MTBC Gene Atlas

hycQ Resolved · high auto-curated

H37Rv Rv0086 · MTBC0 mtbc0_000096 · 488 aa · 94114–95580 (+) · RefSeq NP_214600.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hydrogenase HycQ
MTBC0 PGAP re-annotationhydrogenase HycQ
Revised (this work)Hydrogenase HycQ. Pfam: Proton_antipo_M (PF00361.26).

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

Curated reference (UniProt)

UniProt Q10883 TrEMBL · unreviewed · Predicted
UniProt namePossible hydrogenase HycQ

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category C Energy production and conversion
P Inorganic ion transport and metabolism
Preferred namehycQ
eggNOG descriptionProton-conducting membrane transporter
Orthologous groupCOG0651
KEGG orthology K12141

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 0.317 · purifying
Polymorphic sites (≥ 0.1% of strains) 9 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)

PfamAccessioni-EvalueResiduesDescription
Proton_antipo_MPF00361.26 1.0e-44124–421 NADH:quinone oxidoreductase/Mrp antiporter, TM

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

Closest characterised functional partner: hycE (formate hydrogenase HycE), high confidence from genomic context alone (score 1000 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv0087 hycE formate hydrogenase HycE 999 1000 ctx neighborhood:892 cooccurence:774 coexpression:925 experimental:995 textmining:850
Rv0084 hycD formate hydrogenlyase HycD 999 999 ctx neighborhood:874 cooccurence:774 coexpression:801 experimental:787
Rv0082 oxidoreductase 998 999 ctx neighborhood:874 cooccurence:770 coexpression:840 experimental:784
Rv0085 hycP hydrogenase HycP 999 996 ctx neighborhood:882 cooccurence:774 coexpression:860 textmining:826
Rv0083 oxidoreductase 987 987 ctx neighborhood:874 coexpression:860
Rv3156 nuoL NADH-quinone oxidoreductase subunit L 955 950 coexpression:672 experimental:823
Rv0081 HTH-type transcriptional regulator 928 907 ctx neighborhood:874
Rv3153 nuoI NADH-quinone oxidoreductase subunit I 767 736 experimental:697
Rv0088 polyketide cyclase/dehydrase 667 668 ctx neighborhood:658
Rv3146 nuoB NADH-quinone oxidoreductase subunit B 657 627 experimental:449
Rv3148 nuoD NADH-quinone oxidoreductase subunit D 574 574 experimental:449
Rv0080 hyp hypothetical protein 541 541 ctx neighborhood:538
Rv0079 hyp hypothetical protein 540 540 ctx neighborhood:538
Rv3147 nuoC NADH-quinone oxidoreductase subunit C 503 445 experimental:405
Rv0089 methyltransferase 435 435 ctx neighborhood:427

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: hydrogenase HycQ
  • MTBC0 PGAP product: hydrogenase HycQ
  • Pfam (hmmscan --cut_ga): Proton_antipo_M PF00361.26 (E=1e-44)
  • (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_214600.1)
  • Domains: Pfam-A via hmmscan --cut_ga — Proton_antipo_M (PF00361.26)
  • 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 COG0651
  • Curated reference: UniProt Q10883 (TrEMBL, unreviewed; Predicted)
  • 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 — 23 functional partner(s); context anchor hycE
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000096|Rv0086|hycQ
MTGLLLAAILAPLAASIASLITGWRRTTATLTALSATTVLACAVAMGFWMGSGAQFGLGGLLRADALTVVMLVVIGIVGTLATAASIGYIDTELAHGHIDGRSARLYGVLTPAFLCAMVLAVCANNIGVIWVAIEATTVITAFLVGHRRTRTALEATWKYVVICSVGIAVAFLGTVLLYFAARDSGAAAAGALNLDILAEHAAGLDPGVARLAGGLLLIGYGAKAGLFPFHTWLADAHSQAPAPVSALMSGVLLAVAFSVLIRLRPILDAVSGPAYLRNGLLVVGLATLLVAVLMLTVTGDVKRMLAYSSMEHMGLIAIAAAAGTTLAIAALLLHVLAHGIGKTVLFLAGGQLQAAHDSTAIADITGVMRRSRLIGVSFAVGLIVLLGLPPFAMFASELAIARSLANERLAWVLGAALLLIAIGFTALARNSGRMLLGTPAAGAPAITVPATAAAALMVGIVVSAALGITAGPLADLLGIAASNVGLP