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SEQSORT documentation |
> Q9YBD5^.^1^95^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^55.30^0.000e+00^2.000e-11 VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP > Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^42.60^0.000e+00^1.000e-07 INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP > Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^72.70^0.000e+00^1.000e-16 VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP > P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^42.20^0.000e+00^1.000e-07 GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP > Q08462^.^1^167^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^49.70^0.000e+00^3.000e-09 DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEPERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEETSLVL > Q03101^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^70.90^0.000e+00^1.000e-15 NNACVFFLDIAGFTRFSSIHSPEQVIQVLIKIFNSMDLLCAKHGIEKIKTIGDAYMATCGIFPKCDDIRHNTYKMLGFAMDVLEFIPKEMSFHLGLQVRVGIHCGPVISGVISGYAKPHFDVWGDTVNVASRMESTGIAGQIHVSDRVY > Q02153^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^75.90^0.000e+00^4.000e-17 HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCL > P46197^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^84.40^0.000e+00^1.000e-19 VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDELGCFQLEL > P40137^.^1^139^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^50.90^0.000e+00^1.000e-09 VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQELETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK > P23466^.^1^154^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^55.90^0.000e+00^4.000e-11 PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEAEWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS > O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^80.20^0.000e+00^2.000e-18 DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL |
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> Q9YBD5^.^1^95^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^55.30^0.000e+00^2.000e-11 VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP > Q97FS4^.^1^90^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^42.60^0.000e+00^1.000e-07 INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFPTALIMNAISKKNKAKDIIKIENVMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP > Q7MX57^.^1^92^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^72.70^0.000e+00^1.000e-16 VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDKRITIGNNLRSRSHGSKGVIKIEDKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP > P96111^.^1^98^SCOP^.^54894^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain^.^42.20^0.000e+00^1.000e-07 GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLPDRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP |
> Q08462^.^1^167^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^49.70^0.000e+00^3.000e-09 DCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSAVPSQEHSQEPERQYMHIGTMVEFAFALVGKLDAINKHSFNDFKLRVGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEETSLVL > Q03101^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^70.90^0.000e+00^1.000e-15 NNACVFFLDIAGFTRFSSIHSPEQVIQVLIKIFNSMDLLCAKHGIEKIKTIGDAYMATCGIFPKCDDIRHNTYKMLGFAMDVLEFIPKEMSFHLGLQVRVGIHCGPVISGVISGYAKPHFDVWGDTVNVASRMESTGIAGQIHVSDRVY > Q02153^.^1^165^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^75.90^0.000e+00^4.000e-17 HKRPVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCL > P46197^.^1^168^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^84.40^0.000e+00^1.000e-19 VQAEAFDSVTIYFSDIVGFTALSAESTPMQVVTLLNDLYTCFDAIIDNFDVYKVETIGDAYMVVSGLPGRNGQRHAPEIARMALALLDAVSSFRIRHRPHDQLRLRIGVHTGPVCAGVVGLKMPRYCLFGDTVNTASRMESNGQALKIHVSSTTKDALDELGCFQLEL > P40137^.^1^139^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^50.90^0.000e+00^1.000e-09 VTLLFADIRDFTSLSERLRPEQVVTLLNEYYGRMVEVVFRHGGTLDKFIGDALMVYFGAPIADPAHARRGVQCALDMVQELETVNALRSARGEPCLRIGVGVHTGPAVLGNIGSATRRLEYTAIGDTVNLASRIESLTK > P23466^.^1^154^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^55.90^0.000e+00^4.000e-11 PTGNVAIVFTDIKNSTFLWELFPDAMRAAIKTHNDIMRRQLRIYGGYEVKTEGDAFMVAFPTPTSALVWCLSVQLKLLEAEWPEEITSIQDGCLITDNSGTKVYLGLSVRMGVHWGCPVPEIDLVTQRMDYLGPVVNKAARVSGVADGGQITLS > O30820^.^1^149^SCOP^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^.^80.20^0.000e+00^2.000e-18 DEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQALADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERL |
Standard (Mandatory) qualifiers (* if not always prompted):
[-dhfindir] directory [./] This option specifies the location of
DHF files (domain hits files) (input). A
'domain hits file' contains database hits
(sequences) with domain classification
information, in the DHF format (FASTA or
EMBL-like). The hits are relatives to a SCOP
or CATH family and are found from a search
of a sequence database. Files containing
hits retrieved by PSIBLAST are generated by
using SEQSEARCH.
-overlap integer [10] This option specifies the number of
overlapping residues required for merging of
two hits. Each family is also processed so
that ovlerapping hits (hits with identical
accesssion number that overlap by at least a
user-defined number of residues) are
replaced by a hit that is produced from
merging the two overlapping hits. (Any
integer value)
-dofamilies toggle [N] This option specifies to write a domain
families file. If this option is set a
domain families file is written.
-doambiguities toggle [N] This option specifies whether to write a
domain ambiguities file. If this option is
set a domain ambiguities file is written.
[-dhfoutdir] outdir [./] This option specifies the location of
DHF files (domain hits files) (output). A
'domain hits file' contains database hits
(sequences) with domain classification
information, in the DHF format (FASTA or
EMBL-like). The hits are relatives to a SCOP
or CATH family and are found from a search
of a sequence database. Files containing
hits retrieved by PSIBLAST are generated by
using SEQSEARCH.
* -hitsfile outfile [fam.dhf] This option specifies the name of
domain families file (output). A 'domain
families file' contains sequence relatives
(hits) for each of a number of different
SCOP or CATH families found from searching a
sequence database, e.g. by using SEQSEARCH
(psiblast). The file contains the collated
search results for the indvidual families;
only those hits of unambiguous family
assignment are included. Hits of ambiguous
family assignment are assigned as relatives
to a SCOP or CATH superfamily or fold
instead and are collated into a 'domain
ambiguities file'. The domain families and
ambiguities files are generated by using
SEQSORT and use the same format as a DHF
file (domain hits file).
* -ambigfile outfile [oth.dhf] This option specifies the name of
domain ambiguities file (output). A 'domain
families file' contains sequence relatives
(hits) for each of a number of different
SCOP or CATH families found from searching a
sequence database, e.g. by using SEQSEARCH
(psiblast). The file contains the collated
search results for the indvidual families;
only those hits of unambiguous family
assignment are included. Hits of ambiguous
family assignment are assigned as relatives
to a SCOP or CATH superfamily or fold
instead and are collated into a 'domain
ambiguities file'. The domain families and
ambiguities files are generated by using
SEQSORT and use the same format as a DHF
file (domain hits file).
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-hitsfile" associated qualifiers
-odirectory string Output directory
"-ambigfile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. 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
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-dhfindir] (Parameter 1) |
This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. | Directory | ./ |
| -overlap | This option specifies the number of overlapping residues required for merging of two hits. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits. | Any integer value | 10 |
| -dofamilies | This option specifies to write a domain families file. If this option is set a domain families file is written. | Toggle value Yes/No | No |
| -doambiguities | This option specifies whether to write a domain ambiguities file. If this option is set a domain ambiguities file is written. | Toggle value Yes/No | No |
| [-dhfoutdir] (Parameter 2) |
This option specifies the location of DHF files (domain hits files) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. | Output directory | ./ |
| -hitsfile | This option specifies the name of domain families file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). | Output file | fam.dhf |
| -ambigfile | This option specifies the name of domain ambiguities file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). | Output file | oth.dhf |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
% seqsort Remove ambiguous classified sequences from DHF files. Domain hits directory [./]: ../seqnr-keep/hitsnr Number of overlapping residues required for merging of two hits. [10]: 10 Write domain families file. [N]: Y Write domain ambiguities file. [N]: Y Domain hits file output directory [./]: |
Go to the output files for this example
| FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
| Domain hits file | DHF format (FASTA-like). | Database hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a discriminating element (e.g. a protein signature, hidden Markov model, simple frequency matrix, Gribskov profile or Hennikoff profile) against a sequence database. | SEQSEARCH (hits retrieved by PSIBLAST). SIGSCAN (hits retrieved by sparse protein signature). LIBSCAN (hits retrieved by various types of HMM and profile). | N.A. |
| Domain families & ambiguities file | Contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from PSIBLAST searches of a sequence database. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. | The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). | N.A. | |
| Domain validation file | Contains sequence relatives (hits) for each of a number of different SCOP or CATH families, superfamilies and folds. The file contains the collated results from PSIBLAST searches of a sequence database for the indvidual families; hits of unambiguous family assignment are listed under their respective family, otherwise a hit is assigned as relatives to a superfamily or fold instead. | The domain validation file is generated by using SEQNR and uses the same format as a DHF file (domain hits file). | N.A. |
| Program name | Description |
|---|---|
| contacts | Generate intra-chain CON files from CCF files |
| domainalign | Generate alignments (DAF file) for nodes in a DCF file |
| domainrep | Reorder DCF file to identify representative structures |
| domainreso | Remove low resolution domains from a DCF file |
| interface | Generate inter-chain CON files from CCF files |
| libgen | Generate discriminating elements from alignments |
| matgen3d | Generate a 3D-1D scoring matrix from CCF files |
| psiphi | Calculates phi and psi torsion angles from protein coordinates |
| rocon | Generates a hits file from comparing two DHF files |
| rocplot | Performs ROC analysis on hits files |
| seqalign | Extend alignments (DAF file) with sequences (DHF file) |
| seqfraggle | Removes fragment sequences from DHF files |
| seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file |
| seqwords | Generates DHF files from keyword search of UniProt |
| siggen | Generates a sparse protein signature from an alignment |
| siggenlig | Generates ligand-binding signatures from a CON file |
| sigscan | Generates hits (DHF file) from a signature search |
| sigscanlig | Searches ligand-signature library & writes hits (LHF file) |
See also http://emboss.sourceforge.net/