MTBC Gene Atlas

Rv1887 Family assigned · low

H37Rv Rv1887 · MTBC0 mtbc0_002001 · 380 aa · 2154312–2155454 (+) · RefSeq NP_216403.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationhypothetical protein
Revised (this work)Exopolyphosphatase-like fold (PDB 3HI0); putative phosphatase/hydrolase.

Curated reference (UniProt)

UniProt O07745 TrEMBL · unreviewed · Evidence at protein level
UniProt nameDUF7159 domain-containing protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

Orthologous group29WFR

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 1.655 · diversifying/relaxed
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 9 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
DUF7159PF23717.2 1.8e-742–230 Family of unknown function (DUF7159)

Structural neighbours (Foldseek on the ESMFold model, exploratory)

ESMFold model confidence: mean pLDDT 85.4 (confident). A confident model makes the fold comparison meaningful.

Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.

TargetProbTME-valueDescription
3hi0-assembly1_B 1.00 0.52 3.9e-07 sig 3hi0-assembly1_B Crystal structure of Putative exopolyphosphatase (17739545) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.30 A resolution
6pc2-assembly1_A 1.00 0.42 2.9e-08 sig 6pc2-assembly1_A Crystal structure of Helicobacter pylori PPX/GppA in complex with GNP
6pc1-assembly2_C 1.00 0.42 2.6e-07 sig 6pc1-assembly2_C Crystal structure of Helicobacter pylori PPX/GppA (E143A) in complex with ppGpp
7t1h-assembly1_B 1.00 0.53 4.5e-04 sig 7t1h-assembly1_B Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae in complex with compound YU281445
6uj5-assembly1_B 1.00 0.42 3.1e-04 sig 6uj5-assembly1_B Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae
7t1h-assembly1_A 1.00 0.45 5.1e-04 sig 7t1h-assembly1_A Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae in complex with compound YU281445
7t1g-assembly1_A 0.99 0.49 1.0e-03 sig 7t1g-assembly1_A Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae in complex with compound YU385595
6uj5-assembly1_A 0.99 0.47 1.2e-03 sig 6uj5-assembly1_A Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv1611 trpC indole-3-glycerol phosphate synthase 783 783 coexpression:783
Rv0704 rplB 50S ribosomal protein L2 553 553 coexpression:553
Rv0544c transmembrane protein 457 458 coexpression:458
Rv0702 rplD 50S ribosomal protein L4 431 431 coexpression:431
Rv0198c zmp1 zinc metalloprotease 425 425 coexpression:414
Rv1630 rpsA 30S ribosomal protein S1 422 423 coexpression:423
Rv1884c rpfC resuscitation-promoting factor RpfC 417 418
Rv1084 hyp hypothetical protein 401 400
Rv1886c fbpB diacylglycerol acyltransferase/mycolyltransferase Ag85B 416 374
Rv0175 Mce associated membrane protein 604 284 textmining:470
Rv1096 glycosyl hydrolase 659 83 textmining:644
Rv3835 hyp hypothetical protein 639 78 textmining:625
Rv3491 hyp hypothetical protein 757 57 textmining:753
Rv2799 membrane protein 807 55 textmining:805
Rv2754c thyX thymidylate synthase ThyX 442 50 textmining:438

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

  • MTBC0 PGAP product: hypothetical protein
  • Pfam: DUF7159 PF23717.2
  • Foldseek best: 3hi0-assembly1_B Crystal structure of Putative exopolyphosphatase (17739545) fro (prob 1.00, E=4e-07, TM=0.52)
  • (structure-only promotion reviewed by hand, 2026-06-01)

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_216403.1)
  • Domains: Pfam-A via hmmscan --cut_ga — DUF7159 (PF23717.2)
  • 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 29WFR
  • Curated reference: UniProt O07745 (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)
  • Model confidence: ESMFold per-residue pLDDT (mean 85.4, confident)
  • 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_002001|Rv1887|
MDTVLGLSITPTTLGWVLAEGHGADGAILDRNELELHSGRNAQAIHTAEQLAAEVLLAHEVAAAGDHRLRVIGVTWNAEASAQAALLVESLTGAGFDNVVPVRRLRAIETLAQAIAPVIGYEQIAVCVLEHESATVVMVDTHDGKTQIAVKHVCRGLSGLTSWLTGMFGRDAWRPAGVVVVGSDSEVSEFSWQLERVLPVPVFAQTMAQVTVARGAALAAAQSTEFTDAQLVADSVSQPTVAPRRSRHYAGAAAALAAAAVTFVASLSLAVGIQLAPHNDTGTAKHGAHKPTPRIAKAVAPAVPPPPTVTPPVPARAPRPAAQHEPPARVTSGEALTEPNPPEEQPNASAPQQDRNDSQPITRVLEHIPGAYGDSAPPAE