The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

Table 3. HMM hit isotype classes.

HMM Hit Class	Annotative meaning
Equivalog	All proteins scoring above the trusted cutoff have the exact same function
Equivalog Domain	All domains scoring above the trusted cutoff have the same function; can be part of a multi-function protein
Domain	Defines a region of homology that may or may not have a known function, and need not be the full length of the polypeptide
Subfamily	Hits in this category represent full-length homology within a subgroup comtained within a gene family
Superfamily	This defines a set of proteins with full-length homology of sequence and domain architecture, but not necessarily the same function
Hypothetical - isotype	Unknown function
Uncharacterized	PFAM model cannot be assigned

JCVI classifies HMMs into more than a dozen categories (isology types, or “isotypes”), each of which represents a different degree of confidence about the functional classification.

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