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Table 4 Nonpathogen-linked gene circuits in bacterial strains. The columns identify pathways, circuits, nonpathogen-linked orthologs within the circuit; and genera expressing the circuit

From: Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity – a large-scale system analysis of decoded bacterial genomes

  Pathway Circuit Orthologs Genera
1 Steroid biosynthesis Squalene to 24,25-Dihydro-lanosterol SQLE, ERG1, E5.4.99.7, LSS, ERG7, DHCR24 C. coralloides*, F. taffensis, M. capsulatus*, M. alcaliphilum, S. aurantiaca
7 Arginine and proline metabolism N-Acetyl-glutamate - N-Acetyl-ornithine argB, ARG56, argC, lysY, ARG56, E2.6.1.11, argD, argD, lysJ E. coli*, S. enterica*, S. aureus*, L. monocytogenes, M. tuberculosis*
3 Biosynthesis of 12-, 14- and 16-membered macrolides Propanoyl-CoA to Erythromycin A E2.3.1.94, eryF, eryBV, eryCIII, eryCII, eryG, eryK F. alni, S. erythraea,
2 Lysine biosynthesis L-2-Amino adipate to Pyrrolysine lysX, lysZ, lysY, lysJ, E2.4.1.173, pylB, pylC, pylD T. thermophilus*, P. mucilaginosus, C. sp., D. hafniense, M. ruber
5 Glycine, serine and threonine metabolism Choline - Glycine codA, gbsB, BHMT, DMGDH, SARDH B. amyloliquefaciens, B. subtilis, S. meliloti, R. sphaeroides, B. licheniformis
6 Arginine and proline metabolism Creatine Pathway GAMT, E2.7.3.2, E3.5.3.3, E3.5.1.59, hyuA, hyuB, E3.5.4.21 H. pylori*, P. putida, C. sp., A. mediterranei, G. sp.
11 Type I polyketide structures Rifamycin B rifA, rif14, rifB, rif20, rifC_D, rifE, rifF, asm9, rif19 A. mediterranei*, F. sp., A. mirum, M. aurantiaca, M. sp.
4 Biosynthesis of 12-, 14- and 16-membered macrolides 2-Methylbutanoyl to Avermectin aveA, aveE, aveF, aveD, aveBI S. avermitilis.
8 Streptomycin biosynthesis scyllo-inosamine stsE, strB1, E2.4.2.27, strK, K12570, aphD, strA S. griseus
9 Type I polyketide structures Erythromycin A eryK, E2.3.1.94, eryF, E2.3.1.94, eryCIII, eryCII, E2.3.1.94, eryBV F. alni, S. erythraea.
10 Type I polyketide structures Avermectin A1a aveA, aveBI, aveE, aveF, aveD S. avermitilis,
12 Type I polyketide structures Myalamid S mxaB, mxaE_D, mxaF G. violaceus, H. ochraceum, H. aurantiacus, M. xanthus, N. punctiforme
13 Biosynthesis of type II polyketide backbone 7,9,12-Octaketides actI1, actI2, actI3, actIII, actVII A. mediterranei*, F. sp., A. missouriensis, C. acidiphila*, C. epipsammum
14 Biosynthesis of type II polyketide products 7,9,12-Octaketides - Actinorhodin actVI1, RED1, actVI3, actVI2, actIV, actVI4, actVA6, actVIA, actVA5, actVB A. mediterranei*, F. sp., M. abscessus, S. cattleya, A. ferrooxidans
15 Serotonergic synapse Signal transduction PLA2G4, CPLA2, ALOX5, PTGS2, COX2, PTGS2, COX2 R. sphaeroides*, C. coralloides, G. obscurus, M. nodulans, M. sp.
16 Insulin signaling pathway Glycogenesis/ antilipolysos GYS, CALM, PHKA_B, PRKAR S. sp., C. sp., A. sp., B. coagulans, C. sp.
17 Chemical carcinogenesis Azo dyes/Liver cancer/Bladder cancer PTGS2, COX2, CYP1A1 R. sphaeroides*, G. obscurus, M. mediterranea, M. nodulans, M. sp.
  1. The symbol * indicates those genera for which the circuitry was linked to synergy via within genus comparison
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BMC Genomics

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