Rv0457c Family assigned · medium auto-curated
H37Rv Rv0457c · MTBC0 mtbc0_000481 ·
673 aa · 550951–552972 (-) ·
RefSeq NP_214971.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | peptidase |
|---|---|
| MTBC0 PGAP re-annotation | prolyl oligopeptidase family protein |
| Revised (this work) | Prolyl oligopeptidase family protein. Pfam: Peptidase_S9_N (PF02897.22), Peptidase_S9 (PF00326.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07178
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable peptidase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | Prolyl oligopeptidase |
| Orthologous group | COG1505 |
| EC number |
EC 3.4.21.26
|
| KEGG orthology |
K01322
|
| KEGG pathways |
map04614
|
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 | 1.33 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 missense, 2 nonsense, 2 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 17.54% of strains (25465) · convergent |
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_S9_N | PF02897.22 | 3.6e-23 | 10–391 | Prolyl oligopeptidase, N-terminal beta-propeller domain |
Peptidase_S9 | PF00326.28 | 1.9e-42 | 470–671 | Prolyl oligopeptidase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0458 (aldehyde dehydrogenase), high confidence from genomic context alone (score 775 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0458 |
aldehyde dehydrogenase | 783 | 775 ctx | neighborhood:763 |
Rv0459 hyp |
hypothetical protein | 772 | 772 ctx | neighborhood:772 |
Rv0781 ptrBa |
Rv0781, (MTCY369.25), len: 236 aa. Probable ptrBa,first part of protease II, equivalent to N-terminus of NP_302455.1|NC_002677 protease II f | 767 | 759 ctx | fusion:518 cooccurence:469 |
Rv0460 hyp |
hypothetical protein | 708 | 709 ctx | neighborhood:708 |
Rv0456c echA2 |
enoyl-CoA hydratase EchA2 | 683 | 683 ctx | neighborhood:681 |
Rv0461 |
transmembrane protein | 681 | 681 ctx | neighborhood:680 |
Rv0455c hyp |
hypothetical protein | 635 | 636 ctx | neighborhood:635 |
Rv0456A mazF1 |
toxin MazF1 | 589 | 589 ctx | neighborhood:588 |
Rv0456B mazE1 |
antitoxin MazE1 | 587 | 588 ctx | neighborhood:588 |
Rv0463 |
membrane protein | 488 | 489 ctx | neighborhood:487 |
Rv0198c zmp1 |
zinc metalloprotease | 669 | 486 ctx | cooccurence:444 |
Rv0462 lpdC |
dihydrolipoamide dehydrogenase | 465 | 465 ctx | neighborhood:462 |
Rv0782 ptrBb |
Rv0782, (MTCY369.26), len: 552 aa. Probable ptrBb,second part of protease II, equivalent to C-terminus of NP_302455.1|NC_002677 protease II | 568 | 340 | |
Rv1284 canA |
beta-carbonic anhydrase | 439 | 55 | textmining:431 |
Rv3588c canB |
carbonic anhydrase | 512 | 41 | textmining:512 |
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: peptidase
- MTBC0 PGAP product: prolyl oligopeptidase family protein
- Pfam (hmmscan --cut_ga): Peptidase_S9_N PF02897.22 (E=4e-23), Peptidase_S9 PF00326.28 (E=2e-42)
- (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_214971.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_S9_N (PF02897.22), Peptidase_S9 (PF00326.28)
- 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
COG1505 - Curated reference: UniProt O07178 (TrEMBL, unreviewed; 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 —
15 functional partner(s); context anchor
Rv0458 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000481|Rv0457c| MTFEPAPDGADPYLWLEDVTGAEALDWVRARNKPTTAAFCDAEFERMRVEALEVLDTDARIPYVNRRGNYLYNFWRDAANPRGLWRRTTLDSYRTDSPGWDVLIDVDELGRADDQKWVWGGAGVIEPDYTRALIGLSPGGSDASIVREFDMLTREFVEDGFQLPPAKSQITWEDPDTVLLGTDFGGDSLTTSGYPRVIKRWRRGKPLADAETIFEGAGTDVRVNASADRTPGFERTLLGRALDFWNEEVYELRGSELIRIEAPTDASVSIHRDWLLIELRTDWTVATTRYTAGSLLAAEYDEFLAGSAELQVVFEPDEHTALYQYAWTRDRLLIVTLADVASRVEIATPGSWRREPLSGIPAATNTVIVSADSHGDEFFLDSSGFDTPSRLMRGTDDGRLAEIKSAPAFFDAENMAVTQYFATSDDGTSIPYFVVRRTDADNPGPTLLNGYGGFETSRTPTYDGVLGRLWLARGGTYALANIRGGGEYGPGWHTQAMREGRDKVAQDFAAVATDLVTRGITTAEQLGARGGSNGGLLMGIMLTGYPEKFGALVCDVPLLDMKRYHLLLAGASWMAEYGDPDNPDDWKFISEYSPYQNISANRKYPPVLMTTSTRDDRVHPGHARKMTAALQAAGHPVWYYENIEGGHAGAADNAQIAFKSALSFAFLWRMLAG