sucD Family assigned · medium auto-curated
H37Rv Rv0952 · MTBC0 - ·
303 aa · 1063140–1064051 (+) ·
RefSeq NP_215467.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | succinyl-CoA ligase subunit alpha |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Succinyl-CoA ligase subunit alpha. Pfam: CoA_binding (PF02629.26), Succ_CoA_lig (PF13607.12), Ligase_CoA (PF00549.25). |
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 |
P9WGC7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Succinate--CoA ligase [ADP-forming] subunit alpha |
| EC (curated) |
EC 6.2.1.5
|
| Curated function | Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The alpha subunit of the enzyme binds the substrates coenzyme A and phosphate, while succinate binding and nucleotide specificity is provided by the beta subunit. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | sucD |
| eggNOG description | Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The alpha subunit of the enzyme binds the substrates coenzyme A and phosphate, while succinate binding and nucleotide specificity is provided by the beta subunit |
| Orthologous group | COG0074 |
| EC number |
EC 6.2.1.5
|
| KEGG orthology |
K01902
|
| KEGG pathways |
map00020, map00640, map00660, map00720, map01100, map01110, map01120, map01130, map01200
|
| KEGG modules |
M00009, M00011, M00173, M00374, M00620
|
| Gene Ontology (15) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, GO:0044424 +3 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 | 0.341 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
CoA_binding | PF02629.26 | 1.4e-24 | 10–111 | CoA binding domain |
Succ_CoA_lig | PF13607.12 | 6.3e-11 | 159–288 | Succinyl-CoA ligase like flavodoxin domain |
Ligase_CoA | PF00549.25 | 3.6e-19 | 165–283 | CoA-ligase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sucC (succinyl-CoA ligase subunit beta), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0951 sucC |
succinyl-CoA ligase subunit beta | 999 | 1000 ctx | neighborhood:869 fusion:899 cooccurence:774 coexpression:968 experimental:928 database:984 textmining:854 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 998 | 996 | coexpression:982 database:540 textmining:479 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 985 | 979 | coexpression:651 database:900 |
Rv0247c |
succinate dehydrogenase iron-sulfur subunit | 979 | 976 | coexpression:668 database:900 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 980 | 974 | coexpression:726 database:900 |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 981 | 973 | coexpression:570 database:900 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 980 | 970 | coexpression:662 database:900 |
Rv0248c |
succinate dehydrogenase flavoprotein subunit | 979 | 969 | coexpression:588 database:900 |
Rv1553 frdB |
fumarate reductase iron-sulfur subunit | 971 | 967 ctx | cooccurence:467 coexpression:649 database:800 |
Rv1552 frdA |
fumarate reductase flavoprotein subunit | 961 | 949 | coexpression:565 database:800 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 979 | 948 | database:900 textmining:628 |
Rv2495c bkdC |
branched-chain keto acid dehydrogenase E2 component | 950 | 937 | coexpression:648 database:800 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 954 | 936 | database:900 |
Rv1493 mutB |
methylmalonyl-CoA mutase large subunit | 944 | 919 | database:900 |
Rv2454c korB |
2-oxoglutarate oxidoreductase subunit KorB | 945 | 916 | 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): succinyl-CoA ligase subunit alpha
- Pfam (hmmscan --cut_ga): CoA_binding PF02629.26 (E=1e-24), Succ_CoA_lig PF13607.12 (E=6e-11), Ligase_CoA PF00549.25 (E=4e-19)
- (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_215467.1)
- Domains: Pfam-A via hmmscan --cut_ga — CoA_binding (PF02629.26), Succ_CoA_lig (PF13607.12), Ligase_CoA (PF00549.25)
- 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
COG0074 - Curated reference: UniProt P9WGC7 (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 —
154 functional partner(s); context anchor
sucC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0952|sucD MTHMSIFLSRDNKVIVQGITGSEATVHTARMLRAGTQIVGGVNARKAGTTVTHEDKGGRLIKLPVFGSVAEAMEKTGADVSIIFVPPTFAKDAIIEAIDAEIPLLVVITEGIPVQDTAYAWAYNLEAGHKTRIIGPNCPGIISPGQSLAGITPANITGPGPIGLVSKSGTLTYQMMFELRDLGFSTAIGIGGDPVIGTTHIDAIEAFERDPDTKLIVMIGEIGGDAEERAADFIKTNVSKPVVGYVAGFTAPEGKTMGHAGAIVSGSSGTAAAKQEALEAAGVKVGKTPSATAALAREILLSL