All families / PF13901
PF13901: RH_dom
Rubicon Homology Domain
- Curation status
- SEEDED
- Seed status
- EX DUF
- Characterization
- UNSCORED
Grounding
PF13901: Rubicon Homology Domain
IPR025258: integrated entry for Rubicon Homology Domain
Source description
This is the Rubicon homology domain (RH) characterised at the C-terminal of Rubicon, PLEKHM1 and Pacer, proteins that modulate late steps in autophagy [InterPro reference PUB00100995,InterPro reference PUB00100997]. Rubicon (RUBCN) negatively regulates autophagy and endolysosomal trafficking by inhibiting PI3K complex II (PI3KC3-C2), which impairs autophagosome maturation process. PLEKHM1 is an adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways [InterPro reference PUB00100999,InterPro reference PUB00100998]. On the other hand, Pacer positively regulates autophagy, promoting autophagosome maturation by facilitating the biogenesis of phosphatidylinositol 3-phosphate (PtdIns3P) in late steps of autophagy; it antagonises RUBCN [InterPro reference PUB00101000]. This domain contains nine conserved cysteines and one conserved histidine, which have been predicted to bind divalent zinc cations being required for Rubicon and PLEKHM1 to interact with Rab7.
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
12 verified sequence examples. FASTA
| UniProt | Protein / organism | Sequence | Provenance |
|---|---|---|---|
| O01738 | Differentially expressed in FDCP 8 homolog Caenorhabditis elegans | 486 aa; version 2 UniProt 2026_03 | UNIPROT FETCH2 sibling references |
| Q3TD16 | Protein associated with UVRAG as autophagy enhancer Mus musculus | 648 aa; version 2 UniProt 2026_03 | PTM REGISTRY MIRROR |
| Q6ZN54 | Differentially expressed in FDCP 8 homolog Homo sapiens | 512 aa; version 2 UniProt 2026_03 | UNIPROT FETCH2 sibling references |
| Q6ZWE6 | Pleckstrin homology domain-containing family M member 3 Homo sapiens | 761 aa; version 2 UniProt 2026_03 | UNIPROT FETCH |
| Q7TSI1 | Pleckstrin homology domain-containing family M member 1 Mus musculus | 1074 aa; version 1 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| Q80U62 | Run domain Beclin-1-interacting and cysteine-rich domain-containing protein Mus musculus | 956 aa; version 2 UniProt 2026_03 | UNIPROT FETCH11 sibling references
|
| Q8BM47 | Pleckstrin homology domain-containing family M member 3 Mus musculus | 761 aa; version 1 UniProt 2026_03 | UNIPROT FETCH |
| Q92622 | Run domain Beclin-1-interacting and cysteine-rich domain-containing protein Homo sapiens | 972 aa; version 4 UniProt 2026_03 | UNIPROT FETCH11 sibling references
|
| Q99J78 | Differentially expressed in FDCP 8 Mus musculus | 448 aa; version 1 UniProt 2026_03 | UNIPROT FETCH2 sibling references |
| Q9H714 | Protein associated with UVRAG as autophagy enhancer Homo sapiens | 662 aa; version 3 UniProt 2026_03 | UNIPROT FETCH |
First 10 shown; the FASTA and family JSON contain all examples.
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
- 8,015
- matches
- 8,152
- proteomes
- 1,750
- taxa
- 5,484
- structures
- 1
- alphafold models
- 6,861
- domain architectures
- 123
Classification basis
pfam previous unknown name
No scoring reasons supplied.
Related Mech records
This family joined the worklist after the frozen cross-Mech scan, so other Mechs were not searched for it. Missing links here are not evidence that other Mechs lack it; rows shown come from mentions of a former DUF/UPF name.
No cross-Mech examples are present in the supplied snapshot.
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.