ripD Family assigned · medium auto-curated
H37Rv Rv1566c · MTBC0 mtbc0_001674 ·
230 aa · 1785892–1786584 (-) ·
RefSeq NP_216082.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | NlpC/P60 family peptidoglycan-binding protein RipD |
| Revised (this work) | NlpC/P60 family peptidoglycan-binding protein RipD. 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 |
O06624
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Peptidoglycan-binding protein RipD |
| Curated function | Binds peptidoglycan but does not show peptidoglycan hydrolase activity. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | ripA_1 |
| eggNOG description | COG0791 Cell wall-associated hydrolases (invasion-associated proteins) |
| Orthologous group | COG0791 |
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 | 0.263 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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 | 9.6e-25 | 55–166 | NlpC/P60 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1565c (acyltransferase), high confidence from genomic context alone (score 778 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) |
|---|---|---|---|---|
Rv1477 ripA |
peptidoglycan endopeptidase RipA | 848 | 834 | coexpression:807 |
Rv1478 ripB |
peptidoglycan endopeptidase RipB | 843 | 824 | coexpression:799 |
Rv3810 pirG |
cell surface protein | 809 | 802 | coexpression:802 |
Rv1565c |
acyltransferase | 785 | 778 ctx | neighborhood:774 |
Rv1158c hyp |
hypothetical protein | 882 | 751 | coexpression:751 textmining:548 |
Rv2525c hyp |
hypothetical protein | 761 | 750 | coexpression:745 |
Rv1157c hyp |
hypothetical protein | 759 | 749 | coexpression:748 |
Rv1564c treX |
maltooligosyl trehalose synthase | 748 | 748 ctx | neighborhood:740 |
Rv1563c treY |
maltooligosyl trehalose synthase | 740 | 740 ctx | neighborhood:740 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 740 | 740 ctx | neighborhood:740 |
Rv2721c hyp |
hypothetical protein | 747 | 738 | coexpression:738 |
Rv0040c mtc28 hyp |
hypothetical protein | 747 | 734 | coexpression:734 |
Rv0312 hyp |
hypothetical protein | 730 | 730 | coexpression:730 |
Rv1567c |
membrane protein | 580 | 581 ctx | neighborhood:581 |
Rv3414c sigD |
ECF RNA polymerase sigma factor SigD | 487 | 485 |
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: NlpC/P60 family peptidoglycan-binding protein RipD
- Pfam (hmmscan --cut_ga): NLPC_P60 PF00877.26 (E=1e-24)
- (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_216082.1)
- 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 O06624 (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 —
21 functional partner(s); context anchor
Rv1565c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001674|Rv1566c|ripD MKRSMKSGSFAIGLAMMLAPMVAAPGLAAADPATRPVDYQQITDVVIARGLSQRGVPFSWAGGGISGPTRGTGTGINTVGFDASGLIQYAYAGAGLKLPRSSGQMYKVGQKVLPQQARKGDLIFYGPEGTQSVALYLGKGQMLEVGDVVQVSPVRTNGMTPYLVRVLGTQPTPVQQAPVQPAPVQQAPVQQAPVQQAPVQQAPVQQAPVQQAPVQQAPVQPPPFGTARSR