CATH

Useful websites: https://www.cathdb.info/ http://sfam.cathdb.info/

Part I: Steps followed for naming a superfamily

• Look through representative domains as: ‘domain only’ to understand common secondary structures; as ‘domain in chain’ to observe the location of the domain in the chain; as ‘domain in PDB’ to understand the domain’s function and location in the protein.
• Check through FunFams/SwissProt/Keywords and refer to the most abundant name when naming.
• Check through enzymes (EC number if available), GO terms and species to get a rough idea of domain function.
• Refer to Pfam and InterPro entries for general idea of protein domain function and/or structure.
• Check through papers associated with PDB entry for better understanding of protein and protein domain structure and/or function .
• In ‘Description section’, provide an overview of structure and function. In larger superfamilies, you may have to refer to specific PDB IDs.
• Check references are correct: [InterPro:] [Pfam:] [PMID:] [DOI:]
• Check other names in the database, either to avoid duplicate names or to identify potential cross-hits
• Check names of other domains in the same chain to keep the name similar.

Part II: General observations and tips

Dos

• Check other names in CATH to not make duplicates (i.e. make sure the assigned name is unique)
• Make superfamily names consistent with other domains of same protein
• Start with smaller families until you get the hang of it
• For larger superfamily- it is a good idea to check FunFam
• When looking at a protein on InterPro, see if there are other domains that don’t have a name yet on the same protein - it will be easy to name that one
• Work in groups for larger superfamilies
• Choose superfamily entries with FunFams, Pfams, or InterPro associated

Don’ts

• Make description without sourcing references
• Make description without actually really understanding it
• Spend 3 hours on a very small superfamily
• Look at every single PDB for big superfamilies
• For smaller representative domains, don’t put too much confidence in InterPro/Pfam - it may be better to look at PDB paper for the specific domain
• Assume it is the exact same domain if it has good mapping to Pfam
• Choose a superfamily entry with no annotation or too many annotation

(Last updated in September 2023, Written by summer interns since 2020-2023 (Barbara, Oliver, Natalie, Charling, Ruiqi, Lorna, Katie, Charlotte, Hazuki) and CATH curators (Vaishali Waman, Ian Sillitoe)