pcd Resolved · high auto-curated
H37Rv Rv3293 · MTBC0 - ·
494 aa · 3673602–3675086 (+) ·
RefSeq YP_177953.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | piperideine-6-carboxylic acid dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Piperideine-6-carboxylic acid dehydrogenase. Pfam: Aldedh (PF00171.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
L7N650
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | aldehyde dehydrogenase |
| EC (curated) |
EC 1.2.1.3
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | pcd |
| eggNOG description | Belongs to the aldehyde dehydrogenase family |
| Orthologous group | COG1012 |
| EC number |
EC 1.2.1.3
|
| KEGG orthology |
K00128
|
| KEGG pathways |
map00010, map00053, map00071, map00280, map00310, map00330, map00340, map00380, map00410, map00561, map00620, map00625, map00903, map00981, map01100, map01110, map01120, map01130
|
| KEGG modules |
M00135
|
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 | 0.311 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.22% of strains (319) · 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 |
|---|---|---|---|---|
Aldedh | PF00171.28 | 2.6e-135 | 22–474 | Aldehyde dehydrogenase family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3292 hyp |
hypothetical protein | 978 | 979 ctx | neighborhood:843 coexpression:799 |
Rv3667 acs |
acetyl-CoAsynthetase | 950 | 947 | coexpression:420 database:900 |
Rv2589 gabT |
4-aminobutyrate aminotransferase | 937 | 933 | database:900 |
Rv0409 ackA |
acetate kinase | 929 | 925 | database:900 |
Rv0860 fadB |
fatty oxidation protein FadB | 926 | 922 | database:900 |
Rv0162c adhE1 |
zinc-type alcohol dehydrogenase subunit E | 924 | 921 | database:900 |
Rv0761c adhB |
alcohol dehydrogenase B | 924 | 921 | database:900 |
Rv1530 adh |
alcohol dehydrogenase | 924 | 920 | database:900 |
Rv3432c gadB |
glutamate decarboxylase GadB | 921 | 917 | database:900 |
Rv1862 adhA |
alcohol dehydrogenase A | 920 | 915 | database:900 |
Rv3045 adhC |
NADP-dependent alcohol dehydrogenase | 917 | 913 | database:900 |
Rv0751c mmsB |
3-hydroxyisobutyrate dehydrogenase | 915 | 912 | database:900 |
Rv0753c mmsA |
methylmalonate-semialdehyde dehydrogenase | 909 | 910 | database:900 |
Rv3170 aofH |
flavin-containing monoamine oxidase | 911 | 906 | database:900 |
Rv3535c hsaG |
acetaldehyde dehydrogenase | 908 | 904 | database:900 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): piperideine-6-carboxylic acid dehydrogenase
- Pfam (hmmscan --cut_ga): Aldedh PF00171.28 (E=3e-135)
- (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 YP_177953.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aldedh (PF00171.28)
- 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
COG1012 - Curated reference: UniProt L7N650 (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 — 89 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3293|pcd MLEACQAIGVTAALGEPGEHSLPASTPITGDVLFSIAPTTPEQADHAIAAAAATFTAWRSTPAPVRGALVARLGELLTAHQQDLATLVTVEVGKITAEARGEVQEMIDVCQFSVGLSRQLYGRTIASERAGHRLLETWHPLGVVGVITAFNFPVAVWAWNTAVALVCGDTVVWKPSELTPLTALACQALLSRAAADVGAPAAVGGLLLGGAERGAQLVDDPRVALLSATGSVRMGQQVGPRVARRFGRVLLELGGNNAAIVAPSADLELAVRGIVFAAAGTAGQRCTSLRRLIVHRSVADDVVARVVGAYRQLAIGDPSAPDTLVGPLIHEAAYRDMVAALERARTDGGEVIGGDRREVGSPGAYYVAPAVVRMPSQTAIVATETFAPILYVLTYDDLDEAIALNNAVPQGLSSSIFTTDLREAEHFLDQSDCGIANVNIGTSGAEIGGAFGGEKQTGGGRESGSDAWKAYMRRATNTVNYSSELPLAQGVKFG