Grouping Pfam entries into Clans

Structural properties are often more conserved than the underlying sequence. Therefore, a single profile HMM is often insufficient to model an entire, diverse, structural superfamily. In Pfam there is a hierarchical level of classification which integrates evolutionary related entries in to sets, termed Clans, see Figure 6.

The relationship between entries in a Clan may be defined by:

• sequence similarity (whilst still originating from a common ancestor)
• similarity of known three-dimensional structures
• functional similarity
• and/or similarity between their profile HMMs (as determined by algorithms such as HHsearch) [2]

The majority of Pfam Clans are groupings of domains and families.