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Table 1 Summary of results obtained by Function Discovery V1.0 when applied to ten known-function TRs

From: Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions

TRa Pathway name Known pathway genes Genes clustered with the TRb TRE Ref
betI (B1590) glycine betaine synthesis betABTI betABTI choline [21]
catR (A2107) benzoate degradation catABCR catABCR cis, cis-muconate [22]
cymR (A3550) p-cumate catabolism cymAaAbAcAdBCDEFHG cymAaAbAcAd─CDE─ ─ ─ p-cumate [23]
cysB (A2466) sulfur metabolism cysABPTWA cysABPTW N-acetyl-serine [24]
glpR (A0643) glycerol metabolism glpABCDKFR glp─ ─ ─DKFR glycerol-3-phosphate [25]
hpaR (B2027) hydroxyphenylacetate catabolism hpaGEDFHIR hpaGEDFHIR 4-hydroxy-phenylacetate [26]
kynR (A0736) oxidative tryptophan degradation kynABU kynABU L-kynurenine [27]
hutC (A2946) histidine degradation hutHUIFGC hutHUIFGC urocanate [28, 29]
rcoM (A2142) carbon monoxide oxidation coxBCMSLDEFGHIK cox ─ ─SMLDE ─G ─ ─ ─ carbon monoxide [30]
modEB2851) molybdate transport modABCDE modABC─E molybdenum [31]
  1. aTranscriptional regulators of interest, the locus tag of the gene is in parentheses and excludes the “bxe_” prefix.
  2. bGenes missing in the cluster are identified by a dash (─). This table summarizes the analysis of 10 genes upstream and 10 genes downstream of the TR of interest.