Rv0658c Family assigned · medium auto-curated
H37Rv Rv0658c · MTBC0 mtbc0_000696 ·
238 aa · 757779–758495 (-) ·
RefSeq NP_215172.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | CPBP family intramembrane glutamic endopeptidase |
| Revised (this work) | CPBP family intramembrane glutamic endopeptidase. 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.
Curated reference (UniProt)
| UniProt |
O06781
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | CAAX protease self-immunity |
| 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 | 1.437 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 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 |
|---|---|---|---|---|
Rce1-like | PF02517.22 | 3.8e-16 | 133–222 | Type II CAAX prenyl endopeptidase Rce1-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD1 (ESX-1 secretion system protein EccD1), high confidence from genomic context alone (score 722 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 721 | 722 ctx | cooccurence:719 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 719 | 719 ctx | cooccurence:715 |
Rv1632c hyp |
hypothetical protein | 647 | 648 ctx | cooccurence:639 |
Rv1375 hyp |
hypothetical protein | 654 | 633 | coexpression:620 |
Rv0657c vapB6 |
antitoxin VapB6 | 621 | 621 ctx | neighborhood:615 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 605 | 605 ctx | cooccurence:592 |
Rv3875 esxA |
ESAT-6 protein EsxA | 556 | 556 ctx | cooccurence:555 |
Rv2360c hyp |
hypothetical protein | 547 | 547 ctx | cooccurence:526 |
Rv3737 |
transmembrane protein | 544 | 544 ctx | cooccurence:541 |
Rv3212 hyp |
hypothetical protein | 533 | 534 ctx | cooccurence:520 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK | 532 | 531 ctx | cooccurence:530 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 529 | 528 ctx | cooccurence:505 |
Rv0556 |
transmembrane protein | 521 | 521 ctx | cooccurence:508 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 523 | 506 | coexpression:400 |
Rv3438 hyp |
hypothetical protein | 503 | 503 ctx | cooccurence:502 |
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: integral membrane protein
- MTBC0 PGAP product: CPBP family intramembrane glutamic endopeptidase
- Pfam (hmmscan --cut_ga): Rce1-like PF02517.22 (E=4e-16)
- (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_215172.1)
- 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 O06781 (TrEMBL, unreviewed; Predicted)
- 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 —
49 functional partner(s); context anchor
eccD1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000696|Rv0658c| MEAGRADTVAPSHRWGLGAFLVVELVFLVASTSLAVVLTGHGPVSAGVLALALAAPTVVAAGLAILITRLRGNGPRTDLRLRWSWRGLRLGLMFGFGGMLVTIPASLVYTAIVGPEANSAVVRIFGGVRASWPWALVVFLVVVFVAPLCEEIIYRGLLWGAVDRRWGRWAALVVTTVVFALAHLEFARAPLLVVVAIPIALARFYSGGLLASIVTHQVTNLLPGIVLLLGLTGAISLP