12:31:28 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon Aug 23 12:32:14 2004
Subject: [Bioperl-l] Displaying an alignment using Bio::Graphics
In-Reply-To: 
References: 
Message-ID: <200408231231.28526.lstein@cshl.edu>

There's a colorized multiple alignment display in the GBrowse package 
(http://www.mod.org).  It's in the module 
Bio::Graphics::Browser::PadAlignment.

There's also a very handy module called Bio::Graphics::Browser::Markup 
that can be used to add HTML text style strings (colors, boldface, 
italics and various combinations) to arbitrary DNA and protein 
sequences.  It takes care of all the line-wrapping and collisions 
among the tags.  You just need to provide the base pair range and a 
symbolic style name.

Lincoln

On Tuesday 10 August 2004 07:52 am, Iain Wallace wrote:
> Hi all,
>
> I was wondering if any one knows how to display a multiple sequence
> alignment using the Bio::Graphics modules.
> Ideally I would like to colour in certain columns depending on a
> mask that I have created ?
> (FYI The particular project is to colour in the columns of a test
> alignment which have corresponing columns in a reference
> alignment).
>
> thanks
>
> Iain Wallace
>
>
>
> ____________
> Virus checked by G DATA AntiVirusKit
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> _______________________________________________
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> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
From sdavis2 at mail.nih.gov  Mon Aug 23 12:56:38 2004
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Mon Aug 23 12:55:55 2004
Subject: [Bioperl-l] Displaying an alignment using Bio::Graphics
In-Reply-To: <200408231231.28526.lstein@cshl.edu>
References: 
	<200408231231.28526.lstein@cshl.edu>
Message-ID: <666434EF-F525-11D8-BADD-000A95D7BA10@mail.nih.gov>


On Aug 23, 2004, at 12:31 PM, Lincoln Stein wrote:

> There's a colorized multiple alignment display in the GBrowse package
> (http://www.mod.org).  It's in the module
> Bio::Graphics::Browser::PadAlignment

Just a detail:

I'm assuming http://www.gmod.org above....

Sean

From cjfields at uiuc.edu  Mon Aug 23 12:46:25 2004
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon Aug 23 12:56:29 2004
Subject: [Bioperl-l] (RNAfold)Convert bracktes structure to aligned
	like tructure
In-Reply-To: 
References: 
	
Message-ID: <6.1.1.1.2.20040823113604.01c7c1a8@express.cites.uiuc.edu>

I don't think there is a Bioperl module for  this, but I haven't looked for 
one extensively.  I think mfold can make output like this but I'm not sure 
if it can be done from paranthetical (Vienna RNAFold) format.

Chris

At 09:50 PM 8/21/2004, Yousef Malik wrote:

>  Hi
>  I would like to get your help on the following problem:
>  How could one convert the output of RNAfold within the brackets structure
> 
>GGCCAGUGUUGAGAGGCGGAGACUUGGGCAAUUGCUGGACGCUGCCCUGGGCAUUGCACUUGUCUCGGUCUGACAGUGCCGGCC
> 
>((((.((..((..((((.(((((..(((((((.(((((.......))..)))))))).)).))))).))))..))..)).))))
>  (-36.00)
>
>  To aligned like structure:
>     A UG   AG    G     UU G     U   --  AC
>  GGCC G  UUG  AGGC GAGAC  G GCAAU GCU  GG  G
>  |||| |  |||  |||| |||||  | ||||| |||  ||  C
>  CCGG C  GAC  UCUG CUCUG  C CGUUA CGG  CC  U
>     C GU   AG    G     UU A     -   GU  CG
>
>  Please reply to yousef@cs.haifa.ac.il
>  Reagrds
>  Malik
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l

__________________________________

Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer

Address:

University of Illinois at Urbana-Champaign
Dept. of Biochemistry - 323 RAL
600 S. Mathews Ave.
Urbana, IL 61801

Phone : (217) 333-7098
Fax : (217) 244-5858 

From julipao at terra.es  Mon Aug 23 16:28:34 2004
From: julipao at terra.es (=?ISO-8859-1?Q?Julio_Fern=E1ndez_Banet?=)
Date: Mon Aug 23 16:30:31 2004
Subject: [Bioperl-l] How to change gap open penalty
Message-ID: <018D7C09-F543-11D8-9CA9-000D932C62A2@terra.es>

Hello.
i would like to know if it is posible to change the gap open penalty 
value of bl2seq.
My code looks like this:
   # Run bl2seq with the two sequences
     $factory=Bio::Tools::Run::StandAloneBlast->new('program'=>'blastn', 
'G'=>'0' ,'outfile'=>"$Seq.out");
     my $bl2seq_report=$factory->bl2seq($Seq1, $Seq2);

But it seems that it doesn't not work. any suggestion????
Thanks

From skchan at cs.usask.ca  Mon Aug 23 18:23:45 2004
From: skchan at cs.usask.ca (Simon K. Chan)
Date: Mon Aug 23 18:24:31 2004
Subject: [Bioperl-l] Feedback on AGAVE xml parser
Message-ID: <1093299825.412a6e714b81c@webmail.usask.ca>

Hello All,

I've added my AGAVE xml parser to Bio/SeqIO a few weeks back and have since then
cleaned up the code a bit and added POD docs and made some bug fixes.

Similar to the TIGR XML parser, tigr.pm, agave.pm uses regexp to parse a subset
of tags from AGAVE xml.  agave.pm allows files to be converted to and from
AGAVE xml.

Where can I get some feedback on my code? (I suppose sending this message to the
list is a good start... :-)

Work continues.

Many thanks.


--
Warmest Regards,
Simon K. Chan
Bioinformatics, Crosby Lab
skchan@cs.usask.ca




From jason at cgt.duhs.duke.edu  Tue Aug 24 09:11:50 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Aug 24 09:13:05 2004
Subject: [Bioperl-l] Bioperl Blast
In-Reply-To: <32952.128.237.244.179.1093030930.squirrel@128.237.244.179>
References: <32952.128.237.244.179.1093030930.squirrel@128.237.244.179>
Message-ID: 

What is your question - which module are you asking about?

I assume StandAloneBlast is up to date - people have reported bugs for
certain features that might not work.  It really needs a maintainer (and a
some re-writes to be more flexible for changes to cmdline options I would
say)  if we want to track all the changes that happen wrt cmdline options.

As for remote blast - you can set everything that the CGI needs if you
know what options you want to send in to the webserver - figuring out
those options of course is the fun part. This also needs a maintainer to
track them and document them.

-jason
On Fri, 20 Aug 2004, Neil C. Christopher wrote:

> I was wondering if the Blast API is up to date?  Does it work with the
> current blast?
>
> Please let me know ASAP.
>
> Thanks,
>
> Neil Christopher
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From miroslavac at health.nb.ca  Tue Aug 24 09:46:55 2004
From: miroslavac at health.nb.ca (Miroslava Cuperlovic-Culf)
Date: Tue Aug 24 09:48:45 2004
Subject: [Bioperl-l] Bio::Tools:Sim4::Results
Message-ID: <412B46CF.2080102@health.nb.ca>

Dear All,
I am trying to parse output from sim4  to gff format using something like:
    while(my $exonset = $sim4->next_exonset()) {

       foreach my $exon ( $exonset->sub_SeqFeature() ) {
.....
}
}

This works fine if exon alignment is in the the first group of seq1/seq2  :
seq1 = ..
seq2 = ..

 >fasta info
 >fasta info

1-66  (31346313-31346378)   100% ->
67-222  (31372915-31373070)   100% ->
223-798  (31376360-31376935)   100%

But  if the sim4 outputs shows alignment to multiple sections of the 
Chromosome input and if the exon info is not in the first group of data 
(seq1 \n seq2 ...) this loop doesn't find it. parse_next_alignment 
didn't seem to be able to solve this problem either.
Is there any way to loop around all seq1/seq2 parts of the input from 
Bioperl or not to write the empty alignments from sim4?
Sorry for this most likely trivial question!
Thanks for the on-going help
Mira


From jason at cgt.duhs.duke.edu  Tue Aug 24 10:00:54 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Aug 24 10:02:12 2004
Subject: [Bioperl-l] Bio::Tools:Sim4::Results
In-Reply-To: <412B46CF.2080102@health.nb.ca>
References: <412B46CF.2080102@health.nb.ca>
Message-ID: 

Did you try Bio::SearchIO::sim4?  More effort for proper sim4 parsing has
been paid there.

I don't know if it handles this situation - if it doesn't we'd need you
submit an example report file that isn't working to buzilla.

-jason
On Tue, 24 Aug 2004, Miroslava Cuperlovic-Culf wrote:

> Dear All,
> I am trying to parse output from sim4  to gff format using something like:
>     while(my $exonset = $sim4->next_exonset()) {
>
>        foreach my $exon ( $exonset->sub_SeqFeature() ) {
> .....
> }
> }
>
> This works fine if exon alignment is in the the first group of seq1/seq2  :
> seq1 = ..
> seq2 = ..
>
>  >fasta info
>  >fasta info
>
> 1-66  (31346313-31346378)   100% ->
> 67-222  (31372915-31373070)   100% ->
> 223-798  (31376360-31376935)   100%
>
> But  if the sim4 outputs shows alignment to multiple sections of the
> Chromosome input and if the exon info is not in the first group of data
> (seq1 \n seq2 ...) this loop doesn't find it. parse_next_alignment
> didn't seem to be able to solve this problem either.
> Is there any way to loop around all seq1/seq2 parts of the input from
> Bioperl or not to write the empty alignments from sim4?
> Sorry for this most likely trivial question!
> Thanks for the on-going help
> Mira
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From szhan at uoguelph.ca  Tue Aug 24 17:37:19 2004
From: szhan at uoguelph.ca (szhan@uoguelph.ca)
Date: Tue Aug 24 17:37:55 2004
Subject: [Bioperl-l] gene ontology
Message-ID: <1093383438.412bb50f03049@webmail.uoguelph.ca>

Hello,
I'd like to do gene function analysis using gene ontology. But I don't know how
to do it uising bioper. I saw the script:load_ontology.pl someone used to load
ontology in the list. But I don't where to download this script and what kind
of programs I need to downlod first in order to use this script. Any
information will be highly appreciated!
Josh

From barry.moore at genetics.utah.edu  Tue Aug 24 18:02:38 2004
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue Aug 24 18:03:30 2004
Subject: [Bioperl-l] gene ontology
In-Reply-To: <1093383438.412bb50f03049@webmail.uoguelph.ca>
References: <1093383438.412bb50f03049@webmail.uoguelph.ca>
Message-ID: <412BBAFE.20608@genetics.utah.edu>

Josh,

Have you installed and are you familiar with Perl and Bioperl?  That 
script loads a relational database that is using the biosql schema, so 
you would need to have a relational database management system (RDBMS) 
installed, and have created a database with the biosql schema.  The most 
common RDBMS in use by Bioperl users is probably MySQL, but other RDBMSs 
are supported as well.  Those are the minimum requirements needed to run 
the script.  You can find that script at 
http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/scripts/biosql/load_ontology.pl.  
I found that with Google "load_ontology.pl site:bioperl.org".

Barry

szhan@uoguelph.ca wrote:

>Hello,
>I'd like to do gene function analysis using gene ontology. But I don't know how
>to do it uising bioper. I saw the script:load_ontology.pl someone used to load
>ontology in the list. But I don't where to download this script and what kind
>of programs I need to downlod first in order to use this script. Any
>information will be highly appreciated!
>Josh
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>  
>

-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT



From lstein at cshl.edu  Tue Aug 24 18:22:43 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Tue Aug 24 18:23:27 2004
Subject: [Bioperl-l] Re: [Gmod-gbrowse] New glyphs in bio::graphics
In-Reply-To: 
References: 
Message-ID: <200408241822.43190.lstein@cshl.edu>

There's a "jagged" glyph that has jagged ends.

Lincoln

On Friday 20 August 2004 06:09 pm, Todd Harris wrote:
> Nice!
>
> I'll add these to the examples script so that we can keep an easy
> visual accounting of all available glyphs.  We still need a really
> nice glyph to indicate that the end of a line is approximate (ie
> for fingerprinted clones or genetic spans).
>
> t
>
> > On 8/20/04 9:18 AM, Lincoln Stein wrote:
> >
> > Hi All,
> >
> > This is a quick note to let everyone know that "Vsevolod (Simon)
> > Ilyushchenko"  has just contributed a whole set
> > of new Bio::Graphics glyphs that could be useful for
> > high-magnification images.  The design for these glyphs comes
> > from Mari Watanabe of HGC Japan.
> >
> > The glyphs are available in the CVS version of bioperl.
> >
> > Have fun!
> >
> > Lincoln
>
> -------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank
> Media 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only
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> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
From jason at cgt.duhs.duke.edu  Tue Aug 24 23:20:11 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Aug 24 23:21:31 2004
Subject: [Bioperl-l] Trans-Splicing Coding Sequences
In-Reply-To: 
References: 
Message-ID: 

Yeah there is an outstanding bug about this rev-complementing I believe.

I'm not happy with how split locations and rev complement are handled but
I just don't have the time anymore to apply a good soln.

It just hasn't been fixed or addressed properly by someone so thanks for
giving this a go.

-jason

On Tue, 24 Aug 2004, James Thompson wrote:

> Jason,
>
> Removing the sort was definitely a step in the right direction, but I've found
> another slight problem.  The following snippet from  SeqFeatureI.pm (lines
> 560-567) reverse complements each of the subsequences of the CDS if the section
> is on the reverse strand:
>
> if( $loc->strand == 1 ) {
>    $seqstr .= $called_seq->subseq($loc->start,$loc->end);
> } else {
>    $seqstr .= $called_seq->trunc($loc->start,$loc->end)->revcom->seq();
> }
>
> I don't think that the body of the second else clause does what is intended.
> Reverse complementing each individual exon and splicing them together doesn't
> give the same result as splicing together all of the exons and then reversing
> (and complementing) the product. The correct way to do this would be the second
> way, i.e:
>    1. Splice together all of the exons in a CDS.
>    2. Reverse complement the spliced sequence if necessary.
>
> The current method breaks on reverse complemented coding sequences, such as:
>      CDS             complement(join(25482..27077,28659..28733))
>
> I've made a patch that incorporates two changes into the spliced_seq method
> of SeqFeatureI.pm:
>    1. Adds an optional argument for turning off the sorting of locations.
>    2. Moves reverse complementing of the spliced sequence occur after the
>    entire sequence has been concatenated.
>
> If anyone has any questions on this patch or any input on what I may have
> broken, please e-mail me.
>
> Thanks,
>
> James Thompson
> RIT Bioinformatics
>
> On Sun, 22 Aug 2004, Jason Stajich wrote:
>
> > The problem is that we sort the order of the locations in the calling of
> > spliced_seq at around line 697 in Bio::SeqFeatureI so all you need to do
> > remove the sorting - if you want to add an optional 3rd argument to this
> > method which when true does not try and sort the sub locations.  Make
> > sense?  If it works, post a patch and we'll incorporate it.
> >
> > -jason
> >
> >  On Fri, 20 Aug 2004, James Thompson wrote:
> >
> > > Dear Bioperlers,
> > >
> > > I'm currently working on a project involving some trans-spliced coding sequences
> > > from Arabidopsis, and I was wondering if BioPerl provided an easy way of taking a
> > > trans-spliced CDS feature and correctly splicing it into a Bio::Seq object.
> > >
> > > Here's my naive stab at doing this using the Bioperl methods that I know:
> > >
> > > use strict;
> > > use Bio::SeqIO;
> > >
> > > my $seqio = Bio::SeqIO->new( -file => 'NC_001284.gbk', -format => 'genbank' );
> > > my $genome = $seqio->next_seq;
> > >
> > > foreach my $cds (grep { $_->primary_tag =~ /CDS/i } $genome->get_SeqFeatures) {
> > >    print $cds->start, " -> ", $cds->end, "\n";
> > >    print $cds->spliced_seq->translate->seq, "\n";
> > >
> > >    last;
> > > }
> > >
> > > This just tries to use the spliced_seq method to splice the CDS into a sequence,
> > > and here's the output:
> > >
> > > 79740 -> 333105
> > > LFHDLWVYWSYPLRSISQDFDRIRNHWCSI*WYFYGDSVYRCRIPIQDHCSSFSYVGTRYL*GFTHPGYSIPFYCA*NLYFC
> > > *YFTCFYLWFLWSYIATNLLFLQHCFYDLRSTGRHGPNESQKTSSS*FNWTCRLYSYWFLMWNHRRNSITTNWYLYLCINDD
> > > GCIRHSFSITANPCQIYSGFGRSSQNESYFGYYLLHYYVLIRRNTPVSRLL*QILFVLRRFGLWGLLSSPSGSSD*RYRSFL
> > > LYTLSEKNVF*YT*DMDSI*TNGS**VVTTSNDFLFHYFILAIPLSFVLSYSSNGTQFISLNESRIRSDPPTHVQSFFSGFP
> > > RDLYH*CNLHFAHSWSCI*YL*EI*LSAVSQ*CGLAWIT*CSNNLASARRWRTSPNYCPFILE*SF*EGQFYIFLPNLSIIK
> > > YGWYHFDVFRFFRPREV*CF*IHCINSTSYSRYALYDLGS*FNCHVFSY*ASKFMFLCNRSIKKKV*IFHGSRLEIFDLRCI
> > > FLWNIIVW
> > >
> > > The translated sequence for this coding sequence should look like this:
> > >
> > > MKAEFVRILPHMFNLFLAVSPEIFIINATSILLIHGVVFSTSKK
> > > YDYPPLASNVGWLGLLSVLITLLLLAAGAPLLTIAHLFWNNLFRRDNFTYFCQIFLLL
> > > STAGTISMCFDSSDQERFDAFEFIVLIPLPTRGMLFMISAHDLIAMYLAIEPQSLCFY
> > > VIAASKRKSEFSTEAGSKYLILGAFSSGILLFGCSMIYGSTGATHFDQLAKILTGYEI
> > > TGARSSGIFMGILSIAVGFLFKITAVPFHMWAPDIYEGSPTPVTAFLSIAPKISISAN
> > > ILRVSIYGSYGATLQQIFFFCSIASMILGALAAMAQTKVKRPLAHSSIGHVGYIRTGF
> > > SCGTIEGIQSLLIGIFIYALMTMDAFAIVSALRQTRVKYIADLGALAKTNPISAITFS
> > > ITMFSYAGIPPLAGFCSKFYLFFAALGCGAYFLAPVGVVTSVIGRFYYIRLVKRMFFD
> > > TPRTWILYEPMDRNKSLLLAMTSFFITSSLLYPSPLFSVTHQMALSSYL
> > >
> > > I'm guessing that the spliced_seq method in Bio::SeqFeatureI isn't correctly
> > > recognizing the Location definition for this coding sequence, which looks like this:
> > > CDS             complement(join(327890..328078,329735..330306,
> > >                 332945..333105,79740..80132,81113..81297))
> > >
> > > Could anyone help me shed any light on this? Ideally I'd like to translate all
> > > of these CDS features into individual Bio::Seq objects for further analysis,
> > > and I thought I'd ask for a bit of help before I wrote my own parser. Should I
> > > try sub-classing Bio::SeqFeature to overwrite the spliced_seq method, or has
> > > someone else already figured out this problem? Any suggestions would be very
> > > helpful.
> > >
> > > Thanks,
> > >
> > > James Thompson
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
>
>
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From whs at ebi.ac.uk  Wed Aug 25 04:36:50 2004
From: whs at ebi.ac.uk (Will Spooner)
Date: Wed Aug 25 04:37:34 2004
Subject: [Bioperl-l] Bio::Tools::Run::Search proposal
Message-ID: 

I have a proposal for a new BioPerl component which provides a common 
programatic interface to tools used for searching sequence databases 
(wublast, ncbiblast, blat, ssaha etc). It lives in the 
Bio::Tools::Run::Search namespace, but this could easily be changed if 
appropriate. Also, the code already exists, and is being used in anger 
(which is nice).

Functionality is similar to StandAloneBlast, which could easily be 
modified to interface this new system.

If this is of interest, and someone would like to 'sponsor' its inclusion 
into BioPerl, please let me know.

Here's some detail;

NAME
       Bio::Tools::Run::Search - Driver for running Sequence
       Database Searches

SYNOPSIS
       use Bio::Tools::Run::Search;
       # Create a new search object
       my $search = new Bio::Tools::Run::Search(-method=>'wublast');

       # Initialise search
       $search->database( '/path/to/my_cdna.fa' ); #method-specific
       $search->seq( $seq );  #Bio::SeqI object
       $search->option( 'E','1' );

       # Run search
       print "Command: ". $search->command . "\n";
       $search->run;
       while( $search->running ){ wait( 10 ) }
       if( $search->error ){ die( $search->error );

       # Get results
       print "Report: " . $runnable->report; # Method-specific report
       while( my $res = $runnable->next_result ){ # ResultI object
         foreach my $hsp( map{$_->hits} $res->hits ){ # HSPI object
           # Do stuff
         }
       }


DESCRIPTION
       A driver for running Sequence Database Searches (blast,
       ssaha etc). This object serves as a wrapper for the meth-
       ods in Bio::Tools::Run::Search::*, (similar approach SeqIO
       and SearchIO).

       Search results are available as
       Bio::Search::Result::ResultI objects, or as raw output
       produced by the search method.

----

Regards,

Will
---
William Spooner
whs@ebi.ac.uk




From jlegato at helix.nih.gov  Wed Aug 25 07:43:29 2004
From: jlegato at helix.nih.gov (John Legato)
Date: Wed Aug 25 07:44:04 2004
Subject: [Bioperl-l] BioPerl Bundle::BioPerl
Message-ID: 


I am having trouble installing Bundle::BioPerl on a Red Hat 9 machine,

One of my problems seems to be related to XML::DOM, it fails make test:

Failed Test       Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/dom_jp_attr.t                 23    6  26.09%  3 9 12 14 19 22
t/dom_jp_cdata.t                 3    1  33.33%  3
t/dom_jp_minus.t                 2    1  50.00%  2
t/dom_jp_modify.t               16    1   6.25%  16
t/dom_jp_print.t                 3    2  66.67%  2-3

I have built Perl 5.8.5 and  libxml2-2.6.12 from
source as well as expat 1.95.8. I've tried setting LANG to en_US as
suggested in some news group postings. Is Red Hat 9 a lost cause?
I am encountering one problem after another in my attempts to
install BioPerl via CPAN, I'd like to install the complete distribution.
Building Perl from source seemed to fix some of the issues but there seems
to be quite a few incompatibilities related to older library versions
in Red Hat 9 .
What distribution are most BioPerl developers/users using?
I am considering moving to Debian or Fedora but I've been sticking to
Red Hat 9 because of a need to run Oracle 10g.

John

From birney at ebi.ac.uk  Wed Aug 25 08:02:17 2004
From: birney at ebi.ac.uk (Ewan Birney)
Date: Wed Aug 25 08:03:03 2004
Subject: [Bioperl-l] BioPerl Bundle::BioPerl
In-Reply-To: 
Message-ID: 


John -

I am not sure how many Bioperl modules use XML::Dom; not that many I am 
pretty sure. 


Bioperl behaves very graciously (including the test suite) when other 
components are not there, so the lack of XML::Dom will only effect the 
small amount of bioperl which depends on it.


What were you planning to use Bioperl for, or was it just a general thing 
of getting everything installed and tied down?



-----------------------------------------------------------------
Ewan Birney.  Work:  +44 1223 494420
             Email:  birney "at" ebi.ac.uk 
Clerical Assistant:  shelley "at" ebi.ac.uk
Please cc shelley for urgent or diary-dependent requests
-----------------------------------------------------------------

From jason at cgt.duhs.duke.edu  Wed Aug 25 08:03:25 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Wed Aug 25 08:04:37 2004
Subject: [Bioperl-l] BioPerl Bundle::BioPerl
In-Reply-To: 
References: 
Message-ID: 

Well I would just force it through  - unless you are using
Bio::SeqIO::bsml it really isn't that important of a dependancy.

cpan> force install XML::DOM

I use FC1 and RHL9 with no problem as well as OSX.

-jason
On Wed, 25 Aug 2004, John Legato wrote:

>
> I am having trouble installing Bundle::BioPerl on a Red Hat 9 machine,
>
> One of my problems seems to be related to XML::DOM, it fails make test:
>
> Failed Test       Stat Wstat Total Fail  Failed  List of Failed
> -------------------------------------------------------------------------------
> t/dom_jp_attr.t                 23    6  26.09%  3 9 12 14 19 22
> t/dom_jp_cdata.t                 3    1  33.33%  3
> t/dom_jp_minus.t                 2    1  50.00%  2
> t/dom_jp_modify.t               16    1   6.25%  16
> t/dom_jp_print.t                 3    2  66.67%  2-3
>
> I have built Perl 5.8.5 and  libxml2-2.6.12 from
> source as well as expat 1.95.8. I've tried setting LANG to en_US as
> suggested in some news group postings. Is Red Hat 9 a lost cause?
> I am encountering one problem after another in my attempts to
> install BioPerl via CPAN, I'd like to install the complete distribution.
> Building Perl from source seemed to fix some of the issues but there seems
> to be quite a few incompatibilities related to older library versions
> in Red Hat 9 .
> What distribution are most BioPerl developers/users using?
> I am considering moving to Debian or Fedora but I've been sticking to
> Red Hat 9 because of a need to run Oracle 10g.
>
> John
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From jlegato at helix.nih.gov  Wed Aug 25 08:14:00 2004
From: jlegato at helix.nih.gov (John Legato)
Date: Wed Aug 25 08:14:36 2004
Subject: [Bioperl-l] BioPerl Bundle::BioPerl
In-Reply-To: 
References: 
Message-ID: 


Thanks for the help, A force fixed it. I was trying to avoid
that hoping for a clean install but if it's just a few modules that have
issues with it, it shouldn't be a problem. I did a complete install
because I am sure how we are going to make use of it yet.

John
On Wed, 25 Aug 2004, Ewan Birney wrote:

>
>John -
>
>I am not sure how many Bioperl modules use XML::Dom; not that many I am
>pretty sure.
>
>
>Bioperl behaves very graciously (including the test suite) when other
>components are not there, so the lack of XML::Dom will only effect the
>small amount of bioperl which depends on it.
>
>
>What were you planning to use Bioperl for, or was it just a general thing
>of getting everything installed and tied down?
>
>
>
>-----------------------------------------------------------------
>Ewan Birney.  Work:  +44 1223 494420
>             Email:  birney "at" ebi.ac.uk
>Clerical Assistant:  shelley "at" ebi.ac.uk
>Please cc shelley for urgent or diary-dependent requests
>-----------------------------------------------------------------
>
From bfontain at iupui.edu  Wed Aug 25 12:31:34 2004
From: bfontain at iupui.edu (Fontaine, Burr R)
Date: Wed Aug 25 12:37:20 2004
Subject: [Bioperl-l] locuslink - gene positions?
Message-ID: <710690625AD28941BDAD9D2271264C580188787F@iu-mssg-mbx08.exchange.iu.edu>

I am trying to mirror portions of Locuslink and have figured out how to get all of the data elements I need from the locuslink module except for the gene starting postion (in bp coordinates). Chromosome coordinates would be best but contig coordinates are OK if there is a way to convert them. I've looked at the location modules but don't see any obvious answers there. Can someone help me figure out the best way to do this?

Thanks in advance for your help.

Burr Fontaine

From allenday at ucla.edu  Wed Aug 25 16:10:32 2004
From: allenday at ucla.edu (Allen Day)
Date: Wed Aug 25 16:12:51 2004
Subject: [Bioperl-l] BioPerl Bundle::BioPerl
In-Reply-To: 
References: 
	
Message-ID: 

Bio::SeqIO::interpro uses it too.

On Wed, 25 Aug 2004, Jason Stajich wrote:

> Well I would just force it through  - unless you are using
> Bio::SeqIO::bsml it really isn't that important of a dependancy.
> 
> cpan> force install XML::DOM
> 
> I use FC1 and RHL9 with no problem as well as OSX.
> 
> -jason
> On Wed, 25 Aug 2004, John Legato wrote:
> 
> >
> > I am having trouble installing Bundle::BioPerl on a Red Hat 9 machine,
> >
> > One of my problems seems to be related to XML::DOM, it fails make test:
> >
> > Failed Test       Stat Wstat Total Fail  Failed  List of Failed
> > -------------------------------------------------------------------------------
> > t/dom_jp_attr.t                 23    6  26.09%  3 9 12 14 19 22
> > t/dom_jp_cdata.t                 3    1  33.33%  3
> > t/dom_jp_minus.t                 2    1  50.00%  2
> > t/dom_jp_modify.t               16    1   6.25%  16
> > t/dom_jp_print.t                 3    2  66.67%  2-3
> >
> > I have built Perl 5.8.5 and  libxml2-2.6.12 from
> > source as well as expat 1.95.8. I've tried setting LANG to en_US as
> > suggested in some news group postings. Is Red Hat 9 a lost cause?
> > I am encountering one problem after another in my attempts to
> > install BioPerl via CPAN, I'd like to install the complete distribution.
> > Building Perl from source seemed to fix some of the issues but there seems
> > to be quite a few incompatibilities related to older library versions
> > in Red Hat 9 .
> > What distribution are most BioPerl developers/users using?
> > I am considering moving to Debian or Fedora but I've been sticking to
> > Red Hat 9 because of a need to run Oracle 10g.
> >
> > John
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
From skirov at utk.edu  Wed Aug 25 17:01:11 2004
From: skirov at utk.edu (Stefan Kirov)
Date: Wed Aug 25 17:02:21 2004
Subject: [Bioperl-l] locuslink - gene positions?
In-Reply-To: <710690625AD28941BDAD9D2271264C580188787F@iu-mssg-mbx08.exchange.iu.edu>
References: <710690625AD28941BDAD9D2271264C580188787F@iu-mssg-mbx08.exchange.iu.edu>
Message-ID: <412CFE17.4050300@utk.edu>

I think you are right- there are no coordinates and there should be 
(contig coordinates of course). Actually the contig accession number is 
in the object as a DBLink object. I don't think DBLink is a suitable 
place for the contig coordinates. Another problem with LLink module is 
that it permits null values for the primary ID for sime DBLink objects 
(LLID 218 for examples). This is definitely a bug.
I guess you can request this to be added to the module- file a bug 
report. I can probably take a look at that but not today, sorry.
You can also check Ensembl API- it may be more straightforward for your 
needs. Something that I am doing (this is not an advertisement) might be 
also helpful: genereg.ornl.gov/gkdb, but we are struggling with some 
update issues, so I wouldn't use it right now.
Have fun,
Stefan

Fontaine, Burr R wrote:

>I am trying to mirror portions of Locuslink and have figured out how to get all of the data elements I need from the locuslink module except for the gene starting postion (in bp coordinates). Chromosome coordinates would be best but contig coordinates are OK if there is a way to convert them. I've looked at the location modules but don't see any obvious answers there. Can someone help me figure out the best way to do this?
>
>Thanks in advance for your help.
>
>Burr Fontaine
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>  
>

From whs at ebi.ac.uk  Thu Aug 26 04:26:07 2004
From: whs at ebi.ac.uk (Will Spooner)
Date: Thu Aug 26 04:26:48 2004
Subject: [Bioperl-l] Bio::Tools::Run::Search proposal
In-Reply-To: <01FEBE53-F6C8-11D8-9C50-000A95765236@bioperl.org>
Message-ID: 

Thanks Steve,

As the module ISA Bio::SearchIO at the moment, could 
Bio::SearchIO::Runnable be the right class?

No tests yet ;)
I will implement something, but the problem is, of course, dependency on 
3rd party binaries.

I'll mail the code to you off-list.

Will

On Wed, 25 Aug 2004, Steve Chervitz wrote:

> Will,
> 
> Sounds good to me. I'd be happy to sponsor you. Couple of things:
> 
> 1) As for where to put it, seems reasonable to put in under 
> bioperl-live rather than bioperl-run, since the StandAlone/RemoteBlast 
> modules would be re-tooled to use it.
> 
> 2) Have you written tests for it?
> 
> Steve
> --
> Steve Chervitz
> sac at bioperl d0t org
> 
> On Aug 25, 2004, at 1:36 AM, Will Spooner wrote:
> 
> > I have a proposal for a new BioPerl component which provides a common
> > programatic interface to tools used for searching sequence databases
> > (wublast, ncbiblast, blat, ssaha etc). It lives in the
> > Bio::Tools::Run::Search namespace, but this could easily be changed if
> > appropriate. Also, the code already exists, and is being used in anger
> > (which is nice).
> >
> > Functionality is similar to StandAloneBlast, which could easily be
> > modified to interface this new system.
> >
> > If this is of interest, and someone would like to 'sponsor' its 
> > inclusion
> > into BioPerl, please let me know.
> >
> > Here's some detail;
> >
> > NAME
> >        Bio::Tools::Run::Search - Driver for running Sequence
> >        Database Searches
> >
> > SYNOPSIS
> >        use Bio::Tools::Run::Search;
> >        # Create a new search object
> >        my $search = new Bio::Tools::Run::Search(-method=>'wublast');
> >
> >        # Initialise search
> >        $search->database( '/path/to/my_cdna.fa' ); #method-specific
> >        $search->seq( $seq );  #Bio::SeqI object
> >        $search->option( 'E','1' );
> >
> >        # Run search
> >        print "Command: ". $search->command . "\n";
> >        $search->run;
> >        while( $search->running ){ wait( 10 ) }
> >        if( $search->error ){ die( $search->error );
> >
> >        # Get results
> >        print "Report: " . $runnable->report; # Method-specific report
> >        while( my $res = $runnable->next_result ){ # ResultI object
> >          foreach my $hsp( map{$_->hits} $res->hits ){ # HSPI object
> >            # Do stuff
> >          }
> >        }
> >
> >
> > DESCRIPTION
> >        A driver for running Sequence Database Searches (blast,
> >        ssaha etc). This object serves as a wrapper for the meth-
> >        ods in Bio::Tools::Run::Search::*, (similar approach SeqIO
> >        and SearchIO).
> >
> >        Search results are available as
> >        Bio::Search::Result::ResultI objects, or as raw output
> >        produced by the search method.
> >
> > ----
> >
> > Regards,
> >
> > Will
> > ---
> > William Spooner
> > whs@ebi.ac.uk
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> 

From jason at cgt.duhs.duke.edu  Thu Aug 26 04:45:03 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Thu Aug 26 04:46:16 2004
Subject: [Bioperl-l] Bio::Tools::Run::Search proposal
In-Reply-To: 
References: 
Message-ID: 

hmm - SearchIO should be for parsers only - have you merged running and
parsing in the same module? Bio::Tools::Run::Search is a fine place in
terms of namespace but as steve said they could could live in the
bioperl-live CVS module.

-jason
On Thu, 26 Aug 2004, Will Spooner wrote:

> Thanks Steve,
>
> As the module ISA Bio::SearchIO at the moment, could
> Bio::SearchIO::Runnable be the right class?
>
> No tests yet ;)
> I will implement something, but the problem is, of course, dependency on
> 3rd party binaries.
>
> I'll mail the code to you off-list.
>
> Will
>
> On Wed, 25 Aug 2004, Steve Chervitz wrote:
>
> > Will,
> >
> > Sounds good to me. I'd be happy to sponsor you. Couple of things:
> >
> > 1) As for where to put it, seems reasonable to put in under
> > bioperl-live rather than bioperl-run, since the StandAlone/RemoteBlast
> > modules would be re-tooled to use it.
> >
> > 2) Have you written tests for it?
> >
> > Steve
> > --
> > Steve Chervitz
> > sac at bioperl d0t org
> >
> > On Aug 25, 2004, at 1:36 AM, Will Spooner wrote:
> >
> > > I have a proposal for a new BioPerl component which provides a common
> > > programatic interface to tools used for searching sequence databases
> > > (wublast, ncbiblast, blat, ssaha etc). It lives in the
> > > Bio::Tools::Run::Search namespace, but this could easily be changed if
> > > appropriate. Also, the code already exists, and is being used in anger
> > > (which is nice).
> > >
> > > Functionality is similar to StandAloneBlast, which could easily be
> > > modified to interface this new system.
> > >
> > > If this is of interest, and someone would like to 'sponsor' its
> > > inclusion
> > > into BioPerl, please let me know.
> > >
> > > Here's some detail;
> > >
> > > NAME
> > >        Bio::Tools::Run::Search - Driver for running Sequence
> > >        Database Searches
> > >
> > > SYNOPSIS
> > >        use Bio::Tools::Run::Search;
> > >        # Create a new search object
> > >        my $search = new Bio::Tools::Run::Search(-method=>'wublast');
> > >
> > >        # Initialise search
> > >        $search->database( '/path/to/my_cdna.fa' ); #method-specific
> > >        $search->seq( $seq );  #Bio::SeqI object
> > >        $search->option( 'E','1' );
> > >
> > >        # Run search
> > >        print "Command: ". $search->command . "\n";
> > >        $search->run;
> > >        while( $search->running ){ wait( 10 ) }
> > >        if( $search->error ){ die( $search->error );
> > >
> > >        # Get results
> > >        print "Report: " . $runnable->report; # Method-specific report
> > >        while( my $res = $runnable->next_result ){ # ResultI object
> > >          foreach my $hsp( map{$_->hits} $res->hits ){ # HSPI object
> > >            # Do stuff
> > >          }
> > >        }
> > >
> > >
> > > DESCRIPTION
> > >        A driver for running Sequence Database Searches (blast,
> > >        ssaha etc). This object serves as a wrapper for the meth-
> > >        ods in Bio::Tools::Run::Search::*, (similar approach SeqIO
> > >        and SearchIO).
> > >
> > >        Search results are available as
> > >        Bio::Search::Result::ResultI objects, or as raw output
> > >        produced by the search method.
> > >
> > > ----
> > >
> > > Regards,
> > >
> > > Will
> > > ---
> > > William Spooner
> > > whs@ebi.ac.uk
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> >
> >
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From whs at ebi.ac.uk  Thu Aug 26 06:00:32 2004
From: whs at ebi.ac.uk (Will Spooner)
Date: Thu Aug 26 06:01:15 2004
Subject: [Bioperl-l] Bio::Tools::Run::Search proposal
In-Reply-To: 
Message-ID: 

Running and parsing in Search are merged in much the same way as 
StandAloneBlast; the SearchIO object is created on the fly, and used when 
the next_result method is called. Search could easily be modified, 
however, to return the SearchIO object itself rather than implementing its 
methods. The advantage of the latter is that the parsed Result tree is 
tied to the user's original Search and its raw results, allowing the whole 
lot to be serialised to a file/database. Is this behaviour (e.g. used for 
offline parsers) likely to be of use to BioPerl developers?

Will

On Thu, 26 Aug 2004, Jason Stajich wrote:

> hmm - SearchIO should be for parsers only - have you merged running and
> parsing in the same module? Bio::Tools::Run::Search is a fine place in
> terms of namespace but as steve said they could could live in the
> bioperl-live CVS module.
> 
> -jason
> On Thu, 26 Aug 2004, Will Spooner wrote:
> 
> > Thanks Steve,
> >
> > As the module ISA Bio::SearchIO at the moment, could
> > Bio::SearchIO::Runnable be the right class?
> >
> > No tests yet ;)
> > I will implement something, but the problem is, of course, dependency on
> > 3rd party binaries.
> >
> > I'll mail the code to you off-list.
> >
> > Will
> >
> > On Wed, 25 Aug 2004, Steve Chervitz wrote:
> >
> > > Will,
> > >
> > > Sounds good to me. I'd be happy to sponsor you. Couple of things:
> > >
> > > 1) As for where to put it, seems reasonable to put in under
> > > bioperl-live rather than bioperl-run, since the StandAlone/RemoteBlast
> > > modules would be re-tooled to use it.
> > >
> > > 2) Have you written tests for it?
> > >
> > > Steve
> > > --
> > > Steve Chervitz
> > > sac at bioperl d0t org
> > >
> > > On Aug 25, 2004, at 1:36 AM, Will Spooner wrote:
> > >
> > > > I have a proposal for a new BioPerl component which provides a common
> > > > programatic interface to tools used for searching sequence databases
> > > > (wublast, ncbiblast, blat, ssaha etc). It lives in the
> > > > Bio::Tools::Run::Search namespace, but this could easily be changed if
> > > > appropriate. Also, the code already exists, and is being used in anger
> > > > (which is nice).
> > > >
> > > > Functionality is similar to StandAloneBlast, which could easily be
> > > > modified to interface this new system.
> > > >
> > > > If this is of interest, and someone would like to 'sponsor' its
> > > > inclusion
> > > > into BioPerl, please let me know.
> > > >
> > > > Here's some detail;
> > > >
> > > > NAME
> > > >        Bio::Tools::Run::Search - Driver for running Sequence
> > > >        Database Searches
> > > >
> > > > SYNOPSIS
> > > >        use Bio::Tools::Run::Search;
> > > >        # Create a new search object
> > > >        my $search = new Bio::Tools::Run::Search(-method=>'wublast');
> > > >
> > > >        # Initialise search
> > > >        $search->database( '/path/to/my_cdna.fa' ); #method-specific
> > > >        $search->seq( $seq );  #Bio::SeqI object
> > > >        $search->option( 'E','1' );
> > > >
> > > >        # Run search
> > > >        print "Command: ". $search->command . "\n";
> > > >        $search->run;
> > > >        while( $search->running ){ wait( 10 ) }
> > > >        if( $search->error ){ die( $search->error );
> > > >
> > > >        # Get results
> > > >        print "Report: " . $runnable->report; # Method-specific report
> > > >        while( my $res = $runnable->next_result ){ # ResultI object
> > > >          foreach my $hsp( map{$_->hits} $res->hits ){ # HSPI object
> > > >            # Do stuff
> > > >          }
> > > >        }
> > > >
> > > >
> > > > DESCRIPTION
> > > >        A driver for running Sequence Database Searches (blast,
> > > >        ssaha etc). This object serves as a wrapper for the meth-
> > > >        ods in Bio::Tools::Run::Search::*, (similar approach SeqIO
> > > >        and SearchIO).
> > > >
> > > >        Search results are available as
> > > >        Bio::Search::Result::ResultI objects, or as raw output
> > > >        produced by the search method.
> > > >
> > > > ----
> > > >
> > > > Regards,
> > > >
> > > > Will
> > > > ---
> > > > William Spooner
> > > > whs@ebi.ac.uk
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l@portal.open-bio.org
> > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > > >
> > >
> > >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 

From skirov at utk.edu  Thu Aug 26 06:23:28 2004
From: skirov at utk.edu (Stefan Kirov)
Date: Thu Aug 26 06:24:08 2004
Subject: [Bioperl-l] locuslink - gene positions?
In-Reply-To: 
References: <710690625AD28941BDAD9D2271264C580188787F@iu-mssg-mbx08.exchange.iu.edu>
	<412CFE17.4050300@utk.edu>
	
Message-ID: <412DBA20.3050609@utk.edu>

Hi Sean,
Thanks! Well, honestly speaking I think the problem is NCBI. They change 
formats, file locations frequently enough to keep us busy. Now they move 
from LocusLink to Entrez Gene, so some stuff is vanishing from LL_tmpl 
and moving to the new ftp dir in a separate file. So we have to write 
new parser, etc. Homologene also is changing the format and this will 
lead to a schema change. MGI map is also not in LL_tmpl so we have to 
get this from  jax. And so forth...
I think H_inv is a nice idea. Another idea we are exploring is Jaspar...
Stefan

Sean Davis wrote:

> Stefan,
>
> Your database design is quite nice!  I'm anxious to try it out.  What 
> are the "update issues"?
>
> We have microarray spot annotation that we have built for custom 
> arrays.  Currently, I link to home-brew tables with annotation 
> information of interest to our users, but it would certainly be nice 
> to have a normalized version of the information.  Also, I would be 
> interested in putting the H-inv data into the schema at some point, as 
> we mainly work in human.
>
> Sean
>
> On Aug 25, 2004, at 5:01 PM, Stefan Kirov wrote:
>
>> I think you are right- there are no coordinates and there should be 
>> (contig coordinates of course). Actually the contig accession number 
>> is in the object as a DBLink object. I don't think DBLink is a 
>> suitable place for the contig coordinates. Another problem with LLink 
>> module is that it permits null values for the primary ID for sime 
>> DBLink objects (LLID 218 for examples). This is definitely a bug.
>> I guess you can request this to be added to the module- file a bug 
>> report. I can probably take a look at that but not today, sorry.
>> You can also check Ensembl API- it may be more straightforward for 
>> your needs. Something that I am doing (this is not an advertisement) 
>> might be also helpful: genereg.ornl.gov/gkdb, but we are struggling 
>> with some update issues, so I wouldn't use it right now.
>> Have fun,
>> Stefan
>>
>> Fontaine, Burr R wrote:
>>
>>> I am trying to mirror portions of Locuslink and have figured out how 
>>> to get all of the data elements I need from the locuslink module 
>>> except for the gene starting postion (in bp coordinates). Chromosome 
>>> coordinates would be best but contig coordinates are OK if there is 
>>> a way to convert them. I've looked at the location modules but don't 
>>> see any obvious answers there. Can someone help me figure out the 
>>> best way to do this?
>>>
>>> Thanks in advance for your help.
>>>
>>> Burr Fontaine
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l@portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>

From sac at portal.open-bio.org  Wed Aug 25 14:53:09 2004
From: sac at portal.open-bio.org (Steve Chervitz)
Date: Fri Aug 27 04:42:22 2004
Subject: [Bioperl-l] Bio::Tools::Run::Search proposal
In-Reply-To: 
References: 
Message-ID: <01FEBE53-F6C8-11D8-9C50-000A95765236@bioperl.org>

Will,

Sounds good to me. I'd be happy to sponsor you. Couple of things:

1) As for where to put it, seems reasonable to put in under 
bioperl-live rather than bioperl-run, since the StandAlone/RemoteBlast 
modules would be re-tooled to use it.

2) Have you written tests for it?

Steve
--
Steve Chervitz
sac at bioperl d0t org

On Aug 25, 2004, at 1:36 AM, Will Spooner wrote:

> I have a proposal for a new BioPerl component which provides a common
> programatic interface to tools used for searching sequence databases
> (wublast, ncbiblast, blat, ssaha etc). It lives in the
> Bio::Tools::Run::Search namespace, but this could easily be changed if
> appropriate. Also, the code already exists, and is being used in anger
> (which is nice).
>
> Functionality is similar to StandAloneBlast, which could easily be
> modified to interface this new system.
>
> If this is of interest, and someone would like to 'sponsor' its 
> inclusion
> into BioPerl, please let me know.
>
> Here's some detail;
>
> NAME
>        Bio::Tools::Run::Search - Driver for running Sequence
>        Database Searches
>
> SYNOPSIS
>        use Bio::Tools::Run::Search;
>        # Create a new search object
>        my $search = new Bio::Tools::Run::Search(-method=>'wublast');
>
>        # Initialise search
>        $search->database( '/path/to/my_cdna.fa' ); #method-specific
>        $search->seq( $seq );  #Bio::SeqI object
>        $search->option( 'E','1' );
>
>        # Run search
>        print "Command: ". $search->command . "\n";
>        $search->run;
>        while( $search->running ){ wait( 10 ) }
>        if( $search->error ){ die( $search->error );
>
>        # Get results
>        print "Report: " . $runnable->report; # Method-specific report
>        while( my $res = $runnable->next_result ){ # ResultI object
>          foreach my $hsp( map{$_->hits} $res->hits ){ # HSPI object
>            # Do stuff
>          }
>        }
>
>
> DESCRIPTION
>        A driver for running Sequence Database Searches (blast,
>        ssaha etc). This object serves as a wrapper for the meth-
>        ods in Bio::Tools::Run::Search::*, (similar approach SeqIO
>        and SearchIO).
>
>        Search results are available as
>        Bio::Search::Result::ResultI objects, or as raw output
>        produced by the search method.
>
> ----
>
> Regards,
>
> Will
> ---
> William Spooner
> whs@ebi.ac.uk
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

From tex at biosysadmin.com  Tue Aug 24 06:48:16 2004
From: tex at biosysadmin.com (James Thompson)
Date: Fri Aug 27 04:43:08 2004
Subject: [Bioperl-l] Trans-Splicing Coding Sequences
In-Reply-To: 
Message-ID: 

Jason,

Removing the sort was definitely a step in the right direction, but I've found
another slight problem.  The following snippet from  SeqFeatureI.pm (lines
560-567) reverse complements each of the subsequences of the CDS if the section
is on the reverse strand:

if( $loc->strand == 1 ) {
   $seqstr .= $called_seq->subseq($loc->start,$loc->end);
} else {
   $seqstr .= $called_seq->trunc($loc->start,$loc->end)->revcom->seq();
}

I don't think that the body of the second else clause does what is intended. 
Reverse complementing each individual exon and splicing them together doesn't
give the same result as splicing together all of the exons and then reversing
(and complementing) the product. The correct way to do this would be the second
way, i.e: 
   1. Splice together all of the exons in a CDS.
   2. Reverse complement the spliced sequence if necessary.

The current method breaks on reverse complemented coding sequences, such as:
     CDS             complement(join(25482..27077,28659..28733))

I've made a patch that incorporates two changes into the spliced_seq method
of SeqFeatureI.pm:
   1. Adds an optional argument for turning off the sorting of locations.
   2. Moves reverse complementing of the spliced sequence occur after the
   entire sequence has been concatenated.

If anyone has any questions on this patch or any input on what I may have 
broken, please e-mail me. 

Thanks,

James Thompson
RIT Bioinformatics

On Sun, 22 Aug 2004, Jason Stajich wrote:

> The problem is that we sort the order of the locations in the calling of
> spliced_seq at around line 697 in Bio::SeqFeatureI so all you need to do
> remove the sorting - if you want to add an optional 3rd argument to this
> method which when true does not try and sort the sub locations.  Make
> sense?  If it works, post a patch and we'll incorporate it.
> 
> -jason
> 
>  On Fri, 20 Aug 2004, James Thompson wrote:
> 
> > Dear Bioperlers,
> >
> > I'm currently working on a project involving some trans-spliced coding sequences
> > from Arabidopsis, and I was wondering if BioPerl provided an easy way of taking a
> > trans-spliced CDS feature and correctly splicing it into a Bio::Seq object.
> >
> > Here's my naive stab at doing this using the Bioperl methods that I know:
> >
> > use strict;
> > use Bio::SeqIO;
> >
> > my $seqio = Bio::SeqIO->new( -file => 'NC_001284.gbk', -format => 'genbank' );
> > my $genome = $seqio->next_seq;
> >
> > foreach my $cds (grep { $_->primary_tag =~ /CDS/i } $genome->get_SeqFeatures) {
> >    print $cds->start, " -> ", $cds->end, "\n";
> >    print $cds->spliced_seq->translate->seq, "\n";
> >
> >    last;
> > }
> >
> > This just tries to use the spliced_seq method to splice the CDS into a sequence,
> > and here's the output:
> >
> > 79740 -> 333105
> > LFHDLWVYWSYPLRSISQDFDRIRNHWCSI*WYFYGDSVYRCRIPIQDHCSSFSYVGTRYL*GFTHPGYSIPFYCA*NLYFC
> > *YFTCFYLWFLWSYIATNLLFLQHCFYDLRSTGRHGPNESQKTSSS*FNWTCRLYSYWFLMWNHRRNSITTNWYLYLCINDD
> > GCIRHSFSITANPCQIYSGFGRSSQNESYFGYYLLHYYVLIRRNTPVSRLL*QILFVLRRFGLWGLLSSPSGSSD*RYRSFL
> > LYTLSEKNVF*YT*DMDSI*TNGS**VVTTSNDFLFHYFILAIPLSFVLSYSSNGTQFISLNESRIRSDPPTHVQSFFSGFP
> > RDLYH*CNLHFAHSWSCI*YL*EI*LSAVSQ*CGLAWIT*CSNNLASARRWRTSPNYCPFILE*SF*EGQFYIFLPNLSIIK
> > YGWYHFDVFRFFRPREV*CF*IHCINSTSYSRYALYDLGS*FNCHVFSY*ASKFMFLCNRSIKKKV*IFHGSRLEIFDLRCI
> > FLWNIIVW
> >
> > The translated sequence for this coding sequence should look like this:
> >
> > MKAEFVRILPHMFNLFLAVSPEIFIINATSILLIHGVVFSTSKK
> > YDYPPLASNVGWLGLLSVLITLLLLAAGAPLLTIAHLFWNNLFRRDNFTYFCQIFLLL
> > STAGTISMCFDSSDQERFDAFEFIVLIPLPTRGMLFMISAHDLIAMYLAIEPQSLCFY
> > VIAASKRKSEFSTEAGSKYLILGAFSSGILLFGCSMIYGSTGATHFDQLAKILTGYEI
> > TGARSSGIFMGILSIAVGFLFKITAVPFHMWAPDIYEGSPTPVTAFLSIAPKISISAN
> > ILRVSIYGSYGATLQQIFFFCSIASMILGALAAMAQTKVKRPLAHSSIGHVGYIRTGF
> > SCGTIEGIQSLLIGIFIYALMTMDAFAIVSALRQTRVKYIADLGALAKTNPISAITFS
> > ITMFSYAGIPPLAGFCSKFYLFFAALGCGAYFLAPVGVVTSVIGRFYYIRLVKRMFFD
> > TPRTWILYEPMDRNKSLLLAMTSFFITSSLLYPSPLFSVTHQMALSSYL
> >
> > I'm guessing that the spliced_seq method in Bio::SeqFeatureI isn't correctly
> > recognizing the Location definition for this coding sequence, which looks like this:
> > CDS             complement(join(327890..328078,329735..330306,
> >                 332945..333105,79740..80132,81113..81297))
> >
> > Could anyone help me shed any light on this? Ideally I'd like to translate all
> > of these CDS features into individual Bio::Seq objects for further analysis,
> > and I thought I'd ask for a bit of help before I wrote my own parser. Should I
> > try sub-classing Bio::SeqFeature to overwrite the spliced_seq method, or has
> > someone else already figured out this problem? Any suggestions would be very
> > helpful.
> >
> > Thanks,
> >
> > James Thompson
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 




-------------- next part --------------
Index: SeqFeatureI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqFeatureI.pm,v
retrieving revision 1.55
diff -u -r1.55 SeqFeatureI.pm
--- SeqFeatureI.pm	13 Mar 2004 01:30:02 -0000	1.55
+++ SeqFeatureI.pm	25 Aug 2004 02:47:21 -0000
@@ -453,18 +453,24 @@
             number of N's (DNA) or X's (protein, though this is unlikely).
 
             This function is deliberately "magical" attempting to second guess
-            what a user wants as "the" sequence for this feature
+            what a user wants as "the" sequence for this feature.
 
             Implementing classes are free to override this method with their
-            own magic if they have a better idea what the user wants
+            own magic if they have a better idea what the user wants.
+
+            Note: This function sorts features according to their starting position,
+            if this is undesirable (e.g in splicing a trans-spliced CDS), pass
+            in a true value as the third argument.
 
   Args    : [optional] A Bio::DB::RandomAccessI compliant object
+            [optional} A true value as the third argument if user does not want
+                       features sorted by start location.
   Returns : A Bio::Seq
 
 =cut
 
 sub spliced_seq {
-    my ($self,$db) = @_;
+    my ($self,$db,$nosort) = @_;
    
     if( ! $self->location->isa("Bio::Location::SplitLocationI") ) {
 	return $self->seq(); # nice and easy!
@@ -496,22 +502,36 @@
 	! $self->absolute ) { 
 	$self->warn("Calling spliced_seq with a Bio::Das::SegmentI which does have absolute set to 1 -- be warned you may not be getting things on the correct strand");
     }
-    
-    my @locs = map { $_->[0] }
-    # sort so that most negative is first basically to order
-    # the features on the opposite strand 5'->3' on their strand
-    # rather than they way most are input which is on the fwd strand
-
-    sort { $a->[1] <=> $b->[1] } # Yes Tim, Schwartzian transformation
-    map { 
-	$fstrand = $_->strand unless defined $fstrand;
-	$mixed = 1 if defined $_->strand && $fstrand != $_->strand;
-	if( defined $_->seq_id ) {
-	    $mixedloc = 1 if( $_->seq_id ne $seqid );
-	}
-	[ $_, $_->start* ($_->strand || 1)];	    
-    } $self->location->each_Location; 
    
+    my @locs;
+    if ( !$nosort ) {
+        @locs = map { $_->[0] }
+        # sort so that most negative is first basically to order
+        # the features on the opposite strand 5'->3' on their strand
+        # rather than they way most are input which is on the fwd strand
+
+        sort { $a->[1] <=> $b->[1] } # Yes Tim, Schwartzian transformation
+        map { 
+            $fstrand = $_->strand unless defined $fstrand;
+            $mixed = 1 if defined $_->strand && $fstrand != $_->strand;
+            if( defined $_->seq_id ) {
+                $mixedloc = 1 if( $_->seq_id ne $seqid );
+            }
+            [ $_, $_->start * ($_->strand || 1)];	    
+        } $self->location->each_Location; 
+    } else {
+        # same as above, just without the sort
+        @locs = map { $_->[0] }
+        map { 
+            $fstrand = $_->strand unless defined $fstrand;
+            $mixed = 1 if defined $_->strand && $fstrand != $_->strand;
+            if( defined $_->seq_id ) {
+                $mixedloc = 1 if( $_->seq_id ne $seqid );
+            }
+            [ $_, $_->start * ($_->strand || 1)];	    
+        } $self->location->each_Location; 
+    }
+
     if ( $mixed ) { 
 	$self->warn("Mixed strand locations, spliced seq using the input order rather than trying to sort");    
 	@locs = $self->location->each_Location; 
@@ -520,6 +540,7 @@
 	@locs = $self->location->each_Location; 
     }
 
+    my $revcom;
     foreach my $loc ( @locs  ) {
 	if( ! $loc->isa("Bio::Location::Atomic") ) {
 	    $self->throw("Can only deal with one level deep locations");
@@ -553,21 +574,24 @@
 	} else {
 	    $called_seq = $self->entire_seq;
 	}
-	
+
 	if( $self->isa('Bio::Das::SegmentI') ) {
 	    my ($s,$e) = ($loc->start,$loc->end);	    
 	    $seqstr .= $called_seq->subseq($s,$e)->seq();
 	} else { 
-	    # This is dumb subseq should work on locations...
-	    if( $loc->strand == 1 ) {
-		$seqstr .= $called_seq->subseq($loc->start,$loc->end);
-	    } else {
-		$seqstr .= $called_seq->trunc($loc->start,$loc->end)->revcom->seq();
-	    }
+	    $seqstr .= $called_seq->subseq($loc->start,$loc->end);
+            # If we have a non-forward strand feature, revcom the entire
+            # sequence later. There may be a better way to do this.
+            if ( $loc->strand != 1 ) {
+               $revcom = 1;
+            }
 	}
     }
+
     my $out = Bio::Seq->new( -id => $self->entire_seq->display_id . "_spliced_feat",
 			     -seq => $seqstr);
+
+    if ( $revcom ) { $out = $out->revcom };
     
     return $out;
 }
From jon_r_manning at yahoo.com  Fri Aug 27 09:46:33 2004
From: jon_r_manning at yahoo.com (=?iso-8859-1?q?Jonathan=20Manning?=)
Date: Fri Aug 27 09:47:08 2004
Subject: [Bioperl-l] Problem with T-Coffee
Message-ID: <20040827134633.80914.qmail@web52705.mail.yahoo.com>

Hi to all,

I've been using T-Coffee via the Bioperl wrapper as
part of a larger project. Though it worked fine on the
development system, it's not working on a different
one. It seems to do the pairwise stuff, at least it
gets to this stage:

......
	AAH76853  CAG05593 : score=  400
	AAH76853  CAE45989 : score=  410
	CAG05593  CAE45989 : score=  460


MAKE NEIGHBOR JOINING DENDROGRAM
	[MODE=fast] [Output dendrogram file=5XIMxfCi1F.dnd]


But then it crashes out with the following messages:

Abnormal Program Termination:[T-COFFEE, Version_1.37]
Please report the fault to:
cedric.notredame@europe.com (Indicate the version
number)
Thank you for your cooperation :-)

------------- EXCEPTION  -------------
MSG: TCoffee call crashed: 256 [command
/usr/bin/t_coffee
-in=/tmp/5XIMxfCi1F,XBLOSUM,Mlalign_id_pair,Mclustalw_pair
 -ktuple=2 -output=clustalw
-outfile=/tmp/6wIuLkvcGl/w7jE5bLbih]

STACK Bio::Tools::Run::Alignment::TCoffee::_run
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:814
STACK Bio::Tools::Run::Alignment::TCoffee::align
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:719
STACK SSIR::align
/usr/lib/perl5/site_perl/5.8.0/SSIR.pm:2094
STACK toplevel /var/www/cgi-bin/ssir.cgi:557

--------------------------------------

Similar commands work fine from the command line.

Does anyone have any ideas?

Many thanks,

Jon



	
	
		
___________________________________________________________ALL-NEW Yahoo! Messenger - all new features - even more fun!  http://uk.messenger.yahoo.com
From jason at cgt.duhs.duke.edu  Fri Aug 27 10:08:43 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Aug 27 10:10:06 2004
Subject: [Bioperl-l] Problem with T-Coffee
In-Reply-To: <20040827134633.80914.qmail@web52705.mail.yahoo.com>
References: <20040827134633.80914.qmail@web52705.mail.yahoo.com>
Message-ID: 

different versions of bioperl/bioperl-run on the dev machine and other
machine?  This happens for every every
alignment you try on the non-dev machine? i.e.
% perl -I. -w t/TCoffee.t
in bioperl-run fails on the new machine too?

An example sequence file and the script with at least the t-coffee part
would help in debugging the problem if all of that is true.

I've also moved to using MUSCLE instead of T-Coffee for some analyses
because it is much faster and seems to be as accurate.  The newest MAFFT
is also rumoured to be as accurate too although one should always do their
own tests on one's own data first...

-jason
On Fri, 27 Aug 2004, [iso-8859-1] Jonathan Manning wrote:

> Hi to all,
>
> I've been using T-Coffee via the Bioperl wrapper as
> part of a larger project. Though it worked fine on the
> development system, it's not working on a different
> one. It seems to do the pairwise stuff, at least it
> gets to this stage:
>
> ......
> 	AAH76853  CAG05593 : score=  400
> 	AAH76853  CAE45989 : score=  410
> 	CAG05593  CAE45989 : score=  460
>
>
> MAKE NEIGHBOR JOINING DENDROGRAM
> 	[MODE=fast] [Output dendrogram file=5XIMxfCi1F.dnd]
>
>
> But then it crashes out with the following messages:
>
> Abnormal Program Termination:[T-COFFEE, Version_1.37]
> Please report the fault to:
> cedric.notredame@europe.com (Indicate the version
> number)
> Thank you for your cooperation :-)
>
> ------------- EXCEPTION  -------------
> MSG: TCoffee call crashed: 256 [command
> /usr/bin/t_coffee
> -in=/tmp/5XIMxfCi1F,XBLOSUM,Mlalign_id_pair,Mclustalw_pair
>  -ktuple=2 -output=clustalw
> -outfile=/tmp/6wIuLkvcGl/w7jE5bLbih]
>
> STACK Bio::Tools::Run::Alignment::TCoffee::_run
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:814
> STACK Bio::Tools::Run::Alignment::TCoffee::align
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:719
> STACK SSIR::align
> /usr/lib/perl5/site_perl/5.8.0/SSIR.pm:2094
> STACK toplevel /var/www/cgi-bin/ssir.cgi:557
>
> --------------------------------------
>
> Similar commands work fine from the command line.
>
> Does anyone have any ideas?
>
> Many thanks,
>
> Jon
>
>
>
>
>
>
> ___________________________________________________________ALL-NEW Yahoo! Messenger - all new features - even more fun!  http://uk.messenger.yahoo.com
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From jpmitchell00 at hotmail.com  Fri Aug 27 14:22:43 2004
From: jpmitchell00 at hotmail.com (James Mitchell)
Date: Fri Aug 27 14:23:18 2004
Subject: [Bioperl-l] Bio::OntologyIO problems
Message-ID: 

I have been having problems with the latest files that I've downloaded from 
geneontology.org.  I use bioperl to parse these files and when I use the new 
files, I get an error from bio-perl now.  Using GO files dated July 15, the 
parsing works.

Any help or suggestions?

This is the call I use in bioperl-1.4.

my $deffile = "GO.defs";
my $comfile = "component.ontology";
my $funfile = "function.ontology";
my $profile = "process.ontology";

my $ont_stream = Bio::OntologyIO->new(-format => 'go',
                                         -files =>  [$comfile,
										$funfile,
										$profile],
                                         -defs_file => $deffile);

$engine = $ont_stream->next_ontology();

This is the error I receive with the new GO files:

------------- EXCEPTION  -------------
MSG: format error: no term id in line ":0017023
"
STACK Bio::OntologyIO::dagflat::_get_first_termid 
C:/Perl/site/lib/Bio/OntologyI
O/dagflat.pm:600
STACK Bio::OntologyIO::dagflat::_parse_flat_file 
C:/Perl/site/lib/Bio/OntologyIO
/dagflat.pm:472
STACK Bio::OntologyIO::dagflat::parse 
C:/Perl/site/lib/Bio/OntologyIO/dagflat.pm
:250
STACK Bio::OntologyIO::dagflat::next_ontology 
C:/Perl/site/lib/Bio/OntologyIO/da
gflat.pm:284
STACK MostInformative::find MostInformative.pm:96
STACK toplevel MostInformative.pl:75

_________________________________________________________________
FREE pop-up blocking with the new MSN Toolbar – get it now! 
http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/

From Annie.Law at nrc-cnrc.gc.ca  Fri Aug 27 14:07:30 2004
From: Annie.Law at nrc-cnrc.gc.ca (Law, Annie)
Date: Fri Aug 27 14:45:53 2004
Subject: [Bioperl-l] Optimizing Bioperl db queries
Message-ID: <10C94843061E094A98C02EB77CFC328722FE7A@nrcmrdex1d.imsb.nrc.ca>

Hi,

I would appreciate help on the following.  I am trying to create an
annotation database and
Am trying to obtain from starting point clone ids and end point being
Locuslink id's and GO terms, gene symbols, gene names.

I have loaded my bioperl-db database with scripts such as load_ontology.pl
and loadseqdatabase.pl.
I am using VB and sql queries to pull out the data.  

I am able to get the data that I want however it is quite slow.  I have 15
clone ids and it takes about 30s to retrieve
The data that I would like to get.  
This is only my test case and there may be times that my input will be 15000
entries.
Aside from the bioperl tables I have some other tables that are used.  So in
total I have about 9 sql queries
And some of these queries are in loops.

How are the people out there optimizing the set of queries to get a faster
retrieval?
I have indexed some tables but I think there is a better solution.

Thanks very much,
Annie.
From jon_r_manning at yahoo.com  Sat Aug 28 12:21:51 2004
From: jon_r_manning at yahoo.com (=?iso-8859-1?q?Jonathan=20Manning?=)
Date: Sat Aug 28 12:22:21 2004
Subject: [Bioperl-l] Possible problems with file output?
Message-ID: <20040828162151.33068.qmail@web52704.mail.yahoo.com>

Hi to all,

I've been developing a large bit of perl-based
software which calls on many Bioperl modules. I've
just moved it from the development system to a new
one, and am having some trouble. 

I e-mailed yesterday concerning a problem I was having
with T-Coffee (which I solved by switching to Muscle-
thanks Jason), but am now having a problem with the
Phylip suite this line in the SeqBoot module (359): 

my $outfile =
$self->io->catfile($self->tempdir,$self->outfile);
    chdir($curpath);
    $self->throw("SeqBoot did not create files
correctly ($outfile)")
        unless (-e $outfile);

It was at a very similar part in the T-Coffee module
the program crashed out before, from which I infer
that there may be some problems with writing to files
(the programs work fine by themselves). This is not an
issue with file permissions, but I thought maybe I
could be short a module or two necessary for this sort
of thing. Could anyone suggest which ones these might
be?

Thanks,

Jon


	
	
		
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From jason at cgt.duhs.duke.edu  Sun Aug 29 05:08:03 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Sun Aug 29 05:09:04 2004
Subject: [Bioperl-l] Trans-Splicing Coding Sequences
In-Reply-To: 
References: 
Message-ID: 

James - hmm the revcom at the end as you've done doesn't exactly work  
because it assumes the rev-complement applies to the whole split  
feature when in fact it could just be related to one of the  
sub-locations.

I think the proper way to do it is prepend the sequence chunk to the  
assembled location which I've done and the tests appear to work fine -  
in fact sorting the sub locations may be a silly default behavior in  
the first place, I can't remember why it was coded that way.

I've committed more tests in t/SeqFeature.t and added the A.thaliana MT  
genome as test data.
-jason

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

On Aug 24, 2004, at 8:48 PM, James Thompson wrote:

> Jason,
>
> Removing the sort was definitely a step in the right direction, but  
> I've found
> another slight problem.  The following snippet from  SeqFeatureI.pm  
> (lines
> 560-567) reverse complements each of the subsequences of the CDS if  
> the section
> is on the reverse strand:
>
> if( $loc->strand == 1 ) {
>    $seqstr .= $called_seq->subseq($loc->start,$loc->end);
> } else {
>    $seqstr .= $called_seq->trunc($loc->start,$loc->end)->revcom->seq();
> }
>
> I don't think that the body of the second else clause does what is  
> intended.
> Reverse complementing each individual exon and splicing them together  
> doesn't
> give the same result as splicing together all of the exons and then  
> reversing
> (and complementing) the product. The correct way to do this would be  
> the second
> way, i.e:
>    1. Splice together all of the exons in a CDS.
>    2. Reverse complement the spliced sequence if necessary.
>
> The current method breaks on reverse complemented coding sequences,  
> such as:
>      CDS             complement(join(25482..27077,28659..28733))
>
> I've made a patch that incorporates two changes into the spliced_seq  
> method
> of SeqFeatureI.pm:
>    1. Adds an optional argument for turning off the sorting of  
> locations.
>    2. Moves reverse complementing of the spliced sequence occur after  
> the
>    entire sequence has been concatenated.
>
> If anyone has any questions on this patch or any input on what I may  
> have
> broken, please e-mail me.
>
> Thanks,
>
> James Thompson
> RIT Bioinformatics
>
> On Sun, 22 Aug 2004, Jason Stajich wrote:
>
>> The problem is that we sort the order of the locations in the calling  
>> of
>> spliced_seq at around line 697 in Bio::SeqFeatureI so all you need to  
>> do
>> remove the sorting - if you want to add an optional 3rd argument to  
>> this
>> method which when true does not try and sort the sub locations.  Make
>> sense?  If it works, post a patch and we'll incorporate it.
>>
>> -jason
>>
>>  On Fri, 20 Aug 2004, James Thompson wrote:
>>
>>> Dear Bioperlers,
>>>
>>> I'm currently working on a project involving some trans-spliced  
>>> coding sequences
>>> from Arabidopsis, and I was wondering if BioPerl provided an easy  
>>> way of taking a
>>> trans-spliced CDS feature and correctly splicing it into a Bio::Seq  
>>> object.
>>>
>>> Here's my naive stab at doing this using the Bioperl methods that I  
>>> know:
>>>
>>> use strict;
>>> use Bio::SeqIO;
>>>
>>> my $seqio = Bio::SeqIO->new( -file => 'NC_001284.gbk', -format =>  
>>> 'genbank' );
>>> my $genome = $seqio->next_seq;
>>>
>>> foreach my $cds (grep { $_->primary_tag =~ /CDS/i }  
>>> $genome->get_SeqFeatures) {
>>>    print $cds->start, " -> ", $cds->end, "\n";
>>>    print $cds->spliced_seq->translate->seq, "\n";
>>>
>>>    last;
>>> }
>>>
>>> This just tries to use the spliced_seq method to splice the CDS into  
>>> a sequence,
>>> and here's the output:
>>>
>>> 79740 -> 333105
>>> LFHDLWVYWSYPLRSISQDFDRIRNHWCSI*WYFYGDSVYRCRIPIQDHCSSFSYVGTRYL*GFTHPGY 
>>> SIPFYCA*NLYFC
>>> *YFTCFYLWFLWSYIATNLLFLQHCFYDLRSTGRHGPNESQKTSSS*FNWTCRLYSYWFLMWNHRRNSI 
>>> TTNWYLYLCINDD
>>> GCIRHSFSITANPCQIYSGFGRSSQNESYFGYYLLHYYVLIRRNTPVSRLL*QILFVLRRFGLWGLLSS 
>>> PSGSSD*RYRSFL
>>> LYTLSEKNVF*YT*DMDSI*TNGS**VVTTSNDFLFHYFILAIPLSFVLSYSSNGTQFISLNESRIRSD 
>>> PPTHVQSFFSGFP
>>> RDLYH*CNLHFAHSWSCI*YL*EI*LSAVSQ*CGLAWIT*CSNNLASARRWRTSPNYCPFILE*SF*EG 
>>> QFYIFLPNLSIIK
>>> YGWYHFDVFRFFRPREV*CF*IHCINSTSYSRYALYDLGS*FNCHVFSY*ASKFMFLCNRSIKKKV*IF 
>>> HGSRLEIFDLRCI
>>> FLWNIIVW
>>>
>>> The translated sequence for this coding sequence should look like  
>>> this:
>>>
>>> MKAEFVRILPHMFNLFLAVSPEIFIINATSILLIHGVVFSTSKK
>>> YDYPPLASNVGWLGLLSVLITLLLLAAGAPLLTIAHLFWNNLFRRDNFTYFCQIFLLL
>>> STAGTISMCFDSSDQERFDAFEFIVLIPLPTRGMLFMISAHDLIAMYLAIEPQSLCFY
>>> VIAASKRKSEFSTEAGSKYLILGAFSSGILLFGCSMIYGSTGATHFDQLAKILTGYEI
>>> TGARSSGIFMGILSIAVGFLFKITAVPFHMWAPDIYEGSPTPVTAFLSIAPKISISAN
>>> ILRVSIYGSYGATLQQIFFFCSIASMILGALAAMAQTKVKRPLAHSSIGHVGYIRTGF
>>> SCGTIEGIQSLLIGIFIYALMTMDAFAIVSALRQTRVKYIADLGALAKTNPISAITFS
>>> ITMFSYAGIPPLAGFCSKFYLFFAALGCGAYFLAPVGVVTSVIGRFYYIRLVKRMFFD
>>> TPRTWILYEPMDRNKSLLLAMTSFFITSSLLYPSPLFSVTHQMALSSYL
>>>
>>> I'm guessing that the spliced_seq method in Bio::SeqFeatureI isn't  
>>> correctly
>>> recognizing the Location definition for this coding sequence, which  
>>> looks like this:
>>> CDS             complement(join(327890..328078,329735..330306,
>>>                 332945..333105,79740..80132,81113..81297))
>>>
>>> Could anyone help me shed any light on this? Ideally I'd like to  
>>> translate all
>>> of these CDS features into individual Bio::Seq objects for further  
>>> analysis,
>>> and I thought I'd ask for a bit of help before I wrote my own  
>>> parser. Should I
>>> try sub-classing Bio::SeqFeature to overwrite the spliced_seq  
>>> method, or has
>>> someone else already figured out this problem? Any suggestions would  
>>> be very
>>> helpful.
>>>
>>> Thanks,
>>>
>>> James Thompson
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l@portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> --
>> Jason Stajich
>> Duke University
>> jason at cgt.mc.duke.edu
>>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

From hz5 at njit.edu  Mon Aug 30 09:22:20 2004
From: hz5 at njit.edu (hz5@njit.edu)
Date: Mon Aug 30 09:22:59 2004
Subject: [Bioperl-l] locuslink - gene positions?
In-Reply-To: <710690625AD28941BDAD9D2271264C580188787F@iu-mssg-mbx08.exchange.iu.edu>
References: <710690625AD28941BDAD9D2271264C580188787F@iu-mssg-mbx08.exchange.iu.edu>
Message-ID: <1093872140.41332a0c90144@webmail.njit.edu>

I believe that there is a flatfile in MapView ftp directory, some kind of md 
file have coordinate of genes relative to both chromosome and contigs.

Haibo

Quoting "Fontaine, Burr R" :

> 
> I am trying to mirror portions of Locuslink and have figured out how to
> get all of the data elements I need from the locuslink module except for
> the gene starting postion (in bp coordinates). Chromosome coordinates
> would be best but contig coordinates are OK if there is a way to convert
> them. I've looked at the location modules but don't see any obvious
> answers there. Can someone help me figure out the best way to do this?
> 
> Thanks in advance for your help.
> 
> Burr Fontaine
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 



=========================================================
Haibo Zhang, PhD student
Computational Biology, NJIT & Rutgers University
Center for Applied Genomics, PHRI
http://afs13.njit.edu/~hz5
From nathanhaigh at ukonline.co.uk  Mon Aug 30 16:03:37 2004
From: nathanhaigh at ukonline.co.uk (Nathan Haigh)
Date: Mon Aug 30 16:04:18 2004
Subject: [Bioperl-l] back translation
Message-ID: 

Is it possible to use BioPerl to back translate a protein sequence into a
nucleotide sequence with ambiguity codes?

Thanks
Nathan


From jon_r_manning at yahoo.com  Fri Aug 27 11:05:52 2004
From: jon_r_manning at yahoo.com (=?iso-8859-1?q?Jonathan=20Manning?=)
Date: Mon Aug 30 19:13:30 2004
Subject: [Bioperl-l] Problem with T-Coffee
In-Reply-To: 
Message-ID: <20040827150552.16636.qmail@web52710.mail.yahoo.com>

Hi Jason,

Thanks for the reply.

My versions of Bioperl, Bioperl-run and T-Coffee are
the same on both machines.

When I run the test I get the following output:


1..22
# Running under perl version 5.008 for linux
# Current time local: Fri Aug 27 10:10:30 2004
# Current time GMT:   Fri Aug 27 14:10:30 2004
# Using Test.pm version 1.23
ok 1
ok 2
ok 3
ok 4
ok 5

Abnormal Program Termination:[T-COFFEE, Version_1.37]
Please report the fault to:
cedric.notredame@europe.com (Indicate the version nu
mber)
Thank you for your cooperation :-)

------------- EXCEPTION  -------------
MSG: TCoffee call crashed: 256 [command
/usr/bin/t_coffee -in=t/data/cysprot.fa,
Xblosum,Mlalign_id_pair,Mclustalw_pair  -ktuple=3
-output=clustalw -outfile=/tmp
/MvE0LpuQko/mPn9bfUyI0 -quiet]

STACK Bio::Tools::Run::Alignment::TCoffee::_run
Bio/Tools/Run/Alignment/TCoffee.
pm:814
STACK Bio::Tools::Run::Alignment::TCoffee::align
Bio/Tools/Run/Alignment/TCoffee
.pm:719
STACK toplevel t/TCoffee.t:62

--------------------------------------
ok 6 # skip TCoffee program not found. Skipping.

ok 7 # skip TCoffee program not found. Skipping.

ok 8 # skip TCoffee program not found. Skipping.

ok 9 # skip TCoffee program not found. Skipping.

ok 10 # skip TCoffee program not found. Skipping.

ok 11 # skip TCoffee program not found. Skipping.

ok 12 # skip TCoffee program not found. Skipping.

ok 13 # skip TCoffee program not found. Skipping.

ok 14 # skip TCoffee program not found. Skipping.

ok 15 # skip TCoffee program not found. Skipping.

ok 16 # skip TCoffee program not found. Skipping.

ok 17 # skip TCoffee program not found. Skipping.

ok 18 # skip TCoffee program not found. Skipping.

ok 19 # skip TCoffee program not found. Skipping.

ok 20 # skip TCoffee program not found. Skipping.

ok 21 # skip TCoffee program not found. Skipping.

ok 22 # skip TCoffee program not found. Skipping.


I guess that explains something- it's not seeing the
T-Coffee program for some reason. I don't know why it
shouldn't- I placed it in /usr/bin using a soft-link
(ln -s).

Nothing unusual with my sequence file, but I'm
attaching it anyway, and relevant snippet of code is
below (it's a subroutine passed an arrayref of
sequences):

 sub align {

	# T-COFFEE USED TO CREATE A Bio::SimpleAlign OBJECT

    my ($self) = shift;
    my ( $relatives, $params ) = @_;
    my @params  = @{$params};
    my $Aligner = new
Bio::Tools::Run::Alignment::TCoffee(@params);
    my $aln     = $Aligner->align($relatives);

    return $aln;
}

I don't really have time to swap the program I'm
using, so I hope I can get this to work!

Thanks again- help appreciated. 

Jon


 --- Jason Stajich  wrote: 
> different versions of bioperl/bioperl-run on the dev
> machine and other
> machine?  This happens for every every
> alignment you try on the non-dev machine? i.e.
> % perl -I. -w t/TCoffee.t
> in bioperl-run fails on the new machine too?
> 
> An example sequence file and the script with at
> least the t-coffee part
> would help in debugging the problem if all of that
> is true.
> 
> I've also moved to using MUSCLE instead of T-Coffee
> for some analyses
> because it is much faster and seems to be as
> accurate.  The newest MAFFT
> is also rumoured to be as accurate too although one
> should always do their
> own tests on one's own data first...
> 
> -jason
> On Fri, 27 Aug 2004, [iso-8859-1] Jonathan Manning
> wrote:
> 
> > Hi to all,
> >
> > I've been using T-Coffee via the Bioperl wrapper
> as
> > part of a larger project. Though it worked fine on
> the
> > development system, it's not working on a
> different
> > one. It seems to do the pairwise stuff, at least
> it
> > gets to this stage:
> >
> > ......
> > 	AAH76853  CAG05593 : score=  400
> > 	AAH76853  CAE45989 : score=  410
> > 	CAG05593  CAE45989 : score=  460
> >
> >
> > MAKE NEIGHBOR JOINING DENDROGRAM
> > 	[MODE=fast] [Output dendrogram
> file=5XIMxfCi1F.dnd]
> >
> >
> > But then it crashes out with the following
> messages:
> >
> > Abnormal Program Termination:[T-COFFEE,
> Version_1.37]
> > Please report the fault to:
> > cedric.notredame@europe.com (Indicate the version
> > number)
> > Thank you for your cooperation :-)
> >
> > ------------- EXCEPTION  -------------
> > MSG: TCoffee call crashed: 256 [command
> > /usr/bin/t_coffee
> >
>
-in=/tmp/5XIMxfCi1F,XBLOSUM,Mlalign_id_pair,Mclustalw_pair
> >  -ktuple=2 -output=clustalw
> > -outfile=/tmp/6wIuLkvcGl/w7jE5bLbih]
> >
> > STACK Bio::Tools::Run::Alignment::TCoffee::_run
> >
>
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:814
> > STACK Bio::Tools::Run::Alignment::TCoffee::align
> >
>
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:719
> > STACK SSIR::align
> > /usr/lib/perl5/site_perl/5.8.0/SSIR.pm:2094
> > STACK toplevel /var/www/cgi-bin/ssir.cgi:557
> >
> > --------------------------------------
> >
> > Similar commands work fine from the command line.
> >
> > Does anyone have any ideas?
> >
> > Many thanks,
> >
> > Jon
> >
> >
> >
> >
> >
> >
> >
>
___________________________________________________________ALL-NEW
> Yahoo! Messenger - all new features - even more fun!
>  http://uk.messenger.yahoo.com
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> >
>
http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>  


	
	
		
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-------------- next part --------------
>XP_058513 PREDICTED: similar to RIKEN cDNA 4921513O20; cDNA sequence, clone 3-75 [Homo sapiens].
MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNI
HVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILK
MLTVHNASVNLSVIGLKTLDLLLTSGKITLLILDEESDIFMLIFDAMHSFPANDEVQKLG
CKALHVLFERGNNVEVLMSGNVRCYNIVVEAMKAFPMSERIQEVSCCLLHRLTLGNFFNI
LVLNEVHEFVVKAVQQYPENAALQISALSCLALLTETIFLNQDLEEKNENQENDDEGEED
KLFWLEACYKALTWHRKNKHVQEAACWALNNLLMYQNSLHEKIGDEDGHFPAHREVMLSM
LMHSSSKEVFQASANALSTLLEQNVNFRKILLSKGIHLNVLELMQKHIHSPEVAESGCKM
LNHLFEGSNTSLDIMAAVVPKILTVMKRHETSLPVQLEALRAILHFIVPGMPEESREDTE
FHHKLNMVKKQCFKNDIHKLVLAALNRFIGNPGIQKCGLKVISSIVHFPDALEMLSLEGA
MDSVLHTLQMYPDDQEIQCLGLSLIGYLITKKNVFIGTGHLLAKILVSSLYRFKDVAEIQ
TKGFQTILAILKLSASFSKLLVHHSFDLVIFHQMSSNIMEQKDQQFLNLCCKCFAKVAMD
DYLKNVMLERACDQNNSIMVECLLLLGADANQAKEGSSLICQVCEKESSPKLVELLLNSG
SREQDVRKALTISIGKGDSQIISLLLRRLALDVANNSICLGGFCIGKVEPSWLGPLFPDK
TSNLRKQTNIASTLARMVIRYQMKSAVEEGTASGSDGNFSEDVLSKFDEWTFIPDSSMDS
VFAQSDDLDSEGSEGSFLVKKKSNSISVGEFYRDAVLQRCSPNLQRHSNSLGPIFDHEDL
LKRKRKILSSDDSLRSSKLQSHMRHSDSISSLASEREYITSLDLSANELRDIDALSQKCC
ISVHLEHLEKLELHQNALTSFPQQLCETLKSLTHLDLHSNKFTSFPSYLLKMSCIANLDV
SRNDIGPSVVLDPTVKCPTLKQFNLSYNQLSFVPENLTDVVEKLEQLILEGNKISGICSP
LRLKELKILNLSKNHISSLSENFLEACPKVESFSARMNFLAAMPFLPPSMTILKLSQNKF
SCIPEAILNLPHLRSLDMSSNDIQYLPGPAHWKSLNLRELLFSHNQISILDLSEKAYLWS
RVEKLHLSHNKLKEIPPEIGCLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDELHLN
FDFKHIGCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQ
SATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQ
AEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDY
HFVNATEESDALAKLRKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVPIEF
PVIDRKRLLQLVRENQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCK
IMAQILTVKVEGCPKHPKGIISRRDVEKFLSKKRKFPKNYMSQYFKLLEKFQIALPIGEE
YLLVPSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPYMLSGRER
ALRPNRMYWRQGIYLNWSPEAYCLVGSEVLDNHPESFLKITVPSCRKGCILLGQVVDHID
SLMEEWFPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDDLMKKAEEGDLLVNPDQ
PRLTIPISQIAPDLILADLPRNIMLNNDELEFEQAPEFLLGDGSFGSVYRAAYEGEEVAV
KIFNKHTSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKAS
LTRTLQHRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCC
RMGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTTGGRIVEGLKFPNEFDE
LEIQGKLPDPVKEYGCAPWPMVEKLIKQCLKENPQERPTSAQVFDILNSAELVCLTRRIL
LPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALV
HLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTCLYCNSFSKQSKQKNFLLV
GTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSESTNSTERNVMWGGCGTKIFS
FSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAKQNSPVVEVWDKKTEKLCG
LIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDLSTRRLI
RVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQKEIQSCLTVWDINLPHEVQ
NLEKHIEVRKELAEKMRRTSVE
>CAD39185 hypothetical protein [Homo sapiens].
VFDILNSAELVCLTRRILLPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTE
GYTSEEVADSRILCLALVHLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTC
LYCNSFSKQSKQKNFLLVGTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSEST
NSTERNVMWGGCGTKIFSFSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAK
QNSPVVEVWDKKTEKLCGLIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWI
GTGGGHILLLDLSTRRLIRVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQK
EIQSCLTVWDINLPHEVQNLEKHIEVRKELAEKMRRTSVE
>BAB29628 unnamed protein product [Mus musculus].
MLGAIFERPIPPDTRPWYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCR
MGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLHDIWTTGSRIMEGLRFPNEFDEL
AIQGKLPDPVKEYGCAPWPMVEKLITKCLKENPQERPTSAQVFDILNSAELICLMRHILI
PKNIIVECMVATNLNSKSATLWLGCGNTEKGQLSLFDLNTERYSYEEVADSRILCLALVH
LAAEKESWVVCGTQSGALLVINVEEETKRHTLEKMTDSVTCLHCNSLAKQSKQSNFLLVG
TADGNLMIFEDKAVKCKGAAPLKTLHIGDVSTPLMCLSESLNSSERHITWGGCGTKVFSF
SNDFTIQKLIETKTNQLFSYAAFSDSNIIALAVDTALYIAKKNSPVVEVWDKKTEKLCEL
IDCVHFLKEVMVKLNKESKHQLSYSGRVKALCLQKNTALWIGTGGGHILLLDLSTRRVIR
TIHNFCDSVRAMATAQLGSLKNVMLVLGYKRKSTEGIQEQKEIQSCLSIWDLNLPHEVQN
LEKHIEVRTELADKMRKTSVE
>AAH34074 4921513O20Rik protein [Mus musculus].
SEIIIRLYEMPYFPMGFWSRLINRLLEISPFMLSGRERALRPNRMYWRQGIYLNWSPEAY
CLVGSEVLDNRPESFLKITVPSCRKGCILLGRVVDHIDSLMEEWFPGLLEIDICGEGETL
LKKWALYSFNDGEEHQKILLDELMKKAEEGDLLINPDQPRLTIPISQIAPDLILADLPRN
IMLNNDELEFEEAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQELVVLCHL
HHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVADGLRYLHS
AMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKTSEGTPGFRAPEVARGN
VIYNQQADVYSFGLLLHDIWTTGSRIMEGLRFPNEFDELAIQGKLPDPVKEYGCAPWPMV
EKLITKCLKENPQERPTSAQVFDILNSAELICLMRHILIPKNIIVECMVATNLNSKSATL
WLGCGNTEKGQLSLFDLNTERYSYEEVADSRILCLALVHLAAEKESWVVCGTQSGALLVI
NVEEETKRHTLEKMTDSVTCLHCNSLAKQSKQSNFLLVGTADGNLMIFEDKAVKCKGAAP
LKTLHIGDVSTPLMCLSESLNSSERHITWGGCGTKVFSFSNDFTIQKLIETKTNQLFSYA
AFSDSNIIALAVDTALYIAKKNSPVVEVWDKKTEKLCELIDCVHFLKEVMVKLNKESKHQ
LSYSGRVKALCLQKNTALWIGTGGGHILLLDLSTRRVIRTIHNFCDSVRAMATAQLGSLK
NVMLVLGYKRKSTEGIQEQKEIQSCLSIWDLNLPHEVQNLEKHIEVRTELADKMRKTSVE
>XP_235581 similar to RIKEN cDNA 4921513O20; cDNA sequence, clone 3-75 [Rattus norvegicus].
MASGACQGCDEEEEEEALKKLIVRLNNVQEGKQIETLLQLLEDILVFTYSDRASKLFEGK
NVHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTLQSLIGPQDIGNDWEVLGIHRLI
LKMLTVHHANVNLSIVGLKALDLLLDSGKITLLILDEECDVFLLIFDAMHRYSANEEVQK
LACKALHVLFERVSEEQLTEFVENKDYMTLLSTFRSFKRDEEIVHHVLCCLHSLAVTCSN
VEVLMSGNVRCYNIVVEAMKTFPTSENIQEVSCSLLHKLTLGNFFNILVLNEVHVFVVKA
VQRYPENVALQISALSCLALLNLEERSETQENSDEDSEKPFWLEPCYKALMRHRKNKHVQ
EAACWALNNLLMYQSSLHEKIGDEDGQFPAHREVMLSMLMHSSSKDVFQAAAHALSTLLE
QNGLPLASIINGGMACICTHKVSLVHAPMSSILVLPSSMKILLAKGVYLNVLELMQRHAQ
VPEVAESGCKMLSHLFEGSNPSLDTVAAVIPKILTVMRTHGTSLSVQLEALRALLHFVVP
GVSEDSRDDSRCQPNVLRTQCFRTDIHKLVLAALNRFIGNPGIQKCGLKVISSFAHLPDA
LEMLSLHGAVDSVLHTLQMYPDDQEIQCLGLHLMGCLMTKKNFCIGTGHLLAKILASTLQ
RFKDVAEVQTTGLQTVLSMLDLSVSFSKLLVHYSFDVVMFHQMSSGVLEQKDEQFLNLCC
KCFAKVAVDDELKSKMLERACDQNNSIMVECLLLLGADANQAKGATSLIYQVCEKESSPK
LVELLLNSGCREQDVRKALTVSIQKGDNQVISLLLRRLALDLANNSICLGGFCIGKLDPS
WLGPLFPDKSSNLRKQTNAGSVLARKVLRYQMRNTLQEGVASGSEGNFSEDALAKFGEWT
FIPDSSMDSVFGQSDDLDSEGSESSFLVKKKSNSVSVGEVYRDLALQRCSPNAQRHSSSL
GPVFDHEDLLRRKRKILSSDESLRSSRLQSHTRQSDSSSSLASEREHITSLDLSANELKD
IDALGQKCCLSSHLEHLTKLELHQNSLTSFPQQLCETLKCLTHLDLHSNKFATFPSFMLK
MPSVIHLDASRNDIGPTVVLDPVVKCPSLKQFNLSYNQLSSIPENLDQVVEKLEQLLLEG
NKISGICSPLSLKELKILNLSKNHIPSLPEDFLEACPKVESFSARMNFLAVHTVSLPPTG
FILVCFVKIPPEIGRLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDGLHLNFDFKHI
GCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKMKKSELGMQGATVGI
DVRDWPIQIRGKRKKDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAM
KPWLFNIKARASSSPVILVGTHLDVSDEKQRKACIGKITKELLNKRGFPTIRDYHFVNAT
EESDALAKLRKTIINESLNFKIRDQPVVGQLIPDCYVELEKIILSERKAVPTEFPVINRK
HLLQLVKEHQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCKVMAQIL
TVKVDGCLKHPKGIISRRDVEKFLSKKKRFPKNYMAQYFKLLEKFQIALPIGEEYLLVPS
SLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPFMLSGRERALRPNR
MYWRQGIYLNWSPEAYCLVGSEVLDSRPESFLKITVPSCRKGCILLGRVVDHIDSLMEEW
FPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDELMKKAEEGDLLINPDQPRLTIP
ISQIAPDLILADLPRNIMLNNDELEFEEAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKH
TSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQ
HRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKT
SEGTPGFRAPEVARGNVIYNQQADVYSFGLLLHDIWTTGNRIMEGLRFPNEFDELAIQGK
LPDPVKEYGCAPWPMVEKLITKCLKENPQERPTSAQVFDILNSAELICLMRHIFIPKDIT
VECIAATNLNSKRATLWLGCGNTEKGQLSLLDLNTERYSYEEVTDSRILCLALVHLAAEK
ESWVVCGTQSGALLVINAEDETRRHTLDKMTDSVTCLYCNSFAKQSKQSHFLLVGTADGN
LMIFEDKTIKCKGAAPLKTLHIGDVSTPLMCLSESMNSSERHITWGGCGTKIFSFSNDFT
IQKLIETRTNQLFSYSAFSDSNIIAVAVDTALYIAKKNSPVVENYKSCDAGDRSQATCVQ
NSEMTTALPPSCFKVLAGCTRLGRSVKSLSADRTVNEHILYASREVMVKINKDSKHKLSY
SGRVKALCLQKNTALWIGTGGGHILLLDLSTRRVIRTIHNFCDSKLSMFCFGKGSLKNVM
LVLGYKRKSTEGTQEQKEIQSCLSIWDLNLPHEVQNLEKHIEVRTELADKMRKTSVE
>AAH35949 4921513O20Rik protein [Mus musculus].
CLALVHLAAEKESWVVCGTQSGALLVINVEEETKRHTLEKMTDSVTCLHCNSLAKQSKQS
NFLLVGTADGNLMIFEDKAVKCKGAAPLKTLHIGDVSTPLMCLSESLNSSERHITWGGCG
TKVFSFSNDFTIQKLIETKTNQLFSYAAFSDSNIIALAVDTALYIAKKNSPVVEVWDKKT
EKLCELIDCVHFLKEVMVKLNKESKHQLSYSGRVKALCLQKNTALWIGTGGGHILLLDLS
TRRVIRTIHNFCDSVRAMATAQLGSLKNVMLVLGYKRKSTEGIQEQKEIQSCLSIWDLNL
PHEVQNLEKHIEVRTELADKMRKTSVE
>XP_415940 PREDICTED: similar to hypothetical protein [Gallus gallus].
MKVYEILNSAELICLMRYVSIPSTSTAECMVAANQSCKKAGVWIGNGNTEKAQLSFVNLN
TDGHTCEDIADSKILSLALVTLPTEKENWIVAGTHSGSLWAVNTEDETRRHRLQKMSDSV
TCLYCNSLSKQSKQKNFFLVGTADGTLAVFEDRAVKCKGATPLKILTIGNVSTPLMCLNE
STYLSEKNTIWGGCGTKLIALSSDFSVQKLIETKSSQLFCHNAYSDANIISIAVDKSIYL
AKKNSHFVEIWDKKTEKLSELIDCAHFLKDEVEKLNKESKHKVAYSGRVKTICLQKNTAL
WVGTGGGHILLLDLSTRRPVRVIDNFCDSIRVMLTAQLGSLKNVVLVLGYCYKSDTEDDK
SHKELQSCVSVWDINLPHEVQNLKKHIEHSYNTATARIALWPRTGPGSPCPVTGRSDRAH
SSSPAHTAMAESHRAAHREPCYVSAGPAAFLYLGISAVTWKASVCPRHPQLLQHSKLKRY
TTGAKASAQNNVGWAPFSSQSRADVSPSHPDQTSQEGAFGGEPEAHPLPAALLGQQAALF
PPHLNAVAAALCQQLVAVQSMLSNCIARFLSNCAGYLELSSTQQPLKSLQRSPQGIGEWG
GAPSPGHSQTHHSSSQHDCKLPPEHSAKAGTAAVGP
>AAH76853 Unknown (protein for IMAGE:6637919) [Xenopus laevis].
IAPDIVLADLPRNIMLNAEELEFDQAPEFLLGDGGFGSVYRASYKGEDVAVKIFNKHTSS
RLLRQELTVLSHLHHPSLVYLLAAGVHPRMLVMELAPKGSLDHLLQQDSASLTRTLQHRI
ALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNSAIIAKIADYGIAQYCCRMGIKTSEG
TPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTGGARMVEGLKFPNEFDELAIHGRLPD
PVKEYNCAPWPEVEVLIKKCLKENPQQRPTSVTVYEILNSAELLCLMRNHVIFSMLTAEC
MVAASPLVKKHVVWVGNGCTEKGQMCCIDLNKGGQTCEDFSDSRILCLTLVTLPGEKQNW
IVAGTQSGEIITADLDELKIKHTLHKLTDSVTCLLFSCIQGQSQKKYHILAGTANGRIAI
FENTAVKCAYAAPIKVIDIGDNSTPVMCLCESTYSSEKNSVWGICGTKIFSLSSEFTVQK
TIDTRTATLYSHGSYSESNITCFAIDKYIYVAKKISPYVEIWDKKTEKICEVLDCVQFLK
EDSRKRRKCKQEEAYTSRVKALYLQKNTALWVGTGGGHILLIDLSTRQPIRIITSFCDSI
RSMVPAQLDRGSIKNVVLVLGCRCTPQKEIQSFLSVWDTNLPHEVQNLKKHNEIRQEFAD
KLRGLSMD
>CAG05593 unnamed protein product [Tetraodon nigroviridis].
MVNGEELEEQLRKLLVRLKSQQQERQLGTLIQILQDLLFLAHTDEAAELFEDKDVHVSLT
VALSSYASRRGVQQVGWSLLCRLMEICPGTLERLTAAQPAAEDSQVLPVHKLVLKVLSQH
GADCKVTMVGLRALALLLRSDAVPPLLLEDESEDVLGLVVQAMKVFPVNEEVLLHGCGAL
QVLLETVSEDHLVEFVENQDHVVVLAALQTFLDNPELLLRGLKVLLPLARPGGVRCYSTV
IAAMDAFPEVEDLQETACRLFRAFTLESYYNILVRNGVQRVAACCTALDLHAEEPDVQEA
ASWAIERLLVHGAGPRPAEEDQEERTPVHRQLMAALLLHPKAPSVFQAATSAISTLIQQD
GERSTPRAAVKRCLVPPTFAAFAGRTRAPLLSSGLHVNLVEMMKRHWTSAEVSISACRLL
SLLFQGRPASLDELNMTMSQILCTIKAHNFNPEVQLEALRASLVLLYPDRSLREHGVSVA
DPDMADVSLKVLKNQCVLEGAHTLYLEVLNRFISSSAIQKSGLKVLSALADCSGAVDLLC
QQGAIDTVLHTLQMFPGEREIHYWGFTLLNYLVTKKKLSPMIVPVLASVLVASLVQYRED
SEMTLKCFQVALRMLDASPRSAAELQRENFDRQIFQQLREDTADLCNYPLRKSVCLALFK
MWSDSELRYAMLEKACQDGDATMAECLIELGADVNAKTKSESLLYQVGGENLCVHRSVLT
AGPSVPQVCERGGPLELAELLVRRGAHEQHLRRALAVSVKRADGPAVILLLARLGLDHNS
SALCLGGFRLGRLDAGWLGPLLAERRSARSLCRTSSKAVSLARFVQSFQRSKSHSSVLRS
PVDPCLTSGYISEESDDSNFSFVSVDDGQIPNEDMESDGSDSLPGVLSPEDPQALRRRQG
RQRHPSPEVQPPHQRPGCVGVFFSLFAPVFVFLFQNGQTETEPCDSVQKRYAKSPQKVFR
PADGPAALQKVQDRVRLLDLSANELDALSCLMDDGVVQQQLGHLLRLDLSHNSLQEFPSS
LCQSLSSLTRLDLQGNQLPSLPVELLTLQSLNTLNISRNCVGPQLTFDPAVSCPSLRHLN
LSFNKIAAFPHQLSGAGSQLEELCLEGNCIRELCVPLSLPEIKLLDVSKNSVETVSADFL
TGCPKLETLNVSVNKISSLSHLPSKLTTLKLANNGFAEVSAAILGLPNLRSVDMRTNRIA
ALPGPASWESCNLRELNFSQNRIGTLDLSGPVHRWARLEKLHLSDNQLSEIPPQIGLLEG
LNSLDVSRNANLHSFPDEMGKLGRLWDLPLDGLRLQLDLKLIGNKTKDIVRFLQQRLKKA
VPYHRMKLIVVGNVASGKTTLIQQLMKLKRSQLKSKSTSVGIDVQDWTIKDWDRKKMVLN
VWDFSGGEEFSGSHPHFLTSRALYLVVYNLSRGASQVDALKPWLFNIKAAAPVSPVILVG
THTDVSNELQLQACLTKIREELLSHQSFPAIRDYHMVSASEDSDALTKLRKAIAREVANF
KIQGQPVMGQLVPDSYVELERQLLQERARVPPEFPVLRHREVLQLIQENQLQLEEAELPH
AIHFLSEAGQNFHELFFPLLTVLSDFLDFRSGNVELRSCSEEGRLYSHLLVFPAGVLLHF
DDPALQLQNLYFIDPQWLCHIISQKLTLKSCGFWEPPKGVIQRSLVEKFLSETKCFPKSH
MTQLFKLLEKFQIALPFGEDQLLVPSRWAHGRSVQRQHTAVCVFVSVGNPTDVGSVFGPS
LSKHRPVIELPHGENSEVIVRLYEMPYFPMDFWSRQIIRLLEFSSHLLSGREKAVRPNRI
YWRRGVYLSWSPDAYCLVEAASVEDNPSSFVRITVPSSQKGRVLLGQVVDHVDSLLEEWF
PGLLSTNMHGSGEALLKKWALYSFEDGQEWSKVLLDDLCPHLDAGVLLQDEEQPGLALPL
SQVAPDLVLSDQPAGLMLDSAELSVDLSERLGTPATRPEPRLGVLLSDNVLFPGGGGFGN
VYRGVYRKEDVAVKIFNNHASELYVFRLLRQELVVLSRLRHPSLVALLAASTAARALVME
LAPRGSLDALFQHENGGLNRKLQHRIALQVADGLRYLHSAMIVYRDLKPHNVLLFNLKTD
CEMIAKITDYGIAQHCCSMGVRSCEGTPGGLSSWAWFCSRFLPVQRQFVLGVQALGFRLC
KAPGGERRVVDGCASAGFRAPEVARGNVAYNQQADVFSFGLLLYDLLTCGERISDGMKFP
SEFDEIAVQRKLPDPVKHYGCAPWPGLQALMRDCLKESPQCRPTSAQVFDRLNSGEVLCL
MRELAVPRVPSAECLALSGGCTAWLGGGSSAQRRGSVTAVNLHTNAVTTEAIDTSPVLCL
TTVQIPNQTSDWLVAGTQSGALVVLSSQDALTWHRLQSVRDAVTSLFFHLHPCRNQRKNY
LLVGTADGTVTIYEDSVLKQEDGRPVKTVTVGQLDTPVVCLGQSLHWQDSRCVWAGCGTK
VLSFTADYDLGRSVDTRPSAEFQQEQSWASEACVSRMVVDKHVYLSKAGSPLVEVWDKKS
ERMVDRIDCAHIIRRDSGGTTEGSSSWARVKALLVQSAAALWIGTRGGYLLLLELSKHQP
LQVIGPRCDSVRCMAPALIETPNWKNVVLVLGRRLPQGRNQADEESVLMVWNGMLPMEAK
DLKRHCHRREQVAVRMR
>CAE45989 hypothetical protein [Homo sapiens].
TEKLCGLIDCVHFLREVTVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDL
STRRLIRVIYNFCNSVRVMMTAQLGKFLSFRYFSYSLSLIKYAFILRLHFL
From nathanhaigh at ukonline.co.uk  Mon Aug 30 15:59:00 2004
From: nathanhaigh at ukonline.co.uk (Nathan Haigh)
Date: Mon Aug 30 19:13:39 2004
Subject: [Bioperl-l] back translation
Message-ID: 

Is it possible to use BioPerl to back translate a protein sequence into a
nucleotide sequence with ambiguity codes?



Thanks

Nathan



---
avast! Antivirus: Outbound message clean.
Virus Database (VPS): 0435-2, 28/08/2004
Tested on: 30/08/2004 20:58:57
avast! is copyright (c) 2000-2003 ALWIL Software.
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From reche at research.dfci.harvard.edu  Fri Aug 27 12:52:28 2004
From: reche at research.dfci.harvard.edu (Pedro Antonio Reche)
Date: Mon Aug 30 19:13:45 2004
Subject: [Bioperl-l] phylogenetic question
Message-ID: <7AED452B-F849-11D8-BABB-000393BC20D0@research.dfci.harvard.edu>

Hi all,
I have a couple of questions and I thought some of you may know the  
answers. Here we bo. Given a set of related proteins is there a way to  
tell ancestry in absolute terms?. Also,  given a couple of paralogs, is  
it possible to know which one is the ancestor. Any help, indication,  
etc is very welcomed.
Cheers
======================================================================== 
=====================
Dr. Pedro A Reche, Instructor of Medicine
Dana-Farber Cancer Institute, Harvard Medical School                     
      TL: 617 632 3824
HIM Building, Room 401                                                   
      FX: 617 632 3351
77 Avenue Louis Pasteur                                   EM:  
reche@research.dfci.harvard.edu
Boston, MA 02115, USA                                                 
W3: www.mifoundation.org
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From reche at research.dfci.harvard.edu  Mon Aug 30 18:48:43 2004
From: reche at research.dfci.harvard.edu (Pedro Antonio Reche)
Date: Mon Aug 30 19:13:49 2004
Subject: [Bioperl-l] phylogenetic question
Message-ID: 

Hi all,
For some reason, lately I do not see  my posting in the bioperl list.  
Maybe I need to join again to the list?!  Anyway, let se if I get this  
question posted. Given a set of related proteins is there a way to tell  
ancestry in absolute terms, and how?.  I know, this is not a bioperl  
question, but any help will  be welcomed.
Cheers

======================================================================== 
=====================
Dr. Pedro A Reche, Instructor of Medicine
Dana-Farber Cancer Institute, Harvard Medical School                     
      TL: 617 632 3824
HIM Building, Room 401                                                   
      FX: 617 632 3351
77 Avenue Louis Pasteur                                   EM:  
reche@research.dfci.harvard.edu
Boston, MA 02115, USA                                                 
W3: www.mifoundation.org
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From jason at cgt.duhs.duke.edu  Mon Aug 30 22:50:06 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Mon Aug 30 23:22:46 2004
Subject: [Bioperl-l] back translation
In-Reply-To: 
References: 
Message-ID: <76DB38F4-FAF8-11D8-8097-000393C44276@cgt.mc.duke.edu>

You mean like Bio::Tools::CodonTable revtranslate() ?

-jason

On Aug 31, 2004, at 5:59 AM, Nathan Haigh wrote:

> Is it possible to use BioPerl to back translate a protein sequence 
> into a
> nucleotide sequence with ambiguity codes?
>
>
>
> Thanks
>
> Nathan
>
>
>
> ---
> avast! Antivirus: Outbound message clean.
> Virus Database (VPS): 0435-2, 28/08/2004
> Tested on: 30/08/2004 20:58:57
> avast! is copyright (c) 2000-2003 ALWIL Software.
> http://www.avast.com
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

From jason.stajich at duke.edu  Mon Aug 30 23:27:52 2004
From: jason.stajich at duke.edu (Jason Stajich)
Date: Mon Aug 30 23:28:25 2004
Subject: [Bioperl-l] Problem with T-Coffee
In-Reply-To: <20040827150552.16636.qmail@web52710.mail.yahoo.com>
References: <20040827150552.16636.qmail@web52710.mail.yahoo.com>
Message-ID: 

Did you also symlink mocca and lalign2list in addition to t_coffee as 
those are also depended on by t_coffee?

-jason

On Aug 28, 2004, at 1:05 AM, Jonathan Manning wrote:

> Hi Jason,
>
> Thanks for the reply.
>
> My versions of Bioperl, Bioperl-run and T-Coffee are
> the same on both machines.
>
> When I run the test I get the following output:
>
>
> 1..22
> # Running under perl version 5.008 for linux
> # Current time local: Fri Aug 27 10:10:30 2004
> # Current time GMT:   Fri Aug 27 14:10:30 2004
> # Using Test.pm version 1.23
> ok 1
> ok 2
> ok 3
> ok 4
> ok 5
>
> Abnormal Program Termination:[T-COFFEE, Version_1.37]
> Please report the fault to:
> cedric.notredame@europe.com (Indicate the version nu
> mber)
> Thank you for your cooperation :-)
>
> ------------- EXCEPTION  -------------
> MSG: TCoffee call crashed: 256 [command
> /usr/bin/t_coffee -in=t/data/cysprot.fa,
> Xblosum,Mlalign_id_pair,Mclustalw_pair  -ktuple=3
> -output=clustalw -outfile=/tmp
> /MvE0LpuQko/mPn9bfUyI0 -quiet]
>
> STACK Bio::Tools::Run::Alignment::TCoffee::_run
> Bio/Tools/Run/Alignment/TCoffee.
> pm:814
> STACK Bio::Tools::Run::Alignment::TCoffee::align
> Bio/Tools/Run/Alignment/TCoffee
> .pm:719
> STACK toplevel t/TCoffee.t:62
>
> --------------------------------------
> ok 6 # skip TCoffee program not found. Skipping.
>
> ok 7 # skip TCoffee program not found. Skipping.
>
> ok 8 # skip TCoffee program not found. Skipping.
>
> ok 9 # skip TCoffee program not found. Skipping.
>
> ok 10 # skip TCoffee program not found. Skipping.
>
> ok 11 # skip TCoffee program not found. Skipping.
>
> ok 12 # skip TCoffee program not found. Skipping.
>
> ok 13 # skip TCoffee program not found. Skipping.
>
> ok 14 # skip TCoffee program not found. Skipping.
>
> ok 15 # skip TCoffee program not found. Skipping.
>
> ok 16 # skip TCoffee program not found. Skipping.
>
> ok 17 # skip TCoffee program not found. Skipping.
>
> ok 18 # skip TCoffee program not found. Skipping.
>
> ok 19 # skip TCoffee program not found. Skipping.
>
> ok 20 # skip TCoffee program not found. Skipping.
>
> ok 21 # skip TCoffee program not found. Skipping.
>
> ok 22 # skip TCoffee program not found. Skipping.
>
>
> I guess that explains something- it's not seeing the
> T-Coffee program for some reason. I don't know why it
> shouldn't- I placed it in /usr/bin using a soft-link
> (ln -s).
>
> Nothing unusual with my sequence file, but I'm
> attaching it anyway, and relevant snippet of code is
> below (it's a subroutine passed an arrayref of
> sequences):
>
>  sub align {
>
> 	# T-COFFEE USED TO CREATE A Bio::SimpleAlign OBJECT
>
>     my ($self) = shift;
>     my ( $relatives, $params ) = @_;
>     my @params  = @{$params};
>     my $Aligner = new
> Bio::Tools::Run::Alignment::TCoffee(@params);
>     my $aln     = $Aligner->align($relatives);
>
>     return $aln;
> }
>
> I don't really have time to swap the program I'm
> using, so I hope I can get this to work!
>
> Thanks again- help appreciated.
>
> Jon
>
>
>  --- Jason Stajich  wrote:
>> different versions of bioperl/bioperl-run on the dev
>> machine and other
>> machine?  This happens for every every
>> alignment you try on the non-dev machine? i.e.
>> % perl -I. -w t/TCoffee.t
>> in bioperl-run fails on the new machine too?
>>
>> An example sequence file and the script with at
>> least the t-coffee part
>> would help in debugging the problem if all of that
>> is true.
>>
>> I've also moved to using MUSCLE instead of T-Coffee
>> for some analyses
>> because it is much faster and seems to be as
>> accurate.  The newest MAFFT
>> is also rumoured to be as accurate too although one
>> should always do their
>> own tests on one's own data first...
>>
>> -jason
>> On Fri, 27 Aug 2004, [iso-8859-1] Jonathan Manning
>> wrote:
>>
>>> Hi to all,
>>>
>>> I've been using T-Coffee via the Bioperl wrapper
>> as
>>> part of a larger project. Though it worked fine on
>> the
>>> development system, it's not working on a
>> different
>>> one. It seems to do the pairwise stuff, at least
>> it
>>> gets to this stage:
>>>
>>> ......
>>> 	AAH76853  CAG05593 : score=  400
>>> 	AAH76853  CAE45989 : score=  410
>>> 	CAG05593  CAE45989 : score=  460
>>>
>>>
>>> MAKE NEIGHBOR JOINING DENDROGRAM
>>> 	[MODE=fast] [Output dendrogram
>> file=5XIMxfCi1F.dnd]
>>>
>>>
>>> But then it crashes out with the following
>> messages:
>>>
>>> Abnormal Program Termination:[T-COFFEE,
>> Version_1.37]
>>> Please report the fault to:
>>> cedric.notredame@europe.com (Indicate the version
>>> number)
>>> Thank you for your cooperation :-)
>>>
>>> ------------- EXCEPTION  -------------
>>> MSG: TCoffee call crashed: 256 [command
>>> /usr/bin/t_coffee
>>>
>>
> -in=/tmp/5XIMxfCi1F,XBLOSUM,Mlalign_id_pair,Mclustalw_pair
>>>  -ktuple=2 -output=clustalw
>>> -outfile=/tmp/6wIuLkvcGl/w7jE5bLbih]
>>>
>>> STACK Bio::Tools::Run::Alignment::TCoffee::_run
>>>
>>
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:814
>>> STACK Bio::Tools::Run::Alignment::TCoffee::align
>>>
>>
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Alignment/TCoffee.pm:719
>>> STACK SSIR::align
>>> /usr/lib/perl5/site_perl/5.8.0/SSIR.pm:2094
>>> STACK toplevel /var/www/cgi-bin/ssir.cgi:557
>>>
>>> --------------------------------------
>>>
>>> Similar commands work fine from the command line.
>>>
>>> Does anyone have any ideas?
>>>
>>> Many thanks,
>>>
>>> Jon
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
> ___________________________________________________________ALL-NEW
>> Yahoo! Messenger - all new features - even more fun!
>>  http://uk.messenger.yahoo.com
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l@portal.open-bio.org
>>>
>>
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>> --
>> Jason Stajich
>> Duke University
>> jason at cgt.mc.duke.edu
>>
>
>
> 	
> 	
> 		
> ___________________________________________________________ALL-NEW 
> Yahoo! Messenger - all new features - even more fun!  
> http://uk.messenger.yahoo.comXP_058513 PREDICTED: similar to RIKEN 
> cDNA 4921513O20; cDNA sequence, clone 3-75 [Homo sapiens].
> MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNI
> HVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILK
> MLTVHNASVNLSVIGLKTLDLLLTSGKITLLILDEESDIFMLIFDAMHSFPANDEVQKLG
> CKALHVLFERGNNVEVLMSGNVRCYNIVVEAMKAFPMSERIQEVSCCLLHRLTLGNFFNI
> LVLNEVHEFVVKAVQQYPENAALQISALSCLALLTETIFLNQDLEEKNENQENDDEGEED
> KLFWLEACYKALTWHRKNKHVQEAACWALNNLLMYQNSLHEKIGDEDGHFPAHREVMLSM
> LMHSSSKEVFQASANALSTLLEQNVNFRKILLSKGIHLNVLELMQKHIHSPEVAESGCKM
> LNHLFEGSNTSLDIMAAVVPKILTVMKRHETSLPVQLEALRAILHFIVPGMPEESREDTE
> FHHKLNMVKKQCFKNDIHKLVLAALNRFIGNPGIQKCGLKVISSIVHFPDALEMLSLEGA
> MDSVLHTLQMYPDDQEIQCLGLSLIGYLITKKNVFIGTGHLLAKILVSSLYRFKDVAEIQ
> TKGFQTILAILKLSASFSKLLVHHSFDLVIFHQMSSNIMEQKDQQFLNLCCKCFAKVAMD
> DYLKNVMLERACDQNNSIMVECLLLLGADANQAKEGSSLICQVCEKESSPKLVELLLNSG
> SREQDVRKALTISIGKGDSQIISLLLRRLALDVANNSICLGGFCIGKVEPSWLGPLFPDK
> TSNLRKQTNIASTLARMVIRYQMKSAVEEGTASGSDGNFSEDVLSKFDEWTFIPDSSMDS
> VFAQSDDLDSEGSEGSFLVKKKSNSISVGEFYRDAVLQRCSPNLQRHSNSLGPIFDHEDL
> LKRKRKILSSDDSLRSSKLQSHMRHSDSISSLASEREYITSLDLSANELRDIDALSQKCC
> ISVHLEHLEKLELHQNALTSFPQQLCETLKSLTHLDLHSNKFTSFPSYLLKMSCIANLDV
> SRNDIGPSVVLDPTVKCPTLKQFNLSYNQLSFVPENLTDVVEKLEQLILEGNKISGICSP
> LRLKELKILNLSKNHISSLSENFLEACPKVESFSARMNFLAAMPFLPPSMTILKLSQNKF
> SCIPEAILNLPHLRSLDMSSNDIQYLPGPAHWKSLNLRELLFSHNQISILDLSEKAYLWS
> RVEKLHLSHNKLKEIPPEIGCLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDELHLN
> FDFKHIGCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQ
> SATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQ
> AEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDY
> HFVNATEESDALAKLRKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVPIEF
> PVIDRKRLLQLVRENQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCK
> IMAQILTVKVEGCPKHPKGIISRRDVEKFLSKKRKFPKNYMSQYFKLLEKFQIALPIGEE
> YLLVPSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPYMLSGRER
> ALRPNRMYWRQGIYLNWSPEAYCLVGSEVLDNHPESFLKITVPSCRKGCILLGQVVDHID
> SLMEEWFPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDDLMKKAEEGDLLVNPDQ
> PRLTIPISQIAPDLILADLPRNIMLNNDELEFEQAPEFLLGDGSFGSVYRAAYEGEEVAV
> KIFNKHTSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKAS
> LTRTLQHRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCC
> RMGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTTGGRIVEGLKFPNEFDE
> LEIQGKLPDPVKEYGCAPWPMVEKLIKQCLKENPQERPTSAQVFDILNSAELVCLTRRIL
> LPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALV
> HLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTCLYCNSFSKQSKQKNFLLV
> GTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSESTNSTERNVMWGGCGTKIFS
> FSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAKQNSPVVEVWDKKTEKLCG
> LIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDLSTRRLI
> RVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQKEIQSCLTVWDINLPHEVQ
> NLEKHIEVRKELAEKMRRTSVE
>> CAD39185 hypothetical protein [Homo sapiens].
> VFDILNSAELVCLTRRILLPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTE
> GYTSEEVADSRILCLALVHLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTC
> LYCNSFSKQSKQKNFLLVGTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSEST
> NSTERNVMWGGCGTKIFSFSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAK
> QNSPVVEVWDKKTEKLCGLIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWI
> GTGGGHILLLDLSTRRLIRVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQK
> EIQSCLTVWDINLPHEVQNLEKHIEVRKELAEKMRRTSVE
>> BAB29628 unnamed protein product [Mus musculus].
> MLGAIFERPIPPDTRPWYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCR
> MGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLHDIWTTGSRIMEGLRFPNEFDEL
> AIQGKLPDPVKEYGCAPWPMVEKLITKCLKENPQERPTSAQVFDILNSAELICLMRHILI
> PKNIIVECMVATNLNSKSATLWLGCGNTEKGQLSLFDLNTERYSYEEVADSRILCLALVH
> LAAEKESWVVCGTQSGALLVINVEEETKRHTLEKMTDSVTCLHCNSLAKQSKQSNFLLVG
> TADGNLMIFEDKAVKCKGAAPLKTLHIGDVSTPLMCLSESLNSSERHITWGGCGTKVFSF
> SNDFTIQKLIETKTNQLFSYAAFSDSNIIALAVDTALYIAKKNSPVVEVWDKKTEKLCEL
> IDCVHFLKEVMVKLNKESKHQLSYSGRVKALCLQKNTALWIGTGGGHILLLDLSTRRVIR
> TIHNFCDSVRAMATAQLGSLKNVMLVLGYKRKSTEGIQEQKEIQSCLSIWDLNLPHEVQN
> LEKHIEVRTELADKMRKTSVE
>> AAH34074 4921513O20Rik protein [Mus musculus].
> SEIIIRLYEMPYFPMGFWSRLINRLLEISPFMLSGRERALRPNRMYWRQGIYLNWSPEAY
> CLVGSEVLDNRPESFLKITVPSCRKGCILLGRVVDHIDSLMEEWFPGLLEIDICGEGETL
> LKKWALYSFNDGEEHQKILLDELMKKAEEGDLLINPDQPRLTIPISQIAPDLILADLPRN
> IMLNNDELEFEEAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQELVVLCHL
> HHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVADGLRYLHS
> AMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKTSEGTPGFRAPEVARGN
> VIYNQQADVYSFGLLLHDIWTTGSRIMEGLRFPNEFDELAIQGKLPDPVKEYGCAPWPMV
> EKLITKCLKENPQERPTSAQVFDILNSAELICLMRHILIPKNIIVECMVATNLNSKSATL
> WLGCGNTEKGQLSLFDLNTERYSYEEVADSRILCLALVHLAAEKESWVVCGTQSGALLVI
> NVEEETKRHTLEKMTDSVTCLHCNSLAKQSKQSNFLLVGTADGNLMIFEDKAVKCKGAAP
> LKTLHIGDVSTPLMCLSESLNSSERHITWGGCGTKVFSFSNDFTIQKLIETKTNQLFSYA
> AFSDSNIIALAVDTALYIAKKNSPVVEVWDKKTEKLCELIDCVHFLKEVMVKLNKESKHQ
> LSYSGRVKALCLQKNTALWIGTGGGHILLLDLSTRRVIRTIHNFCDSVRAMATAQLGSLK
> NVMLVLGYKRKSTEGIQEQKEIQSCLSIWDLNLPHEVQNLEKHIEVRTELADKMRKTSVE
>> XP_235581 similar to RIKEN cDNA 4921513O20; cDNA sequence, clone 3-75 
>> [Rattus norvegicus].
> MASGACQGCDEEEEEEALKKLIVRLNNVQEGKQIETLLQLLEDILVFTYSDRASKLFEGK
> NVHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTLQSLIGPQDIGNDWEVLGIHRLI
> LKMLTVHHANVNLSIVGLKALDLLLDSGKITLLILDEECDVFLLIFDAMHRYSANEEVQK
> LACKALHVLFERVSEEQLTEFVENKDYMTLLSTFRSFKRDEEIVHHVLCCLHSLAVTCSN
> VEVLMSGNVRCYNIVVEAMKTFPTSENIQEVSCSLLHKLTLGNFFNILVLNEVHVFVVKA
> VQRYPENVALQISALSCLALLNLEERSETQENSDEDSEKPFWLEPCYKALMRHRKNKHVQ
> EAACWALNNLLMYQSSLHEKIGDEDGQFPAHREVMLSMLMHSSSKDVFQAAAHALSTLLE
> QNGLPLASIINGGMACICTHKVSLVHAPMSSILVLPSSMKILLAKGVYLNVLELMQRHAQ
> VPEVAESGCKMLSHLFEGSNPSLDTVAAVIPKILTVMRTHGTSLSVQLEALRALLHFVVP
> GVSEDSRDDSRCQPNVLRTQCFRTDIHKLVLAALNRFIGNPGIQKCGLKVISSFAHLPDA
> LEMLSLHGAVDSVLHTLQMYPDDQEIQCLGLHLMGCLMTKKNFCIGTGHLLAKILASTLQ
> RFKDVAEVQTTGLQTVLSMLDLSVSFSKLLVHYSFDVVMFHQMSSGVLEQKDEQFLNLCC
> KCFAKVAVDDELKSKMLERACDQNNSIMVECLLLLGADANQAKGATSLIYQVCEKESSPK
> LVELLLNSGCREQDVRKALTVSIQKGDNQVISLLLRRLALDLANNSICLGGFCIGKLDPS
> WLGPLFPDKSSNLRKQTNAGSVLARKVLRYQMRNTLQEGVASGSEGNFSEDALAKFGEWT
> FIPDSSMDSVFGQSDDLDSEGSESSFLVKKKSNSVSVGEVYRDLALQRCSPNAQRHSSSL
> GPVFDHEDLLRRKRKILSSDESLRSSRLQSHTRQSDSSSSLASEREHITSLDLSANELKD
> IDALGQKCCLSSHLEHLTKLELHQNSLTSFPQQLCETLKCLTHLDLHSNKFATFPSFMLK
> MPSVIHLDASRNDIGPTVVLDPVVKCPSLKQFNLSYNQLSSIPENLDQVVEKLEQLLLEG
> NKISGICSPLSLKELKILNLSKNHIPSLPEDFLEACPKVESFSARMNFLAVHTVSLPPTG
> FILVCFVKIPPEIGRLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDGLHLNFDFKHI
> GCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKMKKSELGMQGATVGI
> DVRDWPIQIRGKRKKDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAM
> KPWLFNIKARASSSPVILVGTHLDVSDEKQRKACIGKITKELLNKRGFPTIRDYHFVNAT
> EESDALAKLRKTIINESLNFKIRDQPVVGQLIPDCYVELEKIILSERKAVPTEFPVINRK
> HLLQLVKEHQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCKVMAQIL
> TVKVDGCLKHPKGIISRRDVEKFLSKKKRFPKNYMAQYFKLLEKFQIALPIGEEYLLVPS
> SLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPFMLSGRERALRPNR
> MYWRQGIYLNWSPEAYCLVGSEVLDSRPESFLKITVPSCRKGCILLGRVVDHIDSLMEEW
> FPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDELMKKAEEGDLLINPDQPRLTIP
> ISQIAPDLILADLPRNIMLNNDELEFEEAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKH
> TSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQ
> HRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKT
> SEGTPGFRAPEVARGNVIYNQQADVYSFGLLLHDIWTTGNRIMEGLRFPNEFDELAIQGK
> LPDPVKEYGCAPWPMVEKLITKCLKENPQERPTSAQVFDILNSAELICLMRHIFIPKDIT
> VECIAATNLNSKRATLWLGCGNTEKGQLSLLDLNTERYSYEEVTDSRILCLALVHLAAEK
> ESWVVCGTQSGALLVINAEDETRRHTLDKMTDSVTCLYCNSFAKQSKQSHFLLVGTADGN
> LMIFEDKTIKCKGAAPLKTLHIGDVSTPLMCLSESMNSSERHITWGGCGTKIFSFSNDFT
> IQKLIETRTNQLFSYSAFSDSNIIAVAVDTALYIAKKNSPVVENYKSCDAGDRSQATCVQ
> NSEMTTALPPSCFKVLAGCTRLGRSVKSLSADRTVNEHILYASREVMVKINKDSKHKLSY
> SGRVKALCLQKNTALWIGTGGGHILLLDLSTRRVIRTIHNFCDSKLSMFCFGKGSLKNVM
> LVLGYKRKSTEGTQEQKEIQSCLSIWDLNLPHEVQNLEKHIEVRTELADKMRKTSVE
>> AAH35949 4921513O20Rik protein [Mus musculus].
> CLALVHLAAEKESWVVCGTQSGALLVINVEEETKRHTLEKMTDSVTCLHCNSLAKQSKQS
> NFLLVGTADGNLMIFEDKAVKCKGAAPLKTLHIGDVSTPLMCLSESLNSSERHITWGGCG
> TKVFSFSNDFTIQKLIETKTNQLFSYAAFSDSNIIALAVDTALYIAKKNSPVVEVWDKKT
> EKLCELIDCVHFLKEVMVKLNKESKHQLSYSGRVKALCLQKNTALWIGTGGGHILLLDLS
> TRRVIRTIHNFCDSVRAMATAQLGSLKNVMLVLGYKRKSTEGIQEQKEIQSCLSIWDLNL
> PHEVQNLEKHIEVRTELADKMRKTSVE
>> XP_415940 PREDICTED: similar to hypothetical protein [Gallus gallus].
> MKVYEILNSAELICLMRYVSIPSTSTAECMVAANQSCKKAGVWIGNGNTEKAQLSFVNLN
> TDGHTCEDIADSKILSLALVTLPTEKENWIVAGTHSGSLWAVNTEDETRRHRLQKMSDSV
> TCLYCNSLSKQSKQKNFFLVGTADGTLAVFEDRAVKCKGATPLKILTIGNVSTPLMCLNE
> STYLSEKNTIWGGCGTKLIALSSDFSVQKLIETKSSQLFCHNAYSDANIISIAVDKSIYL
> AKKNSHFVEIWDKKTEKLSELIDCAHFLKDEVEKLNKESKHKVAYSGRVKTICLQKNTAL
> WVGTGGGHILLLDLSTRRPVRVIDNFCDSIRVMLTAQLGSLKNVVLVLGYCYKSDTEDDK
> SHKELQSCVSVWDINLPHEVQNLKKHIEHSYNTATARIALWPRTGPGSPCPVTGRSDRAH
> SSSPAHTAMAESHRAAHREPCYVSAGPAAFLYLGISAVTWKASVCPRHPQLLQHSKLKRY
> TTGAKASAQNNVGWAPFSSQSRADVSPSHPDQTSQEGAFGGEPEAHPLPAALLGQQAALF
> PPHLNAVAAALCQQLVAVQSMLSNCIARFLSNCAGYLELSSTQQPLKSLQRSPQGIGEWG
> GAPSPGHSQTHHSSSQHDCKLPPEHSAKAGTAAVGP
>> AAH76853 Unknown (protein for IMAGE:6637919) [Xenopus laevis].
> IAPDIVLADLPRNIMLNAEELEFDQAPEFLLGDGGFGSVYRASYKGEDVAVKIFNKHTSS
> RLLRQELTVLSHLHHPSLVYLLAAGVHPRMLVMELAPKGSLDHLLQQDSASLTRTLQHRI
> ALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNSAIIAKIADYGIAQYCCRMGIKTSEG
> TPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTGGARMVEGLKFPNEFDELAIHGRLPD
> PVKEYNCAPWPEVEVLIKKCLKENPQQRPTSVTVYEILNSAELLCLMRNHVIFSMLTAEC
> MVAASPLVKKHVVWVGNGCTEKGQMCCIDLNKGGQTCEDFSDSRILCLTLVTLPGEKQNW
> IVAGTQSGEIITADLDELKIKHTLHKLTDSVTCLLFSCIQGQSQKKYHILAGTANGRIAI
> FENTAVKCAYAAPIKVIDIGDNSTPVMCLCESTYSSEKNSVWGICGTKIFSLSSEFTVQK
> TIDTRTATLYSHGSYSESNITCFAIDKYIYVAKKISPYVEIWDKKTEKICEVLDCVQFLK
> EDSRKRRKCKQEEAYTSRVKALYLQKNTALWVGTGGGHILLIDLSTRQPIRIITSFCDSI
> RSMVPAQLDRGSIKNVVLVLGCRCTPQKEIQSFLSVWDTNLPHEVQNLKKHNEIRQEFAD
> KLRGLSMD
>> CAG05593 unnamed protein product [Tetraodon nigroviridis].
> MVNGEELEEQLRKLLVRLKSQQQERQLGTLIQILQDLLFLAHTDEAAELFEDKDVHVSLT
> VALSSYASRRGVQQVGWSLLCRLMEICPGTLERLTAAQPAAEDSQVLPVHKLVLKVLSQH
> GADCKVTMVGLRALALLLRSDAVPPLLLEDESEDVLGLVVQAMKVFPVNEEVLLHGCGAL
> QVLLETVSEDHLVEFVENQDHVVVLAALQTFLDNPELLLRGLKVLLPLARPGGVRCYSTV
> IAAMDAFPEVEDLQETACRLFRAFTLESYYNILVRNGVQRVAACCTALDLHAEEPDVQEA
> ASWAIERLLVHGAGPRPAEEDQEERTPVHRQLMAALLLHPKAPSVFQAATSAISTLIQQD
> GERSTPRAAVKRCLVPPTFAAFAGRTRAPLLSSGLHVNLVEMMKRHWTSAEVSISACRLL
> SLLFQGRPASLDELNMTMSQILCTIKAHNFNPEVQLEALRASLVLLYPDRSLREHGVSVA
> DPDMADVSLKVLKNQCVLEGAHTLYLEVLNRFISSSAIQKSGLKVLSALADCSGAVDLLC
> QQGAIDTVLHTLQMFPGEREIHYWGFTLLNYLVTKKKLSPMIVPVLASVLVASLVQYRED
> SEMTLKCFQVALRMLDASPRSAAELQRENFDRQIFQQLREDTADLCNYPLRKSVCLALFK
> MWSDSELRYAMLEKACQDGDATMAECLIELGADVNAKTKSESLLYQVGGENLCVHRSVLT
> AGPSVPQVCERGGPLELAELLVRRGAHEQHLRRALAVSVKRADGPAVILLLARLGLDHNS
> SALCLGGFRLGRLDAGWLGPLLAERRSARSLCRTSSKAVSLARFVQSFQRSKSHSSVLRS
> PVDPCLTSGYISEESDDSNFSFVSVDDGQIPNEDMESDGSDSLPGVLSPEDPQALRRRQG
> RQRHPSPEVQPPHQRPGCVGVFFSLFAPVFVFLFQNGQTETEPCDSVQKRYAKSPQKVFR
> PADGPAALQKVQDRVRLLDLSANELDALSCLMDDGVVQQQLGHLLRLDLSHNSLQEFPSS
> LCQSLSSLTRLDLQGNQLPSLPVELLTLQSLNTLNISRNCVGPQLTFDPAVSCPSLRHLN
> LSFNKIAAFPHQLSGAGSQLEELCLEGNCIRELCVPLSLPEIKLLDVSKNSVETVSADFL
> TGCPKLETLNVSVNKISSLSHLPSKLTTLKLANNGFAEVSAAILGLPNLRSVDMRTNRIA
> ALPGPASWESCNLRELNFSQNRIGTLDLSGPVHRWARLEKLHLSDNQLSEIPPQIGLLEG
> LNSLDVSRNANLHSFPDEMGKLGRLWDLPLDGLRLQLDLKLIGNKTKDIVRFLQQRLKKA
> VPYHRMKLIVVGNVASGKTTLIQQLMKLKRSQLKSKSTSVGIDVQDWTIKDWDRKKMVLN
> VWDFSGGEEFSGSHPHFLTSRALYLVVYNLSRGASQVDALKPWLFNIKAAAPVSPVILVG
> THTDVSNELQLQACLTKIREELLSHQSFPAIRDYHMVSASEDSDALTKLRKAIAREVANF
> KIQGQPVMGQLVPDSYVELERQLLQERARVPPEFPVLRHREVLQLIQENQLQLEEAELPH
> AIHFLSEAGQNFHELFFPLLTVLSDFLDFRSGNVELRSCSEEGRLYSHLLVFPAGVLLHF
> DDPALQLQNLYFIDPQWLCHIISQKLTLKSCGFWEPPKGVIQRSLVEKFLSETKCFPKSH
> MTQLFKLLEKFQIALPFGEDQLLVPSRWAHGRSVQRQHTAVCVFVSVGNPTDVGSVFGPS
> LSKHRPVIELPHGENSEVIVRLYEMPYFPMDFWSRQIIRLLEFSSHLLSGREKAVRPNRI
> YWRRGVYLSWSPDAYCLVEAASVEDNPSSFVRITVPSSQKGRVLLGQVVDHVDSLLEEWF
> PGLLSTNMHGSGEALLKKWALYSFEDGQEWSKVLLDDLCPHLDAGVLLQDEEQPGLALPL
> SQVAPDLVLSDQPAGLMLDSAELSVDLSERLGTPATRPEPRLGVLLSDNVLFPGGGGFGN
> VYRGVYRKEDVAVKIFNNHASELYVFRLLRQELVVLSRLRHPSLVALLAASTAARALVME
> LAPRGSLDALFQHENGGLNRKLQHRIALQVADGLRYLHSAMIVYRDLKPHNVLLFNLKTD
> CEMIAKITDYGIAQHCCSMGVRSCEGTPGGLSSWAWFCSRFLPVQRQFVLGVQALGFRLC
> KAPGGERRVVDGCASAGFRAPEVARGNVAYNQQADVFSFGLLLYDLLTCGERISDGMKFP
> SEFDEIAVQRKLPDPVKHYGCAPWPGLQALMRDCLKESPQCRPTSAQVFDRLNSGEVLCL
> MRELAVPRVPSAECLALSGGCTAWLGGGSSAQRRGSVTAVNLHTNAVTTEAIDTSPVLCL
> TTVQIPNQTSDWLVAGTQSGALVVLSSQDALTWHRLQSVRDAVTSLFFHLHPCRNQRKNY
> LLVGTADGTVTIYEDSVLKQEDGRPVKTVTVGQLDTPVVCLGQSLHWQDSRCVWAGCGTK
> VLSFTADYDLGRSVDTRPSAEFQQEQSWASEACVSRMVVDKHVYLSKAGSPLVEVWDKKS
> ERMVDRIDCAHIIRRDSGGTTEGSSSWARVKALLVQSAAALWIGTRGGYLLLLELSKHQP
> LQVIGPRCDSVRCMAPALIETPNWKNVVLVLGRRLPQGRNQADEESVLMVWNGMLPMEAK
> DLKRHCHRREQVAVRMR
>> CAE45989 hypothetical protein [Homo sapiens].
> TEKLCGLIDCVHFLREVTVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDL
> STRRLIRVIYNFCNSVRVMMTAQLGKFLSFRYFSYSLSLIKYAFILRLHFL
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

From nathanhaigh at ukonline.co.uk  Tue Aug 31 07:26:53 2004
From: nathanhaigh at ukonline.co.uk (Nathan Haigh)
Date: Tue Aug 31 07:27:24 2004
Subject: [Bioperl-l] phylip - ProtDist Problem
Message-ID: 

I am trying to run the following script at the bottom which takes a
SimpleAlign object and runs SeqBoot on it. I would then like to take this
output and run ProtDist, Neighbor and Consense to produce a bootstrap
consensus tree. However, ProtDist just seems to fail when it gets to this
line in ProtDist.pm:

	open(PROTDIST,"|".$self->executable);		# line 399 in the
latest version of ProtDist.pm from the CVS

I am running this on WinXP from within a cgi script and have phylip v3.61. I
have no idea why this should fail as the similar line in SeqBoot works fine!

Has anyone come across this problem or know why this might be happening!?

Regards
Nathan



# use seqboot to generate bootstrap alignments
my @params_seqboot = ('datatype'=>'SEQUENCE', 'replicates'=>100);
my $seqboot_factory =
Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params_seqboot);
my $aln_ref = $seqboot_factory->run($aln);

# create distance matrices and construct trees using neighbor
my $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
my $neighbor_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new();
my @tree;
foreach my $a (@{$aln_ref}) {
	my $matrix = $protdist_factory->run($a);
	push @tree, $neighbor_factory->run($matrix);
}
# use consense to get a final tree
my $consense_factory = Bio::Tools::Run::Phylo::Phylip::Consense->new();
my $tree = $consense_factory->run(\@tree);

# output treefile
my $outfilename = "outtrees_ur/homologene.nh"; # unrooted tree
my $outtree = new Bio::TreeIO('-format' => 'newick',
				'-file'   => ">$outfilename");
$outtree->write_tree($tree);


---
avast! Antivirus: Outbound message clean.
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Tested on: 31/08/2004 12:26:50
avast! is copyright (c) 2000-2003 ALWIL Software.
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From jason at cgt.duhs.duke.edu  Tue Aug 31 07:47:43 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Aug 31 07:48:26 2004
Subject: [Bioperl-l] phylip - ProtDist Problem
In-Reply-To: 
References: 
Message-ID: <91FE4E9F-FB43-11D8-8877-000393C44276@cgt.mc.duke.edu>

Hmm - there are some changes in PHYLIP 3.6 from 3.5 menus, did you make 
sure your PHYLIP version environment was set by setting the ENV 
variable otherwise the wrong commands are sent in.

PHYLIPVERSION=3.6

Also you are using 3.6.1 which I know has some bug fixes over 3.6 but 
may also have incurred some changes in how the menus act - I don't 
really know though.

I guess either use 3.5 or try debugging the running of 3.6.1 by putting 
some print statements in there - see what is being sent in to protdist 
and then run protdist by hand to see what are the expected menu items 
to get what you want.  That is how Shawn and I built this in the first 
place.

-jason
On Aug 31, 2004, at 9:26 PM, Nathan Haigh wrote:

> I am trying to run the following script at the bottom which takes a
> SimpleAlign object and runs SeqBoot on it. I would then like to take 
> this
> output and run ProtDist, Neighbor and Consense to produce a bootstrap
> consensus tree. However, ProtDist just seems to fail when it gets to 
> this
> line in ProtDist.pm:
>
> 	open(PROTDIST,"|".$self->executable);		# line 399 in the
> latest version of ProtDist.pm from the CVS
>
> I am running this on WinXP from within a cgi script and have phylip 
> v3.61. I
> have no idea why this should fail as the similar line in SeqBoot works 
> fine!
>
> Has anyone come across this problem or know why this might be 
> happening!?
>
> Regards
> Nathan
>
>
>
> # use seqboot to generate bootstrap alignments
> my @params_seqboot = ('datatype'=>'SEQUENCE', 'replicates'=>100);
> my $seqboot_factory =
> Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params_seqboot);
> my $aln_ref = $seqboot_factory->run($aln);
>
> # create distance matrices and construct trees using neighbor
> my $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
> my $neighbor_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new();
> my @tree;
> foreach my $a (@{$aln_ref}) {
> 	my $matrix = $protdist_factory->run($a);
> 	push @tree, $neighbor_factory->run($matrix);
> }
> # use consense to get a final tree
> my $consense_factory = Bio::Tools::Run::Phylo::Phylip::Consense->new();
> my $tree = $consense_factory->run(\@tree);
>
> # output treefile
> my $outfilename = "outtrees_ur/homologene.nh"; # unrooted tree
> my $outtree = new Bio::TreeIO('-format' => 'newick',
> 				'-file'   => ">$outfilename");
> $outtree->write_tree($tree);
>
>
> ---
> avast! Antivirus: Outbound message clean.
> Virus Database (VPS): 0435-2, 28/08/2004
> Tested on: 31/08/2004 12:26:50
> avast! is copyright (c) 2000-2003 ALWIL Software.
> http://www.avast.com
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

From jason at cgt.duhs.duke.edu  Tue Aug 31 08:07:59 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Aug 31 08:08:38 2004
Subject: [Bioperl-l] phylip - ProtDist Problem
In-Reply-To: 
References: 
Message-ID: <669AD99C-FB46-11D8-8877-000393C44276@cgt.mc.duke.edu>

Well for starters what does this print?

print $protdist->executable


On Aug 31, 2004, at 10:04 PM, Nathan Haigh wrote:

> Yes, I have the ENV variable set to 3.6
>
> I first noticed it not working when using V3.6a3, and thought I'd 
> install
> the latest version 3.61 to see if this fixed the problem - but it 
> didn't.
>
> I checked what keystrokes were being piped into ProtDist, and the only 
> the
> menu choice was a 'Y' (which should just run the program, and hasn't
> changed between version). I ran the program manually and gave it the
> filename that had been used by ProtDist.pm and everything worked
> correctly!
>
> I've compared what has been sent to both SeqBoot and ProtDist (in 
> terms of
> menu choices etc) and they seem to have the same syntax etc. However, 
> as
> I've said ProtDist doesn't seem to want to get past the line:
>
> 	open(PROTDIST,"|".$self->executable);
>
> Any ideas, why this particular line is causing the problems? Could it 
> be
> something to do with BioPerl or maybe my OS? If you have any thoughts 
> on
> debugging this, I'd like to know!
>
> Thanks
> Nathan
>
>> -----Original Message-----
>> From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu]
>> Sent: 31 August 2004 12:48
>> To: nathanhaigh@ukonline.co.uk
>> Cc: bioperl
>> Subject: Re: [Bioperl-l] phylip - ProtDist Problem
>>
>> Hmm - there are some changes in PHYLIP 3.6 from 3.5 menus, did you 
>> make
>> sure your PHYLIP version environment was set by setting the ENV
>> variable otherwise the wrong commands are sent in.
>>
>> PHYLIPVERSION=3.6
>>
>> Also you are using 3.6.1 which I know has some bug fixes over 3.6 but
>> may also have incurred some changes in how the menus act - I don't
>> really know though.
>>
>> I guess either use 3.5 or try debugging the running of 3.6.1 by 
>> putting
>> some print statements in there - see what is being sent in to protdist
>> and then run protdist by hand to see what are the expected menu items
>> to get what you want.  That is how Shawn and I built this in the first
>> place.
>>
>> -jason
>> On Aug 31, 2004, at 9:26 PM, Nathan Haigh wrote:
>>
>>> I am trying to run the following script at the bottom which takes a
>>> SimpleAlign object and runs SeqBoot on it. I would then like to take
>>> this
>>> output and run ProtDist, Neighbor and Consense to produce a bootstrap
>>> consensus tree. However, ProtDist just seems to fail when it gets to
>>> this
>>> line in ProtDist.pm:
>>>
>>> 	open(PROTDIST,"|".$self->executable);		# line 399 in the
>>> latest version of ProtDist.pm from the CVS
>>>
>>> I am running this on WinXP from within a cgi script and have phylip
>>> v3.61. I
>>> have no idea why this should fail as the similar line in SeqBoot 
>>> works
>>> fine!
>>>
>>> Has anyone come across this problem or know why this might be
>>> happening!?
>>>
>>> Regards
>>> Nathan
>>>
>>>
>>>
>>> # use seqboot to generate bootstrap alignments
>>> my @params_seqboot = ('datatype'=>'SEQUENCE', 'replicates'=>100);
>>> my $seqboot_factory =
>>> Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params_seqboot);
>>> my $aln_ref = $seqboot_factory->run($aln);
>>>
>>> # create distance matrices and construct trees using neighbor
>>> my $protdist_factory =
> Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
>>> my $neighbor_factory =
> Bio::Tools::Run::Phylo::Phylip::Neighbor->new();
>>> my @tree;
>>> foreach my $a (@{$aln_ref}) {
>>> 	my $matrix = $protdist_factory->run($a);
>>> 	push @tree, $neighbor_factory->run($matrix);
>>> }
>>> # use consense to get a final tree
>>> my $consense_factory =
> Bio::Tools::Run::Phylo::Phylip::Consense->new();
>>> my $tree = $consense_factory->run(\@tree);
>>>
>>> # output treefile
>>> my $outfilename = "outtrees_ur/homologene.nh"; # unrooted tree
>>> my $outtree = new Bio::TreeIO('-format' => 'newick',
>>> 				'-file'   => ">$outfilename");
>>> $outtree->write_tree($tree);
>>>
>>>
>>> ---
>>> avast! Antivirus: Outbound message clean.
>>> Virus Database (VPS): 0435-2, 28/08/2004
>>> Tested on: 31/08/2004 12:26:50
>>> avast! is copyright (c) 2000-2003 ALWIL Software.
>>> http://www.avast.com
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l@portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>> --
>> Jason Stajich
>> Duke University
>> jason at cgt.mc.duke.edu
>
>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

From jason at cgt.duhs.duke.edu  Tue Aug 31 08:35:29 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Aug 31 08:41:49 2004
Subject: [Bioperl-l] phylip - ProtDist Problem
In-Reply-To: 
References: 
Message-ID: <3DE2F7E6-FB4A-11D8-8877-000393C44276@cgt.mc.duke.edu>

Maybe there is something wrong with how windows is doing things - maybe 
it doesn't accept pipes in the same way that unix does.  You can 
simplify by just writing a little script that does the basics of the 
program execution - perhaps

open(RUN, "| I:\Science\Bioinformatics\PhylipV3.61\exe\protdist.exe") 
|| die ( "cannot open pipe to protdist");

If this fails, don't know what to tell you except get a linux box or 
don't rely on phylip programs - I definitely would prefer that Joe 
would make it accept command-line options rather than this jiggery but 
I know that would be a lot of work.

-jason

On Aug 31, 2004, at 10:24 PM, Nathan Haigh wrote:

> Okay here goes:
>
> $protdist->executable is: 
> I:\Science\Bioinformatics\PhylipV3.61\exe\protdist.exe
> $instring is:
> C:\temp\tJytmRILW9\thukMCrDl3
> Y
>
>
>> -----Original Message-----
>> From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu]
>> Sent: 31 August 2004 13:08
>> To: nathanhaigh@ukonline.co.uk
>> Cc: bioperl
>> Subject: Re: [Bioperl-l] phylip - ProtDist Problem
>>
>> Well for starters what does this print?
>>
>> print $protdist->executable
>>
>>
>> On Aug 31, 2004, at 10:04 PM, Nathan Haigh wrote:
>>
>>> Yes, I have the ENV variable set to 3.6
>>>
>>> I first noticed it not working when using V3.6a3, and thought I'd
>>> install
>>> the latest version 3.61 to see if this fixed the problem - but it
>>> didn't.
>>>
>>> I checked what keystrokes were being piped into ProtDist, and the 
>>> only
>>> the
>>> menu choice was a 'Y' (which should just run the program, and hasn't
>>> changed between version). I ran the program manually and gave it the
>>> filename that had been used by ProtDist.pm and everything worked
>>> correctly!
>>>
>>> I've compared what has been sent to both SeqBoot and ProtDist (in
>>> terms of
>>> menu choices etc) and they seem to have the same syntax etc. However,
>>> as
>>> I've said ProtDist doesn't seem to want to get past the line:
>>>
>>> 	open(PROTDIST,"|".$self->executable);
>>>
>>> Any ideas, why this particular line is causing the problems? Could it
>>> be
>>> something to do with BioPerl or maybe my OS? If you have any thoughts
>>> on
>>> debugging this, I'd like to know!
>>>
>>> Thanks
>>> Nathan
>>>
>>>> -----Original Message-----
>>>> From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu]
>>>> Sent: 31 August 2004 12:48
>>>> To: nathanhaigh@ukonline.co.uk
>>>> Cc: bioperl
>>>> Subject: Re: [Bioperl-l] phylip - ProtDist Problem
>>>>
>>>> Hmm - there are some changes in PHYLIP 3.6 from 3.5 menus, did you
>>>> make
>>>> sure your PHYLIP version environment was set by setting the ENV
>>>> variable otherwise the wrong commands are sent in.
>>>>
>>>> PHYLIPVERSION=3.6
>>>>
>>>> Also you are using 3.6.1 which I know has some bug fixes over 3.6 
>>>> but
>>>> may also have incurred some changes in how the menus act - I don't
>>>> really know though.
>>>>
>>>> I guess either use 3.5 or try debugging the running of 3.6.1 by
>>>> putting
>>>> some print statements in there - see what is being sent in to
> protdist
>>>> and then run protdist by hand to see what are the expected menu 
>>>> items
>>>> to get what you want.  That is how Shawn and I built this in the
> first
>>>> place.
>>>>
>>>> -jason
>>>> On Aug 31, 2004, at 9:26 PM, Nathan Haigh wrote:
>>>>
>>>>> I am trying to run the following script at the bottom which takes a
>>>>> SimpleAlign object and runs SeqBoot on it. I would then like to 
>>>>> take
>>>>> this
>>>>> output and run ProtDist, Neighbor and Consense to produce a
> bootstrap
>>>>> consensus tree. However, ProtDist just seems to fail when it gets 
>>>>> to
>>>>> this
>>>>> line in ProtDist.pm:
>>>>>
>>>>> 	open(PROTDIST,"|".$self->executable);		# line 399 in the
>>>>> latest version of ProtDist.pm from the CVS
>>>>>
>>>>> I am running this on WinXP from within a cgi script and have phylip
>>>>> v3.61. I
>>>>> have no idea why this should fail as the similar line in SeqBoot
>>>>> works
>>>>> fine!
>>>>>
>>>>> Has anyone come across this problem or know why this might be
>>>>> happening!?
>>>>>
>>>>> Regards
>>>>> Nathan
>>>>>
>>>>>
>>>>>
>>>>> # use seqboot to generate bootstrap alignments
>>>>> my @params_seqboot = ('datatype'=>'SEQUENCE', 'replicates'=>100);
>>>>> my $seqboot_factory =
>>>>> Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params_seqboot);
>>>>> my $aln_ref = $seqboot_factory->run($aln);
>>>>>
>>>>> # create distance matrices and construct trees using neighbor
>>>>> my $protdist_factory =
>>> Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
>>>>> my $neighbor_factory =
>>> Bio::Tools::Run::Phylo::Phylip::Neighbor->new();
>>>>> my @tree;
>>>>> foreach my $a (@{$aln_ref}) {
>>>>> 	my $matrix = $protdist_factory->run($a);
>>>>> 	push @tree, $neighbor_factory->run($matrix);
>>>>> }
>>>>> # use consense to get a final tree
>>>>> my $consense_factory =
>>> Bio::Tools::Run::Phylo::Phylip::Consense->new();
>>>>> my $tree = $consense_factory->run(\@tree);
>>>>>
>>>>> # output treefile
>>>>> my $outfilename = "outtrees_ur/homologene.nh"; # unrooted tree
>>>>> my $outtree = new Bio::TreeIO('-format' => 'newick',
>>>>> 				'-file'   => ">$outfilename");
>>>>> $outtree->write_tree($tree);
>>>>>
>>>>>
>>>>> ---
>>>>> avast! Antivirus: Outbound message clean.
>>>>> Virus Database (VPS): 0435-2, 28/08/2004
>>>>> Tested on: 31/08/2004 12:26:50
>>>>> avast! is copyright (c) 2000-2003 ALWIL Software.
>>>>> http://www.avast.com
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l@portal.open-bio.org
>>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>> --
>>>> Jason Stajich
>>>> Duke University
>>>> jason at cgt.mc.duke.edu
>>>
>>>
>> --
>> Jason Stajich
>> Duke University
>> jason at cgt.mc.duke.edu
>
>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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From jon_r_manning at yahoo.com  Tue Aug 31 08:42:17 2004
From: jon_r_manning at yahoo.com (=?iso-8859-1?q?Jonathan=20Manning?=)
Date: Tue Aug 31 08:42:41 2004
Subject: [Bioperl-l] Problem with T-Coffee
In-Reply-To: 
Message-ID: <20040831124217.36744.qmail@web52704.mail.yahoo.com>

Hi Jason,

Yes I did; but I eventually gave up and used Muscle
instead which works fine!

Thanks,

Jon

 --- Jason Stajich  wrote: 
> Did you also symlink mocca and lalign2list in
> addition to t_coffee as 
> those are also depended on by t_coffee?
> 
> -jason
> 
> On Aug 28, 2004, at 1:05 AM, Jonathan Manning wrote:
> 
> > Hi Jason,
> >
> > Thanks for the reply.
> >
> > My versions of Bioperl, Bioperl-run and T-Coffee
> are
> > the same on both machines.
> >
> > When I run the test I get the following output:
> >
> >
> > 1..22
> > # Running under perl version 5.008 for linux
> > # Current time local: Fri Aug 27 10:10:30 2004
> > # Current time GMT:   Fri Aug 27 14:10:30 2004
> > # Using Test.pm version 1.23
> > ok 1
> > ok 2
> > ok 3
> > ok 4
> > ok 5
> >
> > Abnormal Program Termination:[T-COFFEE,
> Version_1.37]
> > Please report the fault to:
> > cedric.notredame@europe.com (Indicate the version
> nu
> > mber)
> > Thank you for your cooperation :-)
> >
> > ------------- EXCEPTION  -------------
> > MSG: TCoffee call crashed: 256 [command
> > /usr/bin/t_coffee -in=t/data/cysprot.fa,
> > Xblosum,Mlalign_id_pair,Mclustalw_pair  -ktuple=3
> > -output=clustalw -outfile=/tmp
> > /MvE0LpuQko/mPn9bfUyI0 -quiet]
> >
> > STACK Bio::Tools::Run::Alignment::TCoffee::_run
> > Bio/Tools/Run/Alignment/TCoffee.
> > pm:814
> > STACK Bio::Tools::Run::Alignment::TCoffee::align
> > Bio/Tools/Run/Alignment/TCoffee
> > .pm:719
> > STACK toplevel t/TCoffee.t:62
> >
> > --------------------------------------
> > ok 6 # skip TCoffee program not found. Skipping.
> >
> > ok 7 # skip TCoffee program not found. Skipping.
> >
> > ok 8 # skip TCoffee program not found. Skipping.
> >
> > ok 9 # skip TCoffee program not found. Skipping.
> >
> > ok 10 # skip TCoffee program not found. Skipping.
> >
> > ok 11 # skip TCoffee program not found. Skipping.
> >
> > ok 12 # skip TCoffee program not found. Skipping.
> >
> > ok 13 # skip TCoffee program not found. Skipping.
> >
> > ok 14 # skip TCoffee program not found. Skipping.
> >
> > ok 15 # skip TCoffee program not found. Skipping.
> >
> > ok 16 # skip TCoffee program not found. Skipping.
> >
> > ok 17 # skip TCoffee program not found. Skipping.
> >
> > ok 18 # skip TCoffee program not found. Skipping.
> >
> > ok 19 # skip TCoffee program not found. Skipping.
> >
> > ok 20 # skip TCoffee program not found. Skipping.
> >
> > ok 21 # skip TCoffee program not found. Skipping.
> >
> > ok 22 # skip TCoffee program not found. Skipping.
> >
> >
> > I guess that explains something- it's not seeing
> the
> > T-Coffee program for some reason. I don't know why
> it
> > shouldn't- I placed it in /usr/bin using a
> soft-link
> > (ln -s).
> >
> > Nothing unusual with my sequence file, but I'm
> > attaching it anyway, and relevant snippet of code
> is
> > below (it's a subroutine passed an arrayref of
> > sequences):
> >
> >  sub align {
> >
> > 	# T-COFFEE USED TO CREATE A Bio::SimpleAlign
> OBJECT
> >
> >     my ($self) = shift;
> >     my ( $relatives, $params ) = @_;
> >     my @params  = @{$params};
> >     my $Aligner = new
> > Bio::Tools::Run::Alignment::TCoffee(@params);
> >     my $aln     = $Aligner->align($relatives);
> >
> >     return $aln;
> > }
> >
> > I don't really have time to swap the program I'm
> > using, so I hope I can get this to work!
> >
> > Thanks again- help appreciated.
> >
> > Jon
> >
> >
> >  --- Jason Stajich 
> wrote:
> >> different versions of bioperl/bioperl-run on the
> dev
> >> machine and other
> >> machine?  This happens for every every
> >> alignment you try on the non-dev machine? i.e.
> >> % perl -I. -w t/TCoffee.t
> >> in bioperl-run fails on the new machine too?
> >>
> >> An example sequence file and the script with at
> >> least the t-coffee part
> >> would help in debugging the problem if all of
> that
> >> is true.
> >>
> >> I've also moved to using MUSCLE instead of
> T-Coffee
> >> for some analyses
> >> because it is much faster and seems to be as
> >> accurate.  The newest MAFFT
> >> is also rumoured to be as accurate too although
> one
> >> should always do their
> >> own tests on one's own data first...
> >>
> >> -jason
> >> On Fri, 27 Aug 2004, [iso-8859-1] Jonathan
> Manning
> >> wrote:
> >>
> >>> Hi to all,
> >>>
> >>> I've been using T-Coffee via the Bioperl wrapper
> >> as
> >>> part of a larger project. Though it worked fine
> on
> >> the
> >>> development system, it's not working on a
> >> different
> >>> one. It seems to do the pairwise stuff, at least
> >> it
> >>> gets to this stage:
> >>>
> >>> ......
> >>> 	AAH76853  CAG05593 : score=  400
> >>> 	AAH76853  CAE45989 : score=  410
> >>> 	CAG05593  CAE45989 : score=  460
> >>>
> >>>
> >>> MAKE NEIGHBOR JOINING DENDROGRAM
> >>> 	[MODE=fast] [Output dendrogram
> >> file=5XIMxfCi1F.dnd]
> >>>
> >>>
> >>> But then it crashes out with the following
> >> messages:
> >>>
> >>> Abnormal Program Termination:[T-COFFEE,
> >> Version_1.37]
> >>> Please report the fault to:
> >>> cedric.notredame@europe.com (Indicate the
> version
> >>> number)
> >>> Thank you for your cooperation :-)
> >>>
> >>> ------------- EXCEPTION  -------------
> >>> MSG: TCoffee call crashed: 256 [command
> >>> /usr/bin/t_coffee
> >>>
> >>
> >
>
-in=/tmp/5XIMxfCi1F,XBLOSUM,Mlalign_id_pair,Mclustalw_pair
> >>>  -ktuple=2 -output=clustalw
> >>> -outfile=/tmp/6wIuLkvcGl/w7jE5bLbih]
> 
=== message truncated === 


	
	
		
___________________________________________________________ALL-NEW Yahoo! Messenger - all new features - even more fun!  http://uk.messenger.yahoo.com
From barry.moore at genetics.utah.edu  Tue Aug 31 14:10:07 2004
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue Aug 31 23:42:41 2004
Subject: [Bioperl-l] locuslink - gene positions?
In-Reply-To: <1093872140.41332a0c90144@webmail.njit.edu>
References: <710690625AD28941BDAD9D2271264C580188787F@iu-mssg-mbx08.exchange.iu.edu>
	<1093872140.41332a0c90144@webmail.njit.edu>
Message-ID: <4134BEFF.10405@genetics.utah.edu>

Chromosome coordinates for genes and other features are available from 
UCSC genome browser either as file downloads from the ftp site, or as 
table downloads from the table browser.

Barry

hz5@njit.edu wrote:

>I believe that there is a flatfile in MapView ftp directory, some kind of md 
>file have coordinate of genes relative to both chromosome and contigs.
>
>Haibo
>
>Quoting "Fontaine, Burr R" :
>
>  
>
>>I am trying to mirror portions of Locuslink and have figured out how to
>>get all of the data elements I need from the locuslink module except for
>>the gene starting postion (in bp coordinates). Chromosome coordinates
>>would be best but contig coordinates are OK if there is a way to convert
>>them. I've looked at the location modules but don't see any obvious
>>answers there. Can someone help me figure out the best way to do this?
>>
>>Thanks in advance for your help.
>>
>>Burr Fontaine
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l@portal.open-bio.org
>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>    
>>
>
>
>
>=========================================================
>Haibo Zhang, PhD student
>Computational Biology, NJIT & Rutgers University
>Center for Applied Genomics, PHRI
>http://afs13.njit.edu/~hz5
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>  
>

-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT