Rv0504c Family assigned · medium auto-curated
H37Rv Rv0504c · MTBC0 mtbc0_000532 ·
166 aa · 598143–598643 (-) ·
RefSeq NP_215018.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | MaoC family dehydratase N-terminal domain-containing protein |
| Revised (this work) | MaoC family dehydratase N-terminal domain-containing protein. Pfam: FAS1_DH_region (PF13452.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFK3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UPF0336 protein Rv0504c |
UniProt still lists this protein as UPF0336 protein Rv0504c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | Belongs to the UPF0336 family |
| Orthologous group | COG2030 |
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.651 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
FAS1_DH_region | PF13452.12 | 4.6e-27 | 10–140 | FAS1-like, dehydratase domain region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hadB ((3R)-hydroxyacyl-ACP dehydratase subunit HadB), high confidence from genomic context alone (score 997 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0636 hadB |
(3R)-hydroxyacyl-ACP dehydratase subunit HadB | 999 | 997 ctx | cooccurence:756 experimental:987 textmining:860 |
Rv0503c cmaA2 |
cyclopropane mycolic acid synthase | 859 | 859 ctx | neighborhood:853 |
Rv0505c serB1 |
phosphoserine phosphatase SerB | 754 | 754 ctx | neighborhood:747 |
Rv3339c icd1 |
isocitrate dehydrogenase | 632 | 632 | database:476 |
Rv2242 hyp |
hypothetical protein | 608 | 608 ctx | cooccurence:605 |
Rv0125 pepA |
serine protease PepA | 568 | 569 | database:498 |
Rv0860 fadB |
fatty oxidation protein FadB | 590 | 565 | |
Rv3671c marP |
serine protease | 562 | 562 | database:498 |
Rv3274c fadE25 |
acyl-CoA dehydrogenase | 554 | 554 | |
Rv0983 pepD |
serine protease PepD | 551 | 552 | database:498 |
Rv1223 htrA |
serine protease HtrA | 551 | 551 | database:498 |
Rv1043c hyp |
hypothetical protein | 550 | 550 | database:498 |
Rv2146c |
transmembrane protein | 541 | 541 ctx | cooccurence:534 |
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 541 | 522 ctx | cooccurence:502 |
Rv0231 fadE4 |
acyl-CoA dehydrogenase FadE4 | 514 | 513 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: MaoC family dehydratase N-terminal domain-containing protein
- Pfam (hmmscan --cut_ga): FAS1_DH_region PF13452.12 (E=5e-27)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215018.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAS1_DH_region (PF13452.12)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG2030 - Curated reference: UniProt P9WFK3 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
138 functional partner(s); context anchor
hadB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000532|Rv0504c| MTVPEEAQTLIGKHYRAPDHFLVGREKIREFAVAVKDDHPTHYSEPDAAAAGYPALVAPLTFLAIAGRRVQLEIFTKFNIPINIARVFHRDQKFRFHRPILANDKLYFDTYLDSVIESHGTVLAEIRSEVTDAEGKPVVTSVVTMLGEAAHHEADADATVAAIASI