Supplementary Table 2. Candidate ArcA-regulated genes in gamma-proteobacteria. Scores and positions of ArcA binding sites relative to the translation start are given. Notation: (*) the ortholog is not present in the genome; (-) no site is found in the upstream region; () and (),direct and reverse DNA strand, respectively. a. E. сoli genes from the training set. b. Genes potentially regulated by ArcA. The references report transcription to be redox-dependent in at least one of the four bacteria.

Gene	E. coli	Y. pestis	P. multocida	V. vulnificus	Reference
a. The trainig set
cydA	-586  5.94	-345  4.60	-334  4.40	-138  5.15	Lynch et al, 1996
	-632  4.44
lldP	-134  5.94	*	-362  4.30	-	Lynch et al, 1996
			-139  5.03
glcC	-105(-160) 5.76	*	*	*	Pellicer, Fernandez et al, 1999
glcD ¹⁾	-94(-171) 4.39
soda	-79  5.50	-84  5.50	-63  4.53	-	Hassan et al, 1992
aldA	-49  5.08	-209  5.26	*	-117  5.50	Pellicer, Lynch et al, 1999
		-137  4.27
lpdA	-230  4.42	-136  4.68	-	-	Cunningham et al, 1998
	-232  5.06
icdA	-111  4.91	-40  4.73	-133  4.42	-	Chao et al, 1997
gltA	-654  5.15 -393  4.34	-422  4.40	-167  4.91 -112  5.07	-337  5.88	Lynch et al, 1996
		-248  4.83		-231  4.04
		-248  4.83		-146  4.34
sdhC	-69  5.15 -330  4.34	-476  4.83	*	-117  4.20	Lynch et al, 1996
		-302  4.40
		-302  4.40
b. Genes with conserved ArcA sites
cyoA	-249  4.95	-303  4.71	*	-147  4.48	Tseng at al, 1996
	-260  4.92
fadD	-74  5.17	-75  4.19	-	-133  4.53	Campbell et al, 2003
	-72  4.79	-77  5.14		-135  4.71
focA	-219  4.28	-408  4.09 -284  4.34	-202  4.09	91  4.77	Kaiser at al. 1997
			-191  4.22
			-80  4.16
adhE	-304  4.59	-395  4.21	-	-261  4.58	Wyborn et at, 2002
	-299  4.57			-241  4.59
pdhR	-84  4.85	-102  4.85	*	-197  4.89	Quail et al, 194
cstC	-38  4.98	-177  4.21	*	-329  4.19
	-49  4.42
mdh	-263  5.19	-71  4.22	-	-105  4.88	van der Rest et al, 2000
		-92  4.22
argR	-186  5.19	-386  4.22	-	-282  4.88	Colloms et al, 1998
arcA	-565  4.67	-699  4.01	-	-353  4.57	Lynch et al, 1996
putP	-312  4.53	-724  4.14	-72  4.20	-	Wood, 1987
		-160  4.16	-61  4.67
prpR	-225  4.42	-233  4.14	*	-86  4.24
		-444  4.25
trxC	-65  4.42	-24  4.04	-699  4.05	-486  4.21	Ritz et al, 2000
			-404  4.12	-328  4.40
ppa	-203  4.40	-116  4.00	-150  4.27	-
			-119  4.94
tolB	-54  4.34	-53  4.08	-	-62  4.10
slyB	-6  4.30	-210  4.34	-446  4.02	*
glpF	-88  4.28	-85  4.22	-	-289  5.50	Chen et al, 1994
acpP	-62  4.27	-62  4.27	-142  4.09	-
phnA	-193  4.27	-55  4.60	-99  4.24	-
fadB	-77  4.26	-81  4.57	*	-158  4.07	Campbell et al, 2003
ompC	-508  4.96	-152  4.05	-238  4.98	*	Matsubara et al, 2000
			-259  4.00
dcuB	-390  4.95	-8  4.34	-647  4.16 -584  4.16	-267  4.59 -130  4.07 -405  4.10	Golby et al, 1998
pldA	-145  4.91	-149  5.15	-	-192  4.15
ndk	-109  4.83	-	20  4.11	-

¹⁾ The gltCD divergon contains two sites in the intergenic region, so we treat it as two independent genes.

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