Table 3.
Function group and gene name | ID | Product | COGa | Fold upregulation in RM6607Rb |
---|---|---|---|---|
Fatty acid uptake or metabolism | ||||
fadE | Z0278 | Putative acyl-CoA dehydrogenase | COG1960I | 5.7 |
hdhA | Z2624 | NAD-dependent 7-α-hydroxysteroid dehydrogenase | COG1028IQR | 2.0 |
fadD | Z2848 | Acyl-CoA synthetase, long-chain fatty acid–CoA ligase | COG0318IQ | 5.4 |
fadJ | Z3604 | Multifunctional fatty acid oxidation complex subunit α | COG1250I | 3.6 |
fadI | Z3605 | 3-Ketoacyl–CoA thiolase | COG0183I | 3.1 |
fadL | Z3608 | Long-chain fatty acid outer membrane transporter | COG2067I | 4.4 |
ucpA | Z3691 | Short-chain dehydrogenase | COG1028IQR | 4.3 |
fadA | Z5366 | 3-Ketoacyl–CoA thiolase | COG0183I | 4.2 |
fadB | Z5367 | Multifunctional fatty acid oxidation complex subunit α | COG1250I | 5.9 |
acs | Z5668 | Acetyl-CoA synthetase | COG0365I | 5.0 |
phoH | Z1522 | PhoB dependent, putative ATPase, involved in lipid metabolism and RNA modification | COG1702T | 3.7 |
Amino acid uptake or metabolism | ||||
gltL | Z0802 | ATP-binding protein of glutamate/aspartate transport system | COG1126E | 2.4 |
gltK | Z0803 | Glutamate/aspartate transport system permease | COG0765E | 3.0 |
gltJ | Z0804 | Glutamate/aspartate transport system permease | COG0765E | 2.5 |
glnH | Z1033 | Glutamine ABC transporter periplasmic protein | COG0834ET | 2.3 |
Z2223 | Z2223 | Hemin-binding lipoprotein | COG0747E | 3.8 |
Z2224 | Z2224 | Transport system permease protein | COG0601EP | 2.4 |
Z2276 | Z2276 | Transport system permease protein | COG1177E | 6.7 |
Z2277 | Z2277 | Transport system permease protein | COG1176E | 3.8 |
Z2278 | Z2278 | ATP-binding component of a transport system | COG3842E | 5.5 |
Z2279 | Z2279 | Transport protein | COG0687E | 5.7 |
fliY | Z3010 | Cystine transporter subunit | COG0834ET | 6.4 |
hisP | Z3568 | Histidine/lysine/arginine/ornithine transporter subunit | COG4598E | 4.2 |
hisM | Z3569 | Histidine transport, membrane protein M | COG4160E | 2.1 |
hisQ | Z3570 | Histidine transport system permease protein | COG4215E | 2.7 |
hisJ | Z3571 | Histidine-binding periplasmic protein of high-affinity histidine transport system | COG0834ET | 2.8 |
argT | Z3572 | Lysine-, arginine-, and ornithine-binding periplasmic protein | COG0834ET | 3.9 |
oppD | Z2022 | Oligopeptide ABC transporter ATP-binding protein | COG0444EP | 2.2 |
dppA | Z4961 | Dipeptide transport protein | COG0747E | 2.4 |
ylbB | Z0671 | Putative hydantoin utilization protein | COG0624E | 2.9 |
cstA | Z0740 | Carbon starvation protein, cAMP-CRP dependent, involved in peptide utilization. | COG1966T | 3.0 |
cstC | Z2780 | Acetylornithine δ-aminotransferase, participates in catabolism of amino acids | COG4992E | 4.9 |
dadA | Z1952 | d-Amino acid dehydrogenase subunit, catalyzes oxidative deamination of d-amino acids | COG0665E | 2.1 |
ydjS | Z2776 | Succinylglutamate desuccinylase, hydrolyzes N-succinyl-l-glutamate to succinate and l-glutamate, participates in arginine and proline metabolism | COG2988E | 4.5 |
Z2777 | Z2777 | Succinylarginine dihydrolase, catalyzes hydrolysis of 2-N-succinylarginine into 2-N-succinylornithine, ammonia, and carbon dioxide in arginine degradation | COG3724E | 6.0 |
Z2779 | Z2779 | Arginine succinyltransferase, participates in arginine and proline metabolism | COG3138E | 5.8 |
Z3717 | Z3717 | Putative ethanolamine utilization protein EutP | COG4917E | 2.6 |
gcvH | Z4241 | Glycine cleavage system protein H | COG0509E | 2.2 |
gcvT | Z4242 | Glycine cleavage system aminomethyltransferase T | COG0404E | 2.2 |
aspA | Z5744 | Aspartate ammonia lyase, participates in alanine and aspartate metabolism and nitrogen metabolism | COG1027E | 5.3 |
Carbohydrate uptake or metabolism | ||||
nagE | Z0826 | Phosphotransferase system N-acetylglucosamine-specific transporter subunit IIABC | COG1263G | 2.5 |
Z2192 | Z2192 | ABC transporter ATP-binding protein | COG1129G | 2.5 |
ycjV | Z2463 | ABC transporter ATP-binding protein | COG3839G | 2.1 |
ugpE | Z4819 | Glycerol-3-phosphate transporter membrane protein, related to uptake of glycerol-3-phosphate | COG0395G | 2.4 |
ugpA | Z4820 | Glycerol-3-phosphate transporter permease | COG1175G | 3.1 |
ugpB | Z4822 | Glycerol-3-phosphate transporter periplasmic binding protein | COG1653G | 3.2 |
xylF | Z4991 | d-Xylose transporter subunit XylF | COG4213G | 2.0 |
rbsB | Z5252 | d-Ribose transporter subunit RbsB | COG1879G | 2.3 |
Z5691 | Z5691 | Ribose ABC transporter ATP-binding protein | COG1129G | 2.1 |
Z5839 | Z5839 | ABC transporter ATP-binding protein | COG1129G | 2.2 |
Z2189 | Z2189 | Autoinducer-2 ABC transporter, periplasmic autoinducer-2-binding protein LsrB, sugar ABC transporter | COG1879G | 2.7 |
ytfQ | Z5838 | Periplasmic binding domain of ABC-type YtfQ-like transport systems | COG1879G | 2.7 |
mgsA | Z1314 | Methylglyoxal synthase, participates in pyruvate metabolism | COG1803G | 2.4 |
yneB | Z2188 | Aldolase, catalyzes a reversible aldol reaction | COG1830G | 2.6 |
manB | Z3194 | Phosphomannomutase, participate in fructose and mannose metabolism | COG1109G | 2.0 |
yeiQ | Z3431 | Putative oxidoreductase, may be related to metabolic pathways | COG0246G | 3.5 |
yihM | Z5409 | Hypothetical protein contains conserved domain pfam01261 (AP_endonuc_2) and COG1082 [IolE], may be related to carbohydrate transport and metabolism | COG1082G | 2.6 |
The COG category was assigned based on the annotation for E. coli O157:H7 strain EDL933.
The ratio of normalized hybridization intensities of the gene in RM6607R to that in RM6607W. All genes listed passed the significance test as detailed in Materials and Methods.