
                          SIGSCANLIG 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

   Search ligand-signature library & write hits (LHF file)

   Generates LHF files (ligand hits file) of hits from scanning sequences
   against a library of ligand-binding signatures.

2.0 INPUTS & OUTPUTS

   SIGSCANLIG reads one more sequences, e.g. from a sequence database,
   and scans each in turn against a library of ligand-binding signatures
   (directory of signature files). The signatures may be of type 1D or
   3D. To perform the scan, the user provides a scoring matrix which is
   either a residue substitution matrix (1D signatures) or matrix of
   3D:1D (environment:residue) scores (3D). Various other parameters
   including gap insertion and extension penalties and a score mode are
   also set. For each query sequence, 3 files are generated as follows:
   (i) An LHF file (ligand hits file) of hits to the signatures. (ii) A
   SAF file (signature alignment file) of the corresponding
   signature-sequence alignments. (iii) A results file, containing a list
   of hits (ligands), rank-ordered on the basis of score. The user
   specifies the query sequences and also the paths of the signature
   files (input), LHF, SAF and results files (output). The file
   extensions are specified in the ACD file.

3.0 INPUT FILE FORMAT

   The format of the signature file is described in SIGGEN documentation
   (1D signatures) and the SIGGENLIG documentation (3D signatures).
   SIGSCANLIG can read protein sequences in any sequence format supported
   by EMBOSS.

  Input files for usage example

  File: swtiny

> Q9WVI4^.^516^664^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Ad
enylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cata
lytic domain^PSIBLAST^84.40^0.000e+00^2.000e-16
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASG
LHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLF
GNNVTLASKFESGSHPRRINISPTTYQLL
> Q9ERL9^.^480^631^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Ad
enylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cata
lytic domain^PSIBLAST^72.10^0.000e+00^1.000e-12
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLH
RESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGN
NVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9DGG6^.^380^560^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Ad
enylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cata
lytic domain^PSIBLAST^142.00^0.000e+00^8.000e-34
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAG
CPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVW
SNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL
I
> Q99396^.^262^473^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Ad
enylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cata
lytic domain^PSIBLAST^192.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMI
ACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVY
RQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS
LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN

4.0 OUTPUT FILE FORMAT

   LHF file (ligand hits file)
   Each LHF file contains the hits from the search of a single query
   sequence against the library of signatures. The file (Figure 1)
   contains two lines per hit. The first contains a description of the
   hit in 17 text tokens delimited by '^'. The second line contains the
   protein sequence. The tokens are as follows (a '.' is given where a
   token does not have a value).
     * (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) 'LIGAND' is always given.
     * (vi) 4-character PDB identifier code.
     * (vii) 7-character domain identifier code from SCOP or CATH.
     * (viii) Ligand identifier code. A 3-letter abbreviation of the full
       ligand name.
     * (ix) Site number. This uniquely identifies a ligand-binding site
       in the CON file generated by running SITES.
     * (x) The total number of binding sites for a given ligand.
     * (xi) Patch number. The sequential order (from the N-terminus) of
       the patch in the ligand-binding site from which the signature was
       derived.
     * (xii) Number of patches. The total number of patches in this
       ligand-binding site.
     * (xiii) Signature data type, either '1D' or '3D', for sequence or
       structure-based signatures respectively.
     * (xiv) Signature type, either 'P' for patch signatures or 'F' for
       full-length signatures.

   The next 3 tokens refer to the hit, specifically, information about
   the search result as follows:
     * (xv) Score of hit from search algoritm.
     * (xvi) P-value of hit (not written by SIGSCANLIG).
     * (xvii) E-value of hit (not written by SIGSCANLIG).

   SAF file (signature alignment file)
   The format of the SAF file (signature alignment file, Figure 2) is
   more or less identical to DAF (domain alignment file) described in the
   DOMAINALIGN documentation. The file conforms to EMBOSS "simple"
   multiple sequence alignment format. Each file contains the
   signature-sequence alignments corresponding to the search of a single
   query sequence against a library of signatures. The SAF file generated
   by SIGSCANLIG contains some unique features which are summarised here.
   All lines beginning with '#' are comments and the first line is always
   '# DE Alignment of query sequence against library of signatures'. Each
   signature-sequence alignment is contained in one or more blocks in the
   file. These blocks are preceeded by a comment line containing
   information for the corresponding hit from the LHF (above). Each block
   contains contains the signature identifier code and accession number
   of the protein sequence, sequence positions and a section of the
   signature-sequence alignment.
     * The signature identifier code uniquely identifies the signature
       and is of the format ligand identifer code_site number_patch
       number. The ligand identifier, site number and the patch number
       are defined above (a '0' will be given for patch number if the
       site was represented as a single 'full-length' signature rather
       than patches).
     * The sequence positions are the start and end residue positions of
       the appropriate section of sequence. The character '-' is used for
       gaps.
     * The protein sequence is given after the accession number and the
       signature-sequence alignment is given as a markup line underneath
       the sequence (signature positions are marked with a '*').

   Results file
   Each results file (Figure 3) contains the summarised results of the
   search of a single query sequence against the library of signatures.
   The results file contains a list of ligands, rank-ordered on the basis
   of score (highest-scoring ligand is given first). There are four
   columns under the labels 'LIGID, 'PATCHES', 'SITES' and 'SCORE'. These
   give the ligand identifier, the number of patches for that ligand
   binding site, the number of sites for the ligand and the score of the
   sequence-signature match. In the example shown (Figure 3) there is a
   single ligand. Typically, the library would represent all ligands
   represented in PDB.
   Figure 3 Excerpt from a results file (output) 

LIGID     PATCHES   SITES     SCORE
101       0         1         0.48

  Output files for usage example

  Directory: lhf

   This directory contains output files, for example
   Q99396^.^262^473^.lhf Q9DGG6^.^380^560^.lhf Q9ERL9^.^480^631^.lhf and
   Q9WVI4^.^516^664^.lhf.

  File: lhf/Q99396^.^262^473^.lhf

> Q99396^.^262^473^.^55074^Alpha^.^99^138^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^
7.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^97^138^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^5
.33^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^130^210^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^
0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^12^17^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^3
.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^12^56^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^2.
00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^11^55^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^1
.83^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^1.00^0
.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^32^126^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.94^0
.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^22^126^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.74^0
.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.59^0
.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-10
00000.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRF
LRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANT
AARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN

  File: lhf/Q9DGG6^.^380^560^.lhf

> Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.
50^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.5
0^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.
17^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^99^179^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0
.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF
^3.50^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^20^61^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^2.
33^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^74^178^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^1.00^0
.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^84^178^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.82^0
.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.65^0
.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.47^0
.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-10
00000.00^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGM
IKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDG
KVTERVGQSAVADQLKGLKTYLI

  File: lhf/Q9ERL9^.^480^631^.lhf

> Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.5
0^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.
17^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^98^137^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^
4.50^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^6^11^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.
17^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^63^104^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^4
.00^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^22^102^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^2.50^0
.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^4^114^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.60^0.
000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^25^119^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.29^0
.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^12^122^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.24^0
.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^15^119^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.21^0
.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-10
00000.00^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMME
LSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG

  File: lhf/Q9WVI4^.^516^664^.lhf

> Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.5
0^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.
17^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF
^4.50^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.
17^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^25^105^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^3.50^0
.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^43^84^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^3.
33^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^27^121^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.53^0
.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^17^121^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.42^0
.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^6^116^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.33^0.
000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^14^124^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.18^0
.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-10
00000.00^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKM
MELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL

  Directory: aln

   This directory contains output files, for example
   Q99396^.^262^473^.aln Q9DGG6^.^380^560^.aln Q9ERL9^.^480^631^.aln and
   Q9WVI4^.^516^664^.aln.

  File: aln/Q99396^.^262^473^.aln

# DE   Alignment of query sequence against library of signatures
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^99^138^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1D
F^7.00^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSL
IEN 45
101_2_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTT
VFD 90
101_2_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVG
IHT 135
101_2_0           -      ---------*-----------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCET
YHS 180
101_2_0           -      ---*-----------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
    225
101_2_0           -      --------------------------------
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^97^138^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF
^5.33^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSL
IEN 45
MN_1_0            -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTT
VFD 90
MN_1_0            -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVG
IHT 135
MN_1_0            -      -------*-*-----------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCET
YHS 180
MN_1_0            -      ---*-----------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
    225
MN_1_0            -      --------------------------------
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^130^210^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.0
0^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSL
IEN 45
PO4_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTT
VFD 90
PO4_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVG
IHT 135
PO4_1_0           -      ----------------------------------------*----
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCET
YHS 180
PO4_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
    225
PO4_1_0           -      ------------------------------*-
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^12^17^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF
^3.00^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSL
IEN 45
POP_1_0           -      ------------******---------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTT
VFD 90
POP_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVG
IHT 135
POP_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCET
YHS 180


  [Part of this file has been deleted for brevity]

# > Q99396^.^262^473^.^55074^Alpha^.^32^126^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.94
^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSL
IEN 45
HEM_1_0           -      --------------------------------**-**--------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTT
VFD 90
HEM_1_0           -      ---*--**--*-----------------*--**---*-*---**-
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVG
IHT 135
HEM_1_0           -      -*----------------------------------*--------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCET
YHS 180
HEM_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
    225
HEM_1_0           -      --------------------------------
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^22^126^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.74
^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSL
IEN 45
HEM_3_0           -      ----------------------*------*--**-**--------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTT
VFD 90
HEM_3_0           -      ---*--**--*-----------------*--**---*-*---**-
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVG
IHT 135
HEM_3_0           -      -*----------------------------------*--------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCET
YHS 180
HEM_3_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
    225
HEM_3_0           -      --------------------------------
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.59
^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSL
IEN 45
HEM_2_0           -      ----------------*---------**-----------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTT
VFD 90
HEM_2_0           -      ---*--**--**----------------*--**---*-*---**-
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVG
IHT 135
HEM_2_0           -      -*----------------------------------*--------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCET
YHS 180
HEM_2_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
    225
HEM_2_0           -      --------------------------------
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-
1000000.00^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSL
IEN 45
FOK_1_0           -      *--------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTT
VFD 90
FOK_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVG
IHT 135
FOK_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCET
YHS 180
FOK_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
    225
FOK_1_0           -      --------------------------------

  File: aln/Q9DGG6^.^380^560^.aln

# DE   Alignment of query sequence against library of signatures
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^
5.50^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCED
TKC 45
101_1_0           -      --------*---**-------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFC
QEK 90
101_1_0           -      -----***-------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQ
LGV 135
101_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLK
TYL 180
101_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha181    I
    225
101_1_0           -      -
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5
.50^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCED
TKC 45
MG_1_0            -      --------**--*--------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFC
QEK 90
MG_1_0            -      -------*-------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQ
LGV 135
MG_1_0            -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLK
TYL 180
MG_1_0            -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha181    I
    225
MG_1_0            -      -
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^
4.17^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCED
TKC 45
POP_1_0           -      --------******-------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFC
QEK 90
POP_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQ
LGV 135
POP_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLK
TYL 180
POP_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha181    I
    225
POP_1_0           -      -
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^99^179^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00
^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCED
TKC 45
PO4_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFC
QEK 90
PO4_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQ
LGV 135
PO4_1_0           -      ---------*-----------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLK
TYL 180


  [Part of this file has been deleted for brevity]

# > Q9DGG6^.^380^560^.^55074^Alpha^.^84^178^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.82
^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCED
TKC 45
HEM_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFC
QEK 90
HEM_1_0           -      ---------------------------------------**-**-
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQ
LGV 135
HEM_1_0           -      ----------*--**--*-----------------*--**---*-
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLK
TYL 180
HEM_1_0           -      *---**--*----------------------------------*-
Q9DGG6^.^380^560^.^55074^Alpha181    I
    225
HEM_1_0           -      -
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.65
^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCED
TKC 45
HEM_2_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFC
QEK 90
HEM_2_0           -      -----------------------*---------**----------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQ
LGV 135
HEM_2_0           -      ----------*--**--**----------------*--**---*-
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLK
TYL 180
HEM_2_0           -      *---**--*----------------------------------*-
Q9DGG6^.^380^560^.^55074^Alpha181    I
    225
HEM_2_0           -      -
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.47
^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCED
TKC 45
HEM_4_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFC
QEK 90
HEM_4_0           -      -----------------------*---------**----------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQ
LGV 135
HEM_4_0           -      ----------*--**--*--------------------**---*-
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLK
TYL 180
HEM_4_0           -      *---**--*----------------------------------*-
Q9DGG6^.^380^560^.^55074^Alpha181    I
    225
HEM_4_0           -      -
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-
1000000.00^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCED
TKC 45
FOK_1_0           -      *--------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFC
QEK 90
FOK_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQ
LGV 135
FOK_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLK
TYL 180
FOK_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha181    I
    225
FOK_1_0           -      -

  File: aln/Q9ERL9^.^480^631^.aln

# DE   Alignment of query sequence against library of signatures
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5
.50^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELD
VYK 45
MG_1_0            -      ------**--*----------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSP
HGE 90
MG_1_0            -      -----*---------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCS
VPR 135
MG_1_0            -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG
    180
MG_1_0            -      -----------------
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^
5.17^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELD
VYK 45
101_1_0           -      ------*---**---------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSP
HGE 90
101_1_0           -      ---***---------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCS
VPR 135
101_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG
    180
101_1_0           -      -----------------
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^98^137^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1D
F^4.50^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELD
VYK 45
101_2_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSP
HGE 90
101_2_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCS
VPR 135
101_2_0           -      --------*------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG
    180
101_2_0           -      --*--------------
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^6^11^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^
4.17^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELD
VYK 45
POP_1_0           -      ------******---------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSP
HGE 90
POP_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCS
VPR 135
POP_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG
    180
POP_1_0           -      -----------------
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^63^104^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF
^4.00^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELD
VYK 45
MN_1_0            -      ---------------------------------------------


  [Part of this file has been deleted for brevity]

HEM_4_0           -      ----*---------**--------------------*--**--*-
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSP
HGE 90
HEM_4_0           -      -------------------**---*-*---**--*----------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCS
VPR 135
HEM_4_0           -      ------------------------*--------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG
    180
HEM_4_0           -      -----------------
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^25^119^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.29
^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELD
VYK 45
HEM_1_0           -      -------------------------**-**-----------*--*
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSP
HGE 90
HEM_1_0           -      *--*-----------------*--**---*-*---**--*-----
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCS
VPR 135
HEM_1_0           -      -----------------------------*---------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG
    180
HEM_1_0           -      -----------------
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^12^122^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.24
^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELD
VYK 45
HEM_2_0           -      ------------*---------**--------------------*
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSP
HGE 90
HEM_2_0           -      --**--**----------------*--**---*-*---**--*--
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCS
VPR 135
HEM_2_0           -      --------------------------------*------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG
    180
HEM_2_0           -      -----------------
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^15^119^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.21
^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELD
VYK 45
HEM_3_0           -      ---------------*------*--**-**-----------*--*
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSP
HGE 90
HEM_3_0           -      *--*-----------------*--**---*-*---**--*-----
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCS
VPR 135
HEM_3_0           -      -----------------------------*---------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG
    180
HEM_3_0           -      -----------------
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-
1000000.00^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELD
VYK 45
FOK_1_0           -      *--------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSP
HGE 90
FOK_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCS
VPR 135
FOK_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG
    180
FOK_1_0           -      -----------------

  File: aln/Q9WVI4^.^516^664^.aln

# DE   Alignment of query sequence against library of signatures
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5
.50^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGF
LDI 45
MG_1_0            -      --------**--*--------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVL
TPD 90
MG_1_0            -      -------*-------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFES
GSH 135
MG_1_0            -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL
    180
MG_1_0            -      --------------
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^
5.17^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGF
LDI 45
101_1_0           -      --------*---**-------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVL
TPD 90
101_1_0           -      -----***-------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFES
GSH 135
101_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL
    180
101_1_0           -      --------------
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1
DF^4.50^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGF
LDI 45
101_2_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVL
TPD 90
101_2_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFES
GSH 135
101_2_0           -      ----------*----------------------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL
    180
101_2_0           -      ----*---------
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^
4.17^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGF
LDI 45
POP_1_0           -      --------******-------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVL
TPD 90
POP_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFES
GSH 135
POP_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL
    180
POP_1_0           -      --------------
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^25^105^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^3.50
^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGF
LDI 45
PO4_1_0           -      -------------------------*-------------------


  [Part of this file has been deleted for brevity]

HEM_1_0           -      ---------------------------**-**-----------*-
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVL
TPD 90
HEM_1_0           -      -**--*-----------------*--**---*-*---**--*---
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFES
GSH 135
HEM_1_0           -      -------------------------------*-------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL
    180
HEM_1_0           -      --------------
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^17^121^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.42
^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGF
LDI 45
HEM_3_0           -      -----------------*------*--**-**-----------*-
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVL
TPD 90
HEM_3_0           -      -**--*-----------------*--**---*-*---**--*---
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFES
GSH 135
HEM_3_0           -      -------------------------------*-------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL
    180
HEM_3_0           -      --------------
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^6^116^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.33^
0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGF
LDI 45
HEM_4_0           -      ------*---------**--------------------*--**--
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVL
TPD 90
HEM_4_0           -      *--------------------**---*-*---**--*--------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFES
GSH 135
HEM_4_0           -      --------------------------*------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL
    180
HEM_4_0           -      --------------
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^14^124^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.18
^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGF
LDI 45
HEM_2_0           -      --------------*---------**-------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVL
TPD 90
HEM_2_0           -      -*--**--**----------------*--**---*-*---**--*
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFES
GSH 135
HEM_2_0           -      ----------------------------------*----------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL
    180
HEM_2_0           -      --------------
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-
1000000.00^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGF
LDI 45
FOK_1_0           -      *--------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVL
TPD 90
FOK_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFES
GSH 135
FOK_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL
    180
FOK_1_0           -      --------------

  Directory: results

   This directory contains output files, for example
   Q99396^.^262^473^.results Q9DGG6^.^380^560^.results
   Q9ERL9^.^480^631^.results and Q9WVI4^.^516^664^.results.

  File: results/Q99396^.^262^473^.results

LIGID     PATCHES   SITES     SCORE
MN        1         1         5.33
101       2         2         4.42
PO4       1         1         4.00
POP       1         1         3.00
MG        1         1         2.00
HEM       4         4         0.82
FOK       1         1         -1000000.00

  File: results/Q9DGG6^.^380^560^.results

LIGID     PATCHES   SITES     SCORE
MG        1         1         5.50
101       2         2         4.50
POP       1         1         4.17
PO4       1         1         4.00
MN        1         1         2.33
HEM       4         4         0.73
FOK       1         1         -1000000.00

  File: results/Q9ERL9^.^480^631^.results

LIGID     PATCHES   SITES     SCORE
MG        1         1         5.50
101       2         2         4.83
POP       1         1         4.17
MN        1         1         4.00
PO4       1         1         2.50
HEM       4         4         0.33
FOK       1         1         -1000000.00

  File: results/Q9WVI4^.^516^664^.results

LIGID     PATCHES   SITES     SCORE
MG        1         1         5.50
101       2         2         4.83
POP       1         1         4.17
PO4       1         1         3.50
MN        1         1         3.33
HEM       4         4         0.37
FOK       1         1         -1000000.00

5.0 DATA FILES

   SIGSCANLIG requires a matrix of 3D:1D scores (residue:environment
   scoring matrix).

6.0 USAGE

   Standard (Mandatory) qualifiers:
  [-siginfilesdir]     dirlist    [./] This option specifies the directory of
                                  signature files (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.
  [-dbseqall]          seqall     This option specifies the name of the
                                  database of query sequences.
   -sub                matrixf    [EBLOSUM62] This option specifies the
                                  scoring matrix to use, e.g. residue
                                  substitution matrix (1D signatures) or
                                  matrix of 3D:1D (environment:residue) scores
                                  (3D).
   -mode               menu       [1] This option specifies the mode of
                                  scoring ligands. In 'Patch Score Mode' (mode
                                  1) the score for a ligand is the mean of
                                  its patch scores. In 'Site Score Mode' the
                                  score for a ligand is the mean of its site
                                  scores. A site score is the mean of patch
                                  score for all patches for a given site.
                                  (Values: 1 (Patch score mode); 2 (Site score
                                  mode))
   -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))
  [-hitsoutdir]        outdir     [./] This option specifies the directory of
                                  the LHF files (ligand hits files) (output).
                                  A 'ligand hits file' contains database hits
                                  (sequences) with ligand classification
                                  information, in the LHF format (FASTA-like).
                                  The hits are putative ligand-binding
                                  sequences and are found from a search of a
                                  sequence database, in this case, by using
                                  SIGSCANLIG.
  [-alignoutdir]       outdir     [./] This option specifies the name of the
                                  SAF (signature alignment file) (output).A
                                  'signature alignment file' contains one or
                                  more signnature-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.
  [-resultsoutdir]     outdir     [./] This option specifies the directory for
                                  the results files. A results file is
                                  generated for each query sequence and
                                  contains a list of hits (ligands),
                                  rank-ordered on the basis of score.

   Additional (Optional) qualifiers (* if not always prompted):
   -nhits              integer    [100] This option specifies the maximum
                                  number of hits to output. (Any integer
                                  value)
   -domax              toggle     [N] This option specifies whether to
                                  consider a max. number of top-scoring hits
                                  only for each ligand.
*  -maxhits            integer    [0] This option specifies the maximum number
                                  of top-scoring hits to consider for each
                                  ligand. (Any integer value)

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

   "-dbseqall" 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

   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. 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

  6.1 COMMAND LINE ARGUMENTS

