Rv1140 Family assigned · medium auto-curated
H37Rv Rv1140 · MTBC0 - ·
282 aa · 1267347–1268195 (+) ·
RefSeq NP_215656.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Integral membrane protein. Pfam: Rce1-like (PF02517.22). |
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 |
O06540
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Abortive infection protein |
| Orthologous group | COG1266 |
| KEGG orthology |
K07052
|
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 | 0.734 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (197) · 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 |
|---|---|---|---|---|
Rce1-like | PF02517.22 | 6.6e-11 | 184–270 | Type II CAAX prenyl endopeptidase Rce1-like |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1375 hyp |
hypothetical protein | 654 | 633 | coexpression:620 |
Rv1765c hyp |
hypothetical protein | 552 | 553 ctx | cooccurence:552 |
Rv2015c hyp |
hypothetical protein | 528 | 529 ctx | cooccurence:528 |
Rv0904c accD3 |
acetyl-CoAcarboxylase carboxyl transferase subunit beta | 506 | 506 | |
Rv1747 |
ABC transporter ATP-binding protein/permease | 523 | 490 | coexpression:438 |
Rv1586c |
phage integrase | 431 | 431 | |
Rv1571 hyp |
hypothetical protein | 427 | 428 | |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 441 | 421 | coexpression:402 |
Rv3127 hyp |
hypothetical protein | 440 | 420 | coexpression:403 |
Rv2032 acg |
NAD(P)H nitroreductase | 440 | 420 | coexpression:403 |
Rv3131 |
NAD(P)H nitroreductase | 439 | 420 | coexpression:403 |
Rv3368c |
oxidoreductase | 439 | 420 | coexpression:403 |
Rv1457c |
antibiotic ABC transporter permease | 438 | 418 | coexpression:414 |
Rv0306 bluB |
oxidoreductase | 437 | 417 | coexpression:400 |
Rv2938 drrC |
daunorubicin ABC transporter permease DrrC | 437 | 416 | coexpression:412 |
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): integral membrane protein
- Pfam (hmmscan --cut_ga): Rce1-like PF02517.22 (E=7e-11)
- (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_215656.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rce1-like (PF02517.22)
- 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
COG1266 - Curated reference: UniProt O06540 (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 — 21 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1140| MPRDYTAPRWAHAWAGEPRPARWHPANQPAHPDHSNRESPACMSQSTTPYRSSVLAEFRRAITNVAVPHHEPPGIVRRRRVVVGVTLVIGAVMLGFSLRRTPGESSFYWLTLALAAVWIAGALMSGPLHLGGICWRGRNQRPVITGTTVGLLLAGIFGVGAMIVRAIPGAAEPIARVLQFAHQGTLLPILLITLINGIAEEMFFRGALYTALGRRYPVTISTVLYVGATMASANLMLGFAAIFVGTVCALERRASGGVLAPILTHFVWGLIMVFALPPLFAV