sdhD Family assigned · medium auto-curated
H37Rv Rv3317 · MTBC0 mtbc0_003527 ·
144 aa · 3726575–3727009 (+) ·
RefSeq NP_217834.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | succinate dehydrogenase hydrophobic membrane anchor subunit |
|---|---|
| MTBC0 PGAP re-annotation | succinate dehydrogenase hydrophobic membrane anchor subunit |
| Revised (this work) | Succinate dehydrogenase hydrophobic membrane anchor 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 |
O53369
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable succinate dehydrogenase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | sdhD |
| eggNOG description | succinate dehydrogenase |
| Orthologous group | COG2142 |
| KEGG orthology |
K00242
|
| KEGG pathways |
map00020, map00190, map00650, map00720, map01100, map01110, map01120, map01130, map01200
|
| KEGG modules |
M00009, M00011, M00149, M00173
|
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 | 0.62 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 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 | 1.7e-16 | 17–129 | Succinate dehydrogenase/Fumarate reductase transmembrane subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sdhB (succinate dehydrogenase iron-sulphur protein subunit), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 999 | 1000 ctx | neighborhood:758 cooccurence:760 coexpression:673 experimental:997 database:900 textmining:837 |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 999 | 1000 ctx | neighborhood:758 cooccurence:718 coexpression:690 experimental:997 database:900 textmining:880 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:865 experimental:997 database:900 textmining:937 |
Rv1553 frdB |
fumarate reductase iron-sulfur subunit | 997 | 994 | coexpression:666 experimental:784 database:900 textmining:661 |
Rv1552 frdA |
fumarate reductase flavoprotein subunit | 997 | 994 | coexpression:646 experimental:784 database:900 textmining:597 |
Rv0247c |
succinate dehydrogenase iron-sulfur subunit | 998 | 993 | coexpression:670 experimental:784 database:900 textmining:822 |
Rv0248c |
succinate dehydrogenase flavoprotein subunit | 998 | 992 | coexpression:650 experimental:784 database:900 textmining:794 |
Rv0951 sucC |
succinyl-CoA ligase subunit beta | 981 | 976 | coexpression:756 database:900 |
Rv0952 sucD |
succinyl-CoA ligase subunit alpha | 954 | 936 | database:900 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 960 | 923 | coexpression:906 textmining:510 |
Rv1098c fum |
fumarate hydratase | 922 | 911 | database:900 |
Rv1731 gabD2 |
succinate-semialdehyde dehydrogenase | 912 | 907 | database:900 |
Rv0234c gabD1 |
succinate-semialdehyde dehydrogenase | 909 | 906 | database:900 |
Rv1554 frdC |
fumarate reductase membrane anchor subunit | 966 | 901 | database:900 textmining:680 |
Rv1555 frdD |
fumarate reductase membrane anchor subunit | 966 | 901 | database:900 textmining:675 |
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 hydrophobic membrane anchor subunit
- MTBC0 PGAP product: succinate dehydrogenase hydrophobic membrane anchor subunit
- Pfam (hmmscan --cut_ga): Sdh_cyt PF01127.28 (E=2e-16)
- (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_217834.1)
- 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
COG2142 - Curated reference: UniProt O53369 (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 —
57 functional partner(s); context anchor
sdhB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003527|Rv3317|sdhD MSAPVRQRSHDRPASLDNPRSPRRRAGMPNFEKFAWLFMRFSGVVLVFLAIGHLFIMLMWDNGVYRLDFNFVAQRWASPFWQTWDLLLLWLAQLHGGNGLRTIIDDYSRKDTTRFWLNSLLVLSMLFTLMLGTYVIVTFDPNIS