                          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

   Searches ligand-signature library & writes 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^Ade
nylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cataly
tic 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^Ade
nylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cataly
tic 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^Ade
nylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cataly
tic 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^Ade
nylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase cataly
tic 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
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^97^138^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^5.
33^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^130^210^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0
.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^12^17^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^3.
00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^12^56^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^2.0
0^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^11^55^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^1.
83^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^1.00^0.
000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^32^126^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.94^0.
000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^22^126^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.74^0.
000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.59^0.
000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-100
0000.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFL
RLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAA
RTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN

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

> Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.5
0^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50
^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.1
7^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^99^179^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0.
000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^
3.50^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^20^61^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^2.3
3^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^74^178^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^1.00^0.
000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^84^178^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.82^0.
000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.65^0.
000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.47^0.
000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-100
0000.00^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMI
KAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKV
TERVGQSAVADQLKGLKTYLI

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

> Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50
^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.1
7^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^98^137^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^4
.50^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^6^11^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.1
7^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^63^104^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^4.
00^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^22^102^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^2.50^0.
000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^4^114^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.60^0.0
00e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^25^119^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.29^0.
000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^12^122^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.24^0.
000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^15^119^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.21^0.
000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-100
0000.00^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMEL
SNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG

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

> Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50
^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.1
7^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^
4.50^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.1
7^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^25^105^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^3.50^0.
000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^43^84^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^3.3
3^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^27^121^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.53^0.
000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^17^121^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.42^0.
000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^6^116^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.33^0.0
00e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^14^124^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.18^0.
000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-100
0000.00^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMM
ELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL

  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_^101^2^2^0^0^1DF
^7.00^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLI
EN 45
101_2_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTV
FD 90
101_2_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGI
HT 135
101_2_0           -      ---------*-----------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETY
HS 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      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLI
EN 45
MN_1_0            -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTV
FD 90
MN_1_0            -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGI
HT 135
MN_1_0            -      -------*-*-----------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETY
HS 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^4.00
^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLI
EN 45
PO4_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTV
FD 90
PO4_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGI
HT 135
PO4_1_0           -      ----------------------------------------*----
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETY
HS 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      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLI
EN 45
POP_1_0           -      ------------******---------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTV
FD 90
POP_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGI
HT 135
POP_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETY
HS 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      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLI
EN 45
HEM_1_0           -      --------------------------------**-**--------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTV
FD 90
HEM_1_0           -      ---*--**--*-----------------*--**---*-*---**-
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGI
HT 135
HEM_1_0           -      -*----------------------------------*--------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETY
HS 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      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLI
EN 45
HEM_3_0           -      ----------------------*------*--**-**--------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTV
FD 90
HEM_3_0           -      ---*--**--*-----------------*--**---*-*---**-
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGI
HT 135
HEM_3_0           -      -*----------------------------------*--------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETY
HS 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      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLI
EN 45
HEM_2_0           -      ----------------*---------**-----------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTV
FD 90
HEM_2_0           -      ---*--**--**----------------*--**---*-*---**-
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGI
HT 135
HEM_2_0           -      -*----------------------------------*--------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETY
HS 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^-1
000000.00^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLI
EN 45
FOK_1_0           -      *--------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTV
FD 90
FOK_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGI
HT 135
FOK_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETY
HS 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      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDT
KC 45
101_1_0           -      --------*---**-------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQ
EK 90
101_1_0           -      -----***-------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQL
GV 135
101_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKT
YL 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      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDT
KC 45
MG_1_0            -      --------**--*--------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQ
EK 90
MG_1_0            -      -------*-------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQL
GV 135
MG_1_0            -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKT
YL 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      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDT
KC 45
POP_1_0           -      --------******-------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQ
EK 90
POP_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQL
GV 135
POP_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKT
YL 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      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDT
KC 45
PO4_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQ
EK 90
PO4_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQL
GV 135
PO4_1_0           -      ---------*-----------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKT
YL 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      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDT
KC 45
HEM_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQ
EK 90
HEM_1_0           -      ---------------------------------------**-**-
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQL
GV 135
HEM_1_0           -      ----------*--**--*-----------------*--**---*-
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKT
YL 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      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDT
KC 45
HEM_2_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQ
EK 90
HEM_2_0           -      -----------------------*---------**----------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQL
GV 135
HEM_2_0           -      ----------*--**--**----------------*--**---*-
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKT
YL 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      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDT
KC 45
HEM_4_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQ
EK 90
HEM_4_0           -      -----------------------*---------**----------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQL
GV 135
HEM_4_0           -      ----------*--**--*--------------------**---*-
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKT
YL 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^-1
000000.00^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDT
KC 45
FOK_1_0           -      *--------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQ
EK 90
FOK_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQL
GV 135
FOK_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKT
YL 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      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDV
YK 45
MG_1_0            -      ------**--*----------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPH
GE 90
MG_1_0            -      -----*---------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSV
PR 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      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDV
YK 45
101_1_0           -      ------*---**---------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPH
GE 90
101_1_0           -      ---***---------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSV
PR 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_^101^2^2^0^0^1DF
^4.50^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDV
YK 45
101_2_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPH
GE 90
101_2_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSV
PR 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      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDV
YK 45
POP_1_0           -      ------******---------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPH
GE 90
POP_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSV
PR 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      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDV
YK 45
MN_1_0            -      ---------------------------------------------


  [Part of this file has been deleted for brevity]

HEM_4_0           -      ----*---------**--------------------*--**--*-
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPH
GE 90
HEM_4_0           -      -------------------**---*-*---**--*----------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSV
PR 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      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDV
YK 45
HEM_1_0           -      -------------------------**-**-----------*--*
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPH
GE 90
HEM_1_0           -      *--*-----------------*--**---*-*---**--*-----
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSV
PR 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      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDV
YK 45
HEM_2_0           -      ------------*---------**--------------------*
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPH
GE 90
HEM_2_0           -      --**--**----------------*--**---*-*---**--*--
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSV
PR 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      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDV
YK 45
HEM_3_0           -      ---------------*------*--**-**-----------*--*
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPH
GE 90
HEM_3_0           -      *--*-----------------*--**---*-*---**--*-----
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSV
PR 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^-1
000000.00^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDV
YK 45
FOK_1_0           -      *--------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPH
GE 90
FOK_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSV
PR 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      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFL
DI 45
MG_1_0            -      --------**--*--------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLT
PD 90
MG_1_0            -      -------*-------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESG
SH 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      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFL
DI 45
101_1_0           -      --------*---**-------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLT
PD 90
101_1_0           -      -----***-------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESG
SH 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_^101^2^2^0^0^1D
F^4.50^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFL
DI 45
101_2_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLT
PD 90
101_2_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESG
SH 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      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFL
DI 45
POP_1_0           -      --------******-------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLT
PD 90
POP_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESG
SH 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      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFL
DI 45
PO4_1_0           -      -------------------------*-------------------


  [Part of this file has been deleted for brevity]

HEM_1_0           -      ---------------------------**-**-----------*-
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLT
PD 90
HEM_1_0           -      -**--*-----------------*--**---*-*---**--*---
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESG
SH 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      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFL
DI 45
HEM_3_0           -      -----------------*------*--**-**-----------*-
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLT
PD 90
HEM_3_0           -      -**--*-----------------*--**---*-*---**--*---
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESG
SH 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      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFL
DI 45
HEM_4_0           -      ------*---------**--------------------*--**--
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLT
PD 90
HEM_4_0           -      *--------------------**---*-*---**--*--------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESG
SH 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      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFL
DI 45
HEM_2_0           -      --------------*---------**-------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLT
PD 90
HEM_2_0           -      -*--**--**----------------*--**---*-*---**--*
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESG
SH 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^-1
000000.00^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFL
DI 45
FOK_1_0           -      *--------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLT
PD 90
FOK_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESG
SH 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

Searches ligand-signature library & writes hits (LHF file)
Version: EMBOSS:6.2.0

   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 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

