The field codes found in a Pfam flat file help display information for human readabilty and machine-based parsing. A typical entry contains several two-letter Pfam field codes. Table 4-1 provides definitions and descriptions of these codes.
Table 4-1. Pfam field definitions
| Field | Definition | Description |
| AC | Accession number | PFxxxxx or PBxxxxxx. |
| ID | Identification | 15 characters or less. |
| DE | Definition | 80 characters or less. |
| AU | Author | Author of the entry. |
| AL | Alignment method of seed | Method used to align the seed members. Approved AL lines are: - Clustalv
- Clustalw
- Clustalw_mask_xxxx
- Domainer
- HMM_built_from_alignment
- HMM_simulated_annealing
- Manual
- Prosite_pattern
- Prodom
- Structure_superposition
- pftools
- Unknown
|
| BM | HMM building command lines | |
| SE | Source of seed | The source suggesting seed members belong to a family. |
| GA | Gathering threshold | Search threshold to build the full alignment. |
| NC | Noise cutoff | This field refers to the bit scores of the highest scoring match not in the full alignment. |
| TC | Trusted cutoff | This field refers to the bit scores of the lowest scoring match in the full alignment. |
| TP | Type field | The type field is a compulsory field describing the type of family. At present it can be one of: - Family
- Domain
- Repeat
- Motif
|
| PI | Previous IDs | |
| DC | Database Comment | Comment for database reference. |
| DR | Database Reference | Reference to external database. |
| RC | Reference Comment | Comment for literature reference. |
| RN | Reference Number | Digit in square brackets. |
| RM | Reference Medline | Eight digit number. |
| RT | Reference Title | Title of paper. |
| RA | Reference Author | Author of paper. |
| RL | Reference Location | Location of paper. |
| CC | Comment | Comment lines provide annotation and other information. |
| NE | Pfam accession | Indicated those cases where there is a nested domain. |
| SQ | Sequence | Nr of sequences, start of alignment. |
| // | End of alignment | |