Rv2257c Family assigned · medium auto-curated
H37Rv Rv2257c · MTBC0 mtbc0_002400 ·
272 aa · 2556164–2556982 (-) ·
RefSeq NP_216773.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | serine hydrolase domain-containing protein |
| Revised (this work) | Serine hydrolase domain-containing protein. Pfam: Beta-lactamase (PF00144.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53531
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| Preferred name | bla |
| eggNOG description | beta-lactamase |
| Orthologous group | COG1680 |
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 | 0.742 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 missense, 0 nonsense, 0 frameshift |
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 |
|---|---|---|---|---|
Beta-lactamase | PF00144.30 | 1.7e-33 | 13–254 | Beta-lactamase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2258c (transcriptional regulator), high confidence from genomic context alone (score 879 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) |
|---|---|---|---|---|
Rv2258c |
transcriptional regulator | 878 | 879 ctx | neighborhood:872 |
Rv1614 lgt |
prolipoprotein diacylglyceryl transferase | 793 | 794 | coexpression:788 |
Rv2256c hyp |
hypothetical protein | 759 | 760 ctx | neighborhood:759 |
Rv2259 mscR |
S-nitrosomycothiol reductase MscR | 702 | 703 ctx | neighborhood:689 |
Rv2260 hyp |
hypothetical protein | 704 | 695 ctx | neighborhood:689 |
Rv0194 |
multidrug ABC transporter ATPase/permease | 423 | 402 | |
Rv2610c pimA |
alpha-(1-2)-phosphatidylinositol mannosyltransferase | 421 | 302 | |
Rv1209 hyp |
hypothetical protein | 555 | 241 | textmining:438 |
Rv2613c |
AP-4-A phosphorylase | 812 | 86 | textmining:803 |
Rv1301 |
threonylcarbamoyl-AMP synthase | 459 | 85 | textmining:434 |
Rv2681 hyp |
hypothetical protein | 442 | 55 | textmining: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
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: serine hydrolase domain-containing protein
- Pfam (hmmscan --cut_ga): Beta-lactamase PF00144.30 (E=2e-33)
- (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_216773.1)
- Domains: Pfam-A via hmmscan --cut_ga — Beta-lactamase (PF00144.30)
- 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
COG1680 - Curated reference: UniProt O53531 (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 —
11 functional partner(s); context anchor
Rv2258c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002400|Rv2257c| MTALEVLGGWPVPAAAAAVIGPAGVLATHGDTARVFALASVTKPLVARAAQVAVEEGVVNLDTPAGPPGSTVRHLLAHTSGLAMHSDQALARPGTRRMYSNYGFTVLAESVQRESGIEFGRYLTEAVCEPLGMVTTRLDGGPAAAGFGATSTVADLAVFAGDLLRPSTVSAQMHADATTVQFPGLDGVLPGYGVQRPNDWGLGFEIRNSKSPHWTGECNSTRTFGHFGQSGGFIWVDPKADLALVVLTARDFGDWALDLWPAISDAVLAEYT