MTBC Gene Atlas

Rv0111 Family assigned · medium auto-curated

H37Rv Rv0111 · MTBC0 mtbc0_000121 · 685 aa · 134115–136172 (+) · RefSeq NP_214625.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)acyltransferase
MTBC0 PGAP re-annotationacyltransferase family protein
Revised (this work)Acyltransferase family protein. Pfam: Acyl_transf_3 (PF01757.29), SGNH (PF19040.7), DUF459 (PF04311.21).

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

Curated reference (UniProt)

UniProt O53633 TrEMBL · unreviewed · Predicted
UniProt namePossible transmembrane acyltransferase

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category E Amino acid transport and metabolism
I Lipid transport and metabolism
eggNOG descriptionAcyltransferase
Orthologous groupCOG1835

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 0.558 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 8 synonymous, 12 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
Acyl_transf_3PF01757.29 7.1e-2734–387 Acyltransferase domain
SGNHPF19040.7 1.4e-08465–675 SGNH domain (fused to AT3 domains)
DUF459PF04311.21 2.6e-07525–673 Protein of unknown function (DUF459)

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

Closest characterised functional partner: Rv0228 (acyltransferase), medium confidence from genomic context alone (score 541 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv1251c hyp hypothetical protein 752 752 coexpression:751
Rv0228 acyltransferase 540 541 ctx cooccurence:535
Rv1254 acyltransferase 491 492 ctx cooccurence:487
Rv0110 integral membrane protein 930 465 ctx neighborhood:460 textmining:875
Rv1354c hyp hypothetical protein 452 451 coexpression:420
Rv0112 gca GDP-mannose 4,6-dehydratase 469 448 ctx neighborhood:429
Rv1814 erg3 membrane-bound C-5 sterol desaturase 418 419 coexpression:400
Rv2972c hyp hypothetical protein 442 407 coexpression:406
Rv3634c galE1 UDP-glucose 4-epimerase 444 95 textmining:411
Rv1366 hyp hypothetical protein 517 53 textmining:511
Rv0140 hyp hypothetical protein 517 48 textmining:514
Rv0274 hyp hypothetical protein 854 46 textmining:854
Rv1337 integral membrane protein 906 44 textmining:906
Rv1336 cysM O-phosphoserine sulfhydrylase 585 44 textmining:584

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: acyltransferase
  • MTBC0 PGAP product: acyltransferase family protein
  • Pfam (hmmscan --cut_ga): Acyl_transf_3 PF01757.29 (E=7e-27), SGNH PF19040.7 (E=1e-08), DUF459 PF04311.21 (E=3e-07)
  • (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_214625.1)
  • Domains: Pfam-A via hmmscan --cut_ga — Acyl_transf_3 (PF01757.29), SGNH (PF19040.7), DUF459 (PF04311.21)
  • 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 COG1835
  • Curated reference: UniProt O53633 (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 — 14 functional partner(s); context anchor Rv0228
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000121|Rv0111|
MPARSVPRPRWVAPVRRVGRLAVWDRPERRSGIPALDGLRAIAVALVLASHGGIPGMGGGFIGVDAFFVLSGFLITSLLLDELGRTGRIDLSGFWIRRARRLLPALVLMVLTVSAARALFPDQALTGLRSDAIAAFLWTANWRFVAQNTDYFTQGAPPSPLQHTWSLGVEEQYYVVWPLLLIGATLLLAARARRRCRRATVGGVRFAAFLIASLGTMASATAAVAFTSAATRDRIYFGTDTRAQALLIGSAAAALLVRDWPSLNRGWCLIRTRWGRRIARLLPFVGLAGLAVTTHVATGSVGEFRHGLLIVVAGAAVIVVASVAMEQRGAVARILAWRPLVWLGTISYGVYLWHWPIFLALNGQRTGWSGPALFAARCAATVVLAGASWWLIEQPIRRWRPARVPLLPLAAATVASAAAVTMLVVPVGAGPGLREIGLPPGVSAVAAVSPSPPEASQPAPGPRDPNRPFTVSVFGDSIGWTLMHYLPPTPGFRFIDHTVIGCSLVRGTPYRYIGQTLEQRAECDGWPARWSAQVNRDQPDVALLIVGRWETVDRVNEGRWTHIGDPTFDAYLNAELQRALSIVGSTGVRVMVTTVPYSRGGEKPDGRLYPEDQPERVNKWNAMLHNAISQHSNVGMIDLNKKLCPDGVYTAKVDGIKVRSDGVHLTQEGVKWLIPWLEDSVRVAS