Rv0804 Family assigned · medium auto-curated
H37Rv Rv0804 · MTBC0 mtbc0_000853 ·
209 aa · 901148–901777 (+) ·
RefSeq NP_215319.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical 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 |
I6Y4V2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | CAAX prenyl protease 2/Lysostaphin resistance protein A-like domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | 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 | 0.165 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 2 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 | 1.4e-12 | 96–189 | Type II CAAX prenyl endopeptidase Rce1-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purL (phosphoribosylformylglycinamidine synthase 2), high confidence from genomic context alone (score 804 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) |
|---|---|---|---|---|
Rv0803 purL |
phosphoribosylformylglycinamidine synthase 2 | 804 | 804 ctx | neighborhood:801 |
Rv3604c |
transmembrane protein | 747 | 747 ctx | cooccurence:746 |
Rv0955 |
integral membrane protein | 720 | 720 ctx | cooccurence:707 |
Rv2633c hyp |
hypothetical protein | 698 | 699 ctx | cooccurence:698 |
Rv1978 hyp |
hypothetical protein | 697 | 697 ctx | cooccurence:688 |
Rv3896c hyp |
hypothetical protein | 671 | 671 ctx | cooccurence:671 |
Rv3786c hyp |
hypothetical protein | 665 | 665 ctx | cooccurence:650 |
Rv2687c |
antibiotic ABC transporter permease | 646 | 634 ctx | cooccurence:598 |
Rv1375 hyp |
hypothetical protein | 653 | 632 | coexpression:619 |
Rv1159 pimE |
polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase | 631 | 631 ctx | cooccurence:628 |
Rv1682 hyp |
hypothetical protein | 627 | 627 ctx | cooccurence:627 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 621 | 621 ctx | cooccurence:620 |
Rv2686c |
antibiotic ABC transporter permease | 592 | 592 ctx | cooccurence:592 |
Rv0256c PPE2 |
PPE family protein PPE2 | 590 | 590 ctx | cooccurence:589 |
Rv1057 hyp |
hypothetical protein | 588 | 588 ctx | cooccurence:587 |
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: CPBP family intramembrane glutamic endopeptidase
- Pfam (hmmscan --cut_ga): Rce1-like PF02517.22 (E=1e-12)
- (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_215319.1)
- 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 I6Y4V2 (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 —
43 functional partner(s); context anchor
purL - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000853|Rv0804| MSRLRALSLAAGLVGWSLVSPRLPAPWRIPLQAGLGSVLVLVTRATMGLWPPRLWAGLRLGWAAGAAAATAIAATTPVPMVRLSMSARELPASVPVWLVWHIPGGTVWAEEAAFRGALATIGARAFGRSGGRILQAGAFGLSHIADARATGEPLVLTVLATGIAGWMFGWLADRSGSLAAPLLTHLAINEAGAVAAVLVQRRSGISTRL