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. 2005 Jan;187(1):304–319. doi: 10.1128/JB.187.1.304-319.2005

TABLE 4.

Catabolism and respiration

Group Gene Function Log2 pH ratioa
Classb
5/7 8.7/7 8.7/5
Sugar catabolism and TCA cycle aceE Pyruvate dehydrogenase 1.928 0.527 −1.401 NL
aceF Pyruvate dehydrogenase dihydrolipoamide acetyltransferase 1.802 0.402 1.401 NL
aceK Isocitrate dehydrogenase kinase/phosphatase 0.667 0.038 −0.629 AH
acnA Aconitase A, stationary phase induced 0.769 −0.143 −0.912 AH
acnB Aconitase B; 2-methylaconitate hydratase 1.036 −0.041 −1.077 NL
acrR Regulator for acrA and acrB −0.873 0.164 1.037 AL
dcuR (yjdG) Fumurate respiration regulator (anaerobic) −0.220 0.055 0.275 AL
dcuS (yjdH) Fumurate respiration regulator (anaerobic) −0.324 0.065 0.390 AL
dhaK Dihydroxyacetone kinase, subunit I 1.041 −0.379 −1.420 AH
dhaL Dihydroxyacetone kinase, subunit II 0.742 −0.385 −1.127 AH
dld d-Lactate dehydrogenase 0.919 0.566 −0.353 NL
eno Enolase; RNA degradosome 0.299 0.052 −0.247 AH
fucI l-Fucose isomerase −0.693 −0.173 0.520 AL
fucK l-Fuculose kinase −1.259 −0.519 0.740 NH
fucR Positive regulator, fuc operon −0.046 0.495 0.541 BH
galF Putative regulator of galU NL
galK Galactokinase −0.616 −0.562 0.053 BL
galM Galactose mutarotase; aldose-1-epimerase −0.619 −0.647 −0.028
gapA Glyceraldehyde 3-P dehydrogenase A 0.093 −0.752 −0.844 BL
gatA Galactitol-specific enzyme IIA of PTSd 0.929 −0.626 −1.555 AH
gatB Galactitol-specific enzyme IIB of PTS 0.632 −0.895 −1.528 AH
gatC Galactitol-specific enzyme IIC of PTS 0.973 −0.949 −1.922 AH
gatD Galactitol-1-phosphate dehydrogenase 1.037 −0.893 −1.930 AH
gatY d-Tagatose-1,6-bisphosphate aldolase, class II 0.846 −0.483 −1.329 AH
gatZ Enhances GatY activity 0.774 −0.605 −1.380 AH
glpA Glycerol-3-phosphate dehydrogenase large subunit (anaerobic) −0.200 0.558 0.758 AL
glpB Glycerol-3-phosphate membrane anchor (anaerobic) −0.124 0.437 0.562 BH
glpC Glycerol-3-phosphate dehydrogenase (anaerobic) small subunit −0.169 0.469 0.638 BH
glpX Fructose 1,6-bisphosphatase −0.162 0.375 0.537 BH
gltA Citrate synthase 0.288 −0.559 −0.846 AH
gnd Gluconate-6-phosphate dehydrogenase 0.895 0.351 −0.544 NL
gntT High-affinity gluconate transport −0.613 −0.362 0.251 NH
gpsA Glycerol-3-phosphate dehydrogenase −0.492 −0.534 −0.041 NH
gpmA Phosphoglycerate mutase I 0.303 −0.118 −0.421 AH
icdA Isocitrate dehydrogenase 1.211 0.061 −1.272 AH
lldD l-Lactate dehydrogenase 0.613 −0.554 −1.167 AH
lldP l-Lactate permease; glycolate uptake 1.527 0.219 −1.307 NL
lpdA Lipoamide dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenase complexes 1.507 0.281 −1.226 NL
malE Maltose-binding protein, periplasmic −3.425 −2.933 0.491 NH
malF Maltose transport, inner membrane −1.016 −0.935 0.082 NH
malG Maltose transport, inner membrane subunit −1.577 −1.502 0.075 NH
malK Maltose transport, ATP-binding subunit −4.790 −3.748 1.041 NH
malM Periplasmic protein, mal regulon −4.643 −3.780 0.863 NH
malP Maltodextrin phosphorylase −4.000 −3.373 0.627 NH
malQ Amylomaltase −3.322 −2.883 0.439 NH
malT mal positive regulator −0.103 0.617 0.720 BH
pdhR Pyruvate dehydrogenase operon repressor 0.755 −0.109 −0.863 AH
pfkB 6-Phosphofructokinase-2 0.363 0.095 −0.268 NL
pflA Pyruvate formate lyase I activase 0.964 0.667 −0.297 NL
pflB Pyruvate formate lyase I (anaerobic) 0.812 0.578 −0.234 NL
pgi Glucose phosphate isomerase 0.654 0.177 −0.477 NL
pta Phosphotransacetylase 1.167 0.639 −0.528 NL
ptsG Glucose PTS enzyme IIBC 0.841 0.544 −0.287 NL
ptsH PTS system histidine phosphocarrier protein Hpr 0.369 0.564 0.195 NL
ptsI PTS system enzyme I 0.241 0.339 0.098 NL
ptsO NPr, N-regulated HPr-like protein 0.639 0.168 −0.470 NL
rpiA Ribose-5-phosphate isomerase A 0.180 0.364 0.184 BH
srlA Sorbitol-specific enzyme II of PTS −1.156 −1.720 −0.564 BL
srlB Sorbitol-specific enzyme III of PTS −0.908 −1.140 −0.232 BL
srlD Sorbitol-6-phosphate dehydrogenase −0.660 −1.334 −0.674 BL
srlE srl operon protein −1.013 −1.613 −0.599 BL
srlR srl regulator −0.151 0.804 −0.654 BL
sucA 2-Oxoglutarate dehydrogenase, E1 component 0.850 −0.851 −1.701 AH
sucB Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex (E2) 0.566 −1.073 −1.638 AH
sucC Succinyl-CoAc synthase beta subunit 0.494 −1.019 −1.513 AH
sucD Succinyl-CoA synthase alpha subunit 0.526 −1.225 −1.751 AH
tpiA Triosephosphate isomerase 0.772 0.245 −0.526 NL
treB Trehalose-specific PTS enzyme II −3.156 0.739 3.895 AL
treC Trehalose-6-phosphate hydrolase −2.613 0.620 3.233 AL
Proton transport and electron transport chain atpA ATP synthase subunit alpha, F1 0.111 0.460 0.349 BH
atpB ATP synthase subunit a, F0 0.125 0.484 0.609 BH
atpC ATP synthase subunit epsilon, F1 0.266 1.005 0.739 BH
atpD ATP synthase subunit beta, F1 0.542 1.172 0.630 BH
atpE ATP synthase subunit c, F0 0.182 0.503 0.321 BH
atpF ATP synthase subunit b, F0 −0.055 0.321 0.377 BH
atpG ATP synthase subunit gamma, F1 0.372 0.632 0.260 BH
atpH ATP synthase subunit delta, F1 −0.172 0.186 0.358 AL
atpI ATP synthase subunit, F1F0-type proton-ATPase 0.017 0.499 0.482 BH
cydA Cytochrome d (bd-I) terminal oxidase subunit I (microaerobic) −0.268 0.872 1.140 BH
cydB Cytochrome d (bd-I) terminal oxidase subunit II (microaerobic) −0.097 0.777 0.874 BH
cydC Cysteine exporter to periplasm required for Cyd assembly 0.135 0.490 0.355 BH
cydD Cysteine exporter to periplasm required for cytochrome assembly 0.232 0.574 0.342 BH
cyoA Cytochrome o oxidase subunit II 1.160 0.217 −0.943 NL
cyoB Cytochrome o oxidase subunit I 0.812 −0.204 −1.016 NL
cyoC Cytochrome o oxidase subunit III 1.026 0.019 −1.007 NL
cyoD Cytochrome o oxidase subunit IV 0.829 −0.192 −1.021 NL
cyoE Cytochrome o oxidase subunit protoheme IX farnesyltransferase 1.094 0.225 −0.869 NL
fdoG Formate dehydrogenase-O, major selenopeptide subunit 0.353 −0.138 −0.491 AH
fdoH Formate dehydrogenase-O Fe-S subunit 0.003 −0.414 −0.416 BL
frdA Fumarate reductase flavoprotein subunit −0.305 0.046 0.351 AL
frdC Fumarate reductase membrane anchor polypeptide −0.378 −0.008 0.370 AL
fumA Fumarase A 0.595 −0.647 −1.242 AH
nfsA (mdaA) Nitroreductase A 0.561 −0.419 −0.980 AH
mdaB Probable nitroreductase or quinone reductase 0.444 −0.223 −0.667 AH
napC Cytochrome electron source for NapAB, membrane bound −0.797 −0.382 0.416 NH
ndh Respiratory NADH dehydrogenase II; NADH:ubiquinone oxidoreductase II 0.789 0.161 −0.628 NL
nuoC NADH:ubiquinone oxidoreductase subunit C 0.440 −0.084 −0.524 AH
nuoG NADH:ubiquinone oxidoreductase subunit G; NADH dehydrogenase I 0.525 0.103 −0.442 NL
nuoH NADH:ubiquinone oxidoreductase subunit H; NADH dehydrogenase I 0.564 0.185 −0.379 NL
nuoI NADH:ubiquinone oxidoreductase subunit I; NADH dehydrogenase I 0.792 0.310 −0.481 NL
nuoJ NADH:ubiquinone oxidoreductase subunit J; NADH dehydrogenase I 0.468 0.234 −0.234 NL
nuoK NADH:ubiquinone oxidoreductase subunit K; NADH dehydrogenase I 0.766 0.460 −0.306 NL
nuoL NADH:ubiquinone oxidoreductase subunit L; NADH dehydrogenase I 0.311 0.078 −0.233 NL
nuoN NADH:ubiquinone oxidoreductase subunit N; NADH dehydrogenase I 0.126 −0.210 −0.336 AH
sdhA Succinate dehydrogenase flavoprotein subunit 1.438 −0.018 −1.458 AH
sdhB Succinate dehydrogenase iron-sulfur protein 1.833 0.329 −1.505 AH
sdhC Succinate dehydrogenase membrane anchor subunit, cytochrome b556 2.728 0.890 −1.838 NL
sdhD Succinate dehydrogenase hydrophobic subunit 2.349 0.595 −1.754 NL
Amino acid catabolism and transport artI Arginine periplasmic binding protein 0.286 0.655 0.369 BH
artM Arginine periplasmic binding protein −0.115 0.293 0.407 BH
cadA Lysine decarboxylase, degradative 1.024 0.137 −0.887 AH
cysK O-Acetylserine sulfhydrylase A (cysteine synthase) 1.204 1.351 0.147 NL
dadA d-Amino acid dehydrogenase 1.273 −0.229 −1.501 AH
dadX d-Amino acid dehydrogenase 0.683 −0.393 −1.076 AH
dppC Dipeptide permease system −0.346 −0.032 0.315 AL
gdhA Glutamate dehydrogenase −0.080 −0.496 −0.416 BL
hisC Histidinol-phosphate aminotransferase 0.253 0.984 0.731 BH
hisF Imidazole glycerol phosphate synthase (cyclase) 0.150 0.703 0.553 BH
hisH Amidotransferase of imidazole glycerol phosphate synthase 0.034 0.393 0.359 BH
hisI PR-ATP pyrophosphatase and PR-AMP cyclohydrolase 0.234 0.641 0.407 BH
hisJ Histidine-binding protein −0.149 0.400 0.549 BH
lysC Aspartokinase III 1.464 −0.226 −1.690 AH
lysP Lysine permease 2.662 0.963 −1.698 NL
lysU Lysine-tRNA ligase 0.544 −0.077 −0.621 AH
potD Putrescine-ornithine transporter 0.053 0.509 0.456 BH
sdaA l-Serine deaminase, degradative −0.409 0.638 1.048 BH
sdaB l-Serine deaminase −1.111 −0.434 0.678 AL
sdaC H+/serine symporter; regulator of serine deaminase −1.205 −0.410 0.794 AL
tnaA Tryptophan deaminase, degradative; also deaminases serine and cysteine −3.805 0.223 4.028 AL
tnaB Tryptophan transporter −1.840 1.153 2.993 AL
tnaC tnaA leader peptide −5.026 0.490 5.517 AL
tdcB Threonine dehydratase, degradative −0.849 −0.296 0.553 NH
ydfG l-allo-Threonine, l-serine, d-serine dehydrogenase 0.407 0.287 −0.120 NL
a

Values in boldface are significant (α = 0.001).

b

NL, Neutral Low; AH, Acid High; AL, Acid Low; BH, Base High; BL, Base Low; NH, Neutral High.

c

CoA, coenzyme A.

d

PTS, phosphotransferase.