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====== Cath Domain Description File (CDDF) ======

===== Format 1.0 =====

Each entry corresponds to a CATH domain for a given release of the CATH database. 
Note: Different releases of CATH may have different domain definitions.
See below for CATH domain and segment naming conventions.

Information is compiled from the following files:
  * [[CathDomainList]]
  * [[CathDomall]]
  * CathDomain Fasta Sequences
  * CathSegment Fasta Sequences
  * PdbSum file (in CDDF format)
  * ChainLimits file (in CDDF format)

Comment lines start with a '#' character.

MAXIMUM of 80 characters per line (composed of a tag that is always a maximum of 
10 characters; the rest of the line should be no longer than 70 characters).

^ Tags  ^ Description  ^
| FORMAT   | Format definition (CDDF1.0) and first line of each entry   |
| DOMAIN   | CATH domain identifier - six character code (e.g. 1abc01)  |
| PDBID	   | PDB identifier - four character code  \\ (currently only used in PdbSumData files)   |
| VERSION  | CATH version number          |
| VERDATE  | CATH version release date    |
| NAME	   | PDB entry description         |
| SOURCE   | PDB entry organism/source    |
| CATHCODE | CATH superfamily code C.A.T.H e.g. 1.10.10.10   |
| CLASS	   | Text description of class level (default: 'void')   |
| ARCH	   | Text description of architecture level (default: 'void')   |
| TOPOL	   | Text description of topology level (default: 'void')   |
| HOMOL	   | Text description of homologous superfamily level (default: 'void')  |
| DLENGTH  | Length of the domain sequence    |
| DSEQH	   | Domain sequence header in FASTA format (e.g. '>pdb%%|%%1abc01')   |
| DSEQS	   | Domain sequence string in FASTA format    |
| NSEGMENTS | Number of segments that comprise the domain (integer)   |
| SEGMENT   | Segment identifier (e.g. 1abc01:1:2)    |
| SRANGE    | Start and stop PDB residue identifiers that define the range of segment \\ (e.g. START=159  STOP=202)    |
| SLENGTH   | Length of the segment sequence     |
| SSEQH	    | Segment sequence header in FASTA format (e.g. '>pdb%%|%%1abc01:1:2')    |
| SSEQS	    | Segment sequence string in FASTA format    |
| ENDSEG    | Signifies end of segment entry    |
| COMMENTS  | Text    |
| %%//%%    | Signifies end of entry    |


==== Example ====

<code>
FORMAT    CDDF1.0
DOMAIN    9lprA1
VERSION   2.4
VERDATE   14-Jan-2002
NAME      Alpha-lytic protease complex with methoxysuccinyl- Ala- Ala- Pro- Leuc
NAME      ine boronic acid
SOURCE    (Lysobacter enzymogenes 495) cloned and expressed in (escherichia coli
SOURCE    )
CATHCODE  2.40.10.10
CLASS     Mainly Beta
ARCH      Barrel
TOPOL     Thrombin, subunit H
HOMOL     Trypsin-like serine proteases
DLENGTH   87
DSEQH     >pdb|9lprA1
DSEQS     IVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSA
DSEQS     QTLLLQPILSQYGLSLV
NSEGMENTS 2
SEGMENT   9lprA1:1:2
SRANGE    START=16   STOP=115
SLENGTH   74
SSEQH     >pdb|9lprA1:1:2
SSEQS     IVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSA
SSEQS     QTLL
ENDSEG
SEGMENT   9lprA1:2:2
SRANGE    START=231  STOP=242
SLENGTH   13
SSEQH     >pdb|9lprA1:2:2
SSEQS     LQPILSQYGLSLV
ENDSEG
COMMENTS  Blah Blah
//
</code>


NOTE:
The following CATH hierarchy description lines are typically found together 
(derived from CathList and CathNames files)

<code>
CATHCODE  2.40.10.10
CLASS     Mainly Beta
ARCH      Barrel
TOPOL     Thrombin, subunit H
HOMOL     Trypsin-like serine proteases
</code>


The following domain sequence lines are typically found together 
(derived from CathDomain Fasta Sequence File)

<code>
DLENGTH   87
DSEQH     >pdb|9lprA1
DSEQS     IVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSA
DSEQS     QTLLLQPILSQYGLSLV
</code>

Segment sequence lines are always initiated with a 'SEGMENT' tag
and terminated with an 'ENDSEG' tag. The number of segments in the domain
always precedes the first segment using the 'NSEGMENTS' tag.

The following segment sequence lines are typically found together
(derived from CathSegments Fasta Sequence File)


<code>
SEGMENT   9lprA1:1:2
SRANGE    START=16   STOP=115
SLENGTH   74
SSEQH     >pdb|9lprA1:1:2
SSEQS     IVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSA
SSEQS     QTLL
ENDSEG
</code>

===== Cath Domain and Segment Naming Conventions =====

==== CATH Domain Names ====

The domain names have seven characters (e.g. 1oaiA00).

<code>
CHARACTERS 1-4: PDB Code
The first 4 characters determine the PDB code e.g. 1oai

CHARACTER 5: Chain Character
This determines which PDB chain is represented.
Chain characters of zero ('0') indicate that the PDB file has no chain field.

CHARACTER 6-7: Domain Number
The domain number is a 2-figure, zero-padded number (e.g. '01', '02' ... '10', '11', '12'). Where the domain number is a double ZERO ('00') this indicates that the domain is a whole PDB chain with no domain chopping. 
</code>

==== CATH Segment Names ====

CATH segments (continuous regions of sequence within a domain) are described
adding colon separated numbers to the end of the domain name.

The first number is the sequential number of the segment.

The second number is the total number of segments in this domain.

<code>
1abcA01:1:2
xxxxxxxooooo

x = standard CATH six character domain name
o = segment information :ThisSegment:TotalSegments
</code>
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