HAMAP profiles: User Manual for the Web View

The HAMAP family profiles are used to determine family membership of protein sequences. They are automatically generated from manually curated seed alignments of trusted family members of orthologous proteins using a PROSITE procedure. The profiles can be displayed in a user-friendly Web View which consists of the following two main sections and associated sub-sections.

• General profile information
  • Accession
  • Entry name
  • Entry type
  • Date
  • Version
  • Description
  • Taxonomic range
  • InterPro
  • Associated rule(s)
  • Links
• Statistics
  • Number of hits
  • Taxonomic distribution
  • Links

This section indicates the accession number of the family profile, in the form MF_xxxxx.

This section provides the short name of the family profile.

This section indicates the type of the entry. HAMAP family profiles are stored in PROSITE format and are always of the type MATRIX.

This section indicates the date the last time the family profile was modified.

This section indicates the version of the family profile.

This section provides a description of the family profile, usually giving the recommended protein name of the protein family members matched by the profile.

This section indicates the taxonomic coverage of the family profile. It lists all major kingdoms (Archaea, Bacteria, Eukaryota and Viruses) that contain hits to the family profile.

This section contains a cross-reference to InterPro, linking to the InterPro record for this family profile.

This section indicates the HAMAP annotation rule(s) that is (are) associated to the family profile. It provides the rule accession number (clickable to access the rule), the rule short name as well as the taxonomic scope of each rule.

On the right hand of the 'General Profile Information' section, we provide links to:

• The actual family classification profile.
• The seed alignment that was used to generate the profile with highlighted features from the annotation rule.

Note: data from HAMAP may differ from that provided by UniProtKB due to differing release cycles.

In this section, the count of profile hits is indicated for the two sections of UniProtKB:

• Hits in UniProtKB/Swiss-Prot, which are manually annotated and reviewed.
• Hits in UniProtKB/TrEMBL, which are automatically annotated and are not reviewed.

In this section, the count of profile hits in UniProtKB is indicated for each major kingdom.

On the right hand of the 'Statistics' section, we provide links to:

• An interactive, graphical view of the score distribution of matching proteins in UniProtKB, including those that fall below the trusted cutoff.
• An expandable view of the taxonomic distribution of matching proteins in UniProtKB.
• The distribution (presence/absence) of matches on a taxonomic tree of UniProtKB complete proteomes.