gabD1 Resolved · high auto-curated
H37Rv Rv0234c · MTBC0 - ·
511 aa · 279605–281140 (-) ·
RefSeq NP_216247.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | succinate-semialdehyde dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Succinate-semialdehyde 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 |
P9WNX9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Succinate-semialdehyde dehydrogenase [NADP(+)] 1 |
| EC (curated) |
EC 1.2.1.79
|
| Curated function | Catalyzes the NADP(+)-dependent oxidation of succinate semialdehyde to succinate. It is believed to be the main source of succinate semialdehyde dehydrogenase activity in Mycobacterium. NAD(+) can substitute for NADP(+), but enzymatic activity is three times reduced. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | gabD1 |
| eggNOG description | Catalyzes the NADP( )-dependent oxidation of succinate semialdehyde to succinate. It is believed to be the main source of succinate semialdehyde dehydrogenase activity in Mycobacterium |
| Orthologous group | COG1012 |
| EC number |
EC 1.2.1.16, EC 1.2.1.20, EC 1.2.1.79
|
| KEGG orthology |
K00135
|
| KEGG pathways |
map00250, map00310, map00350, map00650, map00760, map01100, map01120
|
| KEGG modules |
M00027
|
| Gene Ontology (32) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006082, GO:0006091, GO:0006099, GO:0006101, GO:0008150, GO:0008152, GO:0009013 +20 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 | 1.027 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 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 | 2.3e-143 | 57–508 | Aldehyde dehydrogenase family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2589 gabT |
4-aminobutyrate aminotransferase | 937 | 933 | database:900 |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 933 | 931 | database:900 |
Rv0248c |
succinate dehydrogenase flavoprotein subunit | 932 | 930 | database:900 |
Rv1731 gabD2 |
succinate-semialdehyde dehydrogenase | 925 | 925 | database:900 |
Rv0247c |
succinate dehydrogenase iron-sulfur subunit | 915 | 912 | database:900 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 915 | 912 | database:900 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 910 | 909 | database:900 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 909 | 906 | database:900 |
Rv1131 prpC |
methylcitrate synthase PrpC | 896 | 889 | database:800 |
Rv0896 gltA2 |
citrate synthase 1 | 894 | 889 | database:800 |
Rv0889c citA |
citrate synthase 2 | 894 | 889 | database:800 |
Rv2852c mqo |
malate:quinone oxidoreductase | 851 | 843 | database:800 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 869 | 830 | database:800 |
Rv1240 mdh |
malate dehydrogenase | 839 | 829 | database:800 |
Rv1098c fum |
fumarate hydratase | 837 | 828 | database:800 |
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): succinate-semialdehyde dehydrogenase
- Pfam (hmmscan --cut_ga): Aldedh PF00171.28 (E=2e-143)
- (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_216247.2)
- 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 P9WNX9 (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 — 73 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0234c|gabD1 MRSVTCSATLVLPVIEPTPADRRPRHLLLGSAGHVSGRLDTGRFVQTHPAKDVSVPIATINPATGETVKTFTAATDDEVDAAIARAHRRFADYRQTSFAQRARWANATADLLEAEADQAAAMMTLEMGKTLAAAKAEALKCAKGFRYYAENAEALLADEPADAAKVGASAAYGRYQPLGVILAVMPWNFPLWQAVRFAAPALMAGNVGLLKHASNVPQCALYLADVIARGGFPDGCFQTLLVSSGAVEAILRDPRVAAATLTGSEPAGQSVGAIAGNEIKPTVLELGGSDPFIVMPSADLDAAVSTAVTGRVQNNGQSCIAAKRFIVHADIYDDFVDKFVARMAALRVGDPTDPDTDVGPLATEQGRNEVAKQVEDAAAAGAVIRCGGKRLDRPGWFYPPTVITDISKDMALYTEEVFGPVASVFRAANIDEAVEIANATTFGLGSNAWTRDETEQRRFIDDIVAGQVFINGMTVSYPELPFGGVKRSGYGRELSAHGIREFCNIKTVWIA