pcp Resolved · high auto-curated
H37Rv Rv0319 · MTBC0 mtbc0_000340 ·
222 aa · 390471–391139 (+) ·
RefSeq NP_214833.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | pyrrolidone-carboxylate peptidase |
|---|---|
| MTBC0 PGAP re-annotation | pyroglutamyl-peptidase I |
| Revised (this work) | Pyroglutamyl-peptidase I. Pfam: Peptidase_C15 (PF01470.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIJ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Pyrrolidone-carboxylate peptidase |
| EC (curated) |
EC 3.4.19.3
|
| Curated function | Removes 5-oxoproline from various penultimate amino acid residues except L-proline. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | pcp |
| eggNOG description | Removes 5-oxoproline from various penultimate amino acid residues except L-proline |
| Orthologous group | COG2039 |
| EC number |
EC 3.4.19.3
|
| KEGG orthology |
K01304
|
| Gene Ontology (9) |
GO:0006508, GO:0006807, GO:0008150, GO:0008152, GO:0019538, GO:0043170, GO:0044238, GO:0071704, GO:1901564
|
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 | 1.776 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 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_C15 | PF01470.23 | 2.7e-95 | 3–208 | Pyroglutamyl peptidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0318c (integral membrane protein), medium confidence from genomic context alone (score 564 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0320 hyp |
hypothetical protein | 757 | 756 ctx | neighborhood:754 |
Rv0318c |
integral membrane protein | 563 | 564 ctx | neighborhood:561 |
Rv0321 dcd |
deoxycytidine triphosphate deaminase | 560 | 560 ctx | neighborhood:560 |
Rv0263c hyp |
hypothetical protein | 482 | 460 | |
Rv0264c hyp |
hypothetical protein | 467 | 448 | |
Rv3468c |
dTDP-glucose 4,6-dehydratase | 570 | 47 | textmining:568 |
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: pyrrolidone-carboxylate peptidase
- MTBC0 PGAP product: pyroglutamyl-peptidase I
- Pfam (hmmscan --cut_ga): Peptidase_C15 PF01470.23 (E=3e-95)
- (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_214833.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_C15 (PF01470.23)
- 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
COG2039 - Curated reference: UniProt P9WIJ5 (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
Rv0318c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000340|Rv0319|pcp MSKVLVTGFGPYGVTPVNPAQLTAEELDGRTIAGATVISRIVPNTFFESIAAAQQAIAEIEPALVIMLGEYPGRSMITVERLAQNVNDCGRYGLADCAGRVLVGEPTDPAGPVAYHATVPVRAMVLAMRKAGVPADVSDAAGTFVCNHLMYGVLHHLAQKGLPVRAGWIHLPCLPSVAALDHNLGVPSMSVQTAVAGVTAGIEAAIRQSADIREPIPSRLQI