Document for "master" file

What is the master file?

This is a documentation on the master file of the GTOP database, developed by the Laboratory of Gene-product Informatics at the National Institute of Genetics. GTOP contains information on assigned 3D-structres, family classifications, domain structures, etc. of the proteomes derived from numerous genome sequences. Please refer to what is GTOP ? for details.

Analytical results of the GTOP database are stored as master files. A master file is a collection of one-line descriptions summarizing analytical results for a protein, with each line initiated by the header, GT:ID and ended by the string, "//". The lines in the master file have a description headed by a header of 15 characters, which describes the source or property of the information. When a protein has multiple pieces of information under one header, multiple lines of the header are entered.

One line descriptions in the master file

GT section : information unique in GTOP

  GT:ID          The GTOP ID
  GT:GENE        The gene name in GTOP
  GT:PRODUCT     The product description in GTOP
  GT:DATABASE    The accession number in the DDBJ/Genbank/EMBL database
  GT:EXON        Information of exon - intron structures.
                 number of exons | first residues - last residue in the first exon:phase of intron | first residues - last residue in the second exon:phase of intron | ....
  GT:ORG         The organism abbreviation in GTOP

GB section : Information from the DDBJ/Genbank/EMBL database

  GB:ACCESSION   The accession number in the DDBJ/Genbank/EMBL database
  GB:LOCATION    The location of the gene in the genome
  GB:FROM        The start position of the gene
  GB:TO          The end position of the gene
  GB:DIRECTION   The orientation of the gene in the genome
  GB:GENE        The information in the "/gene" line in the "CDS" section
  GB:PRODUCT     The information in the "/product" line in the "CDS" section
  GB:FUNCTION    The information in the "/function" line in the "CDS" section
  GB:NOTE        The information in the "/note" line in the "CDS" section
  GB:PROTEIN_ID  The information in the "/protein_id" line in the "CDS" section
  GB:GENE:GENE   The information in the "/gene" line in the "gene" section
  GB:GENE:NOTE   The information in the "/note" line in the "gene" section

LENGTH section : Information on the length of this entry
```
  LENGTH         The length of the entry
```

SQ section : Information on the sequence of this entry

  SQ:AASEQ       The amino acid sequence
  SQ:SECSTR      Secondary structure information obtained by reverse PSI-BLAST search

SW section : Information from the Swiss-Prot database

  Identifications with Swiss-Prot entries are based on sequence similarities. An entry, 
  which has a sequence with more than 90 % identity covering more than a half of the query, is regarded 
as
  the sequence identical with the query.

  SW:ID          The information in the "ID" line
  SW:DE          The information in the "DE" line
  SW:GN          The information in the "GN" line
  SW:KW          The information in the "KW" line(s)
  SW:EXACT       If the sequence is not exactly the same as that in the DDBJ/Genbank/EMBL database, an F is entered in this line.
  SW:FUNC        Sufficiency of functional information. Please refer to How to assign function tag

PROS section: predicted ProSite motifs

  PROS           The region | ProSite ID | motif name | documentation ID of the motif |

SEG sections: low complexity regions predicted by SEG

  SEG            The region | amino acid sequence in the region |

BL section: summary of BLAST search results

  In the master file, we denote only representatives of the family of sequences
 matching the query sequence. When the query has multiple domains hit by different families, 
 one representative of each family is chosen.

  BL:SWS         Information on results of BLAST search against Swiss-Prot
  BL:SWS:NREP    The number of the representative sequences
  BL:SWS:REP     Information on the representative sequences
                 region | Swiss-Prot ID | E value | % identity | (length of the similar region) / (length of the query) |

  BL:PDB         Results of BLAST search against PDB
  BL:PDB:NREP    The number of the representative sequences
  BL:PDB:REP     Information on the representative sequences
                 region | PDB ID | E value | % identity | (length of the similar region) / (length of the query) |

RP section: summary of reverse PSI-BLAST search results

  In the master file, we denote only representatives of the family of sequences
 matching the query sequence. When the query has multiple domains hit by different families, 
 one representative of each family is chosen.

  RP:PDB         Results of reverse PSI-BLAST search against PDB
  RP:PDB:NREP    The number of the representative sequences
  RP:PDB:REP     Information on the representative sequences
                 region | PDB ID | E value | % identity | (length of the similar region) / (length of the query) |

  RP:PFM         Results of reverse PSI-BLAST search against PFAM
  RP:PFM:NREP    The number of the representative PFAM domains
  RP:PFM:REP     Information on the representative PFAM domains
                 region | PFAM ID | E value | % identity | (length of the similar region) / (length of the query) |

  RP:SCP         Results of reverse PSI-BLAST search against SCOP
  RP:SCP:NREP    The number of the representative sequences
  RP:SCP:REP     information on the representative sequences
                 region | SCOP ID | E value | % identity | (length of the similar region) / (length of the query) |

HM section: summary of HMMer search results

 In the master file, we denote only representatives of the family of sequences
matching the query sequence. When the query has multiple domains hit by different families, 
one representative of each family is chosen.

  HM:PFM:REP     Information on the representative PFAM domains
                 region | PFAM ID | E value | % identity | (length of the similar region) / (length of the query) |PFAM name
  HM:SCP:REP     information on the representative SCOP sequences
                 region | SCOP ID | E value | % identity | (length of the similar region) / (length of the query) |SCOP code|SCOP name

 TM section : information on the predicted transmembrane regions by SOSUIb
  TM:NTM         The number of the predicted transmembrane regions
  TM:REGION      The predicted transmembrane region


COIL section : information on the predicted coiled - coil regions.
  COIL:NAA       The length of the total coiled-coil regions in amino acid residues
  COIL:NSEG      The number of the predicted coiled-coil regions
  COIL:REGION    The region


 OP section : information on homologs
  OP:NHOMO       The number of the homologs found in the organisms in GTOP
  OP:NHOMOORG    The number of the organisms to which the homologs belong
  OP:PATTERN     A string summarizing homolog information. Also see the "orgPattern" section in what is GTOP?.


 STR section : Information on the secondary structure predicted by reverse PSI-BLAST
  STR:NPRED      The number of residues in the predicted secondary structure
  STR:RPRED      The coverage of the predicted region in the query
  SQ:SECSTR      The sequence representing secondary structure predicted by reverse PSI-BLAST (#, sites out of the hit regions)


 GO section : information on assigned GO (Gene Ontology)
  A GO is assigned when a query has similarity to any of the Swiss-Prot proteins or the Pfam 
domains.
  The GO(s) assigned to the hit sequences or domains in Swiss-Prot or Pfam is denoted.

  GO:SWS:NREP    The number of GOs assigned by similarity to Swiss-Prot
  GO:SWS         Information on the assigned GOs
                 GO ID | description of the GO | Swiss-Prot keyword linked to the GO
  GO:SWS:TREE    Information on the hierarchal tree of the GO terms assigned by Swiss-Prot key words.
                 The last word in the line is the assigned GO term, and the words appeared former than the assigned word
                 are those located in the lower level of the tree. The details of the tree structure can be referred to Gene Ontology^TMConsortium.

  GO:PFM:NREP    The number of GOs assigned by similarity to Pfam domains
  GO:PFM         Information on the assigned GOs
                 GO ID | description of the GO | Pfam ID linked to the GO| InterPro ID linked to the GO
  GO:PFM:TREE    Information on the hierarchal tree of the GO terms assigned by Pfam searches.
                 The last word in the line is the assigned GO term, and the words appeared former than the assigned word
                 are those located in the lower level of the tree. The details of the tree structure can be referred to Gene Ontology^TMConsortium.



DISOP section : information on intrinsically disordered regions predicted by DISOPRED2
  DISOP:02AL     Intrinsically disordered regions.



PSIPRED section : information on the secondary predicted by DISOPRED2
  PSIPRED        The sequence representing predicted secondary structure.