sdhC Family assigned · medium auto-curated
H37Rv Rv3316 · MTBC0 mtbc0_003526 ·
112 aa · 3726240–3726578 (+) ·
RefSeq NP_217833.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | succinate dehydrogenase cytochrome B-556 subunit |
|---|---|
| MTBC0 PGAP re-annotation | succinate dehydrogenase%2C cytochrome b556 subunit |
| Revised (this work) | Succinate dehydrogenase%2C cytochrome b556 subunit. Pfam: Sdh_cyt (PF01127.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53368
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Succinate dehydrogenase 2 membrane subunit SdhC |
| Curated function | Membrane-anchoring subunit of succinate dehydrogenase 2 (Sdh2). Sdh2 may catalyze the two-electron oxidation of succinate to fumarate with a corresponding reduction of quinone to quinol under low oxygen conditions, when the primary aerobic succinate dehydrogenase (Sdh1) is inhibited. Sdh2 seems to be the generator of the proton motive force (PMF) under hypoxia. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | sdhC |
| eggNOG description | succinate dehydrogenase |
| Orthologous group | COG2009 |
| KEGG orthology |
K00241
|
| KEGG pathways |
map00020, map00190, map00650, map00720, map01100, map01110, map01120, map01130, map01200
|
| KEGG modules |
M00009, M00011, M00149, M00173, M00374, M00376
|
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 | 0.314 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
Sdh_cyt | PF01127.28 | 1.5e-17 | 1–96 | Succinate dehydrogenase/Fumarate reductase transmembrane subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sdhA (succinate dehydrogenase flavoprotein subunit), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 999 | 1000 ctx | neighborhood:758 cooccurence:736 coexpression:664 experimental:870 database:960 textmining:967 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 999 | 1000 ctx | neighborhood:758 cooccurence:766 coexpression:698 experimental:997 database:962 textmining:909 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:865 experimental:997 database:900 textmining:937 |
Rv1553 frdB |
fumarate reductase iron-sulfur subunit | 999 | 998 | coexpression:694 experimental:788 database:962 textmining:653 |
Rv0247c |
succinate dehydrogenase iron-sulfur subunit | 999 | 998 | coexpression:696 experimental:788 database:962 textmining:861 |
Rv1552 frdA |
fumarate reductase flavoprotein subunit | 998 | 997 | coexpression:650 experimental:707 database:960 textmining:614 |
Rv0248c |
succinate dehydrogenase flavoprotein subunit | 999 | 996 | coexpression:652 experimental:707 database:960 textmining:812 |
Rv0951 sucC |
succinyl-CoA ligase subunit beta | 986 | 982 | coexpression:811 database:900 |
Rv0952 sucD |
succinyl-CoA ligase subunit alpha | 980 | 974 | coexpression:726 database:900 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 983 | 961 | coexpression:953 textmining:588 |
Rv3537 kstD |
3-oxosteroid 1-dehydrogenase | 962 | 959 | coexpression:650 experimental:707 database:621 |
Rv1817 |
flavoprotein | 962 | 959 | coexpression:650 experimental:707 database:621 |
Rv1098c fum |
fumarate hydratase | 959 | 947 | coexpression:490 database:900 |
Rv1731 gabD2 |
succinate-semialdehyde dehydrogenase | 911 | 910 | database:900 |
Rv0234c gabD1 |
succinate-semialdehyde dehydrogenase | 910 | 909 | 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: succinate dehydrogenase cytochrome B-556 subunit
- MTBC0 PGAP product: succinate dehydrogenase%2C cytochrome b556 subunit
- Pfam (hmmscan --cut_ga): Sdh_cyt PF01127.28 (E=2e-17)
- (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_217833.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sdh_cyt (PF01127.28)
- 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
COG2009 - Curated reference: UniProt O53368 (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 —
109 functional partner(s); context anchor
sdhA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003526|Rv3316|sdhC MWSWVCHRISGATIFFFLFVHVLDAAMLRVSPQTYNAVLATYKTPIVGLMEYGLVAAVLFHALNGIRVILIDFWSEGPRYQRLMLWIIGSVFLLLMVPAGVVVGIHMWEHFR