DUFMech

All families / PF04504

PF04504: GeBP-like_DBD

Glabrous-enhancer-binding protein-like family, DBD domain

Curation status
SEEDED
Seed status
EX DUF
Characterization
UNSCORED

Grounding

PF04504: Glabrous-enhancer-binding protein-like family, DBD domain
IPR053932: integrated entry for Glabrous-enhancer-binding protein-like family, DBD domain

Source description

This entry represents the DNA binding domain (DBD) present in GLABROUS1 enhancer-binding protein (GeBP) and GeBP-like proteins, such us storekeeper and storekeeper-like (STKL) transcription factors. GeBP and GeBP-like proteins play a redundant role in cytokinin hormone pathway regulation [InterPro reference PUB00153966,InterPro reference PUB00153967,InterPro reference PUB00081457]. Storekeeper was identified as a B-box motif binding factor that regulates expression of patatin, a storage protein in potato [InterPro reference PUB00081460]. Storekeeper-like transcription factors STKL1 and STKL2 function as transcription factors in the glucose signalling pathway [InterPro reference PUB00081459]. The overall predicted structure of this DNA binding domain (DBD) reveals a bundle of four helices, with helices alpha1 to alpha3 making up a single myb-type helix-turn-helix (HTH) domain.

Evidence and references

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

13 verified sequence examples. FASTA

UniProtProtein / organismSequenceProvenance
C0SUU6Probable transcription factor At1g11510
Arabidopsis thaliana		352 aa; version 1
UniProt 2026_03		UNIPROT FETCH
1 sibling references
F4K5T4Probable transcription factor At5g28040
Arabidopsis thaliana		427 aa; version 1
UniProt 2026_03		UNIPROT FETCH
1 sibling references
O04608Probable transcription factor At4g01260
Arabidopsis thaliana		325 aa; version 1
UniProt 2026_03		UNIPROT FETCH
1 sibling references
O23063Probable transcription factor At4g00390
Arabidopsis thaliana		364 aa; version 1
UniProt 2026_03		UNIPROT FETCH
1 sibling references
O23077Transcription factor STKL2
Arabidopsis thaliana		319 aa; version 1
UniProt 2026_03		UNIPROT FETCH
3 sibling references
O65270Probable transcription factor At4g00610
Arabidopsis thaliana		328 aa; version 1
UniProt 2026_03		UNIPROT FETCH
1 sibling references
Q8LG05Transcription factor STKL1
Arabidopsis thaliana		345 aa; version 1
UniProt 2026_03		UNIPROT FETCH
4 sibling references
Q8VYD2GLABROUS1 enhancer-binding protein-like 1
Arabidopsis thaliana		386 aa; version 1
UniProt 2026_03		UNIPROT FETCH
2 sibling references
Q9ASZ1GLABROUS1 enhancer-binding protein
Arabidopsis thaliana		302 aa; version 1
UniProt 2026_03		UNIPROT FETCH
2 sibling references
Q9LPF0Probable transcription factor At1g44810
Arabidopsis thaliana		296 aa; version 1
UniProt 2026_03		UNIPROT FETCH
2 sibling references

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
4,360
matches
4,422
proteomes
376
taxa
1,071
structures
0
alphafold models
3,520
domain architectures
95

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

data/families/PF04504.yaml
Family YAML in this build

Download this family (JSON)

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.