frdB Family assigned · medium auto-curated
H37Rv Rv1553 · MTBC0 mtbc0_001660 ·
247 aa · 1769246–1769989 (+) ·
RefSeq NP_216069.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | fumarate reductase iron-sulfur subunit |
|---|---|
| MTBC0 PGAP re-annotation | succinate dehydrogenase iron-sulfur subunit |
| Revised (this work) | Succinate dehydrogenase iron-sulfur subunit. Pfam: Fer2_3 (PF13085.12), Fer4_8 (PF13183.12), Fer4_10 (PF13237.12), Fer4 (PF00037.33), Fer4_7 (PF12838.13), Fer4_17 (PF13534.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN89
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Fumarate reductase iron-sulfur subunit |
| EC (curated) |
EC 1.3.5.1
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | sdhB |
| eggNOG description | 2Fe-2S iron-sulfur cluster binding domain |
| Orthologous group | COG0479 |
| EC number |
EC 1.3.5.1, EC 1.3.5.4
|
| KEGG orthology |
K00240, K00245
|
| KEGG pathways |
map00020, map00190, map00620, map00650, map00720, map01100, map01110, map01120, map01130, map01200, map02020
|
| KEGG modules |
M00009, M00011, M00149, M00150, 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 | 0.105 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 missense, 0 nonsense, 4 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 2.73% of strains (3970) · convergent |
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 |
|---|---|---|---|---|
Fer2_3 | PF13085.12 | 1.5e-32 | 7–110 | 2Fe-2S iron-sulfur cluster binding domain |
Fer4_8 | PF13183.12 | 4.4e-13 | 146–219 | 4Fe-4S dicluster domain |
Fer4_10 | PF13237.12 | 1.1e-08 | 146–216 | 4Fe-4S dicluster domain |
Fer4 | PF00037.33 | 1.6e-05 | 147–164 | 4Fe-4S binding domain |
Fer4_7 | PF12838.13 | 2.9e-08 | 149–219 | 4Fe-4S dicluster domain |
Fer4_17 | PF13534.12 | 3.5e-08 | 149–220 | 4Fe-4S dicluster domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: frdA (fumarate reductase flavoprotein subunit), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1552 frdA |
fumarate reductase flavoprotein subunit | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:925 experimental:454 database:956 textmining:816 |
Rv1555 frdD |
fumarate reductase membrane anchor 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:662 coexpression:912 experimental:549 database:900 textmining:824 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 999 | 998 | coexpression:694 experimental:788 database:962 textmining:653 |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 998 | 997 ctx | cooccurence:771 coexpression:486 experimental:454 database:956 textmining:626 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 997 | 994 | coexpression:666 experimental:784 database:900 textmining:661 |
Rv0248c |
succinate dehydrogenase flavoprotein subunit | 996 | 994 ctx | cooccurence:585 coexpression:484 experimental:454 database:956 textmining:426 |
Rv0951 sucC |
succinyl-CoA ligase subunit beta | 974 | 967 ctx | cooccurence:496 coexpression:645 database:800 |
Rv0952 sucD |
succinyl-CoA ligase subunit alpha | 971 | 967 ctx | cooccurence:467 coexpression:649 database:800 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 969 | 949 | coexpression:930 textmining:420 |
Rv1098c fum |
fumarate hydratase | 953 | 949 | coexpression:419 database:900 |
Rv0247c |
succinate dehydrogenase iron-sulfur subunit | 924 | 915 | database:900 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 915 | 912 | database:900 |
Rv1817 |
flavoprotein | 881 | 875 | coexpression:487 experimental:454 database:578 |
Rv3537 kstD |
3-oxosteroid 1-dehydrogenase | 881 | 875 | coexpression:487 experimental:454 database:578 |
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 iron-sulfur subunit
- MTBC0 PGAP product: succinate dehydrogenase iron-sulfur subunit
- Pfam (hmmscan --cut_ga): Fer2_3 PF13085.12 (E=2e-32), Fer4_8 PF13183.12 (E=4e-13), Fer4_10 PF13237.12 (E=1e-08), Fer4 PF00037.33 (E=2e-05), Fer4_7 PF12838.13 (E=3e-08), Fer4_17 PF13534.12 (E=4e-08)
- (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_216069.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fer2_3 (PF13085.12), Fer4_8 (PF13183.12), Fer4_10 (PF13237.12), Fer4 (PF00037.33), Fer4_7 (PF12838.13), Fer4_17 (PF13534.12)
- 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
COG0479 - Curated reference: UniProt P9WN89 (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 —
118 functional partner(s); context anchor
frdA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001660|Rv1553|frdB MMDRIVMEVSRYRPEIESAPTFQAYEVPLTREWAVLDGLTYIKDHLDGTLSFRWSCRMGICGSSGMTINGDPKLACATFLADYLPGPVRVEPMRNFPVIRDLVVDISDFMAKLPSVKPWLVRHDEPPVEDGEYRQTPAELDAFKQFSMCINCMLCYSACPVYALDPDFLGPAAIALGQRYNLDSRDQGAADRRDVLAAADGAWACTLVGECSTACPKGVDPAGAIQRYKLTAATHALKKLLFPWGGG