SEQSEARCH documentation


 


CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES



1.0 SUMMARY

Generate PSI-BLAST hits (DHF file) from a DAF file


2.0 INPUTS & OUTPUTS

SEQSEARCH reads a directory of i. single protein sequences or ii. set of protein sequences (aligned or unaligned) and generates a DHF file ('domain hits file') of sequence relatives (hits) for each file in the input directory. The hits are sequence relatives to the input sequences and are found by using PSIBLAST. Only unique hits are generated; only one of a set of identical hits returned by PSIBLAST is retained.

Typically, aligned sequences within a DAF file ('domain alignment file') are input and the DHF file output is annotated with domain classification data.

PSIBLAST must be installed on the system that is running SEQSEARCH (see 'Notes' below). The base name of an input file is used as the base name for the corresponding output file. The paths and extensions for the sequence files (input) and domain hits files (output) are specified by the user. The name of the BLAST-indexed database to search are also user-specified. A log file is also written.


3.0 INPUT FILE FORMAT

The format of the domain alignment file is described in DOMAINALIGN documentation.
If other sequences or sequence sets (aligned or unaligned) are used as input, all of the common file formats are supported.

Input files for usage example

File: swsmall

> 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




4.0 OUTPUT FILE FORMAT

SEQSEARCH generates a domain hits file in FASTA-like format (Figure 1).

Figure 1 DHF file (FASTA-like format)
The file (Figure 1) contains two lines per hit. The first contains a description of the hit in 16 text tokens delimited by '^'. The tokens are as follows (a '.' is given where a token does not have a value). The first 4 tokens are specific to the sequence of the hit: The next 9 tokens are specific to the domain (or domain family or other node) for which the hit was generated: The next 4 tokens are specific to the hit itself:

Output files for usage example

File: 54894.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^PSIBLAST^56.10^0.000e+00^9.000e-12
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP
> 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^PSIBLAST^60.00^0.000e+00^6.000e-13
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^PSIBLAST^120.00^0.000e+00^4.000e-31
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^PSIBLAST^93.10^0.000e+00^7.000e-23
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^PSIBLAST^91.60^0.000e+00^2.000e-22
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^PSIBLAST^73.10^0.000e+00^8.000e-17
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^PSIBLAST^71.50^0.000e+00^2.000e-16
VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIVRDYEVDEKRRVDRP
> 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^PSIBLAST^43.40^0.000e+00^6.000e-08
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP
> 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^PSIBLAST^72.70^0.000e+00^8.000e-17
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^PSIBLAST^71.90^0.000e+00^1.000e-16
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^PSIBLAST^58.80^0.000e+00^1.000e-12
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^PSIBLAST^145.00^0.000e+00^8.000e-39
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^PSIBLAST^168.00^0.000e+00^1.401e-45
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^PSIBLAST^83.90^0.000e+00^4.000e-20
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^PSIBLAST^66.10^0.000e+00^9.000e-15
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^PSIBLAST^67.30^0.000e+00^4.000e-15
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^PSIBLAST^61.50^0.000e+00^2.000e-13
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^PSIBLAST^137.00^0.000e+00^4.000e-36
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^PSIBLAST^118.00^0.000e+00^2.000e-30
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^PSIBLAST^115.00^0.000e+00^2.000e-29
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^PSIBLAST^57.70^0.000e+00^3.000e-12
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^PSIBLAST^46.90^0.000e+00^5.000e-09
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^PSIBLAST^122.00^0.000e+00^8.000e-32
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^PSIBLAST^175.00^0.000e+00^0.000e+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^PSIBLAST^118.00^0.000e+00^1.000e-30
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^PSIBLAST^141.00^0.000e+00^2.000e-37
VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIENYEVVKKLPINLP
> 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^PSIBLAST^73.80^0.000e+00^5.000e-17
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP
> 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^PSIBLAST^118.00^0.000e+00^2.000e-30
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^PSIBLAST^53.40^0.000e+00^6.000e-11
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^PSIBLAST^99.30^0.000e+00^9.000e-25
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIENFKVTDKHSLALP
> 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^PSIBLAST^43.00^0.000e+00^9.000e-08
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP
> 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^PSIBLAST^85.00^0.000e+00^2.000e-20
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^PSIBLAST^68.10^0.000e+00^2.000e-15
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^PSIBLAST^133.00^0.000e+00^6.000e-35
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^PSIBLAST^148.00^0.000e+00^1.000e-39
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^PSIBLAST^170.00^0.000e+00^0.000e+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^PSIBLAST^177.00^0.000e+00^0.000e+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^PSIBLAST^86.20^0.000e+00^8.000e-21
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^PSIBLAST^71.10^0.000e+00^3.000e-16
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^PSIBLAST^75.00^0.000e+00^2.000e-17
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVRDYKIVEKAKVRL

File: 55074.dhf

> 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^PSIBLAST^77.00^0.000e+00^2.000e-17
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^PSIBLAST^67.70^0.000e+00^9.000e-15
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^PSIBLAST^124.00^0.000e+00^9.000e-32
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^PSIBLAST^159.00^0.000e+00^2.000e-42
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^PSIBLAST^180.00^0.000e+00^0.000e+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^PSIBLAST^210.00^0.000e+00^0.000e+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^PSIBLAST^51.90^0.000e+00^6.000e-10
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^PSIBLAST^139.00^0.000e+00^2.000e-36
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^PSIBLAST^154.00^0.000e+00^1.000e-40
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^PSIBLAST^51.60^0.000e+00^7.000e-10
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^PSIBLAST^139.00^0.000e+00^2.000e-36
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^PSIBLAST^154.00^0.000e+00^7.000e-41
FHNLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHARNCVKMGLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHLDKAYEVEDGHGQQRDPYLKEMNIRTYLV
> Q29450^.^1^58^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^51.20^0.000e+00^1.000e-09
NSFRLRVGINHGPVIAGVIGARKPQYDIWGNTVNVASRMESTGELGKIQVTEETCTIL
> 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^PSIBLAST^140.00^0.000e+00^1.000e-36
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^PSIBLAST^163.00^0.000e+00^9.949e-44
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^PSIBLAST^184.00^0.000e+00^0.000e+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^PSIBLAST^140.00^0.000e+00^2.000e-36
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^PSIBLAST^75.10^0.000e+00^6.000e-17
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^PSIBLAST^183.00^0.000e+00^0.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHCCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNGDYEVEPGYGHERNSFLKTHNIETFFI
> Q08828^.^1^51^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^45.40^0.000e+00^5.000e-08
NDFVLRVGINVGPVVAGVIGARRPQYDIWGNTVNVASRMDSTGVQGRIQVT
> 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^PSIBLAST^155.00^0.000e+00^4.000e-41
FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKNCVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNGAYKVEEGDGDIRDPYLKQHLVKTYFV
> 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^PSIBLAST^46.20^0.000e+00^4.000e-08
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEPERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEETSLVL
> 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^PSIBLAST^75.80^0.000e+00^4.000e-17
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^PSIBLAST^62.30^0.000e+00^4.000e-13
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^PSIBLAST^245.00^0.000e+00^0.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGMDMIEAISSVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLNYLNGDYEVEPGCGGERNAYLKEHSIETFLIL


  [Part of this file has been deleted for brevity]

PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEAEWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS
> 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^PSIBLAST^61.20^0.000e+00^9.000e-13
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^PSIBLAST^154.00^0.000e+00^1.000e-40
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^PSIBLAST^68.90^0.000e+00^4.000e-15
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^PSIBLAST^78.50^0.000e+00^7.000e-18
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^PSIBLAST^183.00^0.000e+00^0.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHCCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNGDYEVEPGHGHERNSFLKTHNIETFFI
> P19754^.^1^51^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^45.40^0.000e+00^5.000e-08
NDFVLRVGINVGPVVAGVIGARRPQYDIWGNTVNVASRMDSTGVQGRIQVT
> 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^PSIBLAST^72.70^0.000e+00^3.000e-16
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^PSIBLAST^68.50^0.000e+00^5.000e-15
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^PSIBLAST^78.50^0.000e+00^6.000e-18
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^PSIBLAST^79.30^0.000e+00^3.000e-18
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^PSIBLAST^68.90^0.000e+00^4.000e-15
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^PSIBLAST^78.50^0.000e+00^7.000e-18
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^PSIBLAST^77.80^0.000e+00^9.000e-18
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^PSIBLAST^73.90^0.000e+00^1.000e-16
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^PSIBLAST^247.00^0.000e+00^0.000e+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^PSIBLAST^51.60^0.000e+00^8.000e-10
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^PSIBLAST^66.60^0.000e+00^2.000e-14
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^PSIBLAST^124.00^0.000e+00^9.000e-32
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^PSIBLAST^154.00^0.000e+00^8.000e-41
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAVCSILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKGEFDVEPGDGGSRCDYLEEKGIETYLI
> O60266^.^1^54^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^43.50^0.000e+00^2.000e-07
NNFMLRIGMNKGGVLAGVIGARKPHYDIWGNTVNVASRMESTGVMGNIQVVEET
> 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^PSIBLAST^236.00^0.000e+00^0.000e+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^PSIBLAST^51.90^0.000e+00^5.000e-10
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVL
> 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^PSIBLAST^75.40^0.000e+00^6.000e-17
DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL
> 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^PSIBLAST^76.20^0.000e+00^3.000e-17
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^PSIBLAST^77.40^0.000e+00^1.000e-17
DLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIANMSLDILSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRTLGEGYEVE

File: seqsearch.log

//
/homes/user/test/qa/domainalign-keep/daf/54894.daf
//
/homes/user/test/qa/domainalign-keep/daf/55074.daf




5.0 DATA FILES

SEQSEARCH does not requires any data files.


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Generate PSI-BLAST hits (DHF file) from a DAF file.
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
   -mode               menu       [1] This option specifies the mode of
                                  SEQSEARCH operation. SEQSEARCH takes as
                                  input a directory of either i. single
                                  sequences, ii. set of sequences (unaligned
                                  or aligned, but typically aligned sequences
                                  within a domain alignment file)). The user
                                  has to specify which. (Values: 1 (Single
                                  sequences); 2 (Multiple sequences (e.g.
                                  sequence set or alignment)))
  [-inseqspath]        dirlist    [./] This option specifies the location of
                                  sequences, e.g. DAF files (domain alignment
                                  files) (input). SEQSEARCH takes as input a
                                  database of either i. single sequences, ii.
                                  sets of unaligned sequences or iii. sets of
                                  aligned sequences, e.g. a domain alignment
                                  file. 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.
  [-database]          string     [swissprot] Name of BLAST-indexed database
                                  to search. (Any string)
   -niter              integer    [1] This option specifies the number of
                                  PSIBLAST iterations. This option specifies
                                  the number of PSIBLAST iterations that are
                                  performed in a search. (Any integer value)
   -evalue             float      [0.001] This option specifies the threshold
                                  E-value for inclusion in family. This option
                                  specifies the threshold E-value for a
                                  PSIBLAST hit to be retained. (Any numeric
                                  value)
   -maxhits            integer    [1000] This option specifies the maximum
                                  number of hits. This option specifies the
                                  maximum number of PSIBLAST hit that are
                                  retained. It should normally be set high so
                                  that nothing is discarded. (Any integer
                                  value)
  [-dhfoutdir]         outdir     [./] This option specifies the location of
                                  DHF files (domain hits files) (output). A
                                  'domain hits file' contains database hits
                                  (sequences) with domain classification
                                  information, in FASTA format. 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    [seqsearch.log] This option specifies the
                                  name of log file for the build. The log file
                                  contains messages about any errors arising
                                  while SEQSEARCH ran.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-inseqspath" associated qualifiers
   -extension1         string     Default file extension

   "-dhfoutdir" associated qualifiers
   -extension3         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
-mode list This option specifies the mode of SEQSEARCH operation. SEQSEARCH takes as input a directory of either i. single sequences, ii. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file)). The user has to specify which.
1 (Single sequences)
2 (Multiple sequences (e.g. sequence set or alignment))
1
[-inseqspath]
(Parameter 1)
dirlist This option specifies the location of sequences, e.g. DAF files (domain alignment files) (input). SEQSEARCH takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. 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 with files ./
[-database]
(Parameter 2)
string Name of BLAST-indexed database to search. Any string swissprot
-niter integer This option specifies the number of PSIBLAST iterations. This option specifies the number of PSIBLAST iterations that are performed in a search. Any integer value 1
-evalue float This option specifies the threshold E-value for inclusion in family. This option specifies the threshold E-value for a PSIBLAST hit to be retained. Any numeric value 0.001
-maxhits integer This option specifies the maximum number of hits. This option specifies the maximum number of PSIBLAST hit that are retained. It should normally be set high so that nothing is discarded. Any integer value 1000
[-dhfoutdir]
(Parameter 3)
outdir This option specifies the location of DHF files (domain hits files) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in FASTA format. 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 log file for the build. The log file contains messages about any errors arising while SEQSEARCH ran. Output file seqsearch.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-inseqspath" associated dirlist qualifiers
-extension1
-extension_inseqspath
string Default file extension Any string daf
"-dhfoutdir" associated outdir qualifiers
-extension3
-extension_dhfoutdir
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

6.2 EXAMPLE SESSION

An example of interactive use of SEQSEARCH is shown below. Here is a sample session with seqsearch


% seqsearch 
Generate PSI-BLAST hits (DHF file) from a DAF file.
Input mode
         1 : Single sequences
         2 : Multiple sequences (e.g. sequence set or alignment)
Select mode of operation. [1]: 2
Domain alignment directories [./]: ../domainalign-keep/daf
Name of BLAST-indexed database to search. [swissprot]: swsmall
Number of PSIBLAST iterations. [1]: 
Threshold E-value for inclusion in family. [0.001]: 0.0001
Maximum number of hits. [1000]: 100
Domain hits file output directory [./]: 
Domainatrix log output file [seqsearch.log]: 
[blastpgp] WARNING: posFindAlignmentDimensions: Attempting to recover data from multiple alignment file

[blastpgp] WARNING: posProcessAlignment: Alignment recovered successfully

[blastpgp] WARNING: posFindAlignmentDimensions: Attempting to recover data from multiple alignment file

[blastpgp] WARNING: posProcessAlignment: Alignment recovered successfully


PROCESSING /homes/user/test/qa/domainalign-keep/daf/54894.daf
/shared/software/bin/blastpgp -t 1 -i ./seqsearch-1234567890.1234.seqin -B ./seqsearch-1234567890.1234.seqsin -j 1 -e 0.000100 -b 100 -v 100 -d ../../data/structure/swsmall
PROCESSING /homes/user/test/qa/domainalign-keep/daf/55074.daf
/shared/software/bin/blastpgp -t 1 -i ./seqsearch-1234567890.1234.seqin -B ./seqsearch-1234567890.1234.seqsin -j 1 -e 0.000100 -b 100 -v 100 -d ../../data/structure/swsmall

Go to the input files for this example
Go to the output files for this example




7.0 KNOWN BUGS & WARNINGS

None.


8.0 NOTES

1. Use of psiblast
psiblast must be installed on the system that is running SEQSEARCH.

SEQSEARCH requires a blast-indexed database to be present, i.e. both the sequence and index file must be present on the system. The name of the database to search specified in the acd file is that which is given as the -d parameter to blastpgp (e.g. blastpgp -d swissprot).

8.1 GLOSSARY OF FILE TYPES

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.
None


9.0 DESCRIPTION

By using homology search tools such as blast it is possible to find relatives to a group of related proteins (family, superfamily etc), given one or more sequences belonging to the group of interest. For example, when using psiblast it is possible to use a sequence alignment as the seed with which to search a sequence database. Performing such searches for large datasets such as all families within SCOP or CATH potentially requires a lot of time for preparation of datasets, running jobs and so on, in addition to the compute time required for the searches themselves. SEQSEARCH automatically performs a psiblast search of a sequence database for each file in a directory of sequences or sets of sequences. These sequences are used for the searches. Typically, the directory contains DAF files (domain alignment files) and the alignments are for a certain node (e.g. family, superfamily etc) from SCOP or CATH.


10.0 ALGORITHM

None.


11.0 RELATED APPLICATIONS

See also

Program name Description
profit Scan one or more sequences with a simple frequency matrix
prophecy Create frequency matrix or profile from a multiple alignment
prophet Scan one or more sequences with a Gribskov or Henikoff profile
siggen Generates a sparse protein signature from an alignment
siggenlig Generates ligand-binding signatures from a CON file
sigscan Generates hits (DHF file) from a signature search
sigscanlig Searches ligand-signature library and writes hits (LHF file)



12.0 DIAGNOSTIC ERROR MESSAGES

The following 3 types of message might appear in the log file:

WARN Could not open for reading my.file
WARN No PSIBLAST hits therefore no output file my.file
WARN Could not open for writing my.file


13.0 AUTHORS

Ranjeeva Ranasinghe

Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK


14.0 REFERENCES

Please cite the authors and EMBOSS.

Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

14.1 Other useful references

Altschul et al, Nuc. Acids. Res. 25:3389-3402, 1997