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. ņoli 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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