nuoD Family assigned · medium auto-curated
H37Rv Rv3148 · MTBC0 mtbc0_003346 ·
440 aa · 3536040–3537362 (+) ·
RefSeq NP_217664.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | NADH-quinone oxidoreductase subunit D |
|---|---|
| MTBC0 PGAP re-annotation | NADH dehydrogenase (quinone) subunit D |
| Revised (this work) | NADH dehydrogenase (quinone) subunit D. Pfam: Complex1_49kDa (PF00346.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJH5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | NADH-quinone oxidoreductase subunit D |
| 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 a 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. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | nuoD |
| eggNOG description | 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 a 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 |
| Orthologous group | COG0649 |
| EC number |
EC 1.6.5.3
|
| KEGG orthology |
K00333
|
| KEGG pathways |
map00190, map01100
|
| KEGG modules |
M00144
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.4 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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_49kDa | PF00346.25 | 1.4e-111 | 155–440 | Respiratory-chain NADH dehydrogenase, 49 Kd subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nuoF (NADH-quinone oxidoreductase subunit F), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 999 | 1000 ctx | neighborhood:881 coexpression:968 experimental:928 database:583 textmining:426 |
Rv3145 nuoA |
NADH-quinone oxidoreductase subunit A | 999 | 1000 ctx | neighborhood:879 cooccurence:769 coexpression:967 experimental:997 database:731 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 999 | 1000 ctx | neighborhood:760 cooccurence:760 coexpression:882 experimental:928 database:731 textmining:686 |
Rv3156 nuoL |
NADH-quinone oxidoreductase subunit L | 999 | 1000 ctx | neighborhood:760 cooccurence:766 coexpression:939 experimental:928 textmining:462 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 999 | 1000 ctx | neighborhood:724 cooccurence:772 coexpression:983 experimental:997 database:731 textmining:599 |
Rv3146 nuoB |
NADH-quinone oxidoreductase subunit B | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:774 coexpression:979 experimental:997 database:844 textmining:509 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 999 | 1000 ctx | neighborhood:697 cooccurence:773 coexpression:984 experimental:997 database:844 textmining:437 |
Rv3149 nuoE |
NADH-quinone oxidoreductase subunit E | 999 | 1000 ctx | neighborhood:882 fusion:620 coexpression:969 experimental:928 database:583 textmining:518 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 999 | 1000 ctx | neighborhood:882 cooccurence:773 coexpression:967 experimental:997 database:844 |
Rv3158 nuoN |
NADH-quinone oxidoreductase subunit N | 999 | 1000 ctx | neighborhood:760 cooccurence:767 coexpression:948 experimental:928 database:666 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 999 | 1000 ctx | neighborhood:881 cooccurence:574 coexpression:968 experimental:997 database:781 |
Rv3154 nuoJ |
NADH-quinone oxidoreductase subunit J | 999 | 1000 ctx | neighborhood:764 cooccurence:737 coexpression:864 experimental:997 |
Rv3155 nuoK |
NADH-quinone oxidoreductase subunit K | 999 | 1000 ctx | neighborhood:764 cooccurence:763 coexpression:960 experimental:928 |
Rv0310c hyp |
hypothetical protein | 996 | 996 | coexpression:654 experimental:928 database:844 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 985 | 981 | coexpression:808 experimental:904 |
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 D
- MTBC0 PGAP product: NADH dehydrogenase (quinone) subunit D
- Pfam (hmmscan --cut_ga): Complex1_49kDa PF00346.25 (E=1e-111)
- (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_217664.1)
- Domains: Pfam-A via hmmscan --cut_ga — Complex1_49kDa (PF00346.25)
- 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
COG0649 - Curated reference: UniProt P9WJH5 (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 —
185 functional partner(s); context anchor
nuoF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003346|Rv3148|nuoD MTAIADSAGGAGETVLVAGGQDWQQVVDAARSADPGERIVVNMGPQHPSTHGVLRLILEIEGETVVEARCGIGYLHTGIEKNLEYRYWTQGVTFVTRMDYLSPFFNETAYCLGVEKLLGITDEIPERVNVIRVLMMELNRISSHLVALATGGMELGAMTPMFVGFRAREIVLTLFEKITGLRMNSAYIRPGGVAQDLPPNAATEIAEALKQLRQPLREMGELLNENAIWKARTQGVGYLDLTGCMALGITGPILRSTGLPHDLRKSEPYCGYQHYEFDVITDDSCDAYGRYMIRVKEMWESMKIVEQCLDKLRPGPTMISDRKLAWPADLQVGPDGLGNSPKHIAKIMGSSMEALIHHFKLVTEGIRVPAGQVYVAVESPRGELGVHMVSDGGTRPYRVHYRDPSFTNLQSVAAMCEGGMVADLIAAVASIDPVMGGVDR