nirD Family assigned · medium auto-curated
H37Rv Rv0253 · MTBC0 mtbc0_000269 ·
118 aa · 305835–306191 (+) ·
RefSeq NP_214767.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitrite reductase small subunit NirD |
|---|---|
| MTBC0 PGAP re-annotation | nitrite reductase small subunit NirD |
| Revised (this work) | Nitrite reductase small subunit NirD. Pfam: Rieske_2 (PF13806.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53675
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nitrite reductase |
| EC (curated) |
EC 1.7.1.15
|
| Curated function | Required for activity of the reductase. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | nirD |
| eggNOG description | Nitrite reductase |
| Orthologous group | COG2146 |
| EC number |
EC 1.7.1.15
|
| KEGG orthology |
K00363
|
| KEGG pathways |
map00910, map01120
|
| KEGG modules |
M00530
|
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 | 0.357 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
Rieske_2 | PF13806.13 | 3.0e-36 | 10–113 | Rieske-like [2Fe-2S] domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nirB (nitrite reductase large subunit NirB), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0252 nirB |
nitrite reductase large subunit NirB | 999 | 1000 ctx | neighborhood:844 cooccurence:774 coexpression:919 experimental:434 database:900 textmining:768 |
Rv1162 narH |
nitrate reductase subunit beta | 978 | 951 | coexpression:517 database:900 textmining:585 |
Rv1161 narG |
nitrate reductase subunit alpha | 964 | 942 | coexpression:430 database:900 textmining:410 |
Rv1164 narI |
nitrate reductase subunit gamma | 965 | 941 | coexpression:418 database:900 textmining:430 |
Rv1736c narX |
nitrate reductase-like protein NarX | 953 | 941 | coexpression:417 database:900 |
Rv0267 narU |
nitrite extrusion protein NarU | 962 | 938 | database:900 textmining:425 |
Rv2329c narK1 |
nitrate/nitrite transporter | 971 | 936 | database:900 textmining:575 |
Rv0261c narK3 |
nitrate/nitrite transporter | 952 | 936 | database:900 |
Rv1737c narK2 |
nitrate/nitrite transporter | 946 | 932 | database:900 |
Rv2222c glnA2 |
glutamine synthetase | 924 | 902 | database:900 |
Rv1878 glnA3 |
glutamine synthetase GlnA | 907 | 902 | database:900 |
Rv2220 glnA1 |
glutamine synthetase | 929 | 901 | database:900 |
Rv2860c glnA4 |
glutamine synthetase | 906 | 901 | database:900 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 902 | 900 | database:900 |
Rv2781c |
oxidoreductase | 900 | 900 | database:900 |
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: nitrite reductase small subunit NirD
- MTBC0 PGAP product: nitrite reductase small subunit NirD
- Pfam (hmmscan --cut_ga): Rieske_2 PF13806.13 (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_214767.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rieske_2 (PF13806.13)
- 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
COG2146 - Curated reference: UniProt O53675 (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 —
35 functional partner(s); context anchor
nirB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000269|Rv0253|nirD MTLLNDIQVWTTACAYDHLIPGRGVGVLLDDGSQVALFRLDDGSVHAVGNVDPFSGAAVMSRGIVGDRGGRAMVQSPILKQAFALDDGSCLDDPRVSVPVYPARVTPEGRIQVARVAV