nuoJ Family assigned · medium auto-curated
H37Rv Rv3154 · MTBC0 mtbc0_003352 ·
262 aa · 3543841–3544629 (+) ·
RefSeq NP_217670.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | NADH-quinone oxidoreductase subunit J |
|---|---|
| MTBC0 PGAP re-annotation | NADH-quinone oxidoreductase subunit J |
| Revised (this work) | NADH-quinone oxidoreductase subunit J. Pfam: Oxidored_q3 (PF00499.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95172
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | NADH-quinone oxidoreductase subunit J |
| 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. 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 | nuoJ |
| eggNOG description | Belongs to the complex I subunit 6 family |
| Orthologous group | COG0839 |
| EC number |
EC 1.6.5.3
|
| KEGG orthology |
K00339
|
| 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 | 0.094 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 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 |
|---|---|---|---|---|
Oxidored_q3 | PF00499.26 | 3.6e-35 | 31–176 | NADH-ubiquinone/plastoquinone oxidoreductase chain 6 |
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:764 cooccurence:737 coexpression:864 experimental:997 |
Rv3145 nuoA |
NADH-quinone oxidoreductase subunit A | 999 | 1000 ctx | neighborhood:762 cooccurence:766 coexpression:858 experimental:997 textmining:675 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 999 | 1000 ctx | neighborhood:874 cooccurence:720 coexpression:976 experimental:922 textmining:687 |
Rv3156 nuoL |
NADH-quinone oxidoreductase subunit L | 999 | 1000 ctx | neighborhood:874 cooccurence:748 coexpression:976 experimental:997 textmining:714 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 999 | 1000 ctx | neighborhood:882 cooccurence:765 coexpression:970 experimental:922 textmining:734 |
Rv3146 nuoB |
NADH-quinone oxidoreductase subunit B | 999 | 1000 ctx | neighborhood:764 cooccurence:682 coexpression:937 experimental:997 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 999 | 1000 ctx | neighborhood:881 cooccurence:751 coexpression:976 experimental:997 textmining:688 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 999 | 1000 ctx | neighborhood:764 cooccurence:745 coexpression:962 experimental:911 |
Rv3158 nuoN |
NADH-quinone oxidoreductase subunit N | 999 | 1000 ctx | neighborhood:874 cooccurence:756 coexpression:976 experimental:997 textmining:751 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 999 | 1000 ctx | neighborhood:764 cooccurence:771 coexpression:859 experimental:997 textmining:629 |
Rv3155 nuoK |
NADH-quinone oxidoreductase subunit K | 999 | 1000 ctx | neighborhood:882 cooccurence:769 coexpression:951 experimental:997 textmining:821 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 999 | 999 ctx | neighborhood:764 cooccurence:541 coexpression:953 experimental:911 |
Rv3143 |
response regulator | 999 | 999 ctx | cooccurence:695 experimental:997 |
Rv3149 nuoE |
NADH-quinone oxidoreductase subunit E | 999 | 999 ctx | neighborhood:764 cooccurence:615 coexpression:932 experimental:911 |
Rv0172 mce1D |
Mce family protein Mce1D | 799 | 799 | coexpression:799 |
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 J
- MTBC0 PGAP product: NADH-quinone oxidoreductase subunit J
- Pfam (hmmscan --cut_ga): Oxidored_q3 PF00499.26 (E=4e-35)
- (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_217670.1)
- Domains: Pfam-A via hmmscan --cut_ga — Oxidored_q3 (PF00499.26)
- 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
COG0839 - Curated reference: UniProt P95172 (TrEMBL, unreviewed; 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 —
49 functional partner(s); context anchor
nuoD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003352|Rv3154|nuoJ MTAVLASDVIVRTSTGEAVMFWVLSALALLGAVGVVLAVNAVYSAMFLAMTMIILAVFYMAQDALFLGVVQVVVYTGAVMMLFLFVLMLIGVDSAESLKETLRGQRVAAVLTGVGFGVLLISTIGQVATRGFAGLTVANANGNVEGLAALIFSRYLWAFELTSALLITAAVGAMVLAHRERFERRKTQRELSQERFRPGGHPTPLPNPGVYARHNAVDVAALLPDGSYSELSVPRMLRTRGADGLQTPSPGAVSGSLEGGAS