Rv1333 Family assigned · medium auto-curated
H37Rv Rv1333 · MTBC0 mtbc0_001430 ·
344 aa · 1512301–1513335 (+) ·
RefSeq NP_215849.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hydrolase |
|---|---|
| MTBC0 PGAP re-annotation | P1 family peptidase |
| Revised (this work) | P1 family peptidase. Pfam: Peptidase_S58 (PF03576.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM23
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized aminopeptidase Rv1333 |
| EC (curated) |
EC 3.4.11.-
|
| Curated function | Aminopeptidase. |
UniProt still lists this protein as Uncharacterized aminopeptidase Rv1333; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | dmpA |
| eggNOG description | peptidase S58, DmpA |
| Orthologous group | COG3191 |
| KEGG orthology |
K18572
|
| KEGG pathways |
map00332, map01130
|
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 | 0.232 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (156) · 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 |
|---|---|---|---|---|
Peptidase_S58 | PF03576.20 | 1.3e-65 | 2–331 | Peptidase family S58 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: clpS (ATP-dependent Clp protease adapter protein ClpS), high confidence from genomic context alone (score 890 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1331 clpS |
ATP-dependent Clp protease adapter protein ClpS | 895 | 890 ctx | neighborhood:861 |
Rv1334 mec |
[CysO | 887 | 886 ctx | neighborhood:881 |
Rv1332 |
transcriptional regulator | 891 | 875 ctx | neighborhood:861 |
Rv1335 cysO |
sulfur carrier protein CysO | 856 | 856 ctx | neighborhood:851 |
Rv1337 |
integral membrane protein | 874 | 855 ctx | neighborhood:847 |
Rv1338 murI |
glutamate racemase | 854 | 854 ctx | neighborhood:847 |
Rv1336 cysM |
O-phosphoserine sulfhydrylase | 854 | 854 ctx | neighborhood:847 |
Rv1339 hyp |
hypothetical protein | 815 | 816 ctx | neighborhood:813 |
Rv1340 rphA |
ribonuclease PH | 803 | 803 ctx | neighborhood:797 |
Rv1330c pncB1 |
nicotinic acid phosphoribosyltransferase PncB1 | 764 | 764 ctx | neighborhood:763 |
Rv1341 rdgB |
non-canonical purine NTP pyrophosphatase | 761 | 762 ctx | neighborhood:758 |
Rv1329c dinG |
ATP-dependent helicase DinG | 613 | 612 ctx | neighborhood:609 |
Rv2075c hyp |
hypothetical protein | 585 | 60 | textmining:577 |
Rv2479c |
Probable transposase; Rv2479c, (MTV008.35c), len: 328 aa. Probable transposase for IS6110. Identical to many other M. tuberculosis IS6110 tr | 439 | 50 | textmining:434 |
Rv1521 fadD25 |
fatty-acid--CoA ligase FadD25 | 513 | 47 | textmining:510 |
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: hydrolase
- MTBC0 PGAP product: P1 family peptidase
- Pfam (hmmscan --cut_ga): Peptidase_S58 PF03576.20 (E=1e-65)
- (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_215849.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_S58 (PF03576.20)
- 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
COG3191 - Curated reference: UniProt P9WM23 (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 —
17 functional partner(s); context anchor
clpS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001430|Rv1333| MNSITDVGGIRVGHYQRLDPDASLGAGWACGVTVVLPPPGTVGAVDCRGGAPGTRETDLLDPANSVRFVDALLLAGGSAYGLAAADGVMRWLEEHRRGVAMDSGVVPIVPGAVIFDLPVGGWNCRPTADFGYSACAAAGVDVAVGTVGVGVGARAGALKGGVGTASATLQSGVTVGVLAVVNAAGNVVDPATGLPWMADLVGEFALRAPPAEQIAALAQLSSPLGAFNTPFNTTIGVIACDAALSPAACRRIAIAAHDGLARTIRPAHTPLDGDTVFALATGAVAVPPEAGVPAALSPETQLVTAVGAAAADCLARAVLAGVLNAQPVAGIPTYRDMFPGAFGS