MTBC Gene Atlas

Rv3362c Family assigned · medium auto-curated

H37Rv Rv3362c · MTBC0 mtbc0_003577 · 193 aa · 3800282–3800863 (-) · RefSeq NP_217879.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)ATP/GTP-binding protein
MTBC0 PGAP re-annotationATP/GTP-binding protein
Revised (this work)ATP/GTP-binding protein. Pfam: ATP_bind_1 (PF03029.24).

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

Curated reference (UniProt)

UniProt O50391 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable ATP/GTP-binding protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category S Function unknown
eggNOG descriptionConserved hypothetical ATP binding protein
Orthologous groupCOG2229
KEGG orthology K06945

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 0.68 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 1 synonymous, 2 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
ATP_bind_1PF03029.24 6.1e-3318–186 Conserved hypothetical ATP binding protein

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv3364c hyp hypothetical protein 999 1000 ctx neighborhood:882 cooccurence:774 coexpression:807 experimental:917 textmining:838
Rv3363c hyp hypothetical protein 999 995 ctx neighborhood:882 cooccurence:774 coexpression:824 textmining:892
Rv3365c hyp hypothetical protein 992 978 ctx neighborhood:882 cooccurence:758 textmining:656
Rv2921c ftsY signal recognition particle receptor FtsY 980 974 experimental:928 database:647
Rv3361c mfpA hyp hypothetical protein 987 933 ctx neighborhood:882 coexpression:458 textmining:822
Rv1004c membrane protein 825 804 experimental:787
Rv2916c ffh signal recognition particle protein 824 803 experimental:787
Rv0720 rplR 50S ribosomal protein L18 790 790 experimental:787
Rv0701 rplC 50S ribosomal protein L3 779 779 experimental:771
Rv0709 rpmC 50S ribosomal protein L29 779 779 experimental:776
Rv0714 rplN 50S ribosomal protein L14 777 777 experimental:776
Rv3443c rplM 50S ribosomal protein L13 776 776 experimental:771
Rv0704 rplB 50S ribosomal protein L2 773 773 experimental:771
Rv0703 rplW 50S ribosomal protein L23 761 761 experimental:759
Rv0722 rpmD 50S ribosomal protein L30 642 624 experimental:590

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: ATP/GTP-binding protein
  • MTBC0 PGAP product: ATP/GTP-binding protein
  • Pfam (hmmscan --cut_ga): ATP_bind_1 PF03029.24 (E=6e-33)
  • (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_217879.1)
  • Domains: Pfam-A via hmmscan --cut_ga — ATP_bind_1 (PF03029.24)
  • 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 COG2229
  • Curated reference: UniProt O50391 (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 — 38 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_003577|Rv3362c|
MALKHSEASGTASTKIVIAGGFGSGKTTFVGAVSEIMPLRTEAMVTDASAGVDMLEATPDKRSTTVAMDFGRITLGEDLVLYLFGTPGQRRFWFMWDDLVRGAIGAIVLVDCRRLQDSFAAVDFFEHRNLPFLIAINEFDSAPRYPVSAVRDALTLPAHIPVINVDARNRRSATDALIAVSEYALATLSPAGG