Figure 11
From: Domain atrophy creates rare cases of functional partial protein domains
Failure modes of the pipeline. (A) Incorrect gene prediction or partial sequence: sequence fragment or incorrect gene prediction could lead to events that look like domain atrophy, example: Aldo/keto reductase family (UniProt: P43546, Pfam: PF00248) (B) Tandem repeat: a tandem repeat is distinguished from single domain instances that are split/predicted in two parts, by considering its HMM match coordinates; for a tandem domain instances the downstream domain start-HMM-match state is less than the upstream domain end-HMM-match state, example: Peroxidase (Uniprot: A0QXX7, Pfam: PF00141). (C) Nested domain: this architecture results in an atrophy score greater than 1 for domain hosting nested domain(s), example: Peptidase_M20 (UniProt: A0Z6B3, Pfam: PF01546) (D) Unmatched domain region: missing region of the domain containing a nested domain, example: Lon_C (UniProt: A4ILZ1, Pfam: PF05362) (E) Multi-domain family: a single-domain architecture comprising more than one domain. (F) Domain overlap, example: 4Fe-4S single cluster domain (UniProt: A6L094, Pfam: PF13353).