MTBC Gene Atlas

Rv1429 Family assigned · medium auto-curated

H37Rv Rv1429 · MTBC0 mtbc0_001529 · 422 aa · 1614222–1615490 (+) · RefSeq NP_215945.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationPucR family transcriptional regulator
Revised (this work)PucR family transcriptional regulator. Pfam: RsbRD_N (PF14361.13), GGDEF_2 (PF17853.7), HTH_30 (PF13556.13).

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

Curated reference (UniProt)

UniProt O06829 TrEMBL · unreviewed · Evidence at protein level
UniProt nameConserved protein

UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category Q Secondary metabolites biosynthesis, transport and catabolism
T Signal transduction mechanisms
eggNOG descriptionPucR C-terminal helix-turn-helix domain
Orthologous groupCOG2508

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 0.691 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 5 synonymous, 10 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
RsbRD_NPF14361.13 5.5e-1422–160 RsbT co-antagonist protein rsbRD N-terminal domain
GGDEF_2PF17853.7 5.3e-09176–296 GGDEF-like domain
HTH_30PF13556.13 1.1e-16351–408 PucR C-terminal helix-turn-helix domain

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

Closest characterised functional partner: fadD12 (acyl-CoA synthetase), medium confidence from genomic context alone (score 642 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.

PartnerProductScoreNo text-miningChannels (≥400)
Rv1431 hyp hypothetical protein 660 660 ctx cooccurence:466
Rv1428c hyp hypothetical protein 654 654 ctx neighborhood:587
Rv1427c fadD12 acyl-CoA synthetase 642 642 ctx neighborhood:587
Rv1426c lipO esterase LipO 589 590 ctx neighborhood:587
Rv2113 integral membrane protein 526 526 ctx cooccurence:524
Rv0538 membrane protein 511 512 ctx cooccurence:509
Rv1432 dehydrogenase 507 507
Rv0377 HTH-type transcriptional regulator 510 503 ctx cooccurence:501
Rv1963c mce3R transcriptional repressor Mce3R 500 501 ctx cooccurence:499
Rv3903c cpnT hyp hypothetical protein 480 481 ctx cooccurence:478
Rv2939 papA5 phthiocerol/phthiodiolone dimycocerosyl transferase 479 479 ctx cooccurence:479
Rv2237 hyp hypothetical protein 473 474 ctx cooccurence:472
Rv1430 PE16 PE family protein PE16 457 457 ctx neighborhood:457
Rv1132 hyp hypothetical protein 442 442
Rv3843c transmembrane protein 433 434 ctx cooccurence:431

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: PucR family transcriptional regulator
  • Pfam (hmmscan --cut_ga): RsbRD_N PF14361.13 (E=5e-14), GGDEF_2 PF17853.7 (E=5e-09), HTH_30 PF13556.13 (E=1e-16)
  • (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_215945.1)
  • Domains: Pfam-A via hmmscan --cut_ga — RsbRD_N (PF14361.13), GGDEF_2 (PF17853.7), HTH_30 (PF13556.13)
  • 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 COG2508
  • Curated reference: UniProt O06829 (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 — 21 functional partner(s); context anchor fadD12
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001529|Rv1429|
MAEAGGGPISVIARHMQLIRDDFISELFDKMKAEIRGLDYDARMADLWRASITENFVTAVHYLDRDTPQSLVEAPAAALAYARAAAQRDIPLSGLVRAHRLGHARFLEVAMQYVSLLEPADRVSTIIELVNRSARLVDLVADQLIVAYEHEHDRWLSRRSGLQQQWVSELLADTPVDVPRAERALGYRLDGVHIAAVVWVDSAVPIGDVVAQFDQVRCLLAGELGPELGPVANSLMVPTDEREARLWFSPAPTRAFAPSRIRAAFESAGIRARLACGRVGDGLRGFRASLKQAERVKALALAGGARPGGRVMFYDDVAPVALLADDLEELRRFVTDVLGDLSVDDERNSWLRETLREFLLRNRSYVATADAMILHRNTIQYRVIQAMELCGQNLDDPDAAFRVQMALEVCRWMAPAVLRAKQ