Rv1730c Family assigned · medium auto-curated
H37Rv Rv1730c · MTBC0 mtbc0_001842 ·
517 aa · 1967764–1969317 (-) ·
RefSeq NP_216246.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | penicillin-binding 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 |
P71988
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible penicillin-binding protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| 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) pseudogene candidate
| pN/pS | 0.662 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 9 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 21.01% of strains (30511) · 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 |
|---|---|---|---|---|
Beta-lactamase | PF00144.30 | 4.2e-74 | 60–383 | Beta-lactamase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1729c (S-adenosylmethionine-dependent methyltransferase), medium confidence from genomic context alone (score 524 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1728c hyp |
hypothetical protein | 535 | 535 ctx | neighborhood:528 |
Rv1729c |
S-adenosylmethionine-dependent methyltransferase | 525 | 524 ctx | neighborhood:517 |
Rv1923 lipD |
lipase LipD | 496 | 497 ctx | cooccurence:495 |
Rv2000 hyp |
hypothetical protein | 466 | 466 ctx | cooccurence:462 |
Rv1723 |
hydrolase | 418 | 419 ctx | cooccurence:415 |
Rv1367c hyp |
hypothetical protein | 500 | 283 | |
Rv2407 rnz |
ribonuclease Z | 673 | 80 | textmining:660 |
Rv0050 ponA1 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 610 | 69 | textmining:599 |
Rv3682 ponA2 |
bifunctional penicillin-insensitive transglycosylase/penicillin-sensitive transpeptidase | 484 | 66 | textmining:470 |
Rv0712 hyp |
hypothetical protein | 559 | 61 | textmining:550 |
Rv0016c pbpA |
penicillin-binding protein PbpA | 672 | 55 | textmining:668 |
Rv1263 amiB2 |
amidase AmiB | 660 | 52 | textmining:657 |
Rv3627c dacB hyp |
hypothetical protein | 541 | 51 | textmining:537 |
Rv2864c |
penicillin-binding lipoprotein | 469 | 50 | textmining:465 |
Rv2166c mraZ |
transcriptional regulator MraZ | 654 | 49 | textmining:652 |
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: penicillin-binding protein
- MTBC0 PGAP product: serine hydrolase domain-containing protein
- Pfam (hmmscan --cut_ga): Beta-lactamase PF00144.30 (E=4e-74)
- (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_216246.1)
- 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 P71988 (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 —
27 functional partner(s); context anchor
Rv1729c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001842|Rv1730c| MCPPIILSSATPTGTRCGTRHGRAVVTEYVRALDRLPHEIATAVVETVNCADPGAAFDELDAKINAGMKAYAIPGVAVAVWAGGQEYVKGYGVTNVDHPMPVDGDTVFRIGSTTKTFTGTVMMRLVERGKVDLDSPVRRYIPDFAVADESASATVTVRQLLNHTAGWDGRNGQDFGRGDDAVALYVKAMTRLPQLTPPGTAFAYNNSGLVVAGRIIELVAGTTYESTVQRLLLDPLQLAHTRYFSDQIIGLNVAASHSVVDGKPIAVTDFWTFPRSCNPTGGLMSTARDQLRYAQFHLGDGRAPNGEQILSRQSLKAMRSNPGAGGTLWVELTGMGVTWMLRPSAENVTIVEHGGTWKGQRSGFVMVPDRNFAMTVLTNSDGGFHMINDLFASDWALQRFAGLSNLPATPQRLGAVDLAPYEGRYIAKQVAQNGDLETTVIDFRARDGQLAGSMSTDDANPDGQNSANLGLAFYRPDYGLDLGPDNKPTGSRSNFVRGPDGNIAWFCSQHGRLFRRQ