Rv0249c Family assigned · low auto-curated
H37Rv Rv0249c · MTBC0 mtbc0_000265 ·
273 aa · 301216–302037 (-) ·
RefSeq NP_214763.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | succinate dehydrogenase membrane anchor subunit |
|---|---|
| MTBC0 PGAP re-annotation | succinate dehydrogenase membrane anchor subunit |
| Revised (this work) | Succinate dehydrogenase membrane anchor subunit. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53671
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable succinate dehydrogenase [membrane anchor subunit] |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | 2CEY7 |
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 | 0.193 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 3 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0247c (succinate dehydrogenase iron-sulfur subunit), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0247c |
succinate dehydrogenase iron-sulfur subunit | 999 | 1000 ctx | neighborhood:839 cooccurence:774 experimental:997 textmining:870 |
Rv0248c |
succinate dehydrogenase flavoprotein subunit | 998 | 995 ctx | neighborhood:839 cooccurence:771 experimental:870 textmining:655 |
Rv0250c hyp |
hypothetical protein | 940 | 879 ctx | neighborhood:787 cooccurence:451 textmining:527 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 905 | 801 | experimental:784 textmining:543 |
Rv1553 frdB |
fumarate reductase iron-sulfur subunit | 898 | 800 | experimental:784 textmining:511 |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 657 | 512 | experimental:469 |
Rv1552 frdA |
fumarate reductase flavoprotein subunit | 634 | 509 | experimental:469 |
Rv3687c rsfB |
anti-anti-sigma factor RsfB | 478 | 478 ctx | cooccurence:476 |
Rv3537 kstD |
3-oxosteroid 1-dehydrogenase | 409 | 410 | |
Rv1817 |
flavoprotein | 409 | 410 | |
Rv3818 hyp |
hypothetical protein | 401 | 402 | |
Rv0251c hsp |
heat shock protein | 531 | 399 | |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 805 | 53 | textmining:803 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 802 | 49 | textmining:801 |
Rv0392c ndhA |
NADH dehydrogenase NdhA | 511 | 41 | textmining:511 |
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 membrane anchor subunit
- MTBC0 PGAP product: succinate dehydrogenase membrane anchor subunit
- (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_214763.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2CEY7 - Curated reference: UniProt O53671 (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 —
15 functional partner(s); context anchor
Rv0247c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000265|Rv0249c| MSAPTANRPAIGVFTPTRAQIPERTLRTDLWWLPPLLTNLGLLAFICYATTRAFWGSQYWVEKYHYLTPFYSPCVSASCQPGASHLGVWFGHFPGWIPLGAMVLPFLLGFRLTCYYYRKAYYRSVWQSPTSCAVPEPRAHYTGETRLPLIVQNTHRYFFYIAVVVSLINTYDAIAAFHSPSGFGFGLGNVILTINVVLLWAYTISCHSCRHATGGRLKHFSKHPVRYWIWTQVSKLNTRHMQFAWITLGTLALTDFYIMLVASGSITDLRFIG