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    Exercise #4a:

    Homology search in protein databases

    Given are several amino acid sequences. Find all homologous proteins in the database. If a conventional BLAST search doesn't find homologous proteins, try other search algorithms. Which ones do you consider?

    Hrp proteins

    Protein 1 (HrpB1 from Xanthomonas campestris pv. vesicatoria):
            1 mektqcpgsv vsglielitv glthekiqda aavlaavrvl rpelkaldtf dawisikrgn
           61 yvegarllre lesdagskpl cralyacclf amgdpswhgv adglieedad adavalvkal
          121 sgrstptsap aevpvessap mevpnsqylr a
    
    Protein 2 (HrpB2 from Xanthomonas campestris pv. vesicatoria):
            1 mtlippvqai agtsaaatqa lspvatpnqa lvnrfqalmq sssplppamq rvgnpsmmsr
           61 vvdvqndglr tiaehidafs mqaptmglqe maaqqiklmh eltmvgfnln vsvgvaqsgk
          121 navqtlvknq 
    
    Protein 3 (HrpB4 from Xanthomonas campestris pv. vesicatoria):
            1 mdntridnaa rcvqrwtdal aqlaesldaa rvahwlgpva asgwaaapvh rrmrviqaws
           61 gwselspsal glhanqlall mparlakvli aralfsrgla vrrciererl dwleqcvgpa
          121 vlehvrqnas aglpvpllpr dadqaawvgd gwrrmqadgv wsnpvvakll alslplgaaq
          181 vatvaadgas dafltalptl ipeascvcg
    
    Protein 4 (HrpB7 from Xanthomonas campestris pv. vesicatoria):
            1 mrepaytwsv lhqlkarrce rmqerlsdcr ralehcdrel arcrqeaeac ttrlancdaa
           61 lmdktgvggs ididtilqhe rfrtvlvetc raaeqaraaa dqslhsarde lasvqqalsk
          121 lqaqaqvyad kaasarrarq aqrdaaeeed aiealvglrs hraahggar
    
    Protein 5 (HrpD5 from Xanthomonas campestris pv. vesicatoria):
            1 mtmqlrvmtg thagarldla qgrytlgsdp qtdiriddwp gcsliievdq dgqirygsdt
           61 vqetffvafq pvrfgplvlc vgdaaadwpd dvallerlls papppaprts rrkvlrtavg
          121 avlalaaaal lpslqpafls daatrqhpen tlnqakallk qlgfreahae qvgtrvlieg
          181 lvpssadaar lraqvhryhp gvavnvavvd evvatlrdtl adpaltvrye gngvfsvsgs
          241 sdyaerasrr iadvrsdlgp evralhveis qqdpsikppd nydaalladg lhyvetpdgt
          301 khmtslpqqa aq
    
    Protein 6 (HrpD6 from Xanthomonas campestris pv. vesicatoria):
            1 mrdhtmfdam tdavtqdmsk ilqakamdls gerlrnveta ldataqqirv hwsaasdqva
           61 rndfnvlydg itaarnivah iasmp
    
    Protein 7 (HrpE1 from Xanthomonas campestris pv. vesicatoria):
            1 mqifpevssw rsrvgqgmdc ftgglsngis gaaalsgang qmdsllgdms asdeaqksmn
           61 nkitmlkndl dfnvalnkfi gkagdnakql vgq
    
    Protein 8 (HrpF from Xanthomonas campestris pv. vesicatoria):
            1 mslntlstgs npsqllgtsf nessssellg sdsskdgsdl pstmdnifqr iylllealqa
           61 ntpnsasgna pantasgdad tqlsasdwqa tqpiekrtsw pslgydfdpk hikgkdappa
          121 legstvtwnd gtltkselqi vstlnahkdq mpleyknldd kindpstpad lkaalqglkq
          181 dprlffaigs qgdgkcggki saqdlwdfsd shpqvkelgg kndefnpkni kgsnpppaae
          241 gstvtwnegq lnqseleivs vldrhkdqvd slsfdqldak indpstqpdl kkalqglqkd
          301 prlffaigsq kdgkcggkik aqdltdfsyy hpqiaeyndk qaksytqnyi asdspdktka
          361 svmtksdalr elyrysdylp gnlsedefak ivdgdsktgk cppqviaaaq yfrdhpdewk
          421 efagdsgsms tpdflqksts emhltadeqk tldtinshqd afygdgkeit rdkldaiskd
          481 dkadpavkqa atqlladpll fgllnnsitg ykkphhffgg ghvvdsgkis qddfrqfydh
          541 msaanktvdt patheasspd qqkavadmlv gkddppaikk pkkdvgtfqq glheflkwds
          601 kildwmsvgl salngipiig eiadaasial eseaqaaqvv dtaiqggdms lalklaginm
          661 agavvgavgg ptarigakgv akgvaeaaak eaaegaakga akgtaksvak gggktaaerp
          721 saaefakgyv ggtaiskste ilktpvlagl hyeeyqldkq kdgeihqkme naggvpvgkq
          781 iipkgiadnf egdlrqnlrn vrirrr
    

     

    Latest update: October 15, 2009


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