Rv0406c Family assigned · medium auto-curated
H37Rv Rv0406c · MTBC0 - ·
272 aa · 489887–490705 (-) ·
RefSeq NP_214920.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | beta lactamase-like protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Beta lactamase-like protein. Pfam: Lactamase_B (PF00753.34), 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.
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 |
O86336
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Beta lactamase like protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | beta-lactamase |
| Orthologous group | COG0491 |
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 | 0.707 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.18% of strains (264) · 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 | PF00753.34 | 6.7e-37 | 36–245 | Metallo-beta-lactamase superfamily |
Lactamase_B_2 | PF12706.14 | 2.9e-06 | 52–119 | Beta-lactamase superfamily domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pta (phosphate acetyltransferase), high confidence from genomic context alone (score 789 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0408 pta |
phosphate acetyltransferase | 789 | 789 ctx | neighborhood:784 |
Rv0407 fgd1 |
F420-dependent glucose-6-phosphate dehydrogenase | 787 | 787 ctx | neighborhood:784 |
Rv0409 ackA |
acetate kinase | 786 | 786 ctx | neighborhood:784 |
Rv0331 |
dehydrogenase/reductase | 651 | 636 | database:583 |
Rv3455c truA |
tRNA pseudouridine synthase A | 419 | 397 | |
Rv2367c ybeY |
endoribonuclease | 423 | 395 | |
Rv3775 lipE |
lipase LipE | 488 | 243 | |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 591 | 77 | textmining:576 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 524 | 70 | textmining:510 |
Rv2163c pbpB |
penicillin-binding membrane protein PbpB | 543 | 69 | textmining:529 |
Rv0016c pbpA |
penicillin-binding protein PbpA | 520 | 68 | textmining:506 |
Rv2864c |
penicillin-binding lipoprotein | 815 | 66 | textmining:810 |
Rv3330 dacB1 |
penicillin-binding protein DacB | 669 | 51 | textmining:666 |
Rv2911 dacB2 |
penicillin-binding protein DacB2 | 671 | 50 | textmining:669 |
Rv0907 hyp |
hypothetical protein | 810 | 48 | textmining:809 |
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): beta lactamase-like protein
- Pfam (hmmscan --cut_ga): Lactamase_B PF00753.34 (E=7e-37), Lactamase_B_2 PF12706.14 (E=3e-06)
- (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_214920.1)
- Domains: Pfam-A via hmmscan --cut_ga — Lactamase_B (PF00753.34), 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
COG0491 - Curated reference: UniProt O86336 (TrEMBL, unreviewed; 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 —
18 functional partner(s); context anchor
pta - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0406c| MVATRGTRLAALALAPRLAGMAELVQITDKVHLARGHAVNWVLVTDDTGVLLIDAGYPGDRAEVLASLNKLGYTPGDVRAIVLTHAHIDHLGSAIWFAREHSTPVYCHAEEVGHAKREYRENASVFDVALRSWRPRVAVWGIHLLRRGGLTGDGIPTAQPLTAEAAAGLPGQPMAIFTPGHTSGHCSYVVDGVLASGDALITGHPMLRHRGPQLLPAVFSHSQQNSIRSLAALALLETNILAPGHGELWHGPIRKATDEALERAQKSNHVFR