MTBC Gene Atlas

Rv1179c Family assigned · medium auto-curated

H37Rv Rv1179c · MTBC0 mtbc0_001268 · 939 aa · 1318921–1321740 (-) · RefSeq NP_215695.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationDEAD/DEAH box helicase family protein
Revised (this work)DEAD/DEAH box helicase family protein. Pfam: ResIII (PF04851.22).

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

Curated reference (UniProt)

UniProt O50435 TrEMBL · unreviewed · Evidence at protein level
UniProt nameHelicase ATP-binding domain-containing protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category K Transcription
L Replication, recombination and repair
eggNOG descriptionType III restriction enzyme, res subunit
Orthologous groupCOG1061

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 0.791 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 8 synonymous, 17 missense, 0 nonsense, 2 frameshift
Disruption 2 distinct premature-stop/frameshift site(s); most common in 0.39% of strains (564) · clonal

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
ResIIIPF04851.22 3.7e-1815–196 Type III restriction enzyme, res subunit

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv1329c dinG ATP-dependent helicase DinG 892 884 experimental:685 database:622
Rv0667 rpoB DNA-directed RNA polymerase subunit beta 873 871 experimental:578 database:621
Rv3457c rpoA DNA-directed RNA polymerase subunit alpha 853 853 experimental:627 database:621
Rv1390 rpoZ DNA-directed RNA polymerase subunit omega 847 848 experimental:613 database:621
Rv1629 polA DNA polymerase I 787 768 experimental:430 database:580
Rv2090 5'-3' exonuclease 766 753 experimental:430 database:580
Rv1334 mec [CysO 705 705 database:613
Rv2529 hyp hypothetical protein 707 687 database:610
Rv0668 rpoC DNA-directed RNA polymerase subunit beta' 686 686 database:620
Rv2101 helZ helicase HelZ 694 671 database:615
Rv0832 PE_PGRS12 PE-PGRS family protein PE_PGRS12 620 621 database:563
Rv3812 PE_PGRS62 PE-PGRS family protein PE_PGRS62 620 621 database:563
Rv2328 PE23 PE family protein PE23 620 621 database:563
Rv3036c TB22.2 hyp hypothetical protein 620 621 database:563
Rv0938 ligD multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD 592 575 database:556

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: hypothetical protein
  • MTBC0 PGAP product: DEAD/DEAH box helicase family protein
  • Pfam (hmmscan --cut_ga): ResIII PF04851.22 (E=4e-18)
  • (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_215695.1)
  • Domains: Pfam-A via hmmscan --cut_ga — ResIII (PF04851.22)
  • 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 COG1061
  • Curated reference: UniProt O50435 (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 — 49 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001268|Rv1179c|
MDPHRDLESRAFAGNWRVYQQQALDAFDADVAAGDNRAYLVLPPGAGKTMIGLEAARRLGRRSLVLVPNTAVQAQWAAAWDNSFPSSDRSASKCGTERGLASAMNVLTYQSLAVIDAETDSTVRREVLRNRDQQALLDLLHPNGRAVIERAATLGPWTLVLDECHHLLATWGALVSALASVLGAQTALIGLTATPATELTAWQHTLHDELFGTADFVIPTPALVREGDLAPYQELVYLTQPTPEEQAWIGTHRARFADLMLALIDQKVGSMSLAAWLHTRIVDRATREGNQIAWSTFERAEPDLACSGLRFAYDGLIPLPDGVRLREQHRIAPDAQDWVNVLTDFSVGHLQQSADPRDAHALTAIKRVLPGLGYRLTSRGVRVATSPVDRLCALSESKIAATAHILDTEDAVLGARLRALVLCDFESMTGALPTSLKGAPVSEQSGSAQLVAAMLAASDHRRRTPLHALLVTGQTFACPAAIEDDLIAFCAERGALVTAEPLDAHPSLRVMRGTGGFTPRTWVALATEYFLAGRARVLVGTRSLLGEGWDCAAVNVNIDLTSATTQAAITQMRGRAIRNDPSDGHKVADNWSVCCIATEHPRGDADYLRLVRKHDGYYAATPQGLIESGVTHCDPSLSPYGPPVTDTHAITARALQRVAERAQARSWWRIGEPYEGVDVATIRVRSRQPLGVAAPRIPASALTPPVPGQFSPVRLARGAVAAVSVVGASTATAVASANLGMLAGAGTAGAIVAAGVGLVATAAAAESRRLDHAPNALEQLAAVVADALYAAGGAQRGSAALRLASDPEGWIRCQLDGVPTEQSLRFTAALDELLAPLAEPRYLIGRKILTPPARPVARRLFAVRAVVGLSLPGTVAWHAVPRWFARNKDRRQHLAQAWRKHIGPPRQLPADSPQGQAILDLFRGDNPLSVTTQLRTTWR