narK2 Resolved · high auto-curated
H37Rv Rv1737c · MTBC0 mtbc0_001850 ·
395 aa · 1976255–1977442 (-) ·
RefSeq NP_216253.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitrate/nitrite transporter |
|---|---|
| MTBC0 PGAP re-annotation | nitrate transporter NarK |
| Revised (this work) | Nitrate transporter NarK. Pfam: MFS_1 (PF07690.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJY7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable nitrate/nitrite transporter NarK2 |
| Curated function | Permits nitrate and nitrate transport into E.coli..; FUNCTION: Involved in excretion of nitrite produced by the dissimilatory reduction of nitrate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | narK2 |
| eggNOG description | Major facilitator superfamily |
| Orthologous group | COG2223 |
| KEGG orthology |
K02575
|
| KEGG pathways |
map00910
|
| KEGG modules |
M00615
|
| Gene Ontology (16) |
GO:0001666, GO:0006950, GO:0008150, GO:0009628, GO:0019222, GO:0031323, GO:0036293, GO:0050789, GO:0050794, GO:0050896, GO:0051171, GO:0062012 +4 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 | 1.033 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 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 |
|---|---|---|---|---|
MFS_1 | PF07690.22 | 2.5e-36 | 14–345 | Major Facilitator Superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: narX (nitrate reductase-like protein NarX), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1736c narX |
nitrate reductase-like protein NarX | 999 | 1000 ctx | neighborhood:882 cooccurence:762 coexpression:903 database:900 textmining:910 |
Rv1162 narH |
nitrate reductase subunit beta | 996 | 989 ctx | cooccurence:760 coexpression:463 database:900 textmining:703 |
Rv1164 narI |
nitrate reductase subunit gamma | 998 | 988 ctx | cooccurence:766 coexpression:431 database:900 textmining:854 |
Rv1161 narG |
nitrate reductase subunit alpha | 998 | 988 ctx | cooccurence:759 coexpression:449 database:900 textmining:853 |
Rv0261c narK3 |
nitrate/nitrite transporter | 940 | 940 ctx | fusion:855 cooccurence:575 |
Rv0252 nirB |
nitrite reductase large subunit NirB | 975 | 934 | database:900 textmining:645 |
Rv0253 nirD |
nitrite reductase small subunit NirD | 946 | 932 | database:900 |
Rv0267 narU |
nitrite extrusion protein NarU | 948 | 924 ctx | fusion:899 |
Rv2329c narK1 |
nitrate/nitrite transporter | 971 | 920 ctx | fusion:792 cooccurence:606 textmining:651 |
Rv2781c |
oxidoreductase | 909 | 908 | database:900 |
Rv0021c hyp |
hypothetical protein | 908 | 908 | database:900 |
Rv1163 narJ |
nitrate reductase subunit delta | 961 | 887 ctx | cooccurence:748 coexpression:466 textmining:675 |
Rv1738 hyp |
hypothetical protein | 925 | 872 ctx | neighborhood:449 coexpression:778 textmining:436 |
Rv2032 acg |
NAD(P)H nitroreductase | 918 | 862 | coexpression:860 textmining:433 |
Rv2627c hyp |
hypothetical protein | 860 | 861 | 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/nitrite transporter
- MTBC0 PGAP product: nitrate transporter NarK
- Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=3e-36)
- (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_216253.1)
- Domains: Pfam-A via hmmscan --cut_ga — MFS_1 (PF07690.22)
- 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
COG2223 - Curated reference: UniProt P9WJY7 (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 —
46 functional partner(s); context anchor
narX - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001850|Rv1737c|narK2 MRGQAANLVLATWISVVNFWAWNLIGPLSTSYARDMSLSSAEASLLVATPILVGALGRIVTGPLTDRFGGRAMLIAVTLASILPVLAVGVAATMGSYALLVFFGLFLGVAGTIFAVGIPFANNWYQPARRGFSTGVFGMGMVGTALSAFFTPRFVRWFGLFTTHAIVAAALASTAVVAMVVLRDAPYFRPNADPVLPRLKAAARLPVTWEMSFLYAIVFGGFVAFSNYLPTYITTIYGFSTVDAGARTAGFALAAVLARPVGGWLSDRIAPRHVVLASLAGTALLAFAAALQPPPEVWSAATFITLAVCLGVGTGGVFAWVARRAPAASVGSVTGIVAAAGGLGGYFPPLVMGATYDPVDNDYTVGLLLLVATALVACTYTALHAREPVSEEASR