Rv0010c Family assigned · medium auto-curated
H37Rv Rv0010c · MTBC0 mtbc0_000014 ·
141 aa · 13133–13558 (-) ·
RefSeq NP_214524.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | PH domain-containing protein |
| Revised (this work) | PH domain-containing protein. Pfam: bPH_6 (PF10756.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMA3
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv0010c |
UniProt still lists this protein as Uncharacterized protein Rv0010c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Bacterial PH domain |
| Orthologous group | 2ESQF |
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) pseudogene candidate
| pN/pS | 1.647 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 12 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 10.21% of strains (14823) · 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 |
|---|---|---|---|---|
bPH_6 | PF10756.16 | 6.6e-22 | 58–136 | Bacterial PH domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: crgA (cell division protein CrgA), high confidence from genomic context alone (score 797 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0011c crgA |
cell division protein CrgA | 903 | 797 ctx | neighborhood:749 textmining:545 |
Rv3839 hyp |
hypothetical protein | 764 | 764 ctx | cooccurence:764 |
Rv3004 cfp6 |
low molecular weight protein antigen 6 | 740 | 740 ctx | cooccurence:737 |
Rv2732c |
transmembrane protein | 735 | 736 ctx | cooccurence:734 |
Rv2171 lppM |
lipoprotein LppM | 735 | 735 ctx | cooccurence:734 |
Rv1100 hyp |
hypothetical protein | 734 | 734 ctx | cooccurence:733 |
Rv1109c hyp |
hypothetical protein | 718 | 718 ctx | cooccurence:717 |
Rv0431 |
tuberculin-like peptide | 711 | 711 ctx | cooccurence:709 |
Rv2843 hyp |
hypothetical protein | 691 | 691 ctx | cooccurence:691 |
Rv0013 trpG |
anthranilate synthase component II | 674 | 674 ctx | neighborhood:672 |
Rv1222 rseA |
anti-sigma E factor RseA | 650 | 650 ctx | cooccurence:648 |
Rv0012 |
membrane protein | 648 | 649 ctx | neighborhood:646 |
Rv0207c hyp |
hypothetical protein | 648 | 648 ctx | cooccurence:645 |
Rv2520c |
membrane protein | 641 | 641 ctx | cooccurence:638 |
Rv3909 hyp |
hypothetical protein | 639 | 639 ctx | cooccurence:637 |
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: membrane protein
- MTBC0 PGAP product: PH domain-containing protein
- Pfam (hmmscan --cut_ga): bPH_6 PF10756.16 (E=7e-22)
- (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_214524.1)
- Domains: Pfam-A via hmmscan --cut_ga — bPH_6 (PF10756.16)
- 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
2ESQF - Curated reference: UniProt P9WMA3 (SwissProt, reviewed; Predicted)
- 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 —
78 functional partner(s); context anchor
crgA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000014|Rv0010c| MQQTAWAPRTSGIAGCGAGGVVMAIASVTLVTDTPGRVLTGVAALGLILFASATWRARPRLAITPDGLAIRGWFRTQLLRHSNIKIIRIDEFRRYGRLVRLLEIETVSGGLLILSRWDLGTDPVEVLDALTAAGYAGRGQR