frdD Family assigned · medium auto-curated
H37Rv Rv1555 · MTBC0 mtbc0_001662 ·
125 aa · 1770363–1770740 (+) ·
RefSeq NP_216071.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fumarate reductase membrane anchor subunit |
|---|---|
| MTBC0 PGAP re-annotation | fumarate reductase subunit FrdD |
| Revised (this work) | Fumarate reductase subunit FrdD. Pfam: Fumarate_red_D (PF02313.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNB5
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Fumarate reductase subunit D |
| Curated function | Anchors the catalytic components of the fumarate reductase complex to the cell membrane, binds quinones. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | frdD |
| eggNOG description | Seems to be involved in the anchoring of the catalytic components of the fumarate reductase complex to the cytoplasmic membrane |
| Orthologous group | COG3080 |
| KEGG orthology |
K00247
|
| KEGG pathways |
map00020, map00190, map00620, map00650, map00720, map01100, map01110, map01120, map01130, map01200, map02020
|
| KEGG modules |
M00009, M00011, M00150, 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 | 0.759 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Fumarate_red_D | PF02313.23 | 9.9e-34 | 11–123 | Fumarate reductase subunit D |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: frdB (fumarate reductase iron-sulfur subunit), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1553 frdB |
fumarate reductase iron-sulfur subunit | 999 | 1000 ctx | neighborhood:881 cooccurence:674 coexpression:878 experimental:549 database:900 textmining:822 |
Rv1554 frdC |
fumarate reductase membrane anchor subunit | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:939 experimental:895 database:900 textmining:850 |
Rv1552 frdA |
fumarate reductase flavoprotein subunit | 999 | 999 ctx | neighborhood:881 cooccurence:631 coexpression:542 experimental:455 database:900 textmining:887 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 980 | 973 | coexpression:419 experimental:549 database:900 |
Rv0247c |
succinate dehydrogenase iron-sulfur subunit | 981 | 972 | coexpression:417 experimental:549 database:900 |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 981 | 961 | experimental:455 database:900 textmining:540 |
Rv0248c |
succinate dehydrogenase flavoprotein subunit | 971 | 961 | experimental:455 database:900 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 966 | 901 | database:900 textmining:675 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 954 | 900 | database:900 textmining:563 |
Rv1098c fum |
fumarate hydratase | 900 | 900 | database:900 |
Rv0951 sucC |
succinyl-CoA ligase subunit beta | 830 | 803 | database:800 |
Rv1659 argH |
argininosuccinate lyase | 807 | 803 | database:800 |
Rv3221c TB7.3 |
acetyl-CoA carboxylase biotin carboxyl carrier protein subunit | 802 | 802 | database:800 |
Rv0337c aspC |
aspartate aminotransferase | 801 | 801 | database:800 |
Rv2501c accA1 |
acetyl/propionyl-CoA carboxylase subuit alpha | 800 | 801 | 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
- Legacy H37Rv annotation: fumarate reductase membrane anchor subunit
- MTBC0 PGAP product: fumarate reductase subunit FrdD
- Pfam (hmmscan --cut_ga): Fumarate_red_D PF02313.23 (E=1e-33)
- (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_216071.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fumarate_red_D (PF02313.23)
- 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
COG3080 - Curated reference: UniProt P9WNB5 (SwissProt, reviewed; Inferred from homology)
- 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 —
44 functional partner(s); context anchor
frdB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001662|Rv1555|frdD MTPSTSDARSRRRSAEPFLWLLFSAGGMVTALVAPVLLLLFGLAFPLGWLDAPDHGHLLAMVRNPITKLVVLVLVVLALFHAAHRFRFVLDHGLQLGRFDRVIALWCYGMAVLGSATAGWMLLTM