pepC Family assigned · medium auto-curated
H37Rv Rv0800 · MTBC0 mtbc0_000849 ·
433 aa · 896385–897686 (+) ·
RefSeq NP_215315.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | M18 family aminopeptidase |
|---|---|
| MTBC0 PGAP re-annotation | M18 family aminopeptidase |
| Revised (this work) | M18 family aminopeptidase. Pfam: Peptidase_M18 (PF02127.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHT1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable M18 family aminopeptidase 2 |
| EC (curated) |
EC 3.4.11.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | apeB |
| eggNOG description | M18 family aminopeptidase 2 |
| Orthologous group | COG1362 |
| EC number |
EC 3.4.11.21
|
| KEGG orthology |
K01267
|
| Gene Ontology (36) |
GO:0003674, GO:0003824, GO:0004177, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006508, GO:0006518, GO:0006807 +24 more
|
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 | 0.633 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 7 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 |
|---|---|---|---|---|
Peptidase_M18 | PF02127.21 | 4.2e-145 | 11–425 | Aminopeptidase I zinc metalloprotease (M18) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purL (phosphoribosylformylglycinamidine synthase 2), medium confidence from genomic context alone (score 548 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0801 hyp |
hypothetical protein | 873 | 874 ctx | neighborhood:872 |
Rv0798c cfp29 hyp |
hypothetical protein | 794 | 794 ctx | neighborhood:788 |
Rv0799c hyp |
hypothetical protein | 791 | 791 ctx | neighborhood:788 |
Rv0803 purL |
phosphoribosylformylglycinamidine synthase 2 | 547 | 548 ctx | neighborhood:544 |
Rv2461c clpP1 |
ATP-dependent CLP protease proteolytic subunit 1 | 560 | 104 | textmining:530 |
Rv3011c gatA |
glutamyl-tRNA(GLN) amidotransferase subunit A | 421 | 55 | textmining:413 |
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: M18 family aminopeptidase
- MTBC0 PGAP product: M18 family aminopeptidase
- Pfam (hmmscan --cut_ga): Peptidase_M18 PF02127.21 (E=4e-145)
- (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_215315.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_M18 (PF02127.21)
- 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
COG1362 - Curated reference: UniProt P9WHT1 (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 —
6 functional partner(s); context anchor
purL - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000849|Rv0800|pepC MAATAHGLCEFIDASPSPFHVCATVAGRLLGAGYRELREADRWPDKPGRYFTVRAGSLVAWNAEQSGHTQVPFRIVGAHTDSPNLRVKQHPDRLVAGWHVVALQPYGGVWLHSWLDRDLGISGRLSVRDGTGVSHRLVRIDDPILRVPQLAIHLAEDRKSLTLDPQRHINAVWGVGERVESFVGYVAQRAGVAAADVLAADLMTHDLTPSALIGASVNGTASLLSAPRLDNQASCYAGMEALLAVDVDSASSGFVPVLAIFDHEEVGSASGHGAQSDLLSSVLERIVLAAGGTREDFLRRLTTSMLASADMAHATHPNYPDRHEPSHPIEVNAGPVLKVHPNLRYATDGRTAAAFALACQRAGVPMQRYEHRADLPCGSTIGPLAAARTGIPTVDVGAAQLAMHSARELMGAHDVAAYSAALQAFLSAELSEA