nirB Family assigned · medium auto-curated
H37Rv Rv0252 · MTBC0 mtbc0_000268 ·
853 aa · 303248–305809 (+) ·
RefSeq NP_214766.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitrite reductase large subunit NirB |
|---|---|
| MTBC0 PGAP re-annotation | nitrite reductase large subunit NirB |
| Revised (this work) | Nitrite reductase large subunit NirB. Pfam: Pyr_redox_2 (PF07992.21), Pyr_redox (PF00070.34), Rubredoxin_C (PF18267.8), Fer2_BFD (PF04324.21), NIR_SIR_ferr (PF03460.23), NIR_SIR (PF01077.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53674
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | assimilatory sulfite reductase |
| EC (curated) |
EC 1.8.7.1
|
| Curated function | Catalyzes the reduction of sulfite to sulfide, a step in the biosynthesis of sulfur-containing amino acids and cofactors. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | nirB |
| eggNOG description | Belongs to the nitrite and sulfite reductase 4Fe-4S domain family |
| Orthologous group | COG1251 |
| EC number |
EC 1.7.1.15
|
| KEGG orthology |
K00362
|
| 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 | 0.157 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 18 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 |
|---|---|---|---|---|
Pyr_redox_2 | PF07992.21 | 8.8e-51 | 15–302 | Pyridine nucleotide-disulphide oxidoreductase |
Pyr_redox | PF00070.34 | 1.6e-15 | 165–244 | Pyridine nucleotide-disulphide oxidoreductase |
Rubredoxin_C | PF18267.8 | 2.5e-08 | 339–399 | Rubredoxin NAD+ reductase C-terminal domain |
Fer2_BFD | PF04324.21 | 8.4e-10 | 441–488 | BFD-like [2Fe-2S] binding domain |
NIR_SIR_ferr | PF03460.23 | 1.4e-09 | 573–633 | Nitrite/Sulfite reductase ferredoxin-like half domain |
NIR_SIR | PF01077.28 | 1.0e-25 | 645–783 | Nitrite and sulphite reductase 4Fe-4S domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nirD (nitrite reductase small subunit NirD), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0253 nirD |
nitrite reductase small subunit NirD | 999 | 1000 ctx | neighborhood:844 cooccurence:774 coexpression:919 experimental:434 database:900 textmining:768 |
Rv1161 narG |
nitrate reductase subunit alpha | 970 | 948 | coexpression:484 database:900 textmining:465 |
Rv1736c narX |
nitrate reductase-like protein NarX | 973 | 947 | coexpression:473 database:900 textmining:519 |
Rv0267 narU |
nitrite extrusion protein NarU | 976 | 946 | database:900 textmining:586 |
Rv0261c narK3 |
nitrate/nitrite transporter | 971 | 946 | database:900 textmining:496 |
Rv2329c narK1 |
nitrate/nitrite transporter | 967 | 946 | database:900 textmining:423 |
Rv1162 narH |
nitrate reductase subunit beta | 965 | 942 | coexpression:423 database:900 textmining:435 |
Rv1737c narK2 |
nitrate/nitrite transporter | 975 | 934 | database:900 textmining:645 |
Rv1164 narI |
nitrate reductase subunit gamma | 954 | 924 | database:900 textmining:424 |
Rv2222c glnA2 |
glutamine synthetase | 941 | 904 | database:900 textmining:411 |
Rv1878 glnA3 |
glutamine synthetase GlnA | 933 | 904 | database:900 |
Rv2860c glnA4 |
glutamine synthetase | 929 | 904 | database:900 |
Rv2220 glnA1 |
glutamine synthetase | 963 | 903 | database:900 textmining:642 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 903 | 903 | database:900 |
Rv0021c hyp |
hypothetical protein | 906 | 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 large subunit NirB
- MTBC0 PGAP product: nitrite reductase large subunit NirB
- Pfam (hmmscan --cut_ga): Pyr_redox_2 PF07992.21 (E=9e-51), Pyr_redox PF00070.34 (E=2e-15), Rubredoxin_C PF18267.8 (E=2e-08), Fer2_BFD PF04324.21 (E=8e-10), NIR_SIR_ferr PF03460.23 (E=1e-09), NIR_SIR PF01077.28 (E=1e-25)
- (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_214766.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pyr_redox_2 (PF07992.21), Pyr_redox (PF00070.34), Rubredoxin_C (PF18267.8), Fer2_BFD (PF04324.21), NIR_SIR_ferr (PF03460.23), NIR_SIR (PF01077.28)
- 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
COG1251 - Curated reference: UniProt O53674 (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 —
42 functional partner(s); context anchor
nirD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000268|Rv0252|nirB MPTAGSSRAPAAAREIVVVGHGMVGHRLVEAVRARDADGSLRITVLAEEGDAAYDRVGLTSYTESWDRALLALPGNDYAGDQRVRLLLNTRVTQIDRATKSVVTAAGQRHRYDTLVLATGSYAFVPPVPGHDLPACHVYRTFDDLDAIRAGAQRTLDGGHTDGGVVIGGGLLGLEAANALRQFGLQTHVVEMMPRLMAQQIDEAGGALLARMIADLGIAVHVGTGTESIESVKHSDGSVWARVRLSDGEVIDAGVVIFAAGIRPRDELARAAGLAIGDRGGVLTDLSCRTSDPDIYAVGEVAAIDGRCYGLVGPGYTSAEVVADRLLDGSAEFPEADLSTKLKLLGVDVASFGDAMGATENCLEVVINDAVKRTYAKLVLSDDATTLLGGVLVGDASSYGVLRPMVGAELPGDPLALIAPAGSGAGAGALGVGALPDSAQICSCNNVTKGELKCAIADGCGDVPALKSCTAAGTSCGSCVPLLKQLLEAEGVEQSKALCEHFSQSRAELFEIITATEVRTFSGLLDRFGRGKGCDICKPVVASILASTGSDHILDGEQASLQDSNDHFLANIQKNGSYSVVPRVPGGDIKPEHLILIGQIAQDFGLYTKITGGQRIDLFGARVDQLPLIWQRLVDGGMESGHAYGKAVRTVKSCVGSDWCRYGQQDSVQLAIDLELRYRGLRAPHKIKLGVSGCARECAEARGKDVGVIATEKGWNLYVAGNGGMTPKHAQLLASDLDKETLIRYIDRFLIYYIRTADRLQRTAPWVESLGLDHVREVVCEDSLGLAEEFEAAMQRHVANYKCEWKGVLEDPDKLSRFVSFVNAPDAVDSTVTFTERAGRKVPVSIGIPRVRS