Rv0093c Family assigned · medium auto-curated
H37Rv Rv0093c · MTBC0 - ·
282 aa · 102815–103663 (-) ·
RefSeq NP_214607.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Membrane protein. Pfam: zf-HC2 (PF13490.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WM69
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0093c |
UniProt still lists this protein as Uncharacterized protein Rv0093c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Putative zinc-finger |
| Orthologous group | COG5660 |
| 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 | 0.47 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 10 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (169) · 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 |
|---|---|---|---|---|
zf-HC2 | PF13490.12 | 5.1e-09 | 49–83 | Putative zinc-finger |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sigC (ECF RNA polymerase sigma factor SigC), high confidence from genomic context alone (score 891 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2069 sigC |
ECF RNA polymerase sigma factor SigC | 891 | 891 ctx | fusion:734 cooccurence:462 |
Rv0094c hyp |
hypothetical protein | 677 | 677 ctx | neighborhood:630 |
Rv1907c hyp |
hypothetical protein | 637 | 638 ctx | cooccurence:636 |
Rv2468c hyp |
hypothetical protein | 574 | 574 ctx | cooccurence:572 |
Rv0007 |
membrane protein | 485 | 485 ctx | cooccurence:485 |
Rv1090 celA2b |
Rv1090, (MTV017.43), len: 151 aa. Probable celA2b,second part of cellulase (endoglucanase), similar to C-terminus of others e.g. O08468 cell | 478 | 479 ctx | cooccurence:476 |
Rv0262c aac |
aminoglycoside 2'-N-acetyltransferase | 468 | 469 ctx | cooccurence:467 |
Rv2843 hyp |
hypothetical protein | 468 | 468 ctx | cooccurence:468 |
Rv2171 lppM |
lipoprotein LppM | 468 | 468 ctx | cooccurence:468 |
Rv0097 |
oxidoreductase | 464 | 464 | |
Rv2844 hyp |
hypothetical protein | 460 | 460 ctx | cooccurence:460 |
Rv1917c PPE34 |
PPE family protein PPE34 | 458 | 459 ctx | cooccurence:458 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 445 | 445 ctx | cooccurence:445 |
Rv2308 hyp |
hypothetical protein | 440 | 440 ctx | cooccurence:435 |
Rv2179c |
3'-5' exoribonuclease | 434 | 434 ctx | cooccurence:434 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): membrane protein
- Pfam (hmmscan --cut_ga): zf-HC2 PF13490.12 (E=5e-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_214607.1)
- Domains: Pfam-A via hmmscan --cut_ga — zf-HC2 (PF13490.12)
- 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
COG5660 - Curated reference: UniProt P9WM69 (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 —
33 functional partner(s); context anchor
sigC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0093c| MLAQATTAGSFNHHASTVLQGCRGVPAAMWSEPAGAIRRHCATIDGMDCEVAREALSARLDGERAPVPSARVDEHLGECSACRAWFTQVASQAGDLRRLAESRPVVPPVGRLGIRRAPRRQHSPMTWRRWALLCVGIAQIALGTVQGFGLDVGLTHQHPTGAGTHLLNESTSWSIALGVIMVGAALWPSAAAGLAGVLTAFVAILTGYVIVDALSGAVSTTRILTHLPVVIGAVLAIMVWRSASGPRPRPDAVAAEPDIVLPDNASRGRRRGHLWPTDGSAA