MTBC Gene Atlas

Rv1044 Family assigned · medium auto-curated

H37Rv Rv1044 · MTBC0 mtbc0_001121 · 207 aa · 1174391–1175014 (+) · RefSeq NP_215560.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationtype IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
Revised (this work)Type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein. Pfam: AbiEi_4 (PF13338.13).

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

Curated reference (UniProt)

UniProt P96357 TrEMBL · unreviewed · Evidence at protein level
UniProt nameAbiEi antitoxin N-terminal domain-containing protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category K Transcription
eggNOG descriptionPsort location Cytoplasmic, score
Orthologous groupCOG5340

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
AbiEi_4PF13338.13 2.3e-1518–66 Transcriptional regulator, AbiEi antitoxin

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv1045 hyp hypothetical protein 999 990 ctx neighborhood:801 cooccurence:758 coexpression:817 textmining:913
Rv3190c hyp hypothetical protein 482 482 ctx cooccurence:451
Rv1043c hyp hypothetical protein 462 462 ctx neighborhood:460
Rv0836c hyp hypothetical protein 880 181 textmining:860
Rv0837c hyp hypothetical protein 831 180 textmining:803
Rv2826c hyp hypothetical protein 883 87 textmining:878
Rv3189 hyp hypothetical protein 446 52 textmining:440
Rv3188 hyp hypothetical protein 442 50 textmining:437
Rv2827c hyp hypothetical protein 870 47 textmining:870
Rv0918 hyp hypothetical protein 435 44 textmining:434
Rv1989c mbcT hyp hypothetical protein 653 43 textmining:653
Rv0078B hyp hypothetical protein 815 41 textmining:815
Rv0078A hyp hypothetical protein 803 41 textmining:803
Rv0060 darG hyp hypothetical protein 803 41 textmining:803
Rv0059 darT hyp hypothetical protein 656 41 textmining:656

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: type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
  • Pfam (hmmscan --cut_ga): AbiEi_4 PF13338.13 (E=2e-15)
  • (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_215560.1)
  • Domains: Pfam-A via hmmscan --cut_ga — AbiEi_4 (PF13338.13)
  • 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 COG5340
  • Curated reference: UniProt P96357 (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 — 19 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001121|Rv1044|
MCAKPYLIDTIAHMAIWDRLVEVAAEQHGYVTTRDARDIGVDPVQLRLLAGRGRLERVGRGVYRVPVLPRGEHDDLAAAVSWTLGRGVISHESALALHALADVNPSRIHLTVPRNNHPRAAGGELYRVHRRDLQAAHVTSVDGIPVTTVARTIKDCVKTGTDPYQLRAAIERAEAEGTLRRGSAAELRAALDETTAGLRARPKRASA