narI Family assigned · medium auto-curated
H37Rv Rv1164 · MTBC0 mtbc0_001253 ·
246 aa · 1301847–1302587 (+) ·
RefSeq NP_215680.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitrate reductase subunit gamma |
|---|---|
| MTBC0 PGAP re-annotation | respiratory nitrate reductase subunit gamma |
| Revised (this work) | Respiratory nitrate reductase subunit gamma. Pfam: Nitrate_red_gam (PF02665.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06562
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nitrate reductase-like protein NarX |
| Curated function | Does not seem to have nitrate reductase activity. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | narI |
| eggNOG description | nitrate reductase, gamma subunit |
| Orthologous group | COG2181 |
| EC number |
EC 1.7.5.1
|
| KEGG orthology |
K00370, K00374
|
| KEGG pathways |
map00910, map01120, map02020
|
| KEGG modules |
M00529, M00530, M00804
|
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 | 0.337 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Nitrate_red_gam | PF02665.20 | 2.2e-86 | 9–228 | Nitrate reductase gamma subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: narH (nitrate reductase subunit beta), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1162 narH |
nitrate reductase subunit beta | 999 | 1000 ctx | neighborhood:804 cooccurence:774 coexpression:957 experimental:652 database:900 textmining:938 |
Rv1161 narG |
nitrate reductase subunit alpha | 999 | 1000 ctx | neighborhood:763 cooccurence:774 coexpression:797 experimental:773 database:900 textmining:939 |
Rv1163 narJ |
nitrate reductase subunit delta | 999 | 999 ctx | neighborhood:881 cooccurence:774 coexpression:957 textmining:965 |
Rv1736c narX |
nitrate reductase-like protein NarX | 996 | 994 | coexpression:728 experimental:773 database:900 textmining:424 |
Rv1737c narK2 |
nitrate/nitrite transporter | 998 | 988 ctx | cooccurence:766 coexpression:431 database:900 textmining:854 |
Rv0267 narU |
nitrite extrusion protein NarU | 993 | 978 ctx | cooccurence:613 coexpression:434 database:900 textmining:710 |
Rv2329c narK1 |
nitrate/nitrite transporter | 991 | 978 ctx | cooccurence:618 coexpression:435 database:900 textmining:607 |
Rv0261c narK3 |
nitrate/nitrite transporter | 983 | 977 ctx | cooccurence:588 coexpression:433 database:900 |
Rv0253 nirD |
nitrite reductase small subunit NirD | 965 | 941 | coexpression:418 database:900 textmining:430 |
Rv0252 nirB |
nitrite reductase large subunit NirB | 954 | 924 | database:900 textmining:424 |
Rv2781c |
oxidoreductase | 903 | 904 | database:900 |
Rv0021c hyp |
hypothetical protein | 902 | 903 | database:900 |
Rv1165 typA |
GTP-binding translation elongation factor | 829 | 792 ctx | neighborhood:761 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 767 | 767 ctx | neighborhood:755 |
Rv2847c cysG |
multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase | 628 | 629 | coexpression:512 |
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: nitrate reductase subunit gamma
- MTBC0 PGAP product: respiratory nitrate reductase subunit gamma
- Pfam (hmmscan --cut_ga): Nitrate_red_gam PF02665.20 (E=2e-86)
- (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_215680.1)
- Domains: Pfam-A via hmmscan --cut_ga — Nitrate_red_gam (PF02665.20)
- 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
COG2181 - Curated reference: UniProt O06562 (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 —
30 functional partner(s); context anchor
narH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001253|Rv1164|narI MAVLDLVEIFWDAAPYVVVAIAVVGTWWRYRYDKFGWTTRSSQLYESRLLSIGSPMFHFGSLLVIMGHVMGLFIPDSWTRAFGMSDHLYHLQALLLGAPAGFATLLGIGLLIYRRRIQTPVWLATTRNDKLMYLVLVCAIVAGLACTLMGATHEGDMHDYRRSVSVWFRSIWMLAPRGDLMAQATLYYQVHVLIALALFALWPFTRLVHAFSAPIAYLFRPYIVYRSREVAAKHELIGSAPRRRGW