All families / PF13689
PF13689: DUF4154
YfiR/HmsC-like
- Curation status
- SEEDED
- Seed status
- KNOWN HISTORICAL DUF
- Characterization
- UNSCORED
Grounding
PF13689: YfiR/HmsC-like
IPR025293: integrated entry for YfiR/HmsC-like
Source description
This family of proteins is found in bacteria and includes YfiR from E. coli. YfiR has been shown to regulate YfiN, a diguanylate cyclase and a bifunctional protein that produces c-di-GMP in response to reductive stress and then dynamically relocates to the division site to arrest cell division in response to envelope stress in Escherichia coli. YfiR may serve as a periplasmic redox sensor that regulates YfiN activity in response to reducing conditions [InterPro reference PUB00088310,InterPro reference PUB00088309]. HmsC in Yersinia Pestis is the orthologue of YfiR from E. coli [InterPro reference PUB00091013]. HmsC is a periplasmic protein that interacts directly with the periplasmic domain (PD) of HmsD and causes proteolytic degradation of HmsD, which in turn negatively regulates Y. pestis biofilm formation [InterPro reference PUB00091014].
Evidence and references
- InterPro entry and its literature references. PUB identifiers are internal InterPro references, not PubMed identifiers. Unresolved citations link to the originating entry.
- Frozen description source: InterPro/Pfam API
Source descriptions and links are provenance, not independent functional validation.
Evidence counts: not scored.
Curated functional assertions
No curated functional assertions supplied.
Protein sequence examples
3 verified sequence examples. FASTA
| UniProt | Protein / organism | Sequence | Provenance |
|---|---|---|---|
| P64548 | Protein YfiR Escherichia coli (strain K12) | 172 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| P64549 | Protein YfiR Escherichia coli O157:H7 | 172 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| Q9I4L4 | Negative regulator YfiR Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) | 190 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
Pfam membership is not functional evidence. Whole-protein sequences do not establish domain boundaries. A coverage gap here is not absence from UniProt.
Sequences and metadata: UniProt Consortium, CC BY 4.0.
Domain matches
No residue-level domain match evidence is available in this build. Structure and AlphaFold counters do not supply coordinates or establish function.
Snapshot counters
- proteins
- 2,780
- matches
- 2,788
- proteomes
- 1,988
- taxa
- 3,030
- structures
- 12
- alphafold models
- 1,729
- domain architectures
- 17
Classification basis
short name matches duf
No scoring reasons supplied.
Related Mech records
| Family | Mech | Record | Protein | Link basis |
|---|---|---|---|---|
| DUF4154 (PF13689) | ProteinTraitsMech | YfiR/HmsC-like | P64548 Protein YfiR | canonical example family classification |
| DUF4154 (PF13689) | ProteinTraitsMech | YfiR/HmsC-like | P64549 Protein YfiR | canonical example family classification |
| DUF4154 (PF13689) | ProteinTraitsMech | YfiR/HmsC-like | Q9I4L4 Negative regulator YfiR | canonical example family classification |
| DUF4154 (PF13689) | ProteinTraitsMech | YfiR/HmsC-like | trait identifier |
Curation history and reviews
No retained curation events supplied.
No retained review supplied.
Record source
Status and evidence
- Seed status
- A name-based classification of frozen InterPro/Pfam metadata. UNKNOWN CANDIDATE means the metadata explicitly says the function is unknown. KNOWN HISTORICAL DUF means a DUF name matched without that wording; this heuristic is not proof of a known function and does not establish experimental characterization. EX DUF means Pfam renamed the family away from a DUF/UPF name, as recorded in Pfam's previous identifiers; a rename usually follows published work on some members but is naming history, not proof of function for every member. Some EX DUF families' current names or descriptions still say the function is unknown; their classification basis lists this, and scoring does not treat them as characterized. FALSE POSITIVE TEXT HIT means the naming rules did not match.
- Characterization
- A separate evidence-scoring result. UNSCORED means no score has been calculated; it is not evidence that the family lacks a known function. Missing scores are not negative evidence. PARTIALLY CHARACTERIZED has partial support; KNOWN HISTORICAL DUF can inherit the seed label or reflect a known-function signal. Neither label implies experimental validation.
- Evidence counts
- Source-specific signals, not unique proteins, publications, or confidence scores. Known counts Rhea reactions and experimentally supported GO molecular-function annotations. Partial counts functional/domain assignments. Context counts structural, environmental, orthology, interaction and neighborhood signals; context alone does not assign function. Repeated annotations may not be independent.
- Curation status
- Reported separately from seed classification and characterization. SNAPSHOT ONLY means no curated metadata was supplied for this build. SEEDED denotes a source-derived record, not an expert-reviewed functional claim.
- Missing counts
- Not available means the source did not supply that counter. A zero is a reported count. Not scored means evidence counts are unavailable.