Rv1367c Family assigned · medium auto-curated
H37Rv Rv1367c · MTBC0 - ·
377 aa · 1539512–1540645 (-) ·
RefSeq NP_215883.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Beta-lactamase (PF00144.30) domain(s); putative function inferred from the domain architecture. |
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 |
P9WLZ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein Rv1367c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | beta-lactamase |
| Orthologous group | COG1680 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 0.238 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (374) · 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 | 1.6e-63 | 1–341 | Beta-lactamase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipP (esterase/lipase LipP), medium confidence from genomic context alone (score 680 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) |
|---|---|---|---|---|
Rv2463 lipP |
esterase/lipase LipP | 680 | 680 ctx | cooccurence:678 |
Rv1923 lipD |
lipase LipD | 616 | 616 ctx | cooccurence:616 |
Rv1377c |
transferase | 602 | 603 ctx | neighborhood:544 |
Rv1381 pyrC |
dihydroorotase | 566 | 567 ctx | neighborhood:544 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 545 | 545 ctx | neighborhood:544 |
Rv1379 pyrR |
bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase | 545 | 545 ctx | neighborhood:544 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 544 | 544 ctx | neighborhood:544 |
Rv1382 hyp |
hypothetical protein | 542 | 542 ctx | neighborhood:542 |
Rv1497 lipL |
esterase LipL | 541 | 541 ctx | cooccurence:541 |
Rv0399c lpqK |
lipoprotein LpqK | 503 | 503 ctx | cooccurence:496 |
Rv1385 pyrF |
orotidine 5'-phosphate decarboxylase | 488 | 489 ctx | neighborhood:487 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 487 | 487 ctx | neighborhood:487 |
Rv3633 hyp |
hypothetical protein | 414 | 415 ctx | cooccurence:406 |
Rv0907 hyp |
hypothetical protein | 782 | 349 | textmining:679 |
Rv2045c lipT |
carboxylesterase LipT | 435 | 336 |
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): hypothetical protein
- Pfam (hmmscan --cut_ga): Beta-lactamase PF00144.30 (E=2e-63)
- (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_215883.1)
- 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 P9WLZ3 (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 —
36 functional partner(s); context anchor
lipP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1367c| MVWQREKLLQVNEIGYRDIDAGVPMQRDTLFRIASMTKPVTVAAAMSLVDEGKLALRDPITRWAPELCKVAVLDDAAGPLDRTHPARRAILIEDLLTHTSGLAYGFSVSGPISRAYQRLPFGQGPDVWLAALATLPLVHQPGDRVTYSHAIDVLGVIVSRIEDAPLYQIIDERVLGPAGMTDTGFYVSADAQRRAATMYRLDEQDRLRHDVMGPPHVTPPSFCNAGGGLWSTADDYLRFVRMLLGDGTVDGVRVLSPESVRLMRTDRLTDEQKRHSFLGAPFWVGRGFGLNLSVVTDPAKSRPLFGPGGLGTFSWPGAYGTWWQADPSADLILLYLIQHCPDLSVDAAAAVAGNPSLAKLRTAQPKFVRRTYRALGL