## 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 carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.20^0.000e+00^0.000e+00
    VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP
    > P08421^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.20^0.000e+00^0.000e+00
    VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTEEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP
    > Q83IL8^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.20^0.000e+00^0.000e+00
    VEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEEQVDQLALYAPQATVNRIDNYEVVGKSRPSLP
    > Q8Z130^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^3.00^0.000e+00^0.000e+00
    VEAIKCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLTDEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP
    > Q97B28^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.53^0.000e+00^0.000e+00
    ISKIKDGTVIDHIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISIIKNYEISEKFKVELP
    > P19936^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.000e+00
    VEAIKCGTVIDHIPAQIGFKLLTLFKLTATDQRITIGLNLPSNELGRKDLIKIENTFLTEQQANQLAMYAPKATVNRIDNYEVVRKLTLSLP
    > Q7P144^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.000e+00
    VEALKQGTVIDHIPAGEGVKILRLFKLTETGERVTVGLNLVSRHMGSKDLIKVENVALTEEQANELALFAPKATVNVIDNFEVVKKHKLTLP
    > Q8ZB38^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.000e+00
    VEAIKCGTVIDHIPAQIGFKLLSLFKLTATDQRITIGLNLPSKRSGRKDLIKIENTFLTEQQANQLAMYAPDATVNRIDNYEVVKKLTLSLP
    > Q9HKM3^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.40^0.000e+00^0.000e+00
    ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVNYTVSLAIHVPSNKMGFKDVIKIENRFLDRNELDMISLIAPNATISIIKNYEISEKFQVELP
    > P74766^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.20^0.000e+00^0.000e+00
    VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINIVREYEVVKKTKLEVP
    > Q8ZTG2^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.13^0.000e+00^0.000e+00
    VSKIENGTVIDHIPAGRALTVLRILGISGKEGLRVALVMNVESKKLGKKDIVKIEGRELTPEEVNIISAVAPTATINIIRNFAVVKKFKVTPP
    > Q9UX07^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.13^0.000e+00^0.000e+00
    VSKIRNGTVIDHIPAGRALAVLRILGIRGSEGYRVALVMNVESKKIGRKDIVKIEDRVIDEKEASLITLIAPSATINIIRDYVVTEKRHLEVP
    > Q7MZ14^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.07^0.000e+00^0.000e+00
    VEAIRCGTVIDHIPAQVGFKLLSLFKLTETDQRITIGLNLPSNRLGKKDLIKIENTFLTEQQANQLAMYAPNATVNCIENYEVVKKLPINLP
    > Q9HHN3^.^11^91^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.07^0.000e+00^0.000e+00
    VSKIQAGTVIDHIPAGQALQVLQILGTNGASDDQITVGMNVTSERHHRKDIVKIEGRELSQDEVDVLSLIAPDATINIVRDYEVDEKRRVDRP
    > Q9K1K9^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^2.07^0.000e+00^0.000e+00
    VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDNFKVVQKRHLNLP
    > O58452^.^12^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.93^0.000e+00^0.000e+00
    VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNGGSVLLAMNVPSKKLGRKDIVKVEGKFLSEEEVNKIALVAPTATVNIIRNYKVVEKFKVEVP
    > Q87LF7^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.93^0.000e+00^0.000e+00
    VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSSQRVTIGLNLPSSALGHKDLLKIENVFINEEQASKLALYAPHATVNQIENYEVVKKLALELP
    > Q9KP65^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.93^0.000e+00^0.000e+00
    VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSAQRVTIGLNLPSSALGSKDLLKIENVFISEAQANKLALYAPHATVNQIENYEVVKKLALQLP
    > P96175^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.73^0.000e+00^0.000e+00
    VEAICNGYVIDHIPSGQGVKILRLFSLTDTKQRVTVGFNLPSHDGTTKDLIKVENTEITKSQANQLALLAPNATVNIIENFKVTDKHSLALP
    > Q8D1W6^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.73^0.000e+00^0.000e+00
    VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTKERITMGLNLPSNQQKKKDLIKLENVLLNEDQANQLSIYAPLATVNQIKNYIVIKKQKLKLP
    > Q9JWY6^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.73^0.000e+00^0.000e+00
    VEAIEKGTVIDHIPAGRGLTILRQFKLLHYGNAVTVGFNLPSKTQGSKDIIKIKGVCLDDKAADRLALFAPEAVVNTIDHFKVVQKRHLNLP
    > P77919^.^12^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.000e+00
    VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNGGAVLLAMNVPSKKLGRKDIVKVEGRFLSEEEVNKIALVAPNATVNIIRDYKVVEKFKVEVP
    > Q7MHF0^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.000e+00
    VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP
    > Q8DCF7^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.000e+00
    VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSSQRVTIGLNLPSSALGNKDLLKIENVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP
    > Q8K9H8^.^10^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^1.60^0.000e+00^0.000e+00
    VEAIKSGSVIDHIPAHIGFKLLSLFRFTETEKRITIGLNLPSQKLDKKDIIKIENTFLSDDQINQLAIYAPCATVNYIEKYNLVGKIFPSLP

      [Part of this file has been deleted for brevity]

    FHSLYVKRHQNVSILYADIVGFTQLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPTHARNCVKMGLDMCQAIKQVREATGVDINMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHLDKAYEVEDGHGQQRDPYLKEMNIRTYLV
    > P51829^.^90^170^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00
    FHSLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPTHARNCVKMGLDICEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLNHLDKAYEVEDGHGEQRDPYLKEMNIRTYLV
    > Q03343^.^92^172^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00
    MMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRVHCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNGYLKEQCIETFLIL
    > Q07093^.^16^96^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00
    VTILFSDIVGFTSICSRATPFMVISMLEGLYKDFDEFCDFFDVYKVETIGDAYCVASGLHRASIYDAHRCLDGLKMIDACSKHITHDGEQIKMRIGLHTGTVLAGVVGRKMPRYCLFGHSVTIANKFESGSEALKINVSPTTKDWLTKHEGFEFELQP
    > Q08462^.^70^150^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00
    DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEPERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEETSLVL
    > Q26721^.^94^174^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00
    PVTLIFTDIESSTALWAAHPEVMPDAVATHHRLIRTLISKYECYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWGTNAIDESYQQFEQQRAEDDSDYTPPTARLDPKVYSRLWNGLRVRVGIHTGLCDIRRDEVTKGYDYYGRTSNMAARTESVANGGQVLMTHAAYMSLSAEERQQIDVTALGDVPLRGVPKPVEMYRLN
    > Q29450^.^90^170^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00
    FHNLYVKRHQNVSILYADIVGFTRLASDCSPKELVVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHARNCVKMGLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVSLANRMEAAGVPGRVHITEATLKHLDKAYEVEDGHGQQRDPYLKEMNIRTYLV
    > Q8NFM4^.^76^156^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00
    FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAINCVRMGLDMCRAIRKLRAATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
    > Q8NFM4^.^68^148^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00
    VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDAQQDAERSCSHLGTMVEFAVALGSKLDVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEET
    > Q91WF3^.^76^156^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00
    FHSLYVKRHQGVSVLYADIVGFTRLASECSPKELVLMLNELFGKFDQIAKEHECMRIKILGDCYYCVSGLPLSLPDHAINCVRMGLDMCRAIRKLRVATGVDINMRVGVHSGSVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITGATLALL
    > Q91WF3^.^68^148^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.53^0.000e+00^0.000e+00
    VCVLFASVPDFKEFYSESNINHEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATSGQDTQQDSERSCSHLGTMVEFAVALGSKLGVINKHSFNNFRLRVGLNHGPVVAGVIGAQKPQYDIWGNTVNVASRMESTGVLGKIQVTEETARAL
    > Q97FS4^.^8^88^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00
    INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP
    > O60503^.^50^130^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00
    VSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVIERLGQSVVADQLKGLKTYLI
    > P26769^.^1^81^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00
    FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKNCVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNGAYKVEEGDGEIRDPYLKQHLVKTYFV
    > P98999^.^52^132^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00
    EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEETKCEKISTLGDCYYCVAGCPEPRPDHAYCCIEMGLGMIEAIDQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEKTARYLD
    > Q08462^.^1^81^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00
    FHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLPNHAKNCVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLNGAYKVEEGDGDIRDPYLKQHLVKTYFV
    > Q99279^.^119^199^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00
    NNNRAPKEPTDPVTLIFTDIESSTALWAAHPDLMPDAVAAHHRMVRSLIGRYKCYEVKTVGDSFMIASKSPFAAVQLAQELQLCFLHHDWGTNALDDSYREFEEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIIRHDEVTKGYDYYGRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALGDVALRGVSDPVKMYQLN
    > Q9DGG6^.^52^132^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.47^0.000e+00^0.000e+00
    EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
    > O02740^.^59^139^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00
    DLVTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPKRNGMRHAAEIANMSLDILSSVGTFKMRHMPEVPVRIRIGLHSGPVVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSHSTVTILRTLGEGYEVE
    > O19179^.^57^137^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00
    VTLYFSDIVGFTTISAMSEPIEVVDLLNDLYTLFDAIIGSHDVYKVETIGDAYMVASGLPQRNGQRHAAEIANMALDILSAVGSFRMRHMPEVPVRIRIGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVNMSTVRILHALDEGFQTEV
    > O95622^.^77^157^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00
    VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL
    > P19754^.^33^113^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00
    FHKIYIQRHDNVSILFADIVGFTGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCYYCVSGLTQPKTDHAHCCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTLANVMEAAGLPGKVHITKTTLACLNGDYEVEPGHGHERNSFLKTHNIETFFI
    > P30803^.^77^157^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00
    VAVMFASIANFSEFYVELEANNEGVECLRVLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL
    > P40137^.^30^110^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00
    VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQELETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK
    > P40144^.^77^157^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00
    VAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEDRFRQLEKIKTIGSTYMAASGLNDSTYDKVGKTHIKALADFAMKLMDQMKYINEHSFNNFQMKIGLNIGPVVAGVIGARKPQYDIWGNTVNVASRMDSTGVPDRIQVTTDMYQVL
    > P51839^.^59^139^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^SPARSE^0.40^0.000e+00^0.000e+00
    DQVTIYFSDIVGFTTISALSEPIEVVGFLNDLYTMFDAVLDSHDVYKVETIGDAYMVASGLPRRNGNRHAAEIANMALEILSYAGNFRMRHAPDVPIRVRAGLHSGPCVAGVVGLTMPRYCLFGDTVNTASRMESTGLPYRIHVSRNTVQALLSLDEGYKIDV

### 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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-siginfile] (Parameter 1) | 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. | Input file | Required
[-dbsequence] (Parameter 2) | seqall | This option specifies the name of the database to search. | Readable sequence(s) | Required
-sub | matrixf | This option specifies the residue substitution matrix. | Comparison matrix file in EMBOSS data path | EBLOSUM62
-gapo | float | This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAMAT matrix for nucleotide sequences. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence

-gape

float

This option specifies the gap extension penalty. The gap extension penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty.

Floating point number from 0.0 to 10.0

0.5 for any sequence

-nterm

list

This option specifies the N-terminal matching option. This determines how the first signature position is aligned to a sequence from the database.

1 | (Align anywhere and allow only complete signature-sequence fit)
2 | (Align anywhere and allow partial signature-sequence fit)
3 | (Use empirical gaps only)

1

-nhits | integer | This option specifies the maximum number of hits to output. | Any integer value | 100

[-hitsfile]
(Parameter 3)

outfile

This option specifies the name of the DHF file (domain hits file) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA-like). The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database, in this case, by using SIGSCAN. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH or various types of HMM and profile by using LIBSCAN.

Output file

SIGSCAN.dhf

[-alignfile]
(Parameter 4)

outfile

This option specifies the name of the SAF (signature alignment file) (output).A 'signature alignment file' contains one or more signature-sequence alignments. The file is in DAF format (CLUSTAL-like) and is annotated with bibliographic information, either the domain family classification (for SIGSCAN output) or ligand classification (for SIGSCANLIG output). The files generated by SIGSCAN will contain a signature-sequence alignment for a single signature against a library of one or more sequences. The files generated by using SIGSCANLIG will contain a signature-sequence alignment for a single query sequence against a library of one or more signatures.

Output file

SIGSCAN.aln

Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-dbsequence" associated seqall qualifiers
-sbegin2 -sbegin_dbsequence | integer | Start of each sequence to be used | Any integer value | 0
-send2 -send_dbsequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse2 -sreverse_dbsequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask2 -sask_dbsequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide2 -snucleotide_dbsequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein2 -sprotein_dbsequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower2 -slower_dbsequence | boolean | Make lower case | Boolean value Yes/No | N
-supper2 -supper_dbsequence | boolean | Make upper case | Boolean value Yes/No | N
-sformat2 -sformat_dbsequence | string | Input sequence format | Any string |
-sdbname2 -sdbname_dbsequence | string | Database name | Any string |
-sid2 -sid_dbsequence | string | Entryname | Any string |
-ufo2 -ufo_dbsequence | string | UFO features | Any string |
-fformat2 -fformat_dbsequence | string | Features format | Any string |
-fopenfile2 -fopenfile_dbsequence | string | Features file name | Any string |
"-hitsfile" associated outfile qualifiers
-odirectory3 -odirectory_hitsfile | string | Output directory | Any string |
"-alignfile" associated outfile qualifiers
-odirectory4 -odirectory_alignfile | 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 sigscan is shown below. Here is a sample session with sigscan

    % sigscan
    Generates hits (DHF file) from a signature search
    Domainatrix signature file: ../siggen-keep/54894.sig
    Name of database to search.: swsmall
    Residue substitution matrix [EBLOSUM62]:
    Gap insertion penalty [10]:
    Gap extension penalty [0.5]:
    N-terminal matching options
             1 : Align anywhere and allow only complete signature-sequence fit
             2 : Align anywhere and allow partial signature-sequence fit
             3 : Use empirical gaps only
    Select number [1]:
    Max. number of hits to output [100]:
    Domain hits output file [SIGSCAN.dhf]:
    Domainatrix signature alignment output file [SIGSCAN.aln]:

    Signature file read ok
    Signature compiled ok
    Signature aligned to db ok
    Hits file written ok
    Alignments file written ok

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

## 7.0 KNOWN BUGS & WARNINGS

None.

## 8.0 NOTES

SIGSCAN does not generate p-values or E-values. DHF files of hits for which p-values or E-values are calculated may be generated by using LIBSCAN . LIBSCAN provides searches for sparse protein signatures as well as various types of hidden Markov models and other profiles.
In the case a signature file is generated by hand, it is essential that the gap data given is listed in order of increasing gap size (see SIGGEN documentation ).

### 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).

Sequence alignment of domains belonging to the same SCOP or CATH family (or other node in the structural hierarchies). The file is annotated with domain family classification information.

DOMAINALIGN (structure-based sequence alignment of domains of known structure).

DOMAINALIGN alignments can be extended with sequence relatives (of unknown structure) to the family in question by using SEQALIGN.

Hits file

Text file of classified hits

A list of hits (e.g. from a prediction method) that are classified and rank-ordered on the basis of score, p-value, E-value etc.

ROCON and LIBSCAN (hits from searches of a discriminating element (hidden Markov model, profile or signature) against a sequence database).

ROCPLOT is run on the files to perform Receiver Operator Characteristic (ROC) analysis on the hits.

Signature file | SIG format | Contains a sparse sequence signature suitable for use with the SIGSCAN program. Contains a sparse sequence signature. | SIGGEN, SIGGENLIG, LIBGEN | The files are generated by using SIGGEN.

None

## 9.0 DESCRIPTION

See Blades et al., Ison et al. and Daniel et al. for a description of protein signatures and their application.

## 10.0 ALGORITHM

The algorithm is based on approach first described in Daniel et al (1999) that was applied to the definition of protein families (Ison et al, 2000) and later to automatically-generated signatures (Blades et al, 2005).

## 11.0 RELATED APPLICATIONS

## See also

Program name | Description
--- | ---
contacts | Generate intra-chain CON files from CCF files
domainalign | Generate alignments (DAF file) for nodes in a DCF file
domainrep | Reorder DCF file to identify representative structures
domainreso | Remove low resolution domains from a DCF file
interface | Generate inter-chain CON files from CCF files
libgen | Generate discriminating elements from alignments
matgen3d | Generate a 3D-1D scoring matrix from CCF files
psiphi | Calculates phi and psi torsion angles from protein coordinates
rocon | Generates a hits file from comparing two DHF files
rocplot | Performs ROC analysis on hits files
seqalign | Extend alignments (DAF file) with sequences (DHF file)
seqfraggle | Removes fragment sequences from DHF files
seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file
seqsort | Remove ambiguous classified sequences from DHF files
seqwords | Generates DHF files from keyword search of UniProt
siggen | Generates a sparse protein signature from an alignment
siggenlig | Generates ligand-binding signatures from a CON file
sigscanlig | Searches ligand-signature library & writes hits (LHF file)

## 12.0 DIAGNOSTIC ERROR MESSAGES

None.

## 13.0 AUTHORS

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/

Automatic generation and evaluation of sparse protein signatures for families of protein structural domains. MJ Blades, JC Ison, R Ranasinghe, and JBC Findlay. Protein Science. 2005 (accepted)
A key residues approach to the definition of protein families and analysis of sparse family signatures. JC Ison, AJ Bleasby, MJ Blades, SC Daniel, JH Parish, JBC Findlay. PROTEINS: Structure, Function & Genetics. 2000, 40:330-341
Alignment of a sparse protein signature with protein sequences: application to fold prediction for three small globulins. SC Daniel, JH Parish, JC Ison, MJ Blades & JBC Findlay. FEBS Letters. 1999, 459:349-352.

### 14.1 Other useful references