Rv2923c Family assigned · medium auto-curated
H37Rv Rv2923c · MTBC0 mtbc0_003106 ·
137 aa · 3259083–3259496 (-) ·
RefSeq NP_217439.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | OsmC family protein |
| Revised (this work) | OsmC family protein. Pfam: OsmC (PF02566.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL19
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2923c |
UniProt still lists this protein as Uncharacterized protein Rv2923c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| eggNOG description | redox protein, regulator of disulfide bond formation |
| Orthologous group | COG1765 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.34% of strains (488) · clonal |
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 |
|---|---|---|---|---|
OsmC | PF02566.25 | 7.8e-09 | 35–131 | OsmC-like protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: acyP (acylphosphatase), high confidence from genomic context alone (score 883 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) |
|---|---|---|---|---|
Rv2922A acyP |
acylphosphatase | 883 | 883 ctx | neighborhood:882 |
Rv2922c smc |
chromosome partition protein Smc | 878 | 878 ctx | neighborhood:876 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 818 | 818 ctx | neighborhood:810 |
Rv2924c fpg |
formamidopyrimidine-DNA glycosylase | 772 | 773 ctx | neighborhood:773 |
Rv2927c sepIVA hyp |
hypothetical protein | 739 | 740 ctx | neighborhood:645 |
Rv2925c rnc |
ribonuclease III | 668 | 668 ctx | neighborhood:663 |
Rv2926c hyp |
hypothetical protein | 668 | 668 ctx | neighborhood:663 |
Rv2920c amt |
ammonium transporter integral membrane protein | 655 | 655 ctx | neighborhood:647 |
Rv2560 hyp |
hypothetical protein | 573 | 573 ctx | cooccurence:573 |
Rv2918c glnD |
bifunctional uridylyltransferase/uridylyl-removing enzyme | 521 | 521 ctx | neighborhood:417 |
Rv0523c hyp |
hypothetical protein | 513 | 514 ctx | cooccurence:508 |
Rv1249c |
membrane protein | 491 | 491 ctx | cooccurence:414 |
Rv0477 hyp |
hypothetical protein | 489 | 490 ctx | cooccurence:483 |
Rv3205c hyp |
hypothetical protein | 462 | 463 ctx | cooccurence:461 |
Rv3520c |
coenzyme F420-dependent oxidoreductase | 453 | 453 ctx | cooccurence:441 |
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: OsmC family protein
- Pfam (hmmscan --cut_ga): OsmC PF02566.25 (E=8e-09)
- (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_217439.1)
- Domains: Pfam-A via hmmscan --cut_ga — OsmC (PF02566.25)
- 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
COG1765 - Curated reference: UniProt P9WL19 (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 —
30 functional partner(s); context anchor
acyP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003106|Rv2923c| MTQLWVERTGTRRYIGRSTRGAQVLVGSEDVDGVFTPGELLKIALAACSGMASDQPLARRLGDDYQAVVKVSGAADRDQERYPLIEETMELDLSGLTEDEKERLLVVINRAVELACTVGRTLKSGTTVNLEVVDVGA