narH Family assigned · medium auto-curated
H37Rv Rv1162 · MTBC0 - ·
558 aa · 1291065–1292741 (+) ·
RefSeq NP_215678.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitrate reductase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Nitrate reductase subunit beta. Pfam: Fer4_11 (PF13247.12), Fer4_10 (PF13237.12), Nitr_red_bet_C (PF14711.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O06560
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable respiratory nitrate reductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | narH |
| eggNOG description | Nitrate reductase beta subunit |
| Orthologous group | COG1140 |
| EC number |
EC 1.7.5.1
|
| KEGG orthology |
K00371
|
| KEGG pathways |
map00910, map01120, map02020
|
| KEGG modules |
M00529, M00530, M00804
|
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 | 0.534 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 |
|---|---|---|---|---|
Fer4_11 | PF13247.12 | 1.1e-35 | 177–272 | 4Fe-4S dicluster domain |
Fer4_10 | PF13237.12 | 6.7e-09 | 179–229 | 4Fe-4S dicluster domain |
Nitr_red_bet_C | PF14711.12 | 6.7e-29 | 360–441 | Respiratory nitrate reductase beta C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: narG (nitrate reductase subunit alpha), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1161 narG |
nitrate reductase subunit alpha | 999 | 1000 ctx | neighborhood:825 cooccurence:774 coexpression:961 experimental:829 database:900 textmining:921 |
Rv1164 narI |
nitrate reductase subunit gamma | 999 | 1000 ctx | neighborhood:804 cooccurence:774 coexpression:957 experimental:652 database:900 textmining:938 |
Rv1736c narX |
nitrate reductase-like protein NarX | 999 | 999 ctx | cooccurence:774 coexpression:730 experimental:829 database:900 textmining:653 |
Rv1163 narJ |
nitrate reductase subunit delta | 999 | 999 ctx | neighborhood:804 cooccurence:774 coexpression:968 experimental:501 textmining:937 |
Rv1737c narK2 |
nitrate/nitrite transporter | 996 | 989 ctx | cooccurence:760 coexpression:463 database:900 textmining:703 |
Rv2329c narK1 |
nitrate/nitrite transporter | 993 | 985 ctx | cooccurence:723 coexpression:463 database:900 textmining:564 |
Rv0267 narU |
nitrite extrusion protein NarU | 991 | 985 ctx | cooccurence:721 coexpression:469 database:900 textmining:450 |
Rv0261c narK3 |
nitrate/nitrite transporter | 991 | 984 ctx | cooccurence:708 coexpression:461 database:900 textmining:482 |
Rv0253 nirD |
nitrite reductase small subunit NirD | 978 | 951 | coexpression:517 database:900 textmining:585 |
Rv0252 nirB |
nitrite reductase large subunit NirB | 965 | 942 | coexpression:423 database:900 textmining:435 |
Rv2781c |
oxidoreductase | 902 | 903 | database:900 |
Rv0021c hyp |
hypothetical protein | 901 | 902 | database:900 |
Rv1175c fadH |
NADPH dependent 2,4-dienoyl-CoA reductase FadH | 908 | 899 | experimental:899 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 859 | 811 | experimental:790 |
Rv1165 typA |
GTP-binding translation elongation factor | 829 | 795 ctx | neighborhood:783 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): nitrate reductase subunit beta
- Pfam (hmmscan --cut_ga): Fer4_11 PF13247.12 (E=1e-35), Fer4_10 PF13237.12 (E=7e-09), Nitr_red_bet_C PF14711.12 (E=7e-29)
- (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_215678.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fer4_11 (PF13247.12), Fer4_10 (PF13237.12), Nitr_red_bet_C (PF14711.12)
- 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
COG1140 - Curated reference: UniProt O06560 (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 —
51 functional partner(s); context anchor
narG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1162|narH MKVMAQMAMVMNLDKCIGCHTCSVTCKQAWTNRSGTEYVWFNNVETRPGVGYPRTYEDQERWRGGWVRDKKGRLRLRDGGRIHKLLRIFANPKLPTIGDYYEPWTYDYENLTSAPAGDTFPTAAPRSLISGNPMKVSWGSNWDDNLAGSPEIVPNDPVLKKVNQVNQEVKLKLEETFMFYLPRICEHCLNPSCVASCPSGAMYKRTEDGIVLVDQDRCRGWRMCVSGCPYKKVYFNHKTGKAEKCTLCYPRIEVGLPTVCSETCVGRLRYLGLVLYDVDQVLQAASVESDTDLYEAQRRILLDPHDPRVIAGARAEGIADEWIEAAQRSPVYALINTYRVALPLHPEYRTMPMVWYIPPLSPVVDAVSRDGHDGEDLGNLFGALDALRIPIAYLAELFTAGDTEVVAGVLRRLAAMRCYMRDINLGRETQPHIPESVGMTEEQIYQMYRLLAVAKYEERYVIPTSYAGELPAAAMTDDMGCSLSVDGGPGMYESGPFGQGSPTPVPIAVESFHALQHAGSAATGGAGRSRVNLLNWDPNGAAAGLFPEPQPSKDVVQR