CLUSTALW Multiple Sequence Alignment

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1 Version 3.2 CLUSTALW Multiple Sequence Alignment Selected Sequences) FETA_GORGO FETA_HORSE FETA_HUMAN FETA_MOUSE FETA_PANTR FETA_RAT Import Alignments) Return Help Report Bugs Fasta label *) Workbench label FETA_GORGO FETA_GORGO FETA_HORSE FETA_HORSE FETA_HUMAN FETA_HUMAN FETA_MOUSE FETA_MOUSE FETA_PANTR FETA_PANTR FETA_RAT FETA_RAT *) Clustalw cuts off Fasta labels after the first space e.g. ">abc def" becomes ">abc"). Sequence alignment Consensus key see documentation for details) * - single, fully conserved residue : - conservation of strong groups. - conservation of weak groups Page 1 of 6

2 - no consensus CLUSTAL W 1.81) multiple sequence alignment FETA_HUMAN MKWVESIFLIFLLNFTESRTLHRNEYGIASILDSYQCTAEISLADLATIFFAQF FETA_GORGO MKWVESIFLIFLLNFTESRTLHRNEYGIASILDSYQCTAEISLADLATIFFAQF FETA_PANTR MKWVESIFLIFLLNFTESRTLHRNEYGIASILDSYQCTAEINLTDLATIFFAQF FETA_HORSE MKWVVSILLIFLLNSTESRTMHSNAYGIASALDSFQCSPEMNLVDLATIFFAQF FETA_RAT MKQPATMKWSASISFLLLLNFAEPRVLHTNEFGIESTLDSSQCPTEKNMFNVATIVVAQF FETA_MOUSE MKWITPASLILLLHFAASKALHENEFGIASTLDSSQCVTEKNVLSIATITFTQF ***. :::**: :.:.:* * :** * *** **.*.:.:***.:** FETA_HUMAN VQEATYKEVSKMVKDALTAIEKPTGDEQSSGCLENQLPAFLEELCHEKEILEKYGHSDCC FETA_GORGO VQEATYKEVSKMVKDALTAIEKPTGDEQSAGCLENQLPAFLEELCHEKEILEKYGLSDCC FETA_PANTR VQEATYKEVSKMVKDALTAIEKPTGDEQSAGCLENQLPAFLEELCREKEILEKYGHSDCC FETA_HORSE VQEATYKEVSKMVKDVLTVTEKSTGSEQPTGCSENRLSAFLEEICHEEEIPEKYGLSGCC FETA_RAT VQDATKAEVNKMSSDALAAMKENTGD----GCLENQLSVFLDEICHETELSNKYGFSGCC FETA_MOUSE VPEATEEEVNKMTSDVLAAMKKNSGD----GCLESQLSVFLDEICHETELSNKYGLSGCC * :** **.**.*.*:. :: :*. ** *.:*..**:*:*:* *: :*** *.** FETA_HUMAN SQSEEGRHNCFLAHKKPTPASIPLFQVPEPVTSCEAYEEDRETFMNKFIYEIARRHPFLY FETA_GORGO SQSEEGRHNCFLAHKKPTPASIPLFQVPEPVTSCEAYEEDRETFMNKFIYEIARRHPFLY FETA_PANTR SQSEEGRHNCFLAHKKPTPASIPFFQVPEPVTSCEAYEEDRETFMNKFIYEIARRHPFLY FETA_HORSE SQNEEERHNCLLARKKDSPASIPPFQVPEPVTSCKAYEENREMFLNRYLYEIARRHPFLY FETA_RAT NQSGVERHQCLLARKKTAPDSVPPFHFPETAESCPAYEENRAMSINTFIYDVSKRNPFLY FETA_MOUSE SQSGVERHQCLLARKKTAPASVPPFQFPEPAESCKAHEENRAVFMNRFIYEVSRRNPFMY.*. **:*:**:** :* *:* *:.**.. ** *:**:* :* ::*::::*:**:* FETA_HUMAN APTILLWAARYDKIIPSCCKAENAVECFQTKAATVTKELRESSLLNQHACAVMKNFGTRT FETA_GORGO APTILLWAARYDKIIPSCCKAENAVECFQTKAATVTKELRESSLLNQHACAVMKNFGTRT FETA_PANTR APTILLWAARYDKIIPSCCKAENAVECFQTKAATVTKELRESSLLNQHACAVMKNFGTRT FETA_HORSE SSTALYLASHYDKIISACCKSENAVECFQSKAATITKELRETSLLNQHVCAVIRNFGPRT FETA_RAT APTILYLAAQYDKAVPACCKADNMEECFQTKRASMAKELREGSMLNEHVCAVIRKFGSRN FETA_MOUSE APAILSLAAQYDKVVLACCKADNKEECFQTKRASIAKELREGSMLNEHVCSVIRKFGSRN :.: * *::*** : :***::* ****:* *:::***** *:**:*.*:*:::**.*. FETA_HUMAN FQAITVTKLSQKFTKVNFTEIQKLVLDVAHVHEHCCRGDVLDCLQDGEKIMSYICSQQDT FETA_GORGO FQAITVTKLSQKFTKVNFTEIQKLVLDVAHVHEHCCRGDVLDCLQDGEKIMSYICSQQDT FETA_PANTR FQAITVTKLSQKFTKVNFTEIQKLVLDVAHVHEHCCRGDVLDCLQDGEKIMSYICSQQDT FETA_HORSE LQAITVTTLSQRYSKANFTEIQKLVLDVAHAHEECCRGNVEECVQDGEKLISYVCSQEDI FETA_RAT LQAVLIIKLSQKFPKANITEIRKLALDVAHIHEQCCHGNAMECLQDGESVMTHMCSQQEI FETA_MOUSE LQATTIIKLSQKLTEANFTEIQKLALDVAHIHEECCQGNSLECLQDGEKVMTYICSQQNI :** :.***:.:.*:***:**.***** **.**:*: :*:****.:::::***:: FETA_HUMAN LSNKITECCKLTTLERGQCIIHAENDEKPEGLSPNLNRFLGDRDFNQFSSGEKNIFLASF FETA_GORGO LSNKITECCKLTTLERGQCIIHAENDEKPEGLSPNLNRFLGDRDFNQFSSGEKNIFLASF FETA_PANTR LSNKITECCKLTTLERGQCIIHAENDEKPEGLSPNLNRFLGDRDFNQFSSGEKNIFLASF FETA_HORSE LSSSIVECCKLPTVELAQCIIHAENDDKPEGLSPNLNRLLGERDFNQFSSKEKDLFMARF FETA_RAT LSSKTAECCKLPTIELGYCIIHAENGDKPEGLTLNPSEFLGDRNFAQFSSEEKLLFMASF FETA_MOUSE LSSKIAECCKLPMIQLGFCIIHAENGVKPEGLSLNPSQFLGDRNFAQFSSEEKIMFMASF **...*****. ::. *******. *****: *..:**:*:* **** ** :*:* * FETA_HUMAN VHEYSRRHPQLAVSVILRVAKGYQELLEKCFQTENPLECQDKGEEELQKYIQESQALAKR FETA_GORGO VHEYSRRHPQLAVSVILRVAKGYQELLEKCFQTENPLECQDKGEEELQKYIQESQALAKR FETA_PANTR VHEYSRRHPQLAVSVILRVAKGYQELLEKCFQTENPLECQDKGEEELQKYIQESQALAKR FETA_HORSE TYEYSRRHTKLAVPVILRVAKGYQEFLEKCSQSENPLECQDKGEEELQKYIQEGQALAKR FETA_RAT LHEYSRNHPNLPVSVILKTAKSYQEILEKCSQSETPSKCQDNMEEELQKHIQESQALAKQ Page 2 of 6

3 FETA_MOUSE LHEYSRTHPNLPVSVILRIAKTYQEILEKCSQSGNLPGCQDNLEEELQKHIEESQALSKQ :**** *.:*.*.***: ** ***:**** *:. ***: ******:*:*.***:*: FETA_HUMAN SCGLFQKLGEYYLQNAFLVAYTKKAPQLTSSELMAITRKMAATAATCCQLSEDKLLACGE FETA_GORGO SCGLFQKLGEYYLQNAFLVAYTKKAPQLTSSELMAITRKMAATAATCCQLSEDKLLACGE FETA_PANTR SCGLFQKLGEYYLQNAFLVAYTKKAPQLTSSELMAITRKMAATAATCCQLSEDKLLACGE FETA_HORSE SCGLFQKLGDYYLQNAFLVAYTKKAPQLTPPELIALTRKMATAAATCCQLSEDKQLACGE FETA_RAT SCNLYQKLGPYYLQNLFLIGYTRKAPQLTSAELIDLTGKMVSIASTCCQLSEEKRSACGE FETA_MOUSE SCALYQTLGDYKLQNLFLIGYTRKAPQLTSAELIDLTGKMVSIASTCCQLSEEKWSGCGE ** *:*.** * *** **:.**:******..**: :* **.: *:*******:*.*** FETA_HUMAN GAADIIIGHLCIRHEMTPVNPGVGQCCTSSYANRRPCFSSLVVDETYVPPAFSDDKFIFH FETA_GORGO GAADIIIGHLCIRHEMTPVNPGVGQCCTSSYANRRPCFSSLVVDETYVPPAFSDDKFIFH FETA_PANTR GAADIIIGHLCIRHETTPVNPGVGQCCTSSYANRRPCFSSLVVDETYVPPAFSDDKFIFH FETA_HORSE QVAGLIIGQLCIRHEESPINPGVGQCCTSSYANRRPCFSSLVVDETYVPPPFSDDKFIFH FETA_RAT GLADIYIGHLCLRHEANPVNSGINHCCSSSYSNRRLCITSFLRDETYVPPPFSEDKFIFH FETA_MOUSE GMADIFIGHLCIRNEASPVNSGISHCCNSSYSNRRLCITSFLRDETYAPPPFSEDKFIFH *.: **:**:*:*.*:*.*:.:**.***:*** *::*:: ****.**.**:****** FETA_HUMAN KDLCQAQGVALQTMKQEFLINLVKQKPQITEEQLEAVIADFSGLLEKCCQGQEQEVCFAE FETA_GORGO KDLCQAQGVALQTMKQEFLINLVKQKPQITEEQLETVIADFSGLLEKCCQGQEQEVCFAE FETA_PANTR KDLCQAQGVALQTMKQEFLINLVKQKPQITEEQLEAVIADFSGLLEKCCQGQEQEVCFAE FETA_HORSE KDLCQAQGVALQTMKQQFLINLVKQKPQITEEQLEAVIADFSGLLEKCCQGQGQEVCFSE FETA_RAT KDLCQAQGRALQTMKQELLINLVKQKPEMTEEQHAAVTADFSGLLEKCCKDQDQEACFAK FETA_MOUSE KDLCQAQGKALQTMKQELLINLVKQKPELTEEQLAAVTADFSGLLEKCCKAQDQEVCFTE ******** *******::*********::**** :* ***********: * **.**:: FETA_HUMAN EGQKLISKTRAALGV FETA_GORGO EGQKLISKTRTALGV FETA_PANTR EGQKLISKTRAALGV FETA_HORSE EGPQLISKTRAALGV FETA_RAT EGPKLISKTREALGV FETA_MOUSE EGPKLISKTRDALGV ** :****** **** Clustal W dendrogram Unrooted tree generated by Phylip's Drawtree) Page 3 of 6

4 Download a PostScript version of the output Phylip-format dendrogram FETA_RAT: , FETA_MOUSE: ) : , FETA_HORSE: ) : , FETA_PANTR: ) : , FETA_HUMAN: , Page 4 of 6

5 FETA_GORGO: ); Clustal W options and diagnostic messages Alignment type: Protein Alignment order: aligned Pairwise alignment parameters Method: accurate Matrix: Gonnet Gap open penalty: Gap extension penalty: 0.10 Multiple alignment parameters Matrix: Gonnet Negative matrix?: no Gap open penalty: Gap extension penalty: 0.20 % identity for delay: 30 Residue-specific gap penalties: on Penalize end gaps: on Hydrophilic gap penalties: on Gap separation distance: 0 Hydrophilic residues: GPSNDQEKR CLUSTAL W 1.81) Multiple Sequence Alignments Sequence type explicitly set to Protein Sequence format is Pearson Sequence 1: FETA_RAT 611 aa Sequence 2: FETA_PANTR 609 aa Sequence 3: FETA_MOUSE 605 aa Sequence 4: FETA_HUMAN 609 aa Sequence 5: FETA_HORSE 609 aa Sequence 6: FETA_GORGO 609 aa Start of Pairwise alignments Aligning... Sequences 1:2) Aligned. Score: 65 Sequences 1:3) Aligned. Score: 81 Sequences 1:4) Aligned. Score: 65 Sequences 1:5) Aligned. Score: 63 Sequences 1:6) Aligned. Score: 64 Sequences 2:3) Aligned. Score: 65 Sequences 2:4) Aligned. Score: 99 Sequences 2:5) Aligned. Score: 79 Sequences 2:6) Aligned. Score: 98 Sequences 3:4) Aligned. Score: 65 Sequences 3:5) Aligned. Score: 64 Sequences 3:6) Aligned. Score: 65 Sequences 4:5) Aligned. Score: 79 Sequences 4:6) Aligned. Score: 99 Sequences 5:6) Aligned. Score: 79 Time for pairwise alignment: Guide tree file created: [../tmp-dir/4506.clustalw.dnd] Page 5 of 6

6 Start of Multiple Alignment There are 5 groups Aligning... Group 1: Sequences: 2 Score:13254 Group 2: Sequences: 3 Score:13224 Group 3: Sequences: 4 Score:12140 Group 4: Sequences: 2 Score:12162 Group 5: Sequences: 6 Score:10976 Time for multiple alignment: Alignment Score CLUSTAL-Alignment file created [../tmp-dir/4506.clustalw.aln] Import Alignments) Return Help Report Bugs Citation Algorithm Citation: Higgins, D.G., Bleasby, A.J. and Fuchs, R. 1992) CLUSTAL V: improved software for multiple sequence alignment. Computer Applications in the Biosciences CABIOS), 82): Thompson J.D., Higgins D.G., Gibson T.J. "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Res. 22: ). Felsenstein, J PHYLIP -- Phylogeny Inference Package Version 3.2). Cladistics 5: Program Citation: CLUSTAL W: Julie D. Thompson, Desmond G. Higgins and Toby J. Gibson, modified; any errors are due to the modifications. PHYLIP: Felsenstein, J PHYLIP Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle. Copyright C) 1999, Board of Trustees of the University of Illinois. Page 6 of 6

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