pepQ Family assigned · medium auto-curated
H37Rv Rv2535c · MTBC0 mtbc0_002701 ·
372 aa · 2882190–2883308 (-) ·
RefSeq NP_217051.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytoplasmic peptidase PepQ |
|---|---|
| MTBC0 PGAP re-annotation | Xaa-Pro peptidase family protein |
| Revised (this work) | Xaa-Pro peptidase family protein. Pfam: Creatinase_N (PF01321.25), Peptidase_M24 (PF00557.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YDN6
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable cytoplasmic peptidase PepQ |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | pepQ |
| eggNOG description | Creatinase/Prolidase N-terminal domain |
| Orthologous group | COG0006 |
| EC number |
EC 3.4.11.9, EC 3.4.13.9
|
| KEGG orthology |
K01262, K01271
|
| Gene Ontology (35) |
GO:0003674, GO:0003824, GO:0004177, GO:0005488, GO:0005515, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006508, GO:0006807 +23 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 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 |
|---|---|---|---|---|
Creatinase_N | PF01321.25 | 4.3e-26 | 6–134 | Creatinase/Prolidase N-terminal domain |
Peptidase_M24 | PF00557.30 | 2.9e-67 | 142–344 | Metallopeptidase family M24 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: efp (elongation factor P), high confidence from genomic context alone (score 928 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2534c efp |
elongation factor P | 951 | 928 ctx | neighborhood:882 |
Rv2532c hyp |
hypothetical protein | 889 | 889 ctx | neighborhood:882 |
Rv2533c nusB |
N utilization substance protein B | 911 | 888 ctx | neighborhood:882 |
Rv2536 |
transmembrane protein | 795 | 796 ctx | neighborhood:790 |
Rv2531c |
amino acid decarboxylase | 700 | 628 ctx | neighborhood:596 |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 620 | 620 | database:497 |
Rv2537c aroD |
3-dehydroquinate dehydratase | 596 | 596 ctx | fusion:513 |
Rv0480c |
amidohydrolase | 558 | 558 | database:497 |
Rv2996c serA1 |
D-3-phosphoglycerate dehydrogenase | 535 | 536 | |
Rv2530A vapB39 |
antitoxin VapB39 | 517 | 518 ctx | neighborhood:515 |
Rv2530c vapC39 |
ribonuclease VapC39 | 599 | 517 ctx | neighborhood:514 |
Rv3336c trpS |
tryptophan--tRNA ligase | 522 | 502 | |
Rv0194 |
multidrug ABC transporter ATPase/permease | 504 | 486 | |
Rv2218 lipA |
lipoyl synthase | 447 | 448 | database:424 |
Rv0728c serA2 |
D-3-phosphoglycerate dehydrogenase SerA | 441 | 441 |
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: cytoplasmic peptidase PepQ
- MTBC0 PGAP product: Xaa-Pro peptidase family protein
- Pfam (hmmscan --cut_ga): Creatinase_N PF01321.25 (E=4e-26), Peptidase_M24 PF00557.30 (E=3e-67)
- (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_217051.1)
- Domains: Pfam-A via hmmscan --cut_ga — Creatinase_N (PF01321.25), Peptidase_M24 (PF00557.30)
- 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
COG0006 - Curated reference: UniProt I6YDN6 (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 —
70 functional partner(s); context anchor
efp - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002701|Rv2535c|pepQ MTHSQRRDKLKAQIAASGLDAMLISDLINVRYLSGFSGSNGALLVFADERDAVLATDGRYRTQAASQAPDLEVAIERAVGRYLAGRAGEAGVGKLGFESHVVTVDGLDALAGALEGKNTELVRASGTVESLREVKDAGELALLRLACEAADAALTDLVARGGLRPGRTERQVSRELEALMLDHGADAVSFETIVAAGANSAIPHHRPTDAVLQVGDFVKIDFGALVAGYHSDMTRTFVLGKAADWQLEIYQLVAEAQQAGRQALLPGAELRGVDAAARQLIADAGYGEHFGHGLGHGVGLQIHEAPGIGVTSAGTLLAGSVVTVEPGVYLPGRGGVRIEDTLVVAGGTPKMPETAGQTPELLTRFPKELAIL