narX Family assigned · medium auto-curated
H37Rv Rv1736c · MTBC0 mtbc0_001849 ·
652 aa · 1974300–1976258 (-) ·
RefSeq NP_216252.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitrate reductase-like protein NarX |
|---|---|
| MTBC0 PGAP re-annotation | respiratory nitrate reductase subunit gamma |
| Revised (this work) | Respiratory nitrate reductase subunit gamma. Pfam: Molybdopterin (PF00384.28), Nitrate_red_del (PF02613.21), 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 |
P9WJQ1
SwissProt · reviewed
· 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 | COG2180 |
| EC number |
EC 1.7.5.1
|
| KEGG orthology |
K00370, K00374
|
| KEGG pathways |
map00910, map01120, map02020
|
| KEGG modules |
M00529, M00530, M00804
|
| Gene Ontology (7) |
GO:0001666, GO:0006950, GO:0008150, GO:0009628, GO:0036293, GO:0050896, GO:0070482
|
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 | 0.404 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 7 missense, 1 nonsense, 3 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 0.87% of strains (1270) · convergent |
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 |
|---|---|---|---|---|
Molybdopterin | PF00384.28 | 7.7e-15 | 118–245 | Molybdopterin oxidoreductase |
Nitrate_red_del | PF02613.21 | 3.5e-11 | 291–407 | Nitrate reductase delta subunit |
Nitrate_red_gam | PF02665.20 | 5.9e-88 | 419–639 | Nitrate reductase gamma subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: narK2 (nitrate/nitrite transporter), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1737c narK2 |
nitrate/nitrite transporter | 999 | 1000 ctx | neighborhood:882 cooccurence:762 coexpression:903 database:900 textmining:910 |
Rv1162 narH |
nitrate reductase subunit beta | 999 | 999 ctx | cooccurence:774 coexpression:730 experimental:829 database:900 textmining:653 |
Rv1164 narI |
nitrate reductase subunit gamma | 996 | 994 | coexpression:728 experimental:773 database:900 textmining:424 |
Rv0267 narU |
nitrite extrusion protein NarU | 994 | 984 ctx | cooccurence:721 coexpression:450 database:900 textmining:653 |
Rv2329c narK1 |
nitrate/nitrite transporter | 991 | 984 ctx | cooccurence:723 coexpression:445 database:900 textmining:473 |
Rv0261c narK3 |
nitrate/nitrite transporter | 987 | 983 ctx | cooccurence:706 coexpression:448 database:900 |
Rv0252 nirB |
nitrite reductase large subunit NirB | 973 | 947 | coexpression:473 database:900 textmining:519 |
Rv0253 nirD |
nitrite reductase small subunit NirD | 953 | 941 | coexpression:417 database:900 |
Rv1161 narG |
nitrate reductase subunit alpha | 917 | 910 | database:900 |
Rv2781c |
oxidoreductase | 901 | 901 | database:900 |
Rv0021c hyp |
hypothetical protein | 900 | 901 | database:900 |
Rv1163 narJ |
nitrate reductase subunit delta | 931 | 883 | coexpression:729 experimental:510 textmining:439 |
Rv1997 ctpF |
cation transporter ATPase F | 892 | 862 | coexpression:862 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 888 | 860 | coexpression:860 |
Rv2028c |
universal stress protein | 860 | 860 | coexpression:860 |
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-like protein NarX
- MTBC0 PGAP product: respiratory nitrate reductase subunit gamma
- Pfam (hmmscan --cut_ga): Molybdopterin PF00384.28 (E=8e-15), Nitrate_red_del PF02613.21 (E=4e-11), Nitrate_red_gam PF02665.20 (E=6e-88)
- (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_216252.1)
- Domains: Pfam-A via hmmscan --cut_ga — Molybdopterin (PF00384.28), Nitrate_red_del (PF02613.21), 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
COG2180 - Curated reference: UniProt P9WJQ1 (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 —
57 functional partner(s); context anchor
narK2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001849|Rv1736c|narX MTVTPRTGSRIEELLARSGRFFIPGEISADLRTVTRRGGRDGDVFYRDRWSHDKVVRSTHGVNCTGSCSWKIYVKDGIITWETQETDYPSVGPDRPEYEPRGCPRGAAFSWYTYSPTRVRHPYARGVLVEMYREAKARLGDPVAAWADIQADPRRRRRYQRARGKGGLVRVSWAEATEMIAAAHVHTISTYGPDRVAGFSPIPAMSMVSHAAGSRFVELIGGVMTSFYDWYADLPVASPQVFGDQTDVPESGDWWDVVWQCASVLLTYPNSRQLGTAEELLAHIDGPAADLLGRTVSELRRADPLTAATRYVDTFDLRGRATLYLTYWTAGDTRNRGREMLAFAQTYRSTDVAPPRGETPDFLPVVLEFAATVDPEAGRRLLSGYRVPIAALCNALTEAALPYAHTVAAVCRTGDMMGELFWTVVPYVTMTIVAVGSWWRYRYDKFGWTTRSSQLYESRLLRIASPMFHFGILVVIVGHGIGLVIPQSWTQAAGLSEGAYHVQAVVLGSIAGITTLAGVTLLIYRRRTRGPVFMATTVNDKVMYLVLVAAIVAGLGATALGSGVVGEAYNYRETVSVWFRSVWVLQPRGDLMAEAPLYYQIHVLIGLALFALWPFTRLVHAFSAPIGYLFRPYIIYRSREELVLTRPRRRGW