TABLE 3.

Acid-repressed genes

GeneLog2 ratioDesignationAnnotation or description
Cell envelope genes
    Atu0482−1.05Polysaccharide deacetylase
    Atu0887−1.15Acetyltransferase
    Atu3191−2.03Outer membrane protein
Stress response gene
    Atu3121−1.02cspACold shock family protein
Metabolism and cofactor synthesis genes
    Atu0727−1.12Ferredoxin:oxidoreductase, flavin adenine dinucleotide/NAD(P) binding
    Atu0771−1.01coxCCytochrome c oxidase, subunit III
    Atu1529−0.99fixHNitrogen fixation protein
    Atu1534−1.29fixpCytochrome c oxidase, cbb3-type, subunit III
    Atu1535−1.78fixQcbb3-type cytochrome oxidase
    Atu1536−1.95fixOcbb3-type cytochrome oxidase component
    Atu1537−2.23fixNcbb3-type cytochrome oxidase component
    Atu1601−1.51hemNOxygen-independent coproporphyrinogen III oxidase
    Atu1997−1.52Sulfite reductase (NADPH) flavoprotein alpha component
    Atu2073−1.07Electron transport protein SCO1/SenC
    Atu2283−1.62Pseudoazurin; copper binding electron transfer protein
    Atu2613−1.04hemA5-Aminolevulinate synthase
    Atu3977−1.8Large exoprotein involved in heme utilization or adhesion
    Atu4091−1.55cydACytochrome bd ubiquinol oxidase subunit I
    Atu4092−1.47cydBCytochrome d ubiquinol oxidase subunit II
    Atu4823−1.06acaBAcetyl-coenzyme A acetyltransferase
Genes for biodegradation and modification of organic compounds
    Atu1814−1.47Epoxide hydrolase
    Atu2394−1.58Aminoglycoside acetyltransferase
    Atu3664−1.23ephAEpoxide hydrolase
Amino acid synthesis and degradation genes
    Atu0053−1.84Small-subunit 16S rRNA
    Atu0057−1.52Small-subunit 23S rRNA
    Atu2109−1.17RNase P RNA (rnpB)
    Atu2542−1.53Small-subunit 23S rRNA
    Atu2547−1.78Small-subunit 16S rRNA
    Atu3292−1.26alrAlr, alanine racemase
    Atu3937−1.84Small-subunit 16S rRNA
    Atu3941−1.55Small-subunit 23S rRNA
    Atu4180−1.89Small-subunit 16S rRNA
    Atu4186−0.99Small-subunit 5S rRNA
Hypothetical genes
    Atu0515−1.06Hypothetical protein
    Atu0544−1.27Hypothetical protein
    Atu0896−1.19Hypothetical protein
    Atu0904−1.48Hypothetical protein
    Atu0955−1.05Hypothetical protein
    Atu0983−1.88Hypothetical protein
    Atu1031−1.49Hypothetical protein
    Atu1467−1.01Hypothetical protein
    Atu1637−1.05Hypothetical protein
    Atu1667−1.53Hypothetical protein
    Atu1975−0.99Hypothetical protein
    Atu3190−1.01Hypothetical protein
    Atu3321−1.04Hypothetical protein
    Atu3837−1.1Hypothetical protein
    Atu3838−1.03Hypothetical protein
    Atu4185−1.75Hypothetical protein
Conserved hypothetical genes
    Atu1049−2.94Conserved hypothetical protein
    Atu1468−1.21Conserved hypothetical protein
    Atu4443−1.19Conserved hypothetical protein
Transporter genes
    Atu1577−1.27Amino acid ABC transporter, periplasmic binding
    Atu1717−1.23fadLLong-chain fatty acid transport protein
    Atu2744−1.77TRAP dicarboxylate transporter
    Atu3253−1.04TRAP dicarboxylate transporter
    Atu3575−1.33xylHXylose transport permease protein
    Atu3821−1.23rbsBABC-type sugar transport, periplasmic component
    Atu4667−1.65ABC-type multidrug transport, ATPase component
    Atu4687−1.06Amino acid ABC transporter, periplasmic binding
    Atu5268−1.45dctpTRAP dicarboxylate transporter
Genes for extracellular appendages and function
    Atu0373−1.07mcpXMethyl-accepting chemotaxis protein
    Atu0387−1.03mcpAMethyl-accepting chemotaxis protein
    Atu0520−1.08chey2Chemotaxis protein CheYII
    Atu0543−1.24flaBFlagellum-associated protein
    Atu0545−2.35flaAFlagellum-associated protein
    Atu1912−1.19mclAMethyl-accepting chemotaxis protein
    Atu2223−1.65mcpAMethyl-accepting chemotaxis protein
    Atu6132−1.25mcpAMethyl-accepting chemotaxis protein
Nucleic acid synthesis and metabolism genes
    Atu0069−1.24nrdlNrdl protein involved in ribonucleotide reduction
    Atu0070−1.07nrdERibonucleoside-diphosphate reductase 2 alpha chain
    Atu0071−1.54nrdFRibonucleoside-diphosphate reductase 2 beta chain
    Atu3003−1.68Transposase
    Atu3181−2.17cowBCobalamin synthesis protein/P47K family protein