ripB Family assigned · medium auto-curated
H37Rv Rv1478 · MTBC0 mtbc0_001581 ·
241 aa · 1678224–1678949 (+) ·
RefSeq NP_215994.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | peptidoglycan endopeptidase RipB |
|---|---|
| MTBC0 PGAP re-annotation | NlpC/P60 family peptidoglycan endopeptidase RipB |
| Revised (this work) | NlpC/P60 family peptidoglycan endopeptidase RipB. 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 |
P9WHU5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Peptidoglycan endopeptidase RipB |
| EC (curated) |
EC 3.4.-.-
|
| Curated function | Peptidoglycan endopeptidase that cleaves the bond between D-glutamate and meso-diaminopimelate. Binds high-molecular weight peptidoglycan, but does not degrade it. Required for normal separation of daughter cells after cell division and cell wall integrity. Required for host cell invasion. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | ripB |
| eggNOG description | PFAM NLP P60 protein |
| Orthologous group | COG0791 |
| KEGG orthology |
K21474
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, 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 | 0.726 · 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 0.25% of strains (366) · 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 |
|---|---|---|---|---|
NLPC_P60 | PF00877.26 | 4.6e-30 | 124–238 | NlpC/P60 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ripA (peptidoglycan endopeptidase RipA), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1477 ripA |
peptidoglycan endopeptidase RipA | 984 | 983 ctx | neighborhood:874 coexpression:864 |
Rv1566c ripD hyp |
hypothetical protein | 843 | 824 | coexpression:799 |
Rv2721c hyp |
hypothetical protein | 803 | 796 | coexpression:796 |
Rv2154c ftsW |
lipid II flippase FtsW | 768 | 759 | coexpression:759 |
Rv3810 pirG |
cell surface protein | 754 | 754 | coexpression:754 |
Rv0312 hyp |
hypothetical protein | 751 | 751 | coexpression:751 |
Rv1497 lipL |
esterase LipL | 754 | 746 | coexpression:742 |
Rv0040c mtc28 hyp |
hypothetical protein | 738 | 738 | coexpression:738 |
Rv1479 moxR1 |
transcriptional regulator MoxR1 | 813 | 736 ctx | neighborhood:728 |
Rv1157c hyp |
hypothetical protein | 634 | 619 | coexpression:618 |
Rv1481 |
membrane protein | 916 | 594 ctx | neighborhood:575 textmining:803 |
Rv1480 hyp |
hypothetical protein | 573 | 573 ctx | neighborhood:563 |
Rv1476 |
membrane protein | 497 | 497 ctx | neighborhood:494 |
Rv1158c hyp |
hypothetical protein | 441 | 441 | coexpression:441 |
Rv0063 |
oxidoreductase | 406 | 406 |
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: peptidoglycan endopeptidase RipB
- MTBC0 PGAP product: NlpC/P60 family peptidoglycan endopeptidase RipB
- Pfam (hmmscan --cut_ga): NLPC_P60 PF00877.26 (E=5e-30)
- (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_215994.1)
- 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 P9WHU5 (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 —
27 functional partner(s); context anchor
ripA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001581|Rv1478|ripB MRHTRFHPIKLAWITAVVAGLMVGVATPADAEPGQWDPTLPALVSAGAPGDPLAVANASLQATAQATQTTLDLGRQFLGGLGINLGGPAASAPSAATTGASRIPRANARQAVEYVIRRAGSQMGVPYSWGGGSLQGPSKGVDSGANTVGFDCSGLVRYAFAGVGVLIPRFSGDQYNAGRHVPPAEAKRGDLIFYGPGGGQHVTLYLGNGQMLEASGSAGKVTVSPVRKAGMTPFVTRIIEY