                            sigscan 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

   Generates a DHF (domain hits file) of hits (sequences) from scanning a
   signature against a sequence database. Generates hits (DHF file) from a
   signature search

2.0 INPUTS & OUTPUTS

   SIGSCAN reads a signature from a protein signature file, scans the
   signature against a protein sequence database and generates a DHF file
   (domain hits file) of hits to database sequences and a DAF file (domain
   alignment file) of corresponding signature-sequence alignments. The
   names of the signature file, DHF file and DAF file are provided by the
   user. The user specifies a maximum number of high-scoring hits that
   will be generated.

3.0 INPUT FILE FORMAT

   The format of the signature file is described in SIGGEN documentation.

  Input files for usage example

  File: ../siggen-keep/54894.sig

TY   SCOP
XX
TS   1D
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
SI   54894
XX
NP   15
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   H ; 2
XX
GA   12 ; 2
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   P ; 2
XX
GA   1 ; 2
XX
NN   [3]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   P ; 2
XX
GA   26 ; 2
XX
NN   [4]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   T ; 2
XX
GA   15 ; 2
XX
NN   [5]
XX


  [Part of this file has been deleted for brevity]

XX
GA   4 ; 2
XX
NN   [10]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   I ; 2
XX
GA   2 ; 2
XX
NN   [11]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 2
XX
GA   0 ; 2
XX
NN   [12]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   N ; 2
XX
GA   0 ; 2
XX
NN   [13]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   V ; 2
XX
GA   3 ; 2
XX
NN   [14]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   R ; 2
XX
GA   3 ; 2
XX
NN   [15]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 2
XX
GA   2 ; 2
//

  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

   DHF file (domain hits file)
   The format of the DHF file (domain hits file) of hit sequences
   generated by SIGSCAN (Figure 1) is described fully in SEQSEARCH
   documentation and only summarised here. The file contains two lines per
   hit, the first is a description of the hit in 16 text tokens delimited
   by '^'. The second line contains the protein sequence. The first 4
   tokens refer to the hit (sequence) itself, the tokens are
     * (i) Accession number
     * (ii) Database code,
     * (iii - iv) Start and end positions of the hit relative to the full
       length sequence.

   The next 9 tokens refer to the domain family, superfamily etc for which
   the signature was derived and are as follows:
     * (v) Type of domain (one of 'SCOP' or 'CATH'),
     * (vi) SCOP or CATH domain identifier.
     * (vii) SCOP or CATH node unique identifier, e.g. SCOP Family Sunid.
     * (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 refer to the hit, specifically, information about the
   search result as follows:
     * (xiv) Model type. The type of model that was used to generate the
       hit. For DHF files generated by using SIGSCAN a value of SPARSE
       (sparse protein signature) is given. Several other values are
       possible, however, see SEQSEARCH documentation.
     * (xv) SC - Score of hit from search algoritm (not written by
       SIGSCAN).
     * (xvi) P-value of hit (not written by SIGSCAN).
     * (xvii) E-value of hit (not written by SIGSCAN).

   DAF file (domain alignment file)
   The format of the DAF file (domain alignment file, Figure 2) generated
   by SIGSCAN is described fully in DOMAINALIGN documentation and is only
   summarised here.
   It conforms to EMBOSS "simple" multiple sequence alignment format and
   includes domain classification records (in comment lines beginning with
   '#') for the node for which the signature was generated. The
   classification records are TY (domain type, either SCOP or CATH), CL
   (class), FO (fold), SF (superfamily) and FA (family). For CATH domains,
   AR (architecture) and TP (topology) may also be given. A unique
   identifier for the node is given after SI.
   There are multiple blocks that contain the accession numbers, positions
   and aligned sequences. An accession number is given for each hit. The
   positions are the start and end residue positions of the appropriate
   section of sequence. The sequence uses '-' as a gap character. A
   'SIGNATURE' line is given as a markup line underneath the sequence
   (signature positions are marked with a '*').

  Output files for usage example

  File: SIGSCAN.dhf

> P00478^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.20^0.000e+00^0.
000e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDN
YEVVGKSRPSLP
> P08421^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.20^0.000e+00^0.
000e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> Q83IL8^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.20^0.000e+00^0.
000e+00
VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRIDN
YEVVGKSRPSLP
> Q8Z130^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.00^0.000e+00^0.
000e+00
VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRIDN
YDVVGKSRPSLP
> Q97B28^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.53^0.000e+00^0.
000e+00
ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISIIK
NYEISEKFKVELP
> P19936^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.
000e+00
VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRIDN
YEVVRKLTLSLP
> Q7P144^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.
000e+00
VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVIDN
FEVVKKHKLTLP
> Q8ZB38^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.
000e+00
VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRIDN
YEVVKKLTLSLP
> Q9HKM3^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.
000e+00
ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISIIK
NYEISEKFQVELP
> P74766^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.20^0.000e+00^0.
000e+00
VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIVR
EYEVVKKTKLEVP
> Q8ZTG2^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.13^0.000e+00^0.
000e+00
VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINIIR
NFAVVKKFKVTPP
> Q9UX07^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.13^0.000e+00^0.
000e+00
VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINIIR
DYVVTEKRHLEVP
> Q7MZ14^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.07^0.000e+00^0.
000e+00
VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIEN
YEVVKKLPINLP
> Q9HHN3^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.07^0.000e+00^0.
000e+00
VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIVR
DYEVDEKRRVDRP
> Q9K1K9^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.07^0.000e+00^0.
000e+00
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDN
FKVVQKRHLNLP
> O58452^.^12^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.93^0.000e+00^0.
000e+00
VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNII
RNYKVVEKFKVEVP
> Q87LF7^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.93^0.000e+00^0.
000e+00
VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIEN
YEVVKKLALELP
> Q9KP65^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.93^0.000e+00^0.
000e+00
VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIEN
YEVVKKLALQLP
> P96175^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.73^0.000e+00^0.
000e+00
VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIEN
FKVTDKHSLALP
> Q8D1W6^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.73^0.000e+00^0.
000e+00
VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIKN
YIVIKKQKLKLP
> Q9JWY6^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.73^0.000e+00^0.
000e+00
VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDH
FKVVQKRHLNLP
> P77919^.^12^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.
000e+00
VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNII
RDYKVVEKFKVEVP
> Q7MHF0^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.
000e+00
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIED
YQVVKKLALELP
> Q8DCF7^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.
000e+00
VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIED
YQVVKKLALELP
> Q8K9H8^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.
000e+00
VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIEK
YNLVGKIFPSLP


  [Part of this file has been deleted for brevity]

FHSLYVKRHQNVSILYADIVGFTQLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPTHARN
CVKMGLDMCQAIKQVREATGVDINMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHLDK
AYEVEDGHGQQRDPYLKEMNIRTYLV
> P51829^.^90^170^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0
.000e+00
FHSLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPTHARN
CVKMGLDICEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLNHLDK
AYEVEDGHGEQRDPYLKEMNIRTYLV
> Q03343^.^92^172^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0
.000e+00
MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHA
HCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYL
NGDYEVEPGRGGERNGYLKEQCIETFLIL
> Q07093^.^16^96^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^
Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate ca
rbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.
000e+00
VTILFSDIVGFTSICSRATPFMVISMLEGLYKDFDEFCDFFDVYKVETIGDAYCVASGLHRASIYDAHRCLDGLKMIDAC
SKHITHDGEQIKMRIGLHTGTVLAGVVGRKMPRYCLFGHSVTIANKFESGSEALKINVSPTTKDWLTKHEGFEFELQP
> Q08462^.^70^150^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0
.000e+00
DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEP
ERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVT
EETSLVL
> Q26721^.^94^174^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0
.000e+00
PVTLIFTDIESSTALWAAHPEVMPDAVATHHRLIRTLISKYECYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWG
TNAIDESYQQFEQQRAEDDSDYTPPTARLDPKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTSNMAARTESVA
NGGQVLMTHAAYMSLSAEERQQIDVTALGDVPLRGVPKPVEMYRLN
> Q29450^.^90^170^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0
.000e+00
FHNLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHARN
CVKMGLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHLDK
AYEVEDGHGQQRDPYLKEMNIRTYLV
> Q8NFM4^.^76^156^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0
.000e+00
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAIN
CVRMGLDMCRAIRKLRAATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
> Q8NFM4^.^68^148^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0
.000e+00
VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDAQQDAER
SCSHLGTMVEFAVALGSKLDVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEE
T
> Q91WF3^.^76^156^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0
.000e+00
FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAIN
CVRMGLDMCRAIRKLRVATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
> Q91WF3^.^68^148^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0
.000e+00
VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDTQQDSER
SCSHLGTMVEFAVALGSKLGVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEE
TARAL
> Q97FS4^.^8^88^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^SPARSE^0.47^0.000e+00^0.0
00e+00
INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEK
IRQKIQLKLP
> O60503^.^50^130^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0
.000e+00
VSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKA
IEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVIE
RLGQSVVADQLKGLKTYLI
> P26769^.^1^81^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^SPARSE^0.47^0.000e+00^0.0
00e+00
FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKN
CVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNG
AYKVEEGDGEIRDPYLKQHLVKTYFV
> P98999^.^52^132^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0
.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRPDHAYCCIEMGLGMI
EAIDQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEKTARYLD
> Q08462^.^1^81^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^SPARSE^0.47^0.000e+00^0.0
00e+00
FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKN
CVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNG
AYKVEEGDGDIRDPYLKQHLVKTYFV
> Q99279^.^119^199^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-lik
e^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate
carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^
0.000e+00
NNNRAPKEPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRYKCYEVKTVGDSFMIASKSPFAAVQLAQE
LQLCFLHHDWGTNALDDSYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIIRHDEVTKGYDYYGR
TPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALGDVALRGVSDPVKMYQLN
> Q9DGG6^.^52^132^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0
.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> O02740^.^59^139^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0
.000e+00
DLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIANMSLDI
LSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRTLGEGYE
VE
> O19179^.^57^137^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0
.000e+00
VTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPQRNGQRHAAEIANMALDILS
AVGSFRMRHMPEVPVRIRIGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVNMSTVRILHALDEGFQTE
V
> O95622^.^77^157^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0
.000e+00
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIK
ALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL
> P19754^.^33^113^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0
.000e+00
FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHC
CVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNG
DYEVEPGHGHERNSFLKTHNIETFFI
> P30803^.^77^157^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0
.000e+00
VAVMFASIANFSEFYVELEANNEGVECLRVLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIK
ALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL
> P40137^.^30^110^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0
.000e+00
VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQE
LETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK
> P40144^.^77^157^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0
.000e+00
VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIK
ALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL
> P51839^.^59^139^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like
^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate c
arbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0
.000e+00
DQVTIYFSDIVGFTTISALSEPIEVVGFLNDLYTMFDAVLDSHDVYKVETIGDAYMVASGLPRRNGNRHAAEIANMALEI
LSYAGNFRMRHAPDVPIRVRAGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSRNTVQALLSLDEGYK
IDV

  File: SIGSCAN.aln

# DE   Results of signature search
# XX
# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# SI   54894
# XX
P00478    1      VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKI 53
SIGNATURE -      ----------*-*--------------------------*-------------
P00478    54     ENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP               106
SIGNATURE -      --*---*--*----*-*----*--***---*---*--*-
P00478    107    .                                                     159
SIGNATURE -      .
P00478    160    .                                                     212
SIGNATURE -      .
P00478    213    .                                                     265
SIGNATURE -      .
# XX
P08421    1      VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKI 53
SIGNATURE -      ----------*-*--------------------------*-------------
P08421    54     ENTFLTEEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP               106
SIGNATURE -      --*---*--*----*-*----*--***---*---*--*-
P08421    107    .                                                     159
SIGNATURE -      .
P08421    160    .                                                     212
SIGNATURE -      .
P08421    213    .                                                     265
SIGNATURE -      .
# XX
Q83IL8    1      VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKI 53
SIGNATURE -      ----------*-*--------------------------*-------------
Q83IL8    54     ENTFLSEEQVDQLALYAPQATVNRIDNYEVVGKSRPSLP               106
SIGNATURE -      --*---*--*----*-*----*--***---*---*--*-
Q83IL8    107    .                                                     159
SIGNATURE -      .
Q83IL8    160    .                                                     212
SIGNATURE -      .
Q83IL8    213    .                                                     265
SIGNATURE -      .
# XX
Q8Z130    1      VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKI 53
SIGNATURE -      ----------*-*--------------------------*-------------
Q8Z130    54     ENTFLTDEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP               106


  [Part of this file has been deleted for brevity]

SIGNATURE -      ---------*---------------*---*--*----*-*----*--***---
P19754    107    VGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLN 159
SIGNATURE -      *---*--*---------------------------------------------
P19754    160    GDYEVEPGHGHERNSFLKTHNIETFFI                           212
SIGNATURE -      ---------------------------
P19754    213    .                                                     265
SIGNATURE -      .
# XX
P30803    1      VAVMFASIANFSEFYVELEANNEGVECLRVLNEIIADFDEIISEDRFRQLEKI 53
SIGNATURE -      -----------------------------------------------------
P30803    54     KTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQM 106
SIGNATURE -      ------------------------*-*--------------------------
P30803    107    KIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL 159
SIGNATURE -      *---------------*---*--*----*-*----*--***---*---*--*-
P30803    160    .                                                     212
SIGNATURE -      .
P30803    213    .                                                     265
SIGNATURE -      .
# XX
P40137    1      VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDAL 53
SIGNATURE -      ------------------------------*-*--------------------
P40137    54     MVYFGAPIADPAHARRGVQCALDMVQELETVNALRSARGEPCLRIGVGVHTGP 106
SIGNATURE -      ------*---------------*---*--*----*-*----*--***---*--
P40137    107    AVLGNIGSATRRLEYTAIGDTVNLASRIESLTK                     159
SIGNATURE -      -*--*----------------------------
P40137    160    .                                                     212
SIGNATURE -      .
P40137    213    .                                                     265
SIGNATURE -      .
# XX
P40144    1      VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKI 53
SIGNATURE -      -----------------------------------------------------
P40144    54     KTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQM 106
SIGNATURE -      ------------------------*-*--------------------------
P40144    107    KIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL 159
SIGNATURE -      *---------------*---*--*----*-*----*--***---*---*--*-
P40144    160    .                                                     212
SIGNATURE -      .
P40144    213    .                                                     265
SIGNATURE -      .
# XX
P51839    1      DQVTIYFSDIVGFTTISALSEPIEVVGFLNDLYTMFDAVLDSHDVYKVETIGD 53
SIGNATURE -      -----------------------------------------------------
P51839    54     AYMVASGLPRRNGNRHAAEIANMALEILSYAGNFRMRHAPDVPIRVRAGLHSG 106
SIGNATURE -      ------*-*--------------------------*---------------*-
P51839    107    PCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSRNTVQALLSLDEGY 159
SIGNATURE -      --*--*----*-*----*--***---*---*--*-------------------
P51839    160    KIDV                                                  212
SIGNATURE -      ----
P51839    213    .                                                     265
SIGNATURE -      .

5.0 DATA FILES

   SIGSCAN requires a residue substitution matrix.

6.0 USAGE

Generates hits (DHF file) from a signature search
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-siginfile]         infile     This option specifies the name of the
                                  signature file (input). A 'signature file'
                                  contains a sparse sequence signature
                                  suitable for use with the SIGSCAN and
                                  SIGSCANLIG programs. The files are generated
                                  by using SIGGEN and SIGGENLIG.
  [-dbsequence]        seqall     This option specifies the name of the
                                  database to search.
   -sub                matrixf    [EBLOSUM62] This option specifies the
                                  residue substitution matrix.
   -gapo               float      [10.0 for any sequence] This option
                                  specifies the gap insertion penalty. The gap
                                  insertion penalty is the score taken away
                                  when a gap is created. The best value
                                  depends on the choice of comparison matrix.
                                  The default value assumes you are using the
                                  EBLOSUM62 matrix for protein sequences, and
                                  the EDNAMAT matrix for nucleotide sequences.
                                  (Floating point number from 1.0 to 100.0)
   -gape               float      [0.5 for any sequence] This option specifies
                                  the gap extension penalty. The gap
                                  extension penalty is added to the standard
                                  gap penalty for each base or residue in the
                                  gap. This is how long gaps are penalized.
                                  Usually you will expect a few long gaps
                                  rather than many short gaps, so the gap
                                  extension penalty should be lower than the
                                  gap penalty. (Floating point number from 0.0
                                  to 10.0)
   -nterm              menu       [1] This option specifies the N-terminal
                                  matching option. This determines how the
                                  first signature position is aligned to a
                                  sequence from the database. (Values: 1
                                  (Align anywhere and allow only complete
                                  signature-sequence fit); 2 (Align anywhere
                                  and allow partial signature-sequence fit); 3
                                  (Use empirical gaps only))
   -nhits              integer    [100] This option specifies the maximum
                                  number of hits to output. (Any integer
                                  value)
  [-hitsfile]          outfile    [SIGSCAN.dhf] This option specifies the name
                                  of the DHF file (domain hits file)
                                  (output). A 'domain hits file' contains
                                  database hits (sequences) with domain
                                  classification information, in the DHF
                                  format (FASTA-like). The hits are relatives
                                  to a SCOP or CATH family (or other node in
                                  the structural hierarchies) and are found
                                  from a search of a sequence database, in
                                  this case, by using SIGSCAN. Files
                                  containing hits retrieved by PSIBLAST are
                                  generated by using SEQSEARCH or various
                                  types of HMM and profile by using LIBSCAN.
  [-alignfile]         outfile    [SIGSCAN.aln] This option specifies the name
                                  of the SAF (signature alignment file)
                                  (output).A 'signature alignment file'
                                  contains one or more signature-sequence
                                  alignments. The file is in DAF format
                                  (CLUSTAL-like) and is annotated with
                                  bibliographic information, either the domain
                                  family classification (for SIGSCAN output)
                                  or ligand classification (for SIGSCANLIG
                                  output). The files generated by SIGSCAN will
                                  contain a signature-sequence alignment for
                                  a single signature against a library of one
                                  or more sequences. The files generated by
                                  using SIGSCANLIG will contain a
                                  signature-sequence alignment for a single
                                  query sequence against a library of one or
                                  more signatures.

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

   "-dbsequence" associated qualifiers
   -sbegin2            integer    Start of each sequence to be used
   -send2              integer    End of each sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-hitsfile" associated qualifiers
   -odirectory3        string     Output directory

   "-alignfile" associated qualifiers
   -odirectory4        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options 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


  6.1 COMMAND LINE ARGUMENTS

