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PDB Family-Domain File

The PDB Family-Domain File describes boundaries for entries in the Profs database. This file format has a row for each Profs family and eight columns described below.

  • Column 1: PDB code e.g. 3zyo.
  • Column 2: This determines which PDB chain is represented.
  • Column 3: Family name according Profs.
  • Column 4: The location of begin and end for domain taking as reference ATOM record of PDB format.
  • Column 5: Begin and end of domain using nomenclature PDB.
  • Column 6: The location of begin and end for domain taking as reference SEQRES record of PDB format.
  • Column 7: Template type, this indicate as family boundaries were expanded.
    • Zero "0": The enlargements is based on CATH database.
    • One "1": The enlargements is based on alignment with significance matching.
    • Two "2": The alignment hasn't significance matching.
    • Three "3": There aren't families with previous annotations.
  • Column 8: A tag indicating the type of domain.
    • Supradomain "S": Domain is producted from several families.
    • Fragment "F": Domain is formed for some segment.
    • Repeat "R": Reapeat domain e.g. Leucine-rich.
    • Normal "N": Domain is not part of the above cases.

Notes: The domain with template type "2" and "3" are not expanded.

Examples

PDB | Chain | Family | Atom | Definition | Residue | Type | Tag
-- | -- | -- | -- | -- | -- | -- | -- | 10gs|A|GST_N|1:77,186:207|2:78,187:208|2:78,187:208|0|F 10gs|A|GST_C|78:185|79:186|79:186|0|N 10gs|B|GST_N|1:77,186:207|2:78,187:208|2:78,187:208|0|F 10gs|B|GST_C|78:185|79:186|79:186|0|N 3zyo|A|LRRNT+LRR|1:291|58:354|1:301|1|SR 3zyo|A|I-set|292:391|355:454|302:411|1|N 6rlx|C|Insulin|1:23|-2:20|1:23|2|N

Sequence Family-Domain File

The Sequence Family-Domain File describes boundaries of annotated sequences through Profs database.

  • Column 1: Query sequence
  • Column 2: Family name according Profs.
  • Column 3: Begin and end of domain.
  • Column 4: Alignment score, this is obtein from the equation described in the section Annotations of the Uniprot.
  • Column 5: The PDB chain employed as template. The absence of template is denoted by the symbol "-".

Examples

Sequence | Family | Definition | Score | Template
-- | -- | -- | -- | -- | YAAI_ECOK1 | DUF2541 | 1:134 | 1 | - DNAK_ECOK1 | HSP70 |1:604 | 0.997 | 2kho_A NHAA_ECOK1 | Na_H_antiport_1 | 1:388 | 0.985 | 4au5_A

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