MTBC Gene Atlas

Rv3752c Resolved · high auto-curated

H37Rv Rv3752c · MTBC0 mtbc0_003976 · 152 aa · 4223368–4223826 (-) · RefSeq NP_218269.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)cytidine/deoxycytidylate deaminase
MTBC0 PGAP re-annotationnucleoside deaminase
Revised (this work)Nucleoside deaminase. Pfam: dCMP_cyt_deam_1 (PF00383.30), MafB19-deam (PF14437.13).

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

Curated reference (UniProt)

UniProt O69719 TrEMBL · unreviewed · Evidence at protein level
UniProt nametRNA-specific adenosine deaminase
EC (curated) EC 3.5.4.33
Curated functionCatalyzes the deamination of adenosine to inosine at the wobble position 34 of tRNA(Arg2).

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category F Nucleotide transport and metabolism
J Translation, ribosomal structure and biogenesis
Preferred nametadA
eggNOG descriptionCatalyzes the deamination of adenosine to inosine at the wobble position 34 of tRNA(Arg2)
Orthologous groupCOG0590
EC number EC 3.5.4.1, EC 3.5.4.33
KEGG orthology K01485, K11991
KEGG pathways map00240, map00330, map01100

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 n/a
Polymorphic sites (≥ 0.1% of strains) 0 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
dCMP_cyt_deam_1PF00383.30 2.3e-261–102 Cytidine and deoxycytidylate deaminase zinc-binding region
MafB19-deamPF14437.13 6.8e-1817–128 MafB19-like deaminase

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

Closest characterised functional partner: dhmA1 (haloalkane dehalogenase), high confidence from genomic context alone (score 833 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv3753c hyp hypothetical protein 873 873 ctx neighborhood:867
Rv2296 dhmA1 haloalkane dehalogenase 833 833 ctx fusion:830
Rv3754 tyrA prephenate dehydrogenase TyrA 764 753 ctx neighborhood:750
Rv1003 rsmI rRNA small subunit methyltransferase I 684 684 ctx fusion:662
Rv0427c xthA exodeoxyribonuclease III protein XthA 684 667 database:610
Rv2205c hyp hypothetical protein 630 630 ctx fusion:610
Rv2122c hisE phosphoribosyl-ATP pyrophosphatase 638 625 coexpression:625
Rv3393 iunH nucleoside hydrolase 575 559 database:500
Rv0120c fusA2 elongation factor G 555 555 database:550
Rv0684 fusA1 elongation factor G 552 552 database:550
Rv2764c thyA thymidylate synthase ThyA 546 518 database:500
Rv1407 fmu 16S rRNA m5C967 methyltransferase 493 467 ctx cooccurence:431
Rv3279c birA bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase 470 460 coexpression:441
Rv2368c phoH1 phosphate starvation-inducible protein PhoH 458 459 ctx cooccurence:456
Rv0162c adhE1 zinc-type alcohol dehydrogenase subunit E 434 435 coexpression:417

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: cytidine/deoxycytidylate deaminase
  • MTBC0 PGAP product: nucleoside deaminase
  • Pfam (hmmscan --cut_ga): dCMP_cyt_deam_1 PF00383.30 (E=2e-26), MafB19-deam PF14437.13 (E=7e-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_218269.1)
  • Domains: Pfam-A via hmmscan --cut_ga — dCMP_cyt_deam_1 (PF00383.30), MafB19-deam (PF14437.13)
  • 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 COG0590
  • Curated reference: UniProt O69719 (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 — 44 functional partner(s); context anchor dhmA1
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_003976|Rv3752c|
MTTDEDLIRAALAVAATAGPRDVPVGAVVVGADGTELARAVNAREALGDPTAHAEILAMRLAAGVLGDGWRLEGTTLAVTVEPCTMCAGALVLARVARLVFGAWEPKTGAVGSLWDVVRDRRLNHRPEVRGGVLARECAAPLEAFFARQRLG