nuoE Family assigned · medium auto-curated
H37Rv Rv3149 · MTBC0 mtbc0_003347 ·
252 aa · 3537359–3538117 (+) ·
RefSeq NP_217665.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | NADH-quinone oxidoreductase subunit E |
|---|---|
| MTBC0 PGAP re-annotation | NADH-quinone oxidoreductase subunit NuoE |
| Revised (this work) | NADH-quinone oxidoreductase subunit NuoE. Pfam: 2Fe-2S_thioredx (PF01257.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIV5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | NADH-quinone oxidoreductase subunit E |
| 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 | nuoE |
| eggNOG description | NADH dehydrogenase |
| Orthologous group | COG1905 |
| EC number |
EC 1.6.5.3
|
| KEGG orthology |
K00334
|
| KEGG pathways |
map00190, map01100
|
| KEGG modules |
M00144
|
| Gene Ontology (37) |
GO:0003674, GO:0003824, GO:0003954, GO:0005575, GO:0005623, GO:0005886, GO:0006091, GO:0008137, GO:0008150, GO:0008152, GO:0009987, GO:0015980 +25 more
|
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 | 0.262 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
2Fe-2S_thioredx | PF01257.26 | 3.4e-47 | 45–187 | Thioredoxin-like [2Fe-2S] ferredoxin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nuoB (NADH-quinone oxidoreductase subunit B), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3146 nuoB |
NADH-quinone oxidoreductase subunit B | 999 | 1000 ctx | neighborhood:882 coexpression:968 experimental:928 database:800 textmining:564 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 999 | 1000 ctx | neighborhood:704 cooccurence:653 coexpression:968 experimental:928 database:800 textmining:603 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 999 | 1000 ctx | neighborhood:727 coexpression:963 experimental:928 database:620 textmining:590 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 999 | 1000 ctx | neighborhood:881 cooccurence:770 coexpression:976 experimental:997 database:838 textmining:774 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 999 | 1000 ctx | neighborhood:882 cooccurence:523 coexpression:968 experimental:928 database:583 textmining:811 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 999 | 1000 ctx | neighborhood:881 fusion:675 cooccurence:774 coexpression:976 experimental:997 database:838 textmining:851 |
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 999 | 1000 ctx | neighborhood:882 fusion:620 coexpression:969 experimental:928 database:583 textmining:518 |
Rv3145 nuoA |
NADH-quinone oxidoreductase subunit A | 999 | 1000 ctx | neighborhood:879 coexpression:937 experimental:928 database:620 textmining:644 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 999 | 1000 ctx | neighborhood:760 coexpression:952 experimental:928 database:818 textmining:658 |
Rv3154 nuoJ |
NADH-quinone oxidoreductase subunit J | 999 | 999 ctx | neighborhood:764 cooccurence:615 coexpression:932 experimental:911 |
Rv3156 nuoL |
NADH-quinone oxidoreductase subunit L | 999 | 999 ctx | neighborhood:760 coexpression:935 experimental:911 textmining:511 |
Rv3158 nuoN |
NADH-quinone oxidoreductase subunit N | 998 | 998 ctx | neighborhood:760 coexpression:663 experimental:928 database:606 |
Rv3155 nuoK |
NADH-quinone oxidoreductase subunit K | 999 | 996 ctx | neighborhood:764 coexpression:812 experimental:911 textmining:746 |
Rv0310c hyp |
hypothetical protein | 989 | 988 | coexpression:648 experimental:928 database:561 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 987 | 984 | coexpression:803 experimental:922 |
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 E
- MTBC0 PGAP product: NADH-quinone oxidoreductase subunit NuoE
- Pfam (hmmscan --cut_ga): 2Fe-2S_thioredx PF01257.26 (E=3e-47)
- (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_217665.1)
- Domains: Pfam-A via hmmscan --cut_ga — 2Fe-2S_thioredx (PF01257.26)
- 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
COG1905 - Curated reference: UniProt P9WIV5 (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 —
177 functional partner(s); context anchor
nuoB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003347|Rv3149|nuoE MTQPPGQPVFIRLGPPPDEPNQFVVEGAPRSYPPDVLARLEVDAKEIIGRYPDRRSALLPLLHLVQGEDSYLTPAGLRFCADQLGLTGAEVSAVASFYTMYRRRPTGEYLVGVCTNTLCAVMGGDAIFDRLKEHLGVGHDETTSDGVVTLQHIECNAACDYAPVVMVNWEFFDNQTPESARELVDSLRSDTPKAPTRGAPLCGFRQTSRILAGLPDQRPDEGQGGPGAPTLAGLQVARKNDMQAPPTPGADE