narL Resolved · high auto-curated
H37Rv Rv0844c · MTBC0 mtbc0_000899 ·
216 aa · 943607–944257 (-) ·
RefSeq NP_215359.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitrate/nitrite response transcriptional regulator NarL |
|---|---|
| MTBC0 PGAP re-annotation | two-component system response regulator NarL |
| Revised (this work) | Two-component system response regulator NarL. Pfam: Response_reg (PF00072.31), GerE (PF00196.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGM5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein NarL |
| Curated function | Member of the two-component regulatory system NarS/NarL that regulates genes involved in aerobic nitrate metabolism. Upon phosphorylation by NarS, functions as a transcription regulator by direct binding to promoter regions of target genes together with DevR to regulate their expression during aerobic nitrate metabolism. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | narL |
| eggNOG description | response regulator |
| Orthologous group | COG2197 |
| KEGG orthology |
K07684
|
| KEGG pathways |
map02020
|
| KEGG modules |
M00471
|
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 | 2.441 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 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 |
|---|---|---|---|---|
Response_reg | PF00072.31 | 4.1e-25 | 11–122 | Response regulator receiver domain |
GerE | PF00196.26 | 3.0e-15 | 154–207 | Bacterial regulatory proteins, luxR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: narS (sensor histidine kinase NarS), high confidence from genomic context alone (score 970 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0845 narS |
sensor histidine kinase NarS | 987 | 970 ctx | neighborhood:783 cooccurence:767 textmining:596 |
Rv3132c devS |
two component sensor histidine kinase DevS | 877 | 792 ctx | cooccurence:612 textmining:437 |
Rv2788 sirR |
transcriptional repressor SirR | 851 | 790 | coexpression:731 |
Rv2027c dosT |
two component sensor histidine kinase DosT | 912 | 770 ctx | cooccurence:573 textmining:635 |
Rv3208 |
TetR family transcriptional regulator | 751 | 751 | coexpression:751 |
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 743 | 734 | coexpression:734 |
Rv0377 |
HTH-type transcriptional regulator | 734 | 723 | coexpression:687 |
Rv0195 |
two component transcriptional regulator | 712 | 713 ctx | cooccurence:708 |
Rv0273c |
transcriptional regulator | 615 | 615 | coexpression:615 |
Rv1033c trcR |
two component transcriptional regulator TrcR | 698 | 541 | |
Rv0624 vapC30 |
ribonuclease VapC30 | 474 | 474 | coexpression:474 |
Rv0600c |
two component sensor kinase HK1 | 563 | 444 | |
Rv0902c prrB |
two component sensor histidine kinase PrrB | 653 | 406 | textmining:441 |
Rv1027c kdpE |
transcriptional regulator KdpE | 706 | 388 | textmining:540 |
Rv2359 zur |
zinc uptake regulation protein | 430 | 369 |
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 response transcriptional regulator NarL
- MTBC0 PGAP product: two-component system response regulator NarL
- Pfam (hmmscan --cut_ga): Response_reg PF00072.31 (E=4e-25), GerE PF00196.26 (E=3e-15)
- (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_215359.1)
- Domains: Pfam-A via hmmscan --cut_ga — Response_reg (PF00072.31), GerE (PF00196.26)
- 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
COG2197 - Curated reference: UniProt P9WGM5 (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 —
35 functional partner(s); context anchor
narS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000899|Rv0844c|narL MSNPQPEKVRVVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIKAHLPDVALLDYRMPGMDGAQVAAAVRSYELPTRVLLISAHDEPAIVYQALQQGAAGFLLKDSTRTEIVKAVLDCAKGRDVVAPSLVGGLAGEIRQRAAPVAPVLSAREREVLNRIACGQSIPAIAAELYVAPSTVKTHVQRLYEKLGVSDRAAAVAEAMRQRLLD