MTBC Gene Atlas

narJ Family assigned · medium auto-curated

H37Rv Rv1163 · MTBC0 - · 201 aa · 1292798–1293403 (+) · RefSeq NP_215679.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)nitrate reductase subunit delta
MTBC0 PGAP re-annotation—
Revised (this work)Nitrate reductase subunit delta. Pfam: Nitrate_red_del (PF02613.21).

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 O06561 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable respiratory nitrate reductase

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category C Energy production and conversion
Preferred namenarJ
eggNOG descriptionNitrate reductase, delta subunit
Orthologous groupCOG2180
KEGG orthology K00373
KEGG pathways map02020

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 1.517 · diversifying/relaxed
Polymorphic sites (≥ 0.1% of strains) 1 synonymous, 4 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)

PfamAccessioni-EvalueResiduesDescription
Nitrate_red_delPF02613.21 3.9e-1135–149 Nitrate reductase delta subunit

Functional interaction network (STRING v12, guilt-by-association)

Closest characterised functional partner: narI (nitrate reductase subunit gamma), high confidence from genomic context alone (score 999 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv1164 narI nitrate reductase subunit gamma 999 999 ctx neighborhood:881 cooccurence:774 coexpression:957 textmining:965
Rv1162 narH nitrate reductase subunit beta 999 999 ctx neighborhood:804 cooccurence:774 coexpression:968 experimental:501 textmining:937
Rv1161 narG nitrate reductase subunit alpha 999 998 ctx neighborhood:763 cooccurence:774 coexpression:932 experimental:510 textmining:937
Rv1737c narK2 nitrate/nitrite transporter 961 887 ctx cooccurence:748 coexpression:466 textmining:675
Rv1736c narX nitrate reductase-like protein NarX 931 883 coexpression:729 experimental:510 textmining:439
Rv1165 typA GTP-binding translation elongation factor 873 838 ctx neighborhood:785
Rv0267 narU nitrite extrusion protein NarU 944 795 ctx cooccurence:601 coexpression:466 textmining:738
Rv2329c narK1 nitrate/nitrite transporter 867 772 ctx cooccurence:556 coexpression:466 textmining:441
Rv1166 lpqW monoacyl phosphatidylinositol tetramannoside-binding protein LpqW 766 766 ctx neighborhood:755
Rv0261c narK3 nitrate/nitrite transporter 824 752 ctx cooccurence:520 coexpression:462
Rv2847c cysG multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase 734 735 coexpression:696
Rv0869c moaA2 molybdenum cofactor biosynthesis protein MoaA 682 474 coexpression:417 textmining:421
Rv0511 hemD uroporphyrin-III C-methyltransferase 469 469 coexpression:439
Rv0253 nirD nitrite reductase small subunit NirD 660 460 coexpression:443
Rv3109 moaA1 cyclic pyranopterin monophosphate synthase 616 460 coexpression:401

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 delta
  • Pfam (hmmscan --cut_ga): Nitrate_red_del PF02613.21 (E=4e-11)
  • (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_215679.1)
  • Domains: Pfam-A via hmmscan --cut_ga — Nitrate_red_del (PF02613.21)
  • 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 COG2180
  • Curated reference: UniProt O06561 (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 — 33 functional partner(s); context anchor narI
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>H37Rv|Rv1163|narJ
MWQSASLLLAYPDDGLAERLHMVDALRAHQTGPAAALLGRTVAELRALAPMAAAAQYVETFDMRRRSTMYLTYWTAGDTRNRGREMLAFATAYRDAGVKPPRTEAPDYLPVVLEFAATVDPEAGRRLLTEHRVPIDVLRGALADAKSPYEYTVAAICETLPAATNQEVRRAQRLAQSGPPAEAVGLQPFTLTVPPKRAEGA