aldC Resolved · high auto-curated
H37Rv Rv2858c · MTBC0 - ·
455 aa · 3169356–3170723 (-) ·
RefSeq NP_217374.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aldehyde dehydrogenase AldC |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Aldehyde dehydrogenase AldC. 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 |
O33340
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative succinate-semialdehyde dehydrogenase [NADP(+)] 2 |
| EC (curated) |
EC 1.2.1.79
|
UniProt still lists this protein as Putative succinate-semialdehyde dehydrogenase [NADP(+)] 2; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | aldC |
| eggNOG description | Belongs to the aldehyde dehydrogenase family |
| Orthologous group | COG1012 |
| EC number |
EC 1.2.1.3, EC 1.2.1.39, EC 1.2.1.8
|
| KEGG orthology |
K00128, K00130, K00146
|
| KEGG pathways |
map00010, map00053, map00071, map00260, map00280, map00310, map00330, map00340, map00360, map00380, map00410, map00561, map00620, map00625, map00643, map00903, map00981, map01100, map01110, map01120, map01130
|
| KEGG modules |
M00135, M00555
|
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 | 0.536 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 9 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 |
|---|---|---|---|---|
Aldedh | PF00171.28 | 6.0e-154 | 3–447 | Aldehyde dehydrogenase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2857c (3-oxoacyl-ACP reductase), high confidence from genomic context alone (score 952 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2857c |
3-oxoacyl-ACP reductase | 953 | 952 ctx | neighborhood:882 cooccurence:485 |
Rv2860c glnA4 |
glutamine synthetase | 933 | 930 ctx | neighborhood:881 cooccurence:405 |
Rv2859c |
glutamine amidotransferase | 928 | 925 ctx | neighborhood:882 |
Rv1188 |
proline dehydrogenase | 689 | 669 ctx | fusion:558 |
Rv1691 hyp |
hypothetical protein | 614 | 598 | database:542 |
Rv2267c stf3 hyp |
hypothetical protein | 613 | 598 | database:542 |
Rv3529c hyp |
hypothetical protein | 611 | 596 | database:542 |
Rv1819c bacA |
vitamin B12 transport ATP-binding protein BacA | 597 | 586 | database:581 |
Rv2861c mapB |
methionine aminopeptidase | 597 | 581 ctx | neighborhood:503 |
Rv0435c |
ATPase | 561 | 560 | database:526 |
Rv1371 |
membrane protein | 599 | 556 | database:500 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 551 | 550 | database:526 |
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 550 | 550 | database:526 |
Rv3868 eccA1 |
ESX-1 secretion system protein EccA1 | 549 | 548 | database:526 |
Rv2993c |
2-hydroxyhepta-2,4-diene-1,7-dioate isomerase | 547 | 525 | coexpression:445 |
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): aldehyde dehydrogenase AldC
- Pfam (hmmscan --cut_ga): Aldedh PF00171.28 (E=6e-154)
- (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_217374.1)
- 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 O33340 (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 —
67 functional partner(s); context anchor
Rv2857c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2858c|aldC MSTTQLINPATEEVLASVDHTDANAVDDAVQRARAAQRRWARLAPAQRAAGLRAFAAAVQAHLDELAALEVANSGHPIVSAEWEAGHVRDVLAFYAASPERLSGRQIPVAGGVDVTFNEPMGVVGVITPWNFPMVIASWAIAPALAAGNAVLVKPAELTPLTTMRLGELAVEAGLDEDLLQVLPGKGTVVGERFVTHPDIRKIVFTGSTEVGKRVMAGAAAQVKRVTLELGGKSANIVFHDCDLERAATTAPAGVFDNAGQDCCARSRILVQRSVYDRFMELLEPAVHSIVVGDPGSRATEMGPLVSRAHRDKVAGYVPDDAPVAFRGTAPAGRGFWFPPTVLTPKRGDRTVTDEIFGPVVVVLTFDDEADAISLANDTAYGLSGSIWTDDLSRALRVARAVESGNLSVNSHSSVRFNTPFGGFKQSGVGRELGPDAPLQFTETKNVFIAVGEEM