Rv0906 Resolved · high auto-curated
H37Rv Rv0906 · MTBC0 mtbc0_000960 ·
372 aa · 1012158–1013276 (+) ·
RefSeq NP_215421.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | MBL fold metallo-hydrolase |
| Revised (this work) | MBL fold metallo-hydrolase. Pfam: Lactamase_B_3 (PF13483.13), Lactamase_B_2 (PF12706.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKP3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0906 |
UniProt still lists this protein as Uncharacterized protein Rv0906; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Beta-lactamase superfamily domain |
| Orthologous group | COG2220 |
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 | 0.427 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 17.68% of strains (25674) · 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 |
|---|---|---|---|---|
Lactamase_B_3 | PF13483.13 | 2.1e-12 | 107–303 | Beta-lactamase superfamily domain |
Lactamase_B_2 | PF12706.14 | 7.0e-52 | 122–321 | Beta-lactamase superfamily domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA6 (enoyl-CoA hydratase EchA6), high confidence from genomic context alone (score 914 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) |
|---|---|---|---|---|
Rv0905 echA6 |
enoyl-CoA hydratase EchA6 | 914 | 914 ctx | neighborhood:881 |
Rv0904c accD3 |
acetyl-CoAcarboxylase carboxyl transferase subunit beta | 791 | 791 ctx | neighborhood:790 |
Rv0908 ctpE |
metal cation transporter ATPase E | 789 | 790 ctx | neighborhood:787 |
Rv0907 hyp |
hypothetical protein | 636 | 637 ctx | neighborhood:620 |
Rv0909 |
antitoxin | 582 | 583 ctx | neighborhood:544 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 557 | 557 ctx | cooccurence:543 |
Rv0437c psd |
phosphatidylserine decarboxylase | 469 | 469 | |
Rv0911 hyp |
hypothetical protein | 452 | 453 ctx | neighborhood:450 |
Rv0903c prrA |
two component transcriptional regulator PrrA | 400 | 400 | |
Rv3627c dacB hyp |
hypothetical protein | 872 | 63 | textmining:870 |
Rv3811 hyp |
hypothetical protein | 870 | 41 | textmining:870 |
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: MBL fold metallo-hydrolase
- Pfam (hmmscan --cut_ga): Lactamase_B_3 PF13483.13 (E=2e-12), Lactamase_B_2 PF12706.14 (E=7e-52)
- (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_215421.1)
- Domains: Pfam-A via hmmscan --cut_ga — Lactamase_B_3 (PF13483.13), Lactamase_B_2 (PF12706.14)
- 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
COG2220 - Curated reference: UniProt P9WKP3 (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 —
11 functional partner(s); context anchor
echA6 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000960|Rv0906| MVRRALRLAAGTASLAAGTWLLRALHGTPAALGADAASIRAVSEQSPNYRDGAFVNLDPASMFTLDREELRLIVWELVARHSASRPAAPIPLASPNIYRGDASRLAVSWFGHSTALLEIDGYRVLTDPVWSDRCSPSDVVGPQRLHPPPVQLAALPAVDAVVISHDHYDHLDIDTVVALVGMQRAPFLVPLGVGAHLRSWGVPQDRIVELDWNQSAQVDELTVVCVPARHFSGRFLSRNTTLWASWAFVGPNHRAYFGGDTGYTKSFTQIGADHGPFDLTLLPIGAYNTAWPDIHMNPEEAVRAHLDVTDSGSGMLVPVHWGTFRLAPHPWGEPVERLLAAAEPEHVTVAVPLPGQRVDPTGPMRLHPWWRL