4.2 Pfam Field Definitions

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