ripC Resolved · high auto-curated
H37Rv Rv2190c · MTBC0 mtbc0_002325 ·
385 aa · 2478122–2479279 (-) ·
RefSeq NP_216706.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | endopeptidase |
|---|---|
| MTBC0 PGAP re-annotation | peptidoglycan hydrolase RipC |
| Revised (this work) | Peptidoglycan hydrolase RipC. Pfam: NLPC_P60 (PF00877.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHU3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable endopeptidase Rv2190c |
| EC (curated) |
EC 3.4.-.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | NlpC/P60 family |
| Orthologous group | COG0791 |
| KEGG orthology |
K21471
|
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | 1.043 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 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 |
|---|---|---|---|---|
NLPC_P60 | PF00877.26 | 3.7e-23 | 285–368 | NlpC/P60 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pimB (alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase), medium confidence from genomic context alone (score 608 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0950c hyp |
hypothetical protein | 882 | 795 | coexpression:761 textmining:453 |
Rv2189c hyp |
hypothetical protein | 798 | 791 ctx | neighborhood:752 |
Rv1886c fbpB |
diacylglycerol acyltransferase/mycolyltransferase Ag85B | 781 | 757 | coexpression:757 |
Rv1010 ksgA |
rRNA small subunit methyltransferase A | 738 | 738 | coexpression:730 |
Rv0175 |
Mce associated membrane protein | 732 | 732 | coexpression:732 |
Rv2188c pimB |
alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase | 706 | 608 ctx | neighborhood:551 |
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 596 | 596 ctx | cooccurence:582 |
Rv3835 hyp |
hypothetical protein | 577 | 578 ctx | cooccurence:575 |
Rv3909 hyp |
hypothetical protein | 595 | 565 ctx | cooccurence:561 |
Rv1024 |
membrane protein | 434 | 434 ctx | cooccurence:426 |
Rv0007 |
membrane protein | 422 | 422 ctx | cooccurence:403 |
Rv1009 rpfB |
resuscitation-promoting factor RpfB | 727 | 400 | textmining:565 |
Rv3156 nuoL |
NADH-quinone oxidoreductase subunit L | 419 | 398 | |
Rv1478 ripB |
peptidoglycan endopeptidase RipB | 480 | 359 | |
Rv1477 ripA |
peptidoglycan endopeptidase RipA | 557 | 358 |
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: endopeptidase
- MTBC0 PGAP product: peptidoglycan hydrolase RipC
- Pfam (hmmscan --cut_ga): NLPC_P60 PF00877.26 (E=4e-23)
- (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_216706.1)
- Domains: Pfam-A via hmmscan --cut_ga — NLPC_P60 (PF00877.26)
- 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
COG0791 - Curated reference: UniProt P9WHU3 (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 —
29 functional partner(s); context anchor
pimB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002325|Rv2190c|ripC MRLDQRWLIARVIMRSAIGFFASFTVSSGVLAANVLADPADDALAKLNELSRQAEQTTEALHSAQLDLNEKLAAQRAADQKLADNRTALDAARARLATFQTAVNKVAAATYMGGRTHGMDAILTAESPQLLIDRLSVQRVMAHQMSTQMARFKAAGEQAVKAEQAAAKSAADARSAAEQAAAVRANLQHKQSQLQVQIAVVKSQYVALTPEERTALADPGPVPAVAAIAPGAPPAALPPGAPPGDGPAPGVAPPPGGMPGLPFVQPDGAGGDRTAVVQAALTQVGAPYAWGGAAPGGFDCSGLVMWAFQQAGIALPHSSQALAHGGQPVALSDLQPGDVLTFYSDASHAGIYIGDGLMVHSSTYGVPVRVVPMDSSGPIYDARRY