Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aldehyde dehydrogenase |
|---|
| MTBC0 PGAP re-annotation | aldehyde dehydrogenase |
|---|
| Revised (this work) | Aldehyde 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.
Curated reference (UniProt)
| UniProt |
I6X8S7
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Probable aldehyde dehydrogenase |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|
| eggNOG description | Belongs to the aldehyde dehydrogenase family |
|---|
| Orthologous group | COG1012 |
|---|
| EC number |
EC 1.2.1.3, EC 1.2.1.8
|
|---|
| KEGG orthology |
K00128, K00130
|
|---|
| KEGG pathways |
map00010, map00053, map00071, map00260, map00280, map00310, map00330, map00340, map00380, map00410, map00561, map00620, map00625, 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)
pseudogene candidate
| pN/pS |
1.164 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
2 synonymous, 7 missense, 0 nonsense, 2 frameshift
|
|---|
| Disruption |
2 distinct premature-stop/frameshift site(s); most common in
11.31% of strains
(16426) · 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 |
5.1e-168 | 17–478 |
Aldehyde dehydrogenase family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv3667 acs |
acetyl-CoAsynthetase |
952 |
947 |
coexpression:417 database:900 |
Rv2589 gabT |
4-aminobutyrate aminotransferase |
937 |
932 |
database:900 |
Rv0753c mmsA |
methylmalonate-semialdehyde dehydrogenase |
925 |
923 |
database:900 |
Rv0860 fadB |
fatty oxidation protein FadB |
926 |
922 |
database:900 |
Rv0409 ackA |
acetate kinase |
926 |
922 |
database:900 |
Rv0761c adhB |
alcohol dehydrogenase B |
924 |
921 |
database:900 |
Rv0162c adhE1 |
zinc-type alcohol dehydrogenase subunit E |
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 |
919 |
914 |
database:900 |
Rv3045 adhC |
NADP-dependent alcohol dehydrogenase |
936 |
912 |
database:900 |
Rv0751c mmsB |
3-hydroxyisobutyrate dehydrogenase |
915 |
912 |
database:900 |
Rv3535c hsaG |
acetaldehyde dehydrogenase |
909 |
905 |
database:900 |
Rv3170 aofH |
flavin-containing monoamine oxidase |
909 |
904 |
database:900 |
Rv2205c hyp |
hypothetical protein |
906 |
903 |
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
- Legacy H37Rv annotation: aldehyde dehydrogenase
- MTBC0 PGAP product: aldehyde dehydrogenase
- Pfam (hmmscan --cut_ga): Aldedh PF00171.28 (E=5e-168)
- (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_214737.1)
- 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
I6X8S7
(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 —
76 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000237|Rv0223c|
MSDSATEYDKLFIGGKWTKPSTSDVIEVRCPATGEYVGKVPMAAAADVDAAVAAARAAFDNGPWPSTPPHERAAVIAAAVKMLAERKDLFTKLLAAETGQPPTIIETMHWMGSMGAMNYFAGAADKVTWTETRTGSYGQSIVSREPVGVVGAIVAWNVPLFLAVNKIAPALLAGCTIVLKPAAETPLTANALAEVFAEVGLPEGVLSVVPGGIETGQALTSNPDIDMFTFTGSSAVGREVGRRAAEMLKPCTLELGGKSAAIILEDVDLAAAIPMMVFSGVMNAGQGCVNQTRILAPRSRYDEIVAAVTNFVTALPVGPPSDPAAQIGPLISEKQRTRVEGYIAKGIEEGARLVCGGGRPEGLDNGFFIQPTVFADVDNKMTIAQEEIFGPVLAIIPYDTEEDAIAIANDSVYGLAGSVWTTDVPKGIKISQQIRTGTYGINWYAFDPGSPFGGYKNSGIGRENGPEGVEHFTQQKSVLLPMGYTVA
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