                           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:
     * (i) Accession number of the hit.
     * (ii) Database code from Uniprot.
     * (iii - iv) Start and end positions of the hit relative to the full
       length sequence in the uniprot database (files of these type may
       also be generated by using SEQWORDS in which case a '.' will be
       given for these records - see SEQWORDS documentation ).

   The next 9 tokens are specific to the domain (or domain family or other
   node) for which the hit was generated:
     * (v) Type of domain; currently either 'SCOP' or 'CATH' is given.
     * (vi) SCOP or CATH domain identifier. This is a 7-character code
       that uniquely identifies the domain in SCOP or CATH.
     * (vii) SCOP or CATH node unique identifier. For example, if the
       domain alignment file was for a SCOP family, the SCOP Sunid for the
       family would be given. This number uniquely identifies the node
       (i.e. family in this case) in the raw SCOP or CATH parsable files.
     * (viii) Domain class. Textual description of the 'Class' (SCOP and
       CATH domains).
     * (ix) Domain architecture. Textual description of the 'Architecture'
       (CATH only).
     * (x) Domain topology. Textual description of the 'Topology' (CATH
       only).
     * (xi) Domain fold. Textual description of the 'Fold' (SCOP domains
       only).
     * (xii) Domain superfamily. Textual description of the 'Superfamily'
       (SCOP and CATH domains).
     * (xiii) Domain family. Textual description of the 'Fold' (SCOP
       only).

   The next 4 tokens are specific to the hit itself:
     * (xiv) Model type. The type of model that was used to generate the
       hit. May have a value of "PSIBLAST" (from PSIBLAST), "HMMER"
       (hidden Markov model from the HMMER package), "SAM" (hidden Markov
       model from the SAM package), SPARSE (sparse protein signature),
       HENIKOFF (Henikoff profile) or GRIBSKOV (Gribskov profile). A value
       of "PSIBLAST" is written by SEQSEARCH, a value of "KEYWORD" is
       written by SEQWORDS.
     * (xv) SC - Score of hit. A floating point value that is the score
       from psiblast (or other search algorithm).
     * (xvi) P-value of hit from search algorithm.
     * (xvii) E-value of hit from search algorithm. The second line
       contains the protein sequence.

  Output files for usage example

  File: 54894.dhf

> Q9YBD5^.^1^95^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^56.10^0.000e+00^
9.000e+00
VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNV
IEDYKVVEKVKLKLP
> Q9UX07^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^60.00^0.000e+00^
6.000e+00
VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINIIR
DYVVTEKRHLEVP
> Q9KP65^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^120.00^0.000e+00
^4.000e+00
VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIEN
YEVVKKLALQLP
> Q9K1K9^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^93.10^0.000e+00^
7.000e+00
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDN
FKVVQKRHLNLP
> Q9JWY6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^91.60^0.000e+00^
2.000e+00
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDH
FKVVQKRHLNLP
> Q9HKM3^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^73.10^0.000e+00^
8.000e+00
ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISIIK
NYEISEKFQVELP
> Q9HHN3^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^71.50^0.000e+00^
2.000e+00
VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIVR
DYEVDEKRRVDRP
> Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^43.40^0.000e+00^
6.000e+00
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEK
IRQKIQLKLP
> Q97B28^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^72.70^0.000e+00^
8.000e+00
ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISIIK
NYEISEKFKVELP
> Q970X3^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^71.90^0.000e+00^
1.000e+00
VSKIKNGTVIDHIPAGRALAVLRILKIAEGYRIALVMNVESKKMGKKDIVKIENKEVDEKEANLITLIAPTATINIIRDY
EVVEKKKLKIP
> Q8ZTG2^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^58.80^0.000e+00^
1.000e+00
VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINIIR
NFAVVKKFKVTPP
> Q8ZB38^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^145.00^0.000e+00
^8.000e+00
VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRIDN
YEVVKKLTLSLP
> Q8Z130^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^168.00^0.000e+00
^1.000e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> Q8U374^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^83.90^0.000e+00^
4.000e+00
VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNGGAVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNII
REYKVVEKFKVEIP
> Q8TVB1^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^66.10^0.000e+00^
9.000e+00
VKRIEMGTVLDHLPPGTAPQIMRILDIDPTETTLLVAINVESSKMGRKDILKIEGKILSEEEANKVALVAPNATVNIVRD
YSVAEKFQVKPP
> Q8THL3^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^67.30^0.000e+00^
4.000e+00
IQAIENGTVIDHITAGQALNVLRILRISSAFRATVSFVMNAPGARGKKDVVKIEGKELSVEELNRIALISPKATINIIRD
FEVVQKNKVVLP
> Q8PXK6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^61.50^0.000e+00^
2.000e+00
VQAIESGTVIDHIKSGQALNVLRILGISSAFRATISFVMNAPGAGGKKDVVKIEGKELSVEELNRIALISPKATINIIRD
FVVVQKNNVVLP
> Q8K9H8^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^137.00^0.000e+00
^4.000e+00
VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIEK
YNLVGKIFPSLP
> Q8DCF7^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^118.00^0.000e+00
^2.000e+00
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIED
YQVVKKLALELP
> Q8D1W6^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^115.00^0.000e+00
^2.000e+00
VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIKN
YIVIKKQKLKLP
> Q8A9S4^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^57.70^0.000e+00^
3.000e+00
VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCNITIGFNLDSKKLGKKGIIKIADKFFCDEEINRISVVAPYVKLNIIRD
YEVVEKKEVRMP
> Q891I9^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^46.90^0.000e+00^
5.000e+00
ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYSVALIMNVFSSKLGKKDIIKIANKEIDIDFTVLGLIDPTITINIIEDE
KIKEKLNLELP
> Q87LF7^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^122.00^0.000e+00
^8.000e+00
VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIEN
YEVVKKLALELP
> Q83IL8^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^175.00^0.000e+00
^8.000e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRIDN
YEVVGKSRPSLP
> Q7P144^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^118.00^0.000e+00
^1.000e+00
VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVIDN
FEVVKKHKLTLP
> Q7MZ14^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^141.00^0.000e+00
^2.000e+00
VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIEN
YEVVKKLPINLP
> Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^73.80^0.000e+00^
5.000e+00
VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRD
YEVVEKRQVEVP
> Q7MHF0^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^118.00^0.000e+00
^2.000e+00
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIED
YQVVKKLALELP
> Q58801^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^53.40^0.000e+00^
6.000e+00
VKKITNGTVIDHIDAGKALMVFKVLNVPKETSVMIAINVPSKKKGKKDILKIEGIELKKEDVDKISLISPDVTINIIRNG
KVVEKLKPQIP
> P96175^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^99.30^0.000e+00^
9.000e+00
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIEN
FKVTDKHSLALP
> P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^43.00^0.000e+00^
9.000e+00
GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTT
VNIIKNSTVVEKYRIKLP
> P77919^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^85.00^0.000e+00^
2.000e+00
VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNII
RDYKVVEKFKVEVP
> P74766^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^68.10^0.000e+00^
2.000e+00
VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIVR
EYEVVKKTKLEVP
> P57451^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^133.00^0.000e+00
^6.000e+00
VEAIKSGSVIDHIPEYIGFKLLSLFRFTETEKRITIGLNLPSKKLGRKDIIKIENTFLSDEQINQLAIYAPHATVNYINE
YNLVRKVFPTLP
> P19936^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^148.00^0.000e+00
^1.000e+00
VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRIDN
YEVVRKLTLSLP
> P08421^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^170.00^0.000e+00
^4.000e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> P00478^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^177.00^0.000e+00
^2.000e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDN
YEVVGKSRPSLP
> O58452^.^1^94^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^86.20^0.000e+00^
8.000e+00
VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNII
RNYKVVEKFKVEVP
> O30129^.^1^93^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^71.10^0.000e+00^
3.000e+00
VSKIKEGTVIDHINAGKALLVLKILKIQPGTDLTVSMAMNVPSSKMGKKDIVKVEGMFIRDEELNKIALISPNATINLIR
DYEIERKFKVSPP
> O26938^.^1^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
spartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate car
bamoyltransferase, Regulatory-chain, N-terminal domain^PSIBLAST^75.00^0.000e+00^
2.000e+00
VKPIKNGTVIDHITANRSLNVLNILGLPDGRSKVTVAMNMDSSQLGSKDIVKIENRELKPSEVDQIALIAPRATINIVRD
YKIVEKAKVRL

  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 cat
alytic domain^PSIBLAST^77.00^0.000e+00^2.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9ERL9^.^1^152^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^67.70^0.000e+00^9.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9DGG6^.^1^181^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^124.00^0.000e+00^9.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q99396^.^1^212^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^159.00^0.000e+00^2.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99280^.^6^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^180.00^0.000e+00^1.000e+00
KEPTGPVTLIFTDIESSTALWAAHPDLMPDAVATHHRLIRSLITRYECYEVKTVGDSFMIASKSPFAAVQLAQELQLRFL
RLDWETNALDESYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGRTSNMAAR
TESVANGGQVLMTHAAYMSLSGEDRNQLDVTTLGATVLRGVPEPVRMYQLN
> Q99279^.^1^218^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^210.00^0.000e+00^9.000e+00
NNNRAPKEPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRYKCYEVKTVGDSFMIASKSPFAAVQLAQE
LQLCFLHHDWGTNALDDSYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIIRHDEVTKGYDYYGR
TPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALGDVALRGVSDPVKMYQLN
> Q91WF3^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^51.90^0.000e+00^6.000e+00
VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDTQQDSER
SCSHLGTMVEFAVALGSKLGVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEE
TARAL
> Q91WF3^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^139.00^0.000e+00^2.000e+00
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAIN
CVRMGLDMCRAIRKLRVATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
> Q8VHH7^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^154.00^0.000e+00^1.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAVC
SILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKG
EFDVEPGDGGSRCDYLDEKGIETYLI
> Q8NFM4^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^51.60^0.000e+00^7.000e+00
VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDAQQDAER
SCSHLGTMVEFAVALGSKLDVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEE
T
> Q8NFM4^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^139.00^0.000e+00^2.000e+00
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAIN
CVRMGLDMCRAIRKLRAATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
> Q29450^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^154.00^0.000e+00^7.000e+00
FHNLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHARN
CVKMGLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHLDK
AYEVEDGHGQQRDPYLKEMNIRTYLV
> Q29450^.^1^58^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
denylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cata
lytic domain^PSIBLAST^51.20^0.000e+00^1.000e+00
NSFRLRVGINHGPVIAGVIGARKPQYDIWGNTVNVASRMESTGELGKIQVTEETCTIL
> Q27675^.^1^217^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^140.00^0.000e+00^1.000e+00
NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLACE
IQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTKGYDYYGDT
SNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN
> Q26896^.^6^216^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^163.00^0.000e+00^1.000e+00
KEFTDPVTLIFTDIESSTALWAAHPGMMADAVATHHRLIRSLIALYGAYEVKTVGDSFMIACRSAFAAVELARDLQLTLV
HHDWGTVAIDESYRKFEEERAVEDSDYAPPTARLDSAVYCKLWNGLRVRAGIHTGLCDIAHDEVTKGYDYYGRTPNLAAR
TESAANGGQVLVTGATYYSLSVAERARLDATPIGPVPLRGVPEPVEMYQLN
> Q26721^.^1^206^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^184.00^0.000e+00^7.000e+00
PVTLIFTDIESSTALWAAHPEVMPDAVATHHRLIRTLISKYECYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWG
TNAIDESYQQFEQQRAEDDSDYTPPTARLDPKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTSNMAARTESVA
NGGQVLMTHAAYMSLSAEERQQIDVTALGDVPLRGVPKPVEMYRLN
> Q25263^.^1^217^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^140.00^0.000e+00^2.000e+00
NNDAAPKDGDEPVTLLFTDIESSTALWAALPQLMSDAIAAHHRVIRQLVKKYGCYEVKTIGDSFMIACRSAHSAVSLACE
IQTKLLKHDWGTEALDRAYREFELARVDTLDDYEPPTARLSEEEYAALWCGLRVRVGIHTGLTDIRYDEVTRGYDYYGDT
SNMAARTEAVANGGQVVATEAAWWALSNDERAGIAHTAMGPQGLRGVPFAVEMFQLN
> Q09435^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^75.10^0.000e+00^6.000e+00
DSVTVFFSDVVKFTILASKCSPFQTVNLLNDLYSNFDTIIEQHGVYKVESIGDGYLCVSGLPTRNGYAHIKQIVDMSLKF
MEYCKSFNIPHLPRENVELRIGVNSGPCVAGVVGLSMPRYCLFGDTVNTASRMESNGKPSLIHLTNDAHSLLTTHYPNQY
E
> Q08828^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^183.00^0.000e+00^2.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHC
CVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNG
DYEVEPGYGHERNSFLKTHNIETFFI
> Q08828^.^1^51^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
denylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cata
lytic domain^PSIBLAST^45.40^0.000e+00^5.000e+00
NDFVLRVGINVGPVVAGVIGARRPQYDIWGNTVNVASRMDSTGVQGRIQVT
> Q08462^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^155.00^0.000e+00^4.000e+00
FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKN
CVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNG
AYKVEEGDGDIRDPYLKQHLVKTYFV
> Q08462^.^1^167^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^46.20^0.000e+00^4.000e+00
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEP
ERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVT
EETSLVL
> Q07553^.^1^152^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^75.80^0.000e+00^4.000e+00
DCVTILFSDIVGFTELCTTSTPFEVVEMLNDWYTCCDSIISNYDVYKVETIGDAYMVVSGLPLQNGSRHAGEIASLALHL
LETVGNLKIRHKPTETVQLRIGVHSGPCAAGVVGQKMPRYCLFGDTVNTASRMESTGDSMRIHISEATYQLL
> Q07093^.^1^158^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^62.30^0.000e+00^4.000e+00
VTILFSDIVGFTSICSRATPFMVISMLEGLYKDFDEFCDFFDVYKVETIGDAYCVASGLHRASIYDAHRCLDGLKMIDAC
SKHITHDGEQIKMRIGLHTGTVLAGVVGRKMPRYCLFGHSVTIANKFESGSEALKINVSPTTKDWLTKHEGFEFELQP
> Q04400^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^245.00^0.000e+00^3.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHA
HCCVEMGMDMIEAISSVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLNYL
NGDYEVEPGCGGERNAYLKEHSIETFLIL


  [Part of this file has been deleted for brevity]

PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEA
EWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS
> P22717^.^1^147^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^61.20^0.000e+00^9.000e+00
TILFSDVVTFTNICAACEPIQIVNMLNSMYSKFDRLTSVHDVYKVETIGDAYMVVGGVPVPVESHAQRVANFALGMRISA
KEVMNPVTGEPIQIRVGIHTGPVLAGVVGDKMPRYCLFGDTVNTASRMESHGLPSKVHLSPTAHRAL
> P21932^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^154.00^0.000e+00^1.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAVC
SILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKG
EFDVEPGDGGSRCDYLDEKGIETYLI
> P20595^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^68.90^0.000e+00^4.000e+00
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPE
PCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEY
TYRCL
> P20594^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^78.50^0.000e+00^7.000e+00
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIA
RMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDE
LGCFQLEL
> P19754^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^183.00^0.000e+00^2.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHC
CVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNG
DYEVEPGHGHERNSFLKTHNIETFFI
> P19754^.^1^51^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
denylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cata
lytic domain^PSIBLAST^45.40^0.000e+00^5.000e+00
NDFVLRVGINVGPVVAGVIGARRPQYDIWGNTVNVASRMDSTGVQGRIQVT
> P19687^.^1^161^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^72.70^0.000e+00^3.000e+00
AVQAKRFGNVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDRQCGELDVYKVETIGDAYCVAGGLHKESDTHAVQIA
LMALKMMELSHEVVSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCP
G
> P19686^.^1^160^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^68.50^0.000e+00^5.000e+00
VQAKKFNEVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIAL
MALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> P18910^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^78.50^0.000e+00^6.000e+00
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREVA
RMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVLEE
FDGFELEL
> P18293^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^79.30^0.000e+00^3.000e+00
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGQLHAREVA
RMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALRIHLSSETKAVLEE
FDGFELEL
> P16068^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^68.90^0.000e+00^4.000e+00
HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPE
PCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEY
TYRCL
> P16067^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^78.50^0.000e+00^7.000e+00
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIA
RMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDE
LGCFQLEL
> P16066^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^77.80^0.000e+00^9.000e+00
VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAVIDNFDVYKVETIGDAYMVVSGLPVRNGRLHACEVA
RMALALLDAVRSFRIRHRPQEQLRLRIGIHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGEALKIHLSSETKAVLEE
FGGFELEL
> P16065^.^1^143^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^73.90^0.000e+00^1.000e+00
VSIFFSDIVGFTALSAASTPIQVVNLLNDLYTLFDAIISNYDVYKVETIGDAYMLVSGLPLRNGDRHAGQIASTAHHLLE
SVKGFIVPHKPEVFLKLRIGIHSGSCVAGVVGLTMPRYCLFGDTVNTASRMESNGLALRIHVS
> O95622^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^247.00^0.000e+00^1.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHA
HCCVEMGMDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGKAGRIHITKATLNYL
NGDYEVEPGCGGERNAYLKEHSIETFLIL
> O95622^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^51.60^0.000e+00^8.000e+00
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIK
ALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL
> O75343^.^1^147^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^66.60^0.000e+00^2.000e+00
TILFSDVVTFTNICTACEPIQIVNVLNSMYSKFDRLTSVHAVYKVETIGDAYMVVGGVPVPIGNHAQRVANFALGMRISA
KEVTNPVTGEPIQLRVGIHTGPVLADVVGDKMPRYCLFGDTVNTASRMESHGLPNKVHLSPTAYRAL
> O60503^.^1^179^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^124.00^0.000e+00^9.000e+00
VSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKA
IEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVIE
RLGQSVVADQLKGLKTYLI
> O60266^.^1^186^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^154.00^0.000e+00^8.000e+00
FNTMYMYRHENVSILFADIVGFTQLSSACSAQELVKLLNELFARFDKLAAKYHQLRIKILGDCYYCICGLPDYREDHAVC
SILMGLAMVEAISYVREKTKTGVDMRVGVHTGTVLGGVLGQKRWQYDVWSTDVTVANKMEAGGIPGRVHISQSTMDCLKG
EFDVEPGDGGSRCDYLEEKGIETYLI
> O60266^.^1^54^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^A
denylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cata
lytic domain^PSIBLAST^43.50^0.000e+00^2.000e+00
NNFMLRIGMNKGGVLAGVIGARKPHYDIWGNTVNVASRMESTGVMGNIQVVEET
> O43306^.^1^189^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^236.00^0.000e+00^1.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHA
HCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYL
NGDYEVEPGRGGERNAYLKEQHIETFLIL
> O43306^.^1^159^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^51.90^0.000e+00^5.000e+00
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHIT
ALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVL
> O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^75.40^0.000e+00^6.000e+00
DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMT
NVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL
> O19179^.^1^150^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^76.20^0.000e+00^3.000e+00
VTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPQRNGQRHAAEIANMALDILS
AVGSFRMRHMPEVPVRIRIGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVNMSTVRIL
> O02740^.^1^162^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cat
alytic domain^PSIBLAST^77.40^0.000e+00^1.000e+00
DLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIANMSLDI
LSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRTLGEGYE
VE

  File: seqsearch.log

//
/homes/user/test/qa/domainalign-domsearch/daf/54894.daf
//
/homes/user/test/qa/domainalign-domsearch/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:6.6.0.0

   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


