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SEQNR documentation |
// /homes/user/test/qa/seqfraggle-keep/54894.dhf // /homes/user/test/qa/seqfraggle-keep/55074.dhf |
This directory contains output files, for example 54894.dhf and 55074.dhf.
> Q9YBD5^.^1^95^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^56.10^0.000e+00^9.000e+00 VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP > Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^43.40^0.000e+00^6.000e+00 INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP > Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^73.80^0.000e+00^5.000e+00 VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP > P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^43.00^0.000e+00^9.000e+00 GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP |
> Q08462^.^1^167^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^46.20^0.000e+00^4.000e+00 DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEPERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEETSLVL > Q03101^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^65.80^0.000e+00^4.000e+00 NNACVFFLDIAGFTRFSSIHSPEQVIQVLIKIFNSMDLLCAKHGIEKIKTIGDAYMATCGIFPKCDDIRHNTYKMLGFAMDVLEFIPKEMSFHLGLQVRVGIHCGPVISGVISGYAKPHFDVWGDTVNVASRMESTGIAGQIHVSDRVY > Q02153^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^68.90^0.000e+00^4.000e+00 HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCL > P46197^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^78.50^0.000e+00^7.000e+00 VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDELGCFQLEL > P40137^.^1^139^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^48.50^0.000e+00^6.000e+00 VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQELETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK > P23466^.^1^154^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^50.80^0.000e+00^1.000e+00 PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEAEWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS > O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^75.40^0.000e+00^6.000e+00 DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL |
This directory contains output files, for example 54894.dhf and 55074.dhf.
> Q9UX07^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^60.00^0.000e+00^6.000e+00 VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINIIRDYVVTEKRHLEVP > Q9KP65^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^120.00^0.000e+00^4.000e+00 VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIENYEVVKKLALQLP > Q9K1K9^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^93.10^0.000e+00^7.000e+00 VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDNFKVVQKRHLNLP > Q9JWY6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^91.60^0.000e+00^2.000e+00 VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDHFKVVQKRHLNLP > Q9HKM3^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^73.10^0.000e+00^8.000e+00 ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISIIKNYEISEKFQVELP > Q9HHN3^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^71.50^0.000e+00^2.000e+00 VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIVRDYEVDEKRRVDRP > Q97B28^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^72.70^0.000e+00^8.000e+00 ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISIIKNYEISEKFKVELP > Q970X3^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^71.90^0.000e+00^1.000e+00 VSKIKNGTVIDHIPAGRALAVLRILKIAEGYRIALVMNVESKKMGKKDIVKIENKEVDEKEANLITLIAPTATINIIRDYEVVEKKKLKIP > Q8ZTG2^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^58.80^0.000e+00^1.000e+00 VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINIIRNFAVVKKFKVTPP > Q8ZB38^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^145.00^0.000e+00^8.000e+00 VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRIDNYEVVKKLTLSLP > Q8Z130^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^168.00^0.000e+00^1.000e+00 VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP > Q8U374^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^83.90^0.000e+00^4.000e+00 VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNGGAVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNIIREYKVVEKFKVEIP > Q8TVB1^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^66.10^0.000e+00^9.000e+00 VKRIEMGTVLDHLPPGTAPQIMRILDIDPTETTLLVAINVESSKMGRKDILKIEGKILSEEEANKVALVAPNATVNIVRDYSVAEKFQVKPP > Q8THL3^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^67.30^0.000e+00^4.000e+00 IQAIENGTVIDHITAGQALNVLRILRISSAFRATVSFVMNAPGARGKKDVVKIEGKELSVEELNRIALISPKATINIIRDFEVVQKNKVVLP > Q8PXK6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^61.50^0.000e+00^2.000e+00 VQAIESGTVIDHIKSGQALNVLRILGISSAFRATISFVMNAPGAGGKKDVVKIEGKELSVEELNRIALISPKATINIIRDFVVVQKNNVVLP > Q8K9H8^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^137.00^0.000e+00^4.000e+00 VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIEKYNLVGKIFPSLP > Q8DCF7^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^118.00^0.000e+00^2.000e+00 VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP > Q8D1W6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^115.00^0.000e+00^2.000e+00 VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIKNYIVIKKQKLKLP > Q8A9S4^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^57.70^0.000e+00^3.000e+00 VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCNITIGFNLDSKKLGKKGIIKIADKFFCDEEINRISVVAPYVKLNIIRDYEVVEKKEVRMP > Q891I9^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^46.90^0.000e+00^5.000e+00 ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYSVALIMNVFSSKLGKKDIIKIANKEIDIDFTVLGLIDPTITINIIEDEKIKEKLNLELP > Q87LF7^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^122.00^0.000e+00^8.000e+00 VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIENYEVVKKLALELP > Q83IL8^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^175.00^0.000e+00^8.000e+00 VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRIDNYEVVGKSRPSLP > Q7P144^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^118.00^0.000e+00^1.000e+00 VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVIDNFEVVKKHKLTLP > Q7MZ14^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^141.00^0.000e+00^2.000e+00 VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIENYEVVKKLPINLP > Q7MHF0^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^118.00^0.000e+00^2.000e+00 VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP > Q58801^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^53.40^0.000e+00^6.000e+00 VKKITNGTVIDHIDAGKALMVFKVLNVPKETSVMIAINVPSKKKGKKDILKIEGIELKKEDVDKISLISPDVTINIIRNGKVVEKLKPQIP > P96175^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^99.30^0.000e+00^9.000e+00 VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIENFKVTDKHSLALP > P77919^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^85.00^0.000e+00^2.000e+00 VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNIIRDYKVVEKFKVEVP > P74766^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^68.10^0.000e+00^2.000e+00 VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIVREYEVVKKTKLEVP > P57451^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^133.00^0.000e+00^6.000e+00 VEAIKSGSVIDHIPEYIGFKLLSLFRFTETEKRITIGLNLPSKKLGRKDIIKIENTFLSDEQINQLAIYAPHATVNYINEYNLVRKVFPTLP > P19936^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^148.00^0.000e+00^1.000e+00 VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRIDNYEVVRKLTLSLP > P08421^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^170.00^0.000e+00^4.000e+00 VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP > P00478^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^177.00^0.000e+00^2.000e+00 VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP > O58452^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^86.20^0.000e+00^8.000e+00 VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNIIRNYKVVEKFKVEVP > O30129^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^71.10^0.000e+00^3.000e+00 VSKIKEGTVIDHINAGKALLVLKILKIQPGTDLTVSMAMNVPSSKMGKKDIVKVEGMFIRDEELNKIALISPNATINLIRDYEIERKFKVSPP > O26938^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^75.00^0.000e+00^2.000e+00 VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVRDYKIVEKAKVRL |
> Q9WVI4^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^77.00^0.000e+00^2.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9ERL9^.^1^152^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^67.70^0.000e+00^9.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9DGG6^.^1^181^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^124.00^0.000e+00^9.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q99396^.^1^212^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^159.00^0.000e+00^2.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99280^.^6^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^180.00^0.000e+00^1.000e+00 KEPTGPVTLIFTDIESSTALWAAHPDLMPDAVATHHRLIRSLITRYECYEVKTVGDSFMIASKSPFAAVQLAQELQLRFLRLDWETNALDESYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGRTSNMAARTESVANGGQVLMTHAAYMSLSGEDRNQLDVTTLGATVLRGVPEPVRMYQLN > Q99279^.^1^218^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^210.00^0.000e+00^9.000e+00 NNNRAPKEPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRYKCYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWGTNALDDSYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIIRHDEVTKGYDYYGRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALGDVALRGVSDPVKMYQLN > Q91WF3^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^51.90^0.000e+00^6.000e+00 VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDTQQDSERSCSHLGTMVEFAVALGSKLGVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEETARAL > Q91WF3^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^139.00^0.000e+00^2.000e+00 FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAINCVRMGLDMCRAIRKLRVATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL > Q8VHH7^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^154.00^0.000e+00^1.000e+00 FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAVCSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKGEFDVEPGDGGSRCDYLDEKGIETYLI > Q8NFM4^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^51.60^0.000e+00^7.000e+00 VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDAQQDAERSCSHLGTMVEFAVALGSKLDVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEET > Q8NFM4^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^139.00^0.000e+00^2.000e+00 FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAINCVRMGLDMCRAIRKLRAATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL > Q29450^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^154.00^0.000e+00^7.000e+00 FHNLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHARNCVKMGLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHLDKAYEVEDGHGQQRDPYLKEMNIRTYLV > Q27675^.^1^217^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^140.00^0.000e+00^1.000e+00 NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLACEIQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTKGYDYYGDTSNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN > Q26896^.^6^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^163.00^0.000e+00^1.000e+00 KEFTDPVTLIFTDIESSTALWAAHPGMMADAVATHHRLIRSLIALYGAYEVKTVGDSFMIACRSAFAAVELARDLQLTLVHHDWGTVAIDESYRKFEEERAVEDSDYAPPTARLDSAVYCKLWNGLRVRAGIHTGLCDIAHDEVTKGYDYYGRTPNLAARTESAANGGQVLVTGATYYSLSVAERARLDATPIGPVPLRGVPEPVEMYQLN > Q26721^.^1^206^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^184.00^0.000e+00^7.000e+00 PVTLIFTDIESSTALWAAHPEVMPDAVATHHRLIRTLISKYECYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWGTNAIDESYQQFEQQRAEDDSDYTPPTARLDPKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTSNMAARTESVANGGQVLMTHAAYMSLSAEERQQIDVTALGDVPLRGVPKPVEMYRLN > Q25263^.^1^217^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^140.00^0.000e+00^2.000e+00 NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLACEIQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTRGYDYYGDTSNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN > Q09435^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^75.10^0.000e+00^6.000e+00 DSVTVFFSDVVKFTILASKCSPFQTVNLLNDLYSNFDTIIEQHGVYKVESIGDGYLCVSGLPTRNGYAHIKQIVDMSLKFMEYCKSFNIPHLPRENVELRIGVNSGPCVAGVVGLSMPRYCLFGDTVNTASRMESNGKPSLIHLTNDAHSLLTTHYPNQYE > Q08828^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^183.00^0.000e+00^2.000e+00 FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHCCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNGDYEVEPGYGHERNSFLKTHNIETFFI > Q08462^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^155.00^0.000e+00^4.000e+00 FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKNCVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNGAYKVEEGDGDIRDPYLKQHLVKTYFV > Q07553^.^1^152^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^75.80^0.000e+00^4.000e+00 DCVTILFSDIVGFTELCTTSTPFEVVEMLNDWYTCCDSIISNYDVYKVETIGDAYMVVSGLPLQNGSRHAGEIASLALHLLETVGNLKIRHKPTETVQLRIGVHSGPCAAGVVGQKMPRYCLFGDTVNTASRMESTGDSMRIHISEATYQLL > Q07093^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^62.30^0.000e+00^4.000e+00 VTILFSDIVGFTSICSRATPFMVISMLEGLYKDFDEFCDFFDVYKVETIGDAYCVASGLHRASIYDAHRCLDGLKMIDACSKHITHDGEQIKMRIGLHTGTVLAGVVGRKMPRYCLFGHSVTIANKFESGSEALKINVSPTTKDWLTKHEGFEFELQP > Q04400^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^245.00^0.000e+00^3.000e+00 MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGMDMIEAISSVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLNYLNGDYEVEPGCGGERNAYLKEHSIETFLIL > Q04400^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^51.60^0.000e+00^8.000e+00 VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKAGKTHIKALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL > Q03343^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^235.00^0.000e+00^3.000e+00 MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNGYLKEQCIETFLIL > Q03343^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^51.90^0.000e+00^5.000e+00 VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVL [Part of this file has been deleted for brevity] DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAIPSQEHAQEPERQYMHIGTMVEFAYALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEET > P26338^.^1^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^191.00^0.000e+00^4.000e+00 NNLAPKELTDPVTLIFTDIESSTALWAAHPELMPDAVATHHRLIRSLIGRYGCYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWGTNAIDESYQQLEQQRAEEDAKYTPPTARLDLKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTSNMAARTESVGNGGQVLMTTAAYMSLSAEEREQIDVTALGDVPLRGVAKPVEMYQLN > P25092^.^1^150^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^67.70^0.000e+00^9.000e+00 VTIYFSDIVGFTTICKYSTPMEVVDMLNDIYKSFDHIVDHHDVYKVETIGDAYMVASGLPKRNGNRHAIDIAKMALEILSFMGTFELEHLPGLPIWIRIGVHSGPCAAGVVGIKMPRYCLFGDTVNTASRMESTGLPLRIHVSGSTIAIL > P23897^.^1^150^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^67.40^0.000e+00^1.000e+00 VTIYFSDIVGFTTICKYSTPMEVVDMLNDIYKSFDQIVDHHDVYKVETIGDAYVVASGLPMRNGNRHAVDISKMALDILSFMGTFELEHLPGLPVWIRIGVHSGPCAAGVVGIKMPRYCLFGDTVNTASRMESTGLPLRIHMSSSTIAIL > P22717^.^1^147^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^61.20^0.000e+00^9.000e+00 TILFSDVVTFTNICAACEPIQIVNMLNSMYSKFDRLTSVHDVYKVETIGDAYMVVGGVPVPVESHAQRVANFALGMRISAKEVMNPVTGEPIQIRVGIHTGPVLAGVVGDKMPRYCLFGDTVNTASRMESHGLPSKVHLSPTAHRAL > P21932^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^154.00^0.000e+00^1.000e+00 FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAVCSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKGEFDVEPGDGGSRCDYLDEKGIETYLI > P20595^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^68.90^0.000e+00^4.000e+00 HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCL > P20594^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^78.50^0.000e+00^7.000e+00 VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDELGCFQLEL > P19754^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^183.00^0.000e+00^2.000e+00 FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHCCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNGDYEVEPGHGHERNSFLKTHNIETFFI > P19687^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^72.70^0.000e+00^3.000e+00 AVQAKRFGNVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDRQCGELDVYKVETIGDAYCVAGGLHKESDTHAVQIALMALKMMELSHEVVSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > P19686^.^1^160^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^68.50^0.000e+00^5.000e+00 VQAKKFNEVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > P18910^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^78.50^0.000e+00^6.000e+00 VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREVARMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVLEEFDGFELEL > P18293^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^79.30^0.000e+00^3.000e+00 VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREVARMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALRIHLSSETKAVLEEFDGFELEL > P16068^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^68.90^0.000e+00^4.000e+00 HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCL > P16067^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^78.50^0.000e+00^7.000e+00 VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDELGCFQLEL > P16066^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^77.80^0.000e+00^9.000e+00 VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGRLHACEVARMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVLEEFGGFELEL > P16065^.^1^143^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^73.90^0.000e+00^1.000e+00 VSIFFSDIVGFTALSAASTPIQVVNLLNDLYTLFDAIISNYDVYKVETIGDAYMLVSGLPLRNGDRHAGQIASTAHHLLESVKGFIVPHKPEVFLKLRIGIHSGSCVAGVVGLTMPRYCLFGDTVNTASRMESNGLALRIHVS > O95622^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^247.00^0.000e+00^1.000e+00 MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGMDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLNYLNGDYEVEPGCGGERNAYLKEHSIETFLIL > O95622^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^51.60^0.000e+00^8.000e+00 VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL > O75343^.^1^147^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^66.60^0.000e+00^2.000e+00 TILFSDVVTFTNICTACEPIQIVNVLNSMYSKFDRLTSVHAVYKVETIGDAYMVVGGVPVPIGNHAQRVANFALGMRISAKEVTNPVTGEPIQLRVGIHTGPVLADVVGDKMPRYCLFGDTVNTASRMESHGLPNKVHLSPTAYRAL > O60503^.^1^179^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^124.00^0.000e+00^9.000e+00 VSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVIERLGQSVVADQLKGLKTYLI > O60266^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^154.00^0.000e+00^8.000e+00 FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAVCSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKGEFDVEPGDGGSRCDYLEEKGIETYLI > O43306^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^236.00^0.000e+00^1.000e+00 MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNAYLKEQHIETFLIL > O43306^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^51.90^0.000e+00^5.000e+00 VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVL > O19179^.^1^150^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^76.20^0.000e+00^3.000e+00 VTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPQRNGQRHAAEIANMALDILSAVGSFRMRHMPEVPVRIRIGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVNMSTVRIL > O02740^.^1^162^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^77.40^0.000e+00^1.000e+00 DLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIANMSLDILSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRTLGEGYEVE |
Remove redundancy from DHF files.
Version: EMBOSS:6.5.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
[-dhfinpath] dirlist [./] This option specifies the location of
DHF files (domain hits files) (input). A
'domain hits file' contains database hits
(sequences) with domain classification
information, in the DHF format (FASTA or
EMBL-like). The hits are relatives to a SCOP
or CATH family and are found from a search
of a sequence database. Files containing
hits retrieved by PSIBLAST are generated by
using SEQSEARCH.
-[no]dosing toggle [Y] This option specifies whether to use
singlet sequences (e.g. DHF files) to filter
input. Optionally, up to two further
directories of sequences may be read: these
are considered in the redundancy calculation
but never appear in the output files.
* -singletsdir directory [./] This option specifies the location of
singlet filter sequences (e.g. DHF files)
(input). A 'domain hits file' contains
database hits (sequences) with domain
classification information, in the DHF
format (FASTA or EMBL-like). The hits are
relatives to a SCOP or CATH family and are
found from a search of a sequence database.
Files containing hits retrieved by PSIBLAST
are generated by using SEQSEARCH.
-[no]dosets toggle [Y] This option specifies whether to use
sets of sequences (e.g. DHF files) to filter
input. Optionally, up to two further
directories of sequences may be read: these
are considered in the redundancy calculation
but never appear in the output files.
* -insetsdir directory [./] This option specifies location of sets
of filter sequences (e.g. DAF files)
(input). A 'domain alignment file' contains
a sequence alignment of domains belonging to
the same SCOP or CATH family. The file is
in clustal format annotated with domain
family classification information. The files
generated by using SCOPALIGN will contain a
structure-based sequence alignment of
domains of known structure only. Such
alignments can be extended with sequence
relatives (of unknown structure) by using
SEQALIGN.
-mode menu [1] This option specifies whether to remove
redundancy at a single threshold % sequence
similarity or remove redundancy outside a
range of acceptable threshold % similarity.
All permutations of pair-wise sequence
alignments are calculated for each set of
input sequences in turn using the EMBOSS
implementation of the Needleman and Wunsch
global alignment algorithm. Redundant
sequences are removed in one of two modes as
follows: (i) If a pair of proteins achieve
greater than a threshold percentage sequence
similarity (specified by the user) the
shortest sequence is discarded. (ii) If a
pair of proteins have a percentage sequence
similarity that lies outside an acceptable
range (specified by the user) the shortest
sequence is discarded. (Values: 1 (Remove
redundancy at a single threshold % sequence
similarity); 2 (Remove redundancy outside a
range of acceptable threshold % similarity))
* -threshold float [95.0] This option specifies the % sequence
identity redundancy threshold. The %
sequence identity redundancy threshold
determines the redundancy calculation. If a
pair of proteins achieve greater than this
threshold the shortest sequence is
discarded. (Any numeric value)
* -threshlow float [30.0] This option specifies the % sequence
identity redundancy threshold (lower limit).
The % sequence identity redundancy
threshold determines the redundancy
calculation. If a pair of proteins have a
percentage sequence similarity that lies
outside an acceptable range the shortest
sequence is discarded. (Any numeric value)
* -threshup float [90.0] This option specifies the % sequence
identity redundancy threshold (upper limit).
The % sequence identity redundancy
threshold determines the redundancy
calculation. If a pair of proteins have a
percentage sequence similarity that lies
outside an acceptable range the shortest
sequence is discarded. (Any numeric value)
[-dhfoutdir] outdir [./] This option specifies the location of
DHF files (domain hits files) of
non-redundant sequences (output). A 'domain
hits file' contains database hits
(sequences) with domain classification
information, in the DHF format (FASTA or
EMBL-like). The hits are relatives to a SCOP
or CATH family and are found from a search
of a sequence database. Files containing
hits retrieved by PSIBLAST are generated by
using SEQSEARCH.
-dored toggle [N] This option specifies whether to retain
redundant sequences. If this option is set a
DHF file (domain hits file) of redundant
sequences is written.
* -redoutdir outdir [./] This option specifies the location of
DHF files (domain hits files) of redundant
sequences (output). A 'domain hits file'
contains database hits (sequences) with
domain classification information, in the
DHF format (FASTA or EMBL-like). The hits
are relatives to a SCOP or CATH family and
are found from a search of a sequence
database. Files containing hits retrieved by
PSIBLAST are generated by using SEQSEARCH.
-logfile outfile [seqnr.log] This option specifies the name
of SEQNR log file (output). The log file
contains messages about any errors arising
while SEQNR ran.
Additional (Optional) qualifiers:
-matrix matrixf [EBLOSUM62] This option specifies the
residue substitution matrix that is used for
sequence comparison.
-gapopen 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 EDNAFULL matrix for nucleotide
sequences. (Floating point number from 1.0
to 100.0)
-gapextend 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)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dhfinpath" associated qualifiers
-extension1 string Default file extension
"-singletsdir" associated qualifiers
-extension string Default file extension
"-insetsdir" associated qualifiers
-extension string Default file extension
"-dhfoutdir" associated qualifiers
-extension2 string Default file extension
"-redoutdir" associated qualifiers
-extension string Default file extension
"-logfile" associated qualifiers
-odirectory 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 and exit. 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
-version boolean Report version number and exit
| Qualifier | Type | Description | Allowed values | Default | ||||
|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||
| [-dhfinpath] (Parameter 1) |
dirlist | This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. | Directory with files | ./ | ||||
| -[no]dosing | toggle | This option specifies whether to use singlet sequences (e.g. DHF files) to filter input. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files. | Toggle value Yes/No | Yes | ||||
| -singletsdir | directory | This option specifies the location of singlet filter sequences (e.g. DHF files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. | Directory | ./ | ||||
| -[no]dosets | toggle | This option specifies whether to use sets of sequences (e.g. DHF files) to filter input. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files. | Toggle value Yes/No | Yes | ||||
| -insetsdir | directory | This option specifies location of sets of filter sequences (e.g. DAF files) (input). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. | Directory | ./ | ||||
| -mode | list | This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity. All permutations of pair-wise sequence alignments are calculated for each set of input sequences in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded. |
|
1 | ||||
| -threshold | float | This option specifies the % sequence identity redundancy threshold. The % sequence identity redundancy threshold determines the redundancy calculation. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded. | Any numeric value | 95.0 | ||||
| -threshlow | float | This option specifies the % sequence identity redundancy threshold (lower limit). The % sequence identity redundancy threshold determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded. | Any numeric value | 30.0 | ||||
| -threshup | float | This option specifies the % sequence identity redundancy threshold (upper limit). The % sequence identity redundancy threshold determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded. | Any numeric value | 90.0 | ||||
| [-dhfoutdir] (Parameter 2) |
outdir | This option specifies the location of DHF files (domain hits files) of non-redundant sequences (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. | Output directory | ./ | ||||
| -dored | toggle | This option specifies whether to retain redundant sequences. If this option is set a DHF file (domain hits file) of redundant sequences is written. | Toggle value Yes/No | No | ||||
| -redoutdir | outdir | This option specifies the location of DHF files (domain hits files) of redundant sequences (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. | Output directory | ./ | ||||
| -logfile | outfile | This option specifies the name of SEQNR log file (output). The log file contains messages about any errors arising while SEQNR ran. | Output file | seqnr.log | ||||
| Additional (Optional) qualifiers | ||||||||
| -matrix | matrixf | This option specifies the residue substitution matrix that is used for sequence comparison. | Comparison matrix file in EMBOSS data path | EBLOSUM62 | ||||
| -gapopen | float | 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 EDNAFULL matrix for nucleotide sequences. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence | ||||
| -gapextend | float | 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 | ||||
| Advanced (Unprompted) qualifiers | ||||||||
| (none) | ||||||||
| Associated qualifiers | ||||||||
| "-dhfinpath" associated dirlist qualifiers | ||||||||
| -extension1 -extension_dhfinpath |
string | Default file extension | Any string | dhf | ||||
| "-singletsdir" associated directory qualifiers | ||||||||
| -extension | string | Default file extension | Any string | dhf | ||||
| "-insetsdir" associated directory qualifiers | ||||||||
| -extension | string | Default file extension | Any string | daf | ||||
| "-dhfoutdir" associated outdir qualifiers | ||||||||
| -extension2 -extension_dhfoutdir |
string | Default file extension | Any string | dhf | ||||
| "-redoutdir" associated outdir qualifiers | ||||||||
| -extension | string | Default file extension | Any string | dhf | ||||
| "-logfile" associated outfile qualifiers | ||||||||
| -odirectory | string | Output directory | Any string | |||||
| General qualifiers | ||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||
% seqnr
Remove redundancy from DHF files.
Domain hits directories [./]: ../seqfraggle-keep
Use singlet sequences (e.g. DHF files) to filter input. [Y]: N
Use sets of sequences (e.g. DHF files) to filter input. [Y]: Y
Domain alignment directory [./]: ../domainalign-domsearch/daf
Redundancy removal options
1 : Remove redundancy at a single threshold % sequence similarity
2 : Remove redundancy outside a range of acceptable threshold % similarity
Select number. [1]: 1
The % sequence identity redundancy threshold. [95.0]: 70
Domain hits file output directory [./]: hitsnr
Retain redundant sequences. [N]: Y
Domain hits file redundant output directory [./]: hitsred
Domainatrix log output file [seqnr.log]:
Processing /homes/user/test/qa/seqfraggle-keep/54894.dhf
Processing /homes/user/test/qa/seqfraggle-keep/55074.dhf
|
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 format with domain classification information). | Contains a sequence alignment of domains belonging to the same SCOP or CATH family. 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. |
| Program name | Description |
|---|---|
| aaindexextract | Extract amino acid property data from AAINDEX |
| allversusall | Sequence similarity data from all-versus-all comparison |
| cathparse | Generate DCF file from raw CATH files |
| cutgextract | Extract codon usage tables from CUTG database |
| domainer | Generate domain CCF files from protein CCF files |
| domainnr | Remove redundant domains from a DCF file |
| domainseqs | Add sequence records to a DCF file |
| domainsse | Add secondary structure records to a DCF file |
| hetparse | Convert heterogen group dictionary to EMBL-like format |
| jaspextract | Extract data from JASPAR |
| pdbparse | Parse PDB files and writes protein CCF files |
| pdbplus | Add accessibility and secondary structure to a CCF file |
| pdbtosp | Convert swissprot:PDB codes file to EMBL-like format |
| printsextract | Extract data from PRINTS database for use by pscan |
| prosextract | Process the PROSITE motif database for use by patmatmotifs |
| rebaseextract | Process the REBASE database for use by restriction enzyme applications |
| scopparse | Generate DCF file from raw SCOP files |
| sites | Generate residue-ligand CON files from CCF files |
| ssematch | Search a DCF file for secondary structure matches |
| tfextract | Process TRANSFAC transcription factor database for use by tfscan |
See also http://emboss.sourceforge.net/