narK1 Resolved · high auto-curated
H37Rv Rv2329c · MTBC0 mtbc0_002478 ·
515 aa · 2626663–2628210 (-) ·
RefSeq NP_216845.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitrate/nitrite transporter |
|---|---|
| MTBC0 PGAP re-annotation | nitrate/nitrite transporter |
| Revised (this work) | Nitrate/nitrite transporter. 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 |
P71883
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable nitrite extrusion protein 1 NarK1 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | narK |
| eggNOG description | Major Facilitator Superfamily |
| Orthologous group | COG2223 |
| KEGG orthology |
K02575
|
| KEGG pathways |
map00910
|
| KEGG modules |
M00615
|
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 | 0.57 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.27% of strains (396) · clonal |
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 | 1.6e-17 | 62–433 | Major Facilitator Superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: narH (nitrate reductase subunit beta), high confidence from genomic context alone (score 985 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1162 narH |
nitrate reductase subunit beta | 993 | 985 ctx | cooccurence:723 coexpression:463 database:900 textmining:564 |
Rv1161 narG |
nitrate reductase subunit alpha | 993 | 984 ctx | cooccurence:717 coexpression:446 database:900 textmining:627 |
Rv1736c narX |
nitrate reductase-like protein NarX | 991 | 984 ctx | cooccurence:723 coexpression:445 database:900 textmining:473 |
Rv1164 narI |
nitrate reductase subunit gamma | 991 | 978 ctx | cooccurence:618 coexpression:435 database:900 textmining:607 |
Rv0252 nirB |
nitrite reductase large subunit NirB | 967 | 946 | database:900 textmining:423 |
Rv0253 nirD |
nitrite reductase small subunit NirD | 971 | 936 | database:900 textmining:575 |
Rv1737c narK2 |
nitrate/nitrite transporter | 971 | 920 ctx | fusion:792 cooccurence:606 textmining:651 |
Rv0021c hyp |
hypothetical protein | 908 | 908 | database:900 |
Rv2781c |
oxidoreductase | 908 | 908 | database:900 |
Rv1163 narJ |
nitrate reductase subunit delta | 867 | 772 ctx | cooccurence:556 coexpression:466 textmining:441 |
Rv0260c |
transcriptional regulator | 726 | 656 ctx | cooccurence:608 |
Rv2330c lppP |
lipoprotein LppP | 449 | 449 ctx | neighborhood:447 |
Rv0259c hyp |
hypothetical protein | 435 | 435 | |
Rv2650c |
prophage protein | 422 | 422 | coexpression:422 |
Rv1576c |
phage capsid protein | 422 | 422 | coexpression:422 |
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/nitrite transporter
- Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=2e-17)
- (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_216845.1)
- 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 P71883 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
24 functional partner(s); context anchor
narH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002478|Rv2329c|narK1 MEQHTLLQREESPRSPAAPSLRRLGGSRHITHWDPEDLGAWEAGNKGIARRNLLWSVVTVHLGYSVWTLWPVLELLMPQDVYGFSTSDKFLLGTIATLFGAFLRMPYALASAIFGGRNWATFSAIVLLIPAIGTTVLLTHPGLPLWPYLVCAALTGLGGGNFASSMSNANAFYPHRLKGSALGIAGGVGNLGVPAIQLVGLLAIATVGERKPYLVCALYVVLVAIAVIGVSLFMNNVEQHRVQVNRLRPIVSAVLSTRDTWLLSLLYLGTFGSFIGFSFVFGQVLQTNFLACGQSPARATLHAVELAFVGPLLAAVARIYGGRLADRVGGSRLTLIVFVAMTLAAGLLISASTLEGRHVGQHRGATMVGYFVCFVALFVLSGLGNGSVYKMIPTIFEACSRSLDLSEAERRDWSRIISGVVIGFVAAFGALGGVGINMALRESYLSTGSGTDAFWIFMMCYAAAAVLTWKVYDRRTVTDMGMLQAALVRQPASTPAELIGPRTQSDRFSGCSISA