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sigscan documentation |
TY SCOP XX TS 1D XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX SI 54894 XX NP 15 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA H ; 2 XX GA 12 ; 2 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA P ; 2 XX GA 1 ; 2 XX NN [3] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA P ; 2 XX GA 26 ; 2 XX NN [4] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA T ; 2 XX GA 15 ; 2 XX NN [5] XX [Part of this file has been deleted for brevity] XX GA 4 ; 2 XX NN [10] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA I ; 2 XX GA 2 ; 2 XX NN [11] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA D ; 2 XX GA 0 ; 2 XX NN [12] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA N ; 2 XX GA 0 ; 2 XX NN [13] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA V ; 2 XX GA 3 ; 2 XX NN [14] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA R ; 2 XX GA 3 ; 2 XX NN [15] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 2 XX GA 2 ; 2 // |
> Q9WVI4 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASG LHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLF GNNVTLASKFESGSHPRRINISPTTYQLL > Q9ERL9 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLH RESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGN NVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9DGG6 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAG CPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVW SNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL I > Q99396 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMI ACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVY RQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99280 NDSAPKEPTGPVTLIFTDIESSTALWAAHPDLMPDAVATHHRLIRSLITRYECYEVKTVG DSFMIASKSPFAAVQLAQELQLRFLRLDWETNALDESYREFEEQRAEGECEYTPPTAHMD PEVYSRLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGRTSNMAARTESVANGGQVLMTHA AYMSLSGEDRNQLDVTTLGATVLRGVPEPVRMYQLN > Q99279 NNNRAPKEPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRYKCYEVKTV GDSFMIASKSPFAAVQLAQELQLCFLHHDWGTNALDDSYREFEEQRAEGECEYTPPTAHM DPEVYSRLWNGLRVRVGIHTGLCDIIRHDEVTKGYDYYGRTPNMAARTESVANGGQVLMT HAAYMSLSAEDRKQIDVTALGDVALRGVSDPVKMYQLN > Q91WF3 VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTY MAATGLNATSGQDTQQDSERSCSHLGTMVEFAVALGSKLGVINKHSFNNFRLRVGLNHGP VVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEETARAL > Q91WF3 FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKIL GDCYYCVSGLPLSLPDHAINCVRMGLDMCRAIRKLRVATGVDINMRVGVHSGSVLCGVIG LQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL > Q8VHH7 NNFMLRIGMNKGGVLAGVIGARKPHYDIWGNTVNVASRMESTGVMGNIQVVEET > Q8VHH7 FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKIL GDCYYCICGLPDYREDHAVCSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLG QKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKGEFDVEPGDGGSRCDYLDEKG IETYLI > Q8NFM4 VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTY MAATGLNATSGQDAQQDAERSCSHLGTMVEFAVALGSKLDVINKHSFNNFRLRVGLNHGP VVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEET > Q8NFM4 FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKIL GDCYYCVSGLPLSLPDHAINCVRMGLDMCRAIRKLRAATGVDINMRVGVHSGSVLCGVIG [Part of this file has been deleted for brevity] > Q83IL8 VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSE EQVDQLALYAPQATVNRIDNYEVVGKSRPSLP > Q7P144 VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTE EQANELALFAPKATVNVIDNFEVVKKHKLTLP > Q7MZ14 VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTE QQANQLAMYAPNATVNCIENYEVVKKLPINLP > Q7MX57 VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEE EELNRIALIAPNVRLNIIRDYEVVEKRQVEVP > Q7MHF0 VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINE EQASKLALYAPHATVNQIEDYQVVKKLALELP > Q58801 VKKITNGTVIDHIDAGKALMVFKVLNVPKETSVMIAINVPSKKKGKKDILKIEGIELKKE DVDKISLISPDVTINIIRNGKVVEKLKPQIP > P96175 VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITK SQANQLALLAPNATVNIIENFKVTDKHSLALP > P96111 GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLP DRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP > P77919 VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFL SEEEVNKIALVAPNATVNIIRDYKVVEKFKVEVP > P74766 VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEIS DTEANLITLIAPTATINIVREYEVVKKTKLEVP > P57451 VEAIKSGSVIDHIPEYIGFKLLSLFRFTETEKRITIGLNLPSKKLGRKDIIKIENTFLSD EQINQLAIYAPHATVNYINEYNLVRKVFPTLP > P19936 VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTE QQANQLAMYAPKATVNRIDNYEVVRKLTLSLP > P08421 VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTE EQVNQLALYAPQATVNRIDNYDVVGKSRPSLP > P00478 VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSE DQVDQLALYAPQATVNRIDNYEVVGKSRPSLP > O58452 VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFL SEEEVNKIALVAPTATVNIIRNYKVVEKFKVEVP > O30129 VSKIKEGTVIDHINAGKALLVLKILKIQPGTDLTVSMAMNVPSSKMGKKDIVKVEGMFIR DEELNKIALISPNATINLIRDYEIERKFKVSPP > O26938 VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKP SEVDQIALIAPRATINIVRDYKIVEKAKVRL |
> P00478^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.20^0.000e+00^0.000e+00 VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP > P08421^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.20^0.000e+00^0.000e+00 VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP > Q83IL8^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.20^0.000e+00^0.000e+00 VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRIDNYEVVGKSRPSLP > Q8Z130^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.00^0.000e+00^0.000e+00 VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP > Q97B28^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.53^0.000e+00^0.000e+00 ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISIIKNYEISEKFKVELP > P19936^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.000e+00 VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRIDNYEVVRKLTLSLP > Q7P144^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.000e+00 VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVIDNFEVVKKHKLTLP > Q8ZB38^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.000e+00 VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRIDNYEVVKKLTLSLP > Q9HKM3^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.000e+00 ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISIIKNYEISEKFQVELP > P74766^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.20^0.000e+00^0.000e+00 VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIVREYEVVKKTKLEVP > Q8ZTG2^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.13^0.000e+00^0.000e+00 VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINIIRNFAVVKKFKVTPP > Q9UX07^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.13^0.000e+00^0.000e+00 VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINIIRDYVVTEKRHLEVP > Q7MZ14^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.07^0.000e+00^0.000e+00 VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIENYEVVKKLPINLP > Q9HHN3^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.07^0.000e+00^0.000e+00 VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIVRDYEVDEKRRVDRP > Q9K1K9^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.07^0.000e+00^0.000e+00 VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDNFKVVQKRHLNLP > O58452^.^12^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.93^0.000e+00^0.000e+00 VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNIIRNYKVVEKFKVEVP > Q87LF7^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.93^0.000e+00^0.000e+00 VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIENYEVVKKLALELP > Q9KP65^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.93^0.000e+00^0.000e+00 VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIENYEVVKKLALQLP > P96175^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.73^0.000e+00^0.000e+00 VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIENFKVTDKHSLALP > Q8D1W6^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.73^0.000e+00^0.000e+00 VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIKNYIVIKKQKLKLP > Q9JWY6^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.73^0.000e+00^0.000e+00 VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDHFKVVQKRHLNLP > P77919^.^12^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.000e+00 VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNIIRDYKVVEKFKVEVP > Q7MHF0^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.000e+00 VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP > Q8DCF7^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.000e+00 VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP > Q8K9H8^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.000e+00 VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIEKYNLVGKIFPSLP [Part of this file has been deleted for brevity] FHSLYVKRHQNVSILYADIVGFTQLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPTHARNCVKMGLDMCQAIKQVREATGVDINMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHLDKAYEVEDGHGQQRDPYLKEMNIRTYLV > P51829^.^90^170^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00 FHSLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPTHARNCVKMGLDICEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLNHLDKAYEVEDGHGEQRDPYLKEMNIRTYLV > Q03343^.^92^172^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00 MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNGYLKEQCIETFLIL > Q07093^.^16^96^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00 VTILFSDIVGFTSICSRATPFMVISMLEGLYKDFDEFCDFFDVYKVETIGDAYCVASGLHRASIYDAHRCLDGLKMIDACSKHITHDGEQIKMRIGLHTGTVLAGVVGRKMPRYCLFGHSVTIANKFESGSEALKINVSPTTKDWLTKHEGFEFELQP > Q08462^.^70^150^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00 DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEPERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEETSLVL > Q26721^.^94^174^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00 PVTLIFTDIESSTALWAAHPEVMPDAVATHHRLIRTLISKYECYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWGTNAIDESYQQFEQQRAEDDSDYTPPTARLDPKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTSNMAARTESVANGGQVLMTHAAYMSLSAEERQQIDVTALGDVPLRGVPKPVEMYRLN > Q29450^.^90^170^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00 FHNLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHARNCVKMGLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHLDKAYEVEDGHGQQRDPYLKEMNIRTYLV > Q8NFM4^.^76^156^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00 FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAINCVRMGLDMCRAIRKLRAATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL > Q8NFM4^.^68^148^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00 VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDAQQDAERSCSHLGTMVEFAVALGSKLDVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEET > Q91WF3^.^76^156^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00 FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAINCVRMGLDMCRAIRKLRVATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL > Q91WF3^.^68^148^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00 VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDTQQDSERSCSHLGTMVEFAVALGSKLGVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEETARAL > Q97FS4^.^8^88^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00 INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP > O60503^.^50^130^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00 VSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVIERLGQSVVADQLKGLKTYLI > P26769^.^1^81^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00 FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKNCVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNGAYKVEEGDGEIRDPYLKQHLVKTYFV > P98999^.^52^132^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRPDHAYCCIEMGLGMIEAIDQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEKTARYLD > Q08462^.^1^81^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00 FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKNCVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNGAYKVEEGDGDIRDPYLKQHLVKTYFV > Q99279^.^119^199^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00 NNNRAPKEPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRYKCYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWGTNALDDSYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIIRHDEVTKGYDYYGRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALGDVALRGVSDPVKMYQLN > Q9DGG6^.^52^132^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > O02740^.^59^139^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00 DLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIANMSLDILSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRTLGEGYEVE > O19179^.^57^137^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00 VTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPQRNGQRHAAEIANMALDILSAVGSFRMRHMPEVPVRIRIGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVNMSTVRILHALDEGFQTEV > O95622^.^77^157^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00 VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL > P19754^.^33^113^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00 FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHCCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNGDYEVEPGHGHERNSFLKTHNIETFFI > P30803^.^77^157^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00 VAVMFASIANFSEFYVELEANNEGVECLRVLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL > P40137^.^30^110^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00 VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQELETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK > P40144^.^77^157^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00 VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL > P51839^.^59^139^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00 DQVTIYFSDIVGFTTISALSEPIEVVGFLNDLYTMFDAVLDSHDVYKVETIGDAYMVASGLPRRNGNRHAAEIANMALEILSYAGNFRMRHAPDVPIRVRAGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSRNTVQALLSLDEGYKIDV |
# DE Results of signature search # XX # TY SCOP # XX # CL Alpha and beta proteins (a+b) # XX # FO Ferredoxin-like # XX # SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain # XX # FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain # XX # SI 54894 # XX P00478 1 VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKI 53 SIGNATURE - ----------*-*--------------------------*------------- P00478 54 ENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 106 SIGNATURE - --*---*--*----*-*----*--***---*---*--*- P00478 107 . 159 SIGNATURE - . P00478 160 . 212 SIGNATURE - . P00478 213 . 265 SIGNATURE - . # XX P08421 1 VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKI 53 SIGNATURE - ----------*-*--------------------------*------------- P08421 54 ENTFLTEEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 106 SIGNATURE - --*---*--*----*-*----*--***---*---*--*- P08421 107 . 159 SIGNATURE - . P08421 160 . 212 SIGNATURE - . P08421 213 . 265 SIGNATURE - . # XX Q83IL8 1 VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKI 53 SIGNATURE - ----------*-*--------------------------*------------- Q83IL8 54 ENTFLSEEQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 106 SIGNATURE - --*---*--*----*-*----*--***---*---*--*- Q83IL8 107 . 159 SIGNATURE - . Q83IL8 160 . 212 SIGNATURE - . Q83IL8 213 . 265 SIGNATURE - . # XX Q8Z130 1 VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKI 53 SIGNATURE - ----------*-*--------------------------*------------- Q8Z130 54 ENTFLTDEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 106 [Part of this file has been deleted for brevity] SIGNATURE - ---------*---------------*---*--*----*-*----*--***--- P19754 107 VGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLN 159 SIGNATURE - *---*--*--------------------------------------------- P19754 160 GDYEVEPGHGHERNSFLKTHNIETFFI 212 SIGNATURE - --------------------------- P19754 213 . 265 SIGNATURE - . # XX P30803 1 VAVMFASIANFSEFYVELEANNEGVECLRVLNEIIADFDEIISEDRFRQLEKI 53 SIGNATURE - ----------------------------------------------------- P30803 54 KTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQM 106 SIGNATURE - ------------------------*-*-------------------------- P30803 107 KIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL 159 SIGNATURE - *---------------*---*--*----*-*----*--***---*---*--*- P30803 160 . 212 SIGNATURE - . P30803 213 . 265 SIGNATURE - . # XX P40137 1 VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDAL 53 SIGNATURE - ------------------------------*-*-------------------- P40137 54 MVYFGAPIADPAHARRGVQCALDMVQELETVNALRSARGEPCLRIGVGVHTGP 106 SIGNATURE - ------*---------------*---*--*----*-*----*--***---*-- P40137 107 AVLGNIGSATRRLEYTAIGDTVNLASRIESLTK 159 SIGNATURE - -*--*---------------------------- P40137 160 . 212 SIGNATURE - . P40137 213 . 265 SIGNATURE - . # XX P40144 1 VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKI 53 SIGNATURE - ----------------------------------------------------- P40144 54 KTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQM 106 SIGNATURE - ------------------------*-*-------------------------- P40144 107 KIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL 159 SIGNATURE - *---------------*---*--*----*-*----*--***---*---*--*- P40144 160 . 212 SIGNATURE - . P40144 213 . 265 SIGNATURE - . # XX P51839 1 DQVTIYFSDIVGFTTISALSEPIEVVGFLNDLYTMFDAVLDSHDVYKVETIGD 53 SIGNATURE - ----------------------------------------------------- P51839 54 AYMVASGLPRRNGNRHAAEIANMALEILSYAGNFRMRHAPDVPIRVRAGLHSG 106 SIGNATURE - ------*-*--------------------------*---------------*- P51839 107 PCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSRNTVQALLSLDEGY 159 SIGNATURE - --*--*----*-*----*--***---*---*--*------------------- P51839 160 KIDV 212 SIGNATURE - ---- P51839 213 . 265 SIGNATURE - . |
Standard (Mandatory) qualifiers:
[-siginfile] infile This option specifies the name of the
signature file (input). A 'signature file'
contains a sparse sequence signature
suitable for use with the SIGSCAN and
SIGSCANLIG programs. The files are generated
by using SIGGEN and SIGGENLIG.
[-dbsequence] seqall This option specifies the name of the
database to search.
-sub matrixf [EBLOSUM62] This option specifies the
residue substitution matrix.
-gapo float [10.0 for any sequence] This option
specifies the gap insertion penalty. The gap
insertion penalty is the score taken away
when a gap is created. The best value
depends on the choice of comparison matrix.
The default value assumes you are using the
EBLOSUM62 matrix for protein sequences, and
the EDNAMAT matrix for nucleotide sequences.
(Floating point number from 1.0 to 100.0)
-gape float [0.5 for any sequence] This option specifies
the gap extension penalty. The gap
extension penalty is added to the standard
gap penalty for each base or residue in the
gap. This is how long gaps are penalized.
Usually you will expect a few long gaps
rather than many short gaps, so the gap
extension penalty should be lower than the
gap penalty. (Floating point number from 0.0
to 10.0)
-nterm menu [1] This option specifies the N-terminal
matching option. This determines how the
first signature position is aligned to a
sequence from the database. (Values: 1
(Align anywhere and allow only complete
signature-sequence fit); 2 (Align anywhere
and allow partial signature-sequence fit); 3
(Use empirical gaps only))
-nhits integer [100] This option specifies the maximum
number of hits to output. (Any integer
value)
[-hitsfile] outfile [SIGSCAN.dhf] This option specifies the name
of the DHF file (domain hits file)
(output). A 'domain hits file' contains
database hits (sequences) with domain
classification information, in the DHF
format (FASTA-like). The hits are relatives
to a SCOP or CATH family (or other node in
the structural hierarchies) and are found
from a search of a sequence database, in
this case, by using SIGSCAN. Files
containing hits retrieved by PSIBLAST are
generated by using SEQSEARCH or various
types of HMM and profile by using LIBSCAN.
[-alignfile] outfile [SIGSCAN.aln] This option specifies the name
of the SAF (signature alignment file)
(output).A 'signature alignment file'
contains one or more signature-sequence
alignments. The file is in DAF format
(CLUSTAL-like) and is annotated with
bibliographic information, either the domain
family classification (for SIGSCAN output)
or ligand classification (for SIGSCANLIG
output). The files generated by SIGSCAN will
contain a signature-sequence alignment for
a single signature against a library of one
or more sequences. The files generated by
using SIGSCANLIG will contain a
signature-sequence alignment for a single
query sequence against a library of one or
more signatures.
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dbsequence" associated qualifiers
-sbegin2 integer Start of each sequence to be used
-send2 integer End of each sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-sformat2 string Input sequence format
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-hitsfile" associated qualifiers
-odirectory3 string Output directory
"-alignfile" associated qualifiers
-odirectory4 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||
|---|---|---|---|---|---|---|---|---|---|
| [-siginfile] (Parameter 1) |
This option specifies the name of the signature file (input). A 'signature file' contains a sparse sequence signature suitable for use with the SIGSCAN and SIGSCANLIG programs. The files are generated by using SIGGEN and SIGGENLIG. | Input file | Required | ||||||
| [-dbsequence] (Parameter 2) |
This option specifies the name of the database to search. | Readable sequence(s) | Required | ||||||
| -sub | This option specifies the residue substitution matrix. | Comparison matrix file in EMBOSS data path | EBLOSUM62 | ||||||
| -gapo | This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAMAT matrix for nucleotide sequences. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence | ||||||
| -gape | This option specifies the gap extension penalty. The gap extension penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence | ||||||
| -nterm | This option specifies the N-terminal matching option. This determines how the first signature position is aligned to a sequence from the database. |
|
1 | ||||||
| -nhits | This option specifies the maximum number of hits to output. | Any integer value | 100 | ||||||
| [-hitsfile] (Parameter 3) |
This option specifies the name of the DHF file (domain hits file) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA-like). The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database, in this case, by using SIGSCAN. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH or various types of HMM and profile by using LIBSCAN. | Output file | SIGSCAN.dhf | ||||||
| [-alignfile] (Parameter 4) |
This option specifies the name of the SAF (signature alignment file) (output).A 'signature alignment file' contains one or more signature-sequence alignments. The file is in DAF format (CLUSTAL-like) and is annotated with bibliographic information, either the domain family classification (for SIGSCAN output) or ligand classification (for SIGSCANLIG output). The files generated by SIGSCAN will contain a signature-sequence alignment for a single signature against a library of one or more sequences. The files generated by using SIGSCANLIG will contain a signature-sequence alignment for a single query sequence against a library of one or more signatures. | Output file | SIGSCAN.aln | ||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||
| (none) | |||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||
| (none) | |||||||||
% sigscan
Generates hits (DHF file) from a signature search
Domainatrix signature file: ../siggen-keep/54894.sig
Name of database to search.: swsmall
Residue substitution matrix [EBLOSUM62]:
Gap insertion penalty [10]:
Gap extension penalty [0.5]:
N-terminal matching options
1 : Align anywhere and allow only complete signature-sequence fit
2 : Align anywhere and allow partial signature-sequence fit
3 : Use empirical gaps only
Select number [1]:
Max. number of hits to output [100]:
Domain hits output file [SIGSCAN.dhf]:
Domainatrix signature alignment output file [SIGSCAN.aln]:
Signature file read ok
Signature compiled ok
Signature aligned to db ok
Hits file written ok
Alignments file written ok
|
Go to the input files for this example
Go to the output files for this example
| FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO | Domain hits file | DHF format (FASTA-like). | Database hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a discriminating element (e.g. a protein signature, hidden Markov model, simple frequency matrix, Gribskov profile or Hennikoff profile) against a sequence database. | SEQSEARCH (hits retrieved by PSIBLAST). SIGSCAN (hits retrieved by sparse protein signature). LIBSCAN (hits retrieved by various types of HMM and profile). | N.A. |
| Domain alignment file | DAF format (CLUSTAL-like). | Sequence alignment of domains belonging to the same SCOP or CATH family (or other node in the structural hierarchies). The file is annotated with domain family classification information. | DOMAINALIGN (structure-based sequence alignment of domains of known structure). | DOMAINALIGN alignments can be extended with sequence relatives (of unknown structure) to the family in question by using SEQALIGN. |
| Hits file | Text file of classified hits | A list of hits (e.g. from a prediction method) that are classified and rank-ordered on the basis of score, p-value, E-value etc. | ROCON and LIBSCAN (hits from searches of a discriminating element (hidden Markov model, profile or signature) against a sequence database). | ROCPLOT is run on the files to perform Receiver Operator Characteristic (ROC) analysis on the hits. |
| Signature file | SIG format | Contains a sparse sequence signature suitable for use with the SIGSCAN program. Contains a sparse sequence signature. | SIGGEN, SIGGENLIG, LIBGEN | The files are generated by using SIGGEN. |
| Program name | Description |
|---|---|
| contacts | Generate intra-chain CON files from CCF files |
| domainalign | Generate alignments (DAF file) for nodes in a DCF file |
| domainrep | Reorder DCF file to identify representative structures |
| domainreso | Remove low resolution domains from a DCF file |
| interface | Generate inter-chain CON files from CCF files |
| libgen | Generate discriminating elements from alignments |
| matgen3d | Generate a 3D-1D scoring matrix from CCF files |
| psiphi | Calculates phi and psi torsion angles from protein coordinates |
| rocon | Generates a hits file from comparing two DHF files |
| rocplot | Performs ROC analysis on hits files |
| seqalign | Extend alignments (DAF file) with sequences (DHF file) |
| seqfraggle | Removes fragment sequences from DHF files |
| seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file |
| seqsort | Remove ambiguous classified sequences from DHF files |
| seqwords | Generates DHF files from keyword search of UniProt |
| siggen | Generates a sparse protein signature from an alignment |
| siggenlig | Generates ligand-binding signatures from a CON file |
| sigscanlig | Searches ligand-signature library & writes hits (LHF file) |
See also http://emboss.sourceforge.net/
Automatic generation and evaluation of sparse protein signatures for families of protein
structural domains. MJ Blades, JC Ison, R Ranasinghe, and JBC Findlay. Protein Science. 2005 (accepted)
A key residues approach to the definition of protein families and analysis
of sparse family signatures. JC Ison, AJ Bleasby, MJ Blades, SC Daniel,
JH Parish, JBC Findlay. PROTEINS: Structure, Function & Genetics. 2000,
40:330-341
Alignment of a sparse protein signature with protein sequences: application
to fold prediction for three small globulins. SC Daniel, JH Parish,
JC Ison, MJ Blades & JBC Findlay. FEBS Letters. 1999, 459:349-352.