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What tool from the ExPASy "protein identification and characterization" section would you use for identifying a protein for which you only know theamino acid composition?
What is the name of at least one peptide mass fingerprint tool at the ExPASy site?
Generally outline the underlying principles that allow the identification of a protein through peptide mass fingerprinting.
Scroll down on the ExPASy tools webpage to the section entitled "pattern and profile searches". The tools that populate this section are designed toidentify proteins that belong to well characterized protein families, usually identified by conserved domains within family members.Also, well known protein motifs, or domains, are represented independently of their protein families in pattern databases that contain the conservedaspects of the domain sequence. Select the tool entitled "InterPro Scan" (3) to perform an integrated search in PROSITE, Pfam, PRINTS and other familyand domain databases. This tool is useful for identifying specific domains or motifs within a protein, once the sequence has been determined, and cansometimes recognize the protein as a member of an established protein family. Test the efficacy of this tool with the following sequences, one at a time, but make surethe interactive run button is selected. An email address will be required to submit the job, but the results can be viewed in the browser interactively.
>Seq1
MAGIAAKLAKDREAAEGLGSHERAIKYLNQDYEALRNECLEAGTLFQDPSFPAIPSALGFKELGPYSSKTRGIEWKRPTEICADPQFIIGGATRTDICQGALGDCWLLAAIASLTLNEEILARVVPLNQSFQENYAGIFH
FQFWQYGEWVEVVVDDRLPTKDGELLFVHSAEGSEFWSALLEKAYAKINGCYEALSGGATTEGFEDFTGGIAEWYELKKPPPNLFKIIQKALQKGSLLGCSIDITSAADSEAITFQKLVKGHAYSVTGAEEVESNGSLQK
LIRIRNPWGEVEWTGRWNDNCPSWNTIDPEERERLTRRHEDGEFWMSFSDFLRHYSRLEICNLTPDTLTSDTYKKWKLTKMDGNWRRGSTAGGCRNYPNTFWMNPQYLIKLEEEDEDEEDGESGCTFLVGLIQKHRRRQR
KMGEDMHTIGFGIYEVPEELSGQTNIHLSKNFFLTNRARERSDTFINLREVLNRFKLPPGEYILVPSTFEPNKDGDFCIRVFSEKKADYQAVDDEIEANLEEFDISEDDIDDGVRRLFAQLAGEDAEISAFELQTILRRV
LAKRQDIKSDGFSIETCKIMVDMLDSDGSGKLGLKEFYILWTKIQKYQKIYREIDVDRSGTMNSYEMRKALEEAGFKMPCQLHQVIVARFADDQLIIDFDNFVRCLVRLETLFKIFKQLDPENTGTIELDLISWLCFSVL>Seq2
SGPRPVVLSGPSGAGKSTLLKRLLQEHSGIFGFSVSHTTRNPRPGEENGKDYYFVTREVMQRDIAAGDFIEHAEFSGNLYGTSKVAVQAVQAMNRICVLDVDLQGVRNIKATDLRPIYIS
VQPPSLHVLEQRLRQRNTETEESLVKRLAAAQADMESSKEPGLFDVVIINDSLDQAYAELKEALSEEIKKAQRTGA>Seq3
MTEVISNKITAKDGATSLKDIDDKRWVWISDPETAFTKAWIKEDLPDKKYVVRYNNSRDEKIVGEDEIDPVNPAKFDRVNDMAELTYLNEPAVTYNLEQRYLSDQIYTYSGLFLVAVNPY
CGLPIYTKDIIQLYKDKTQERKLPHVFAIADLAYNNLLENKENQSILVTGESGAGKTENTKRIIQYLAAIASSTTVGSSQVEEQIIKTNPVLESFGNARTVRNNNSSRFGKFIKVEFSLS
GEISNAAIEWYLLEKSRVVHQNEFERNYHVFYQLLSGADTALKNKLLLTDNCNDYRYLKDSVHIIDGVDDKEEFKTLLAAFKTLGFDDKENFDLFNILSIILHMGNIDVGADRSGIARLL
NPDEIDKLCHLLGVSPELFSQNLVRPRIKAGHEWVISARSQTQVISSIEALAKAIYERNFGWLVKRLNTSLNHSNAQSYFIGILDIAGFEIFEKNSFEQLCINYTNEKLQQFFNHHMFVL
EQEEYMKEEIVWDFIDFGHDLQPTIDLIEKANPIGILSCLDEECVMPKATDATFTSKLDALWRNKSLKYKPFKFADQGFILTHYAADVPYSTEGWLEKNTDPLNENVAKLLAQSTNKHVA
TLFSDYQETETKTVRGRTKKGLFRTVAQRHKEQLNQLMNQFNSTQPHFIRCIVPNEEKKM
HTFNRPLVLGQLRCNGVLEGIRITRAGFPNRLPFNDFRVRYEIMAHLPTGTYVESRRASVMILEELKIDEASYRIGVSKIFFKAGVLAELEERRVATLQRLMTMLQTRIRGFLQRKIFQK
RLKDIQAIKLLQANLQVYNEFRTFPWAKLFFNLRPLLSSTQNDKQLKKRDAEIIELKYELKKQQNSKSEVERDLVETNNSLTAVENLLTTERAIALDKEEILRRTQERLANIEDSFSETK
QQNENLQRESASLKQINNELESELLEKTSKVETLLSEQNELKEKLSLEEKDLLDTKGELESLRENNATVLSEKAEFNEQCKSLQETIVTKDAELDKLTKYISDYKTEIQEMRLTNQKMNE
KSIQQEGSLSESLKRVKKLERENSTLISDVSILKQQKEELSVLKGVQELTINNLEEKVNYLEADVKQLPKLKKELESLNDKDQLYQLQATKNKELEAKVKECLNNIKSLTKELENKEEKC
QNLSDASLKYIELQEIHENLLLKVSDLENYKKKYEGLQLDLEGLKDVDTNFQELSKKHRDLTFNHESLLRQSASYKEKLSLASSENKDLSNKVSSLTKQVNELSPKASKVPELERKITNL
MHEYSQLGKTFEDEKRKALIASRDNEELRSLKSELESKRKLEVEYQKVLEEVKTTRSLRSEVTLLRNKVADHESIRSKLSEVEMKLVDTRKELNSALDSCKKREAEIHRLKEHRPSGKEN
NIPAVKTTEPVLKNIPQRKTIFDLQQRNANQALYENLKRDYDRLNLEKHNLEKQVNELKGAEVSPQPTGQSLQHVNLAHAIELKALKDQINSEKAKMFSVQVQYEKREQELQKRIASLEK
VNKDSLIDVRALRDRIASLEDELRAA
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