all_entities_Family

Return all instances of the Family entity.

The Kbase will support the maintenance of protein families (as sets of Features with associated translations). We are initially only supporting the notion of a family as composed of a set of isofunctional homologs. That is, the families we initially support should be thought of as containing protein-encoding genes whose associated sequences all implement the same function (we do understand that the notion of "function" is somewhat ambiguous, so let us sweep this under the rug by calling a functional role a "primitive concept"). We currently support families in which the members are translations of features, and we think of Features as having an associated function. Identical protein sequences as products of translating distinct genes may or may not have identical functions, and we allow multiple members of the same Family to share identical protein sequences. This may be justified, since in a very, very, very few cases identical proteins do, in fact, have distinct functions. We would prefer to reach the point where our Families are sets of protein sequence, rather than sets of protein-encoding Features.

Example:

all_entities_Family -a 

would retrieve all entities of type Family and include all fields in the entities in the output.

Related entities

The Family entity has the following relationship links:

HasMember Feature

HasProteinMember ProteinSequence

IsCoupledTo Family

IsCoupledWith Family

IsFamilyFor Role

IsRepresentedIn Genome

Command-Line Options

-a

Return all fields.

-h

Display a list of the fields available for use.

-fields field-list

Choose a set of fields to return. Field-list is a comma-separated list of strings. The following fields are available:

type

release

family_function

alignment

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added for each requested field. Input lines that cannot be extended are written to stderr.