nuoF Family assigned · medium auto-curated
H37Rv Rv3150 · MTBC0 mtbc0_003348 ·
445 aa · 3538114–3539451 (+) ·
RefSeq NP_217666.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | NADH-quinone oxidoreductase subunit F |
|---|---|
| MTBC0 PGAP re-annotation | NADH-quinone oxidoreductase subunit NuoF |
| Revised (this work) | NADH-quinone oxidoreductase subunit NuoF. Pfam: Complex1_51K (PF01512.23), SLBB (PF10531.16), NADH_4Fe-4S (PF10589.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIV7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | NADH-quinone oxidoreductase subunit F |
| EC (curated) |
EC 7.1.1.-
|
| Curated function | NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | nuoF |
| eggNOG description | NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain |
| Orthologous group | COG1894 |
| EC number |
EC 1.6.5.3
|
| KEGG orthology |
K00335
|
| KEGG pathways |
map00190, map01100
|
| KEGG modules |
M00144
|
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 | 0.34 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 5 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 |
|---|---|---|---|---|
Complex1_51K | PF01512.23 | 2.2e-44 | 54–229 | Nuo51 FMN-binding domain |
SLBB | PF10531.16 | 2.0e-08 | 255–299 | SLBB domain |
NADH_4Fe-4S | PF10589.15 | 2.2e-33 | 340–423 | NADH-ubiquinone oxidoreductase-F iron-sulfur binding region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nuoD (NADH-quinone oxidoreductase subunit D), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 999 | 1000 ctx | neighborhood:881 coexpression:968 experimental:928 database:583 textmining:426 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 999 | 1000 ctx | neighborhood:760 coexpression:949 experimental:928 database:800 textmining:474 |
Rv3145 nuoA |
NADH-quinone oxidoreductase subunit A | 999 | 1000 ctx | neighborhood:879 coexpression:927 experimental:928 database:583 textmining:518 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 999 | 1000 ctx | neighborhood:881 cooccurence:759 coexpression:976 experimental:997 database:830 textmining:840 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 999 | 1000 ctx | neighborhood:881 coexpression:955 experimental:928 database:583 textmining:506 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 999 | 1000 ctx | neighborhood:700 cooccurence:620 coexpression:968 experimental:928 database:800 textmining:500 |
Rv3146 nuoB |
NADH-quinone oxidoreductase subunit B | 999 | 1000 ctx | neighborhood:881 coexpression:958 experimental:928 database:800 |
Rv3149 nuoE |
NADH-quinone oxidoreductase subunit E | 999 | 1000 ctx | neighborhood:881 fusion:675 cooccurence:774 coexpression:976 experimental:997 database:838 textmining:851 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 999 | 1000 ctx | neighborhood:725 coexpression:952 experimental:928 database:583 textmining:584 |
Rv3156 nuoL |
NADH-quinone oxidoreductase subunit L | 999 | 999 ctx | neighborhood:760 coexpression:953 experimental:911 textmining:589 |
Rv3154 nuoJ |
NADH-quinone oxidoreductase subunit J | 999 | 999 ctx | neighborhood:764 cooccurence:541 coexpression:953 experimental:911 |
Rv3158 nuoN |
NADH-quinone oxidoreductase subunit N | 999 | 999 ctx | neighborhood:760 coexpression:806 experimental:928 database:566 textmining:454 |
Rv3155 nuoK |
NADH-quinone oxidoreductase subunit K | 998 | 998 ctx | neighborhood:764 coexpression:876 experimental:911 |
Rv0310c hyp |
hypothetical protein | 991 | 990 | coexpression:722 experimental:928 database:561 |
Rv2782c pepR |
zinc protease | 977 | 974 | coexpression:701 experimental:917 |
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: NADH-quinone oxidoreductase subunit F
- MTBC0 PGAP product: NADH-quinone oxidoreductase subunit NuoF
- Pfam (hmmscan --cut_ga): Complex1_51K PF01512.23 (E=2e-44), SLBB PF10531.16 (E=2e-08), NADH_4Fe-4S PF10589.15 (E=2e-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_217666.1)
- Domains: Pfam-A via hmmscan --cut_ga — Complex1_51K (PF01512.23), SLBB (PF10531.16), NADH_4Fe-4S (PF10589.15)
- 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
COG1894 - Curated reference: UniProt P9WIV7 (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 —
192 functional partner(s); context anchor
nuoD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003348|Rv3150|nuoF MTTQATPLTPVISRHWDDPESWTLATYQRHDRYRGYQALQKALTMPPDDVISIVKDSGLRGRGGAGFATGTKWSFIPQGDTGAAAKPHYLVVNADESEPGTCKDIPLMLATPHVLIEGVIIAAYAIRAHHAFVYVRGEVVPVLRRLHNAVAEAYAAGFLGRNIGGSGFDLELVVHAGAGAYICGEETALLDSLEGRRGQPRLRPPFPAVAGLYGCPTVINNVETIASVPSIILGGIDWFRSMGSEKSPGFTLYSLSGHVTRPGQYEAPLGITLRELLDYAGGVRAGHRLKFWTPGGSSTPLLTDEHLDVPLDYEGVGAAGSMLGTKALEIFDETTCVVRAVRRWTEFYKHESCGKCTPCREGTFWLDKIYERLETGRGSHEDIDKLLDISDSILGKSFCALGDGAASPVMSSIKHFRDEYLAHVEGGGCPFDPRDSMLVANGVDA