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

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.