Rv0024 Family assigned · medium auto-curated
H37Rv Rv0024 · MTBC0 mtbc0_000029 ·
281 aa · 28344–29189 (+) ·
RefSeq NP_214538.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | NLP/P60 family protein |
|---|---|
| MTBC0 PGAP re-annotation | C40 family peptidase |
| Revised (this work) | C40 family peptidase. 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 |
P71594
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Secreted protein P60-related protein |
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
|
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) pseudogene candidate
| pN/pS | 0.268 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 4 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 26.25% of strains (38111) · 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 | 7.0e-22 | 182–272 | NlpC/P60 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0023 (transcriptional regulator), high confidence from genomic context alone (score 826 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0023 |
transcriptional regulator | 825 | 826 ctx | neighborhood:816 |
Rv0025 hyp |
hypothetical protein | 727 | 728 ctx | neighborhood:716 |
Rv0022c whiB5 |
transcriptional regulator WhiB5 | 630 | 617 ctx | neighborhood:615 |
Rv0026 hyp |
hypothetical protein | 446 | 446 ctx | neighborhood:438 |
Rv1477 ripA |
peptidoglycan endopeptidase RipA | 511 | 358 | |
Rv2190c ripC |
endopeptidase | 465 | 308 | |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 407 | 284 | |
Rv2974c hyp |
hypothetical protein | 419 | 188 | |
Rv3915 cwlM |
peptidoglycan hydrolase | 674 | 147 | textmining:634 |
Rv2704 hyp |
hypothetical protein | 463 | 100 | textmining:429 |
Rv2389c rpfD |
resuscitation-promoting factor RpfD | 549 | 86 | textmining:528 |
Rv1337 |
integral membrane protein | 664 | 77 | textmining:651 |
Rv1009 rpfB |
resuscitation-promoting factor RpfB | 582 | 71 | textmining:569 |
Rv2864c |
penicillin-binding lipoprotein | 817 | 66 | textmining:812 |
Rv1430 PE16 |
PE family protein PE16 | 534 | 63 | textmining:523 |
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: NLP/P60 family protein
- MTBC0 PGAP product: C40 family peptidase
- Pfam (hmmscan --cut_ga): NLPC_P60 PF00877.26 (E=7e-22)
- (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_214538.1)
- 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 P71594 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
20 functional partner(s); context anchor
Rv0023 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000029|Rv0024| MNYSEVELLSRAHQLFAGDSRRPGLDAGTTPYGDLLSRAADLNVGAGQRRYQLAVDHSRAALLSAARTDAAAGAVITGAQRDRAWARRSTGTVLDEARSDTTVTAVMPIAQREAIRRRVARLRAQRAHVLTARRRARRHLAALRALRYRVAHGPGVALAKLRLPSPSGRAGIAVHAALSRLGRPYVWGATGPNQFDCSGLVQWAYAQAGVHLDRTTYQQINEGIPVPRSQVRPGDLVFPHPGHVQLAIGNNLVVEAPHAGASVRVSSLGNNVQIRRPLSGR