B Median Log2 Ratio of Expression Levels from Comparisons of 35000Hphfq Catto 35000HP In

TABLE S3. Complete list of genes whose expression was most affected by inactivation of hfq as measured by DNA microarray analysisa.

ORF / Gene / Description of gene product / Median log2 ratiob / SD
Amino acid biosynthesisc
HD0750 / glnA / Glutamine synthetase / 1.06 / 0.09
HD0890 / argC / N-acetyl-gamma-glutamyl-phosphate reductase / 1.06 / 0.08
HD0232 / arcB1 / Ornithine carbamoyltransferase / -3.63 / 0.18
Biosynthesis of cofactors, prosthetic groups, and carriers
HD1162 / ribE / Riboflavin synthase, alpha chain / 2.04 / 0.09
HD1165 / ribH / 6,7-dimethyl-8-ribityllumazine synthase / 1.68 / 0.06
HD2012 / lipA / Lipoic acid synthetase / 1.64 / 0.14
HD1628 / ispE / 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase / 1.58 / 0.12
HD1161 / ribD / Riboflavin-specific deaminase / 1.57 / 0.07
HD1007 / bioB / Biotin synthetase / 1.55 / 0.09
HD1084 / HesB family protein / 1.54 / 0.26
HD1088 / fdx2 / Ferredoxin / 1.16 / 0.05
HD0300 / grxA / Glutaredoxin / 1.10 / 0.18
HD0557 / Conserved possible 6-pyruvoyl tetrahydrobiopterin synthase / 1.08 / 0.11
HD1391 / moaC / Molybdenum cofactor biosynthesis protein C / -1.01 / 0.12
HD0214 / pdxH / Pyridoxamine-5-phosphate oxidase / -1.06 / 0.05
HD0621 / menF / Menaquinone-specific isochorismate synthase / -1.07 / 0.33
HD0273 / ribF / Riboflavin biosynthesis protein RibF / -1.07 / 0.06
HD1480 / bioD1 / Probable dethiobiotin synthetase / -1.30 / 0.13
HD1392 / moaA / Molybdenum cofactor biosynthesis protein A / -1.58 / 0.15
Cell envelope
HD1435 / ompP2B / Outer membrane protein P2 homolog / 3.26 / 0.12
HD0386 / apbE / Thiamine biosynthesis lipoprotein / 2.64 / 0.13
HD1163 / ribAB / Riboflavin biosynthesis protein ribA / 2.13 / 0.12
HD0282 / fimB / Possible fimbrial structural subunit / 1.92 / 0.28
HD1189 / lpxD / UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase / 1.73 / 0.08
HD2016 / dacA / Penicillin-binding protein 5 / 1.66 / 0.13
HD0281 / fimA / Possible fimbrial major pilin protein / 1.61 / 0.51
HD1511 / glmU / Bifunctional GlmU protein / 1.54 / 0.10
HD0250 / Conserved hypothetical protein / 1.49 / 0.16
HD1621 / Conserved hypothetical protein / 1.46 / 0.38
HD1678 / Putative integral membrane protein / 1.35 / 0.16
HD1355 / Conserved hypothetical protein / 1.31 / 0.12
HD0450 / amiB / N-acetylmuramoyl-L-alanine amidase / 1.30 / 0.14
HD1589 / nlpI / Lipoprotein NlpI homolog / 1.26 / 0.12
HD2017 / Possible rare lipoprotein A / 1.24 / 0.11
HD0746 / Possible xylanase A / 1.24 / 0.05
HD1006 / Conserved hypothetical protein / 1.19 / 0.10
HD1094 / Possible outer membrane serine protease / 1.17 / 0.08
HD1187 / lpxA / UDP-N-acetylglucosamine O-acyltransferase / 1.12 / 0.06
HD1087 / hscA / Chaperone protein HscA / 1.12 / 0.07
HD1806 / thiI / Thiamine biosynthesis protein ThiI / 1.10 / 0.08
HD0454 / waaA / 3-deoxy-D-manno-octulosonic-acid transferase / 1.10 / 0.16
HD0040 / yidC / 60 kD inner-membrane protein / 1.07 / 0.11
HD1060 / Hypothetical protein / 1.02 / 0.10
HD1814 / Probable transport protein / 1.00 / 0.07
HD1196 / uppS / Undecaprenyl pyrophosphate synthetase / -1.08 / 0.10
HD1078 / ompP1 / Outer membrane protein P1 / -1.09 / 0.11
HD0073 / napD / Possible napD protein / -1.10 / 0.06
HD1280 / Possible serine protease homolog / -1.23 / 0.13
HD0068 / ftpA / Fine tangled pili major subunit / -1.32 / 0.08
HD1278 / Possible serine protease / -1.71 / 0.10
HD1433 / ompP2A / Outer membrane protein P2 homolog / -2.83 / 0.35
Cellular processes
HD1590 / deaD / Cold-shock DEAD box protein-A / 2.70 / 0.07
HD0357 / Probable carbon starvation protein A / 2.54 / 0.10
HD1512 / Acriflavine resistance protein / 2.48 / 0.07
HD0766 / manZ / Mannose-specific phosphotransferase system IID component / 1.87 / 0.10
HD0646 / Conserved hypothetical protein / 1.85 / 0.12
HD0767 / manY / Mannose-specific phosphotransferase system IIC component / 1.77 / 0.09
HD1472 / Conserved hypothetical protein / 1.33 / 0.19
HD1589 / nlpI / Lipoprotein NlpI homolog / 1.26 / 0.12
HD2017 / Possible rare lipoprotein A / 1.24 / 0.11
HD0746 / Possible xylanase A / 1.24 / 0.05
HD1179 / ksgA / Dimethyladenosine transferase / 1.18 / 0.13
HD1773 / tolB / Colicin tolerance protein / 1.17 / 0.07
HD1094 / Possible outer membrane serine protease / 1.17 / 0.08
HD1008 / cspC / Cold shock-like protein CspC / 1.14 / 0.11
HD1180 / surA / Survival protein SurA homolog / 1.11 / 0.07
HD1505 / lspA1 / Large supernatant protein 1 / 1.07 / 0.06
HD0984 / ftsY / Cell division protein FtsY / 1.04 / 0.09
HD1585 / mukF / MukF protein / -1.06 / 0.08
HD0902 / cdtA / Cytolethal distending toxin protein A / -1.06 / 0.04
HD1518 / Hypothetical protein / -1.07 / 0.14
HD0073 / napD / Possible napD protein / -1.10 / 0.06
HD0014 / mesJ / Probable cell-cycle protein MesJ / -1.18 / 0.10
HD1327 / hhdA / Hemolysin / -1.20 / 0.11
HD1280 / Possible serine protease homolog / -1.23 / 0.13
HD1155 / lspB / Large supernatant protein exporter / -1.24 / 0.16
HD1791 / bolA / Putative transcriptional regulator, BolA / -1.41 / 0.07
HD0066 / Hypothetical protein / -1.52 / 0.11
HD1278 / Possible serine protease / -1.71 / 0.10
HD1985 / Possible DNA transformation protein / -3.44 / 0.38
Central intermediary metabolism
HD0781 / phnA / Alkylphosphonate uptake protein / 1.54 / 0.11
Sulfur metabolism
HD1325 / Conserved hypothetical protein / 1.51 / 0.07
HD0603 / dksA / Dosage-dependent DnaK suppressor protein / 1.16 / 0.03
HD1666 / Probable phosphatase / -1.17 / 0.08
HD1028 / gcvA / Glycine cleavage system transcriptional activator / -1.34 / 0.15
DNA metabolism
HD0710 / mutM / Formamidopyrimidine-DNA glycosylase / 2.38 / 0.09
HD0281 / fimA / Possible fimbrial major pilin protein / 1.61 / 0.51
HD1876 / rpoC / RNA polymerase beta subunit / 1.53 / 0.05
HD1342 / recJ / Single-stranded-DNA-specific exonuclease RecJ / 1.44 / 0.07
HD1353 / ihfB / Integration host factor, beta subunit / 1.35 / 0.09
HD1589 / nlpI / Lipoprotein NlpI homolog / 1.26 / 0.12
HD2017 / Possible rare lipoprotein A / 1.24 / 0.11
HD0746 / Possible xylanase A / 1.24 / 0.05
HD1094 / Possible outer membrane serine protease / 1.17 / 0.08
HD0223 / dnaQ / DNA polymerase III epsilon chain / 1.06 / 0.05
HD1786 / mutT / Mutator MutT protein / 1.06 / 0.07
HD1032 / uvrD / DNA helicase II / 1.03 / 0.05
HD0545 / lexA / Probable LexA repressor / -1.00 / 0.16
HD0584 / Conserved hypothetical protein / -1.07 / 0.07
HD0073 / napD / Possible napD protein / -1.10 / 0.06
HD0954 / topB1 / DNA topoisomerase III / -1.11 / 0.11
HD1935 / holB / DNA polymerase III delta subunit / -1.11 / 0.08
HD1115 / nth / Endonuclease III, DNA (apurinic or apyrimidinic site) lyase / -1.15 / 0.14
HD0479 / Possible DNA-binding protein / -1.19 / 0.10
HD1280 / Possible serine protease homolog / -1.23 / 0.13
HD1921 / recG / ATP-dependent DNA helicase RecG / -1.38 / 0.23
HD0090 / ner / Possible DNA-binding protein / -1.49 / 0.14
HD0667 / holC / DNA polymerase III chi subunit / -1.63 / 0.07
HD1278 / Possible serine protease / -1.71 / 0.10
Energy metabolism
HD1591 / Conserved hypothetical protein / 2.93 / 0.17
HD0564 / aspA / Aspartate ammonia-lyase / 2.15 / 0.10
HD1624 / aceF / Dihydrolipoamide acetyltransferase / 1.83 / 0.07
HD0792 / ccmF / Cytochrome c-type biogenesis protein / 1.74 / 0.23
HD0791 / ccmE / Cytochrome c-type biogenesis protein / 1.70 / 0.28
HD1220 / ykgF / Putative iron-sulfur electron transport protein / 1.60 / 0.05
HD1142 / sdaA / L-serine dehydratase / 1.55 / 0.15
HD1142 / sdaA / L-serine dehydratase / 1.55 / 0.15
HD0990 / pflB / Formate acetyltransferase / 1.40 / 0.07
HD0888 / deoC / Deoxyribose-phosphate aldolase / 1.37 / 0.02
HD1221 / ykgE / Conserved putative dehydrogenase subunit / 1.34 / 0.07
HD1472 / Conserved hypothetical protein / 1.33 / 0.19
HD1355 / Conserved hypothetical protein / 1.31 / 0.12
HD0765 / manA / Mannose-6-phosphate isomerase / 1.29 / 0.29
HD1623 / lpdA / Dihydrolipoamide dehydrogenase / 1.24 / 0.03
HD0660 / gpsA / Glycerol-3-phosphate dehydrogenase / 1.22 / 0.04
HD0010 / atpD / ATP synthase beta chain / 1.17 / 0.07
HD1457 / pta / Phosphate acetyltransferase / 1.17 / 0.06
HD0318 / Possible fimbrial biogenesis and twitching motility protein PilF homolog / 1.13 / 0.12
HD1625 / aceE / 2-oxoglutarate dehydrogenase / 1.12 / 0.08
HD0009 / atpG / ATP synthase gamma chain / 1.04 / 0.04
HD1242 / citE / Citrate lyase beta chain / 1.03 / 0.04
HD0584 / Conserved hypothetical protein / -1.07 / 0.07
HD1666 / Probable phosphatase / -1.17 / 0.08
HD0072 / napF / Ferredoxin-type protein NapF / -1.22 / 0.07
HD1077 / ogt / Methylated-DNA--protein-cysteine S-methyltransferase / -1.22 / 0.07
HD1986 / fumC / Fumarate hydratase class II / -1.73 / 0.05
HD1291 / gapA / Glyceraldehyde 3-phosphate dehydrogenase / -1.75 / 0.07
Fatty acid and phospholipid metabolism
HD0649 / psd / Phosphatidylserine decarboxylase / 1.62 / 0.07
HD1188 / fabZ / (3R)-hydroxymyristoyl-acyl carrier protein dehydratase / 1.33 / 0.04
HD0634 / accB / Probable biotin carboxyl carrier protein of acetyl-CoA carboxylase / 1.19 / 0.05
HD0271 / pssA / CDP-diacylglycerol--serine O-phosphatidyltransferase / 1.14 / 0.02
HD1327 / hhdA / Hemolysin / -1.20 / 0.11
HD0066 / Hypothetical protein / -1.52 / 0.11
Mobile and extrachromosomal element functions
HD1518 / Hypothetical protein / -1.07 / 0.14
Protein fate
HD1957 / secY / Preprotein translocase SecY subunit / 1.69 / 0.06
HD0281 / fimA / Possible fimbrial major pilin protein / 1.61 / 0.51
HD1010 / prc / Tail-specific protease / 1.59 / 0.08
HD1629 / lolB / Outer membrane lipoprotein LolB / 1.46 / 0.17
HD1472 / Conserved hypothetical protein / 1.33 / 0.19
HD0989 / pflA / Pyruvate formate-lyase activating enzyme / 1.32 / 0.06
HD1085 / hscB / Chaperone protein HscB / 1.28 / 0.10
HD1589 / nlpI / Lipoprotein NlpI homolog / 1.26 / 0.12
HD2017 / Possible rare lipoprotein A / 1.24 / 0.11
HD0746 / Possible xylanase A / 1.24 / 0.05
HD2013 / lipB / Lipoate-protein ligase B / 1.23 / 0.06
HD1784 / groEL / 60 kDa chaperonin / 1.23 / 0.05
HD0455 / Putative protease / 1.20 / 0.05
HD1094 / Possible outer membrane serine protease / 1.17 / 0.08
HD1607 / lepB / Signal peptidase I / 1.15 / 0.07
HD1340 / dsbC / Thiol:disulfide interchange protein / 1.14 / 0.06
HD1785 / groES / 10 kDa chaperonin / 1.13 / 0.06
HD1087 / hscA / Chaperone protein HscA / 1.12 / 0.07
HD0807 / dsbD / Thiol:disulfide interchange protein / 1.08 / 0.04
HD0471 / gcp / Putative sialylglycoprotease / 1.03 / 0.07
HD0073 / napD / Possible napD protein / -1.10 / 0.06
HD1666 / Probable phosphatase / -1.17 / 0.08
HD1280 / Possible serine protease homolog / -1.23 / 0.13
HD1278 / Possible serine protease / -1.71 / 0.10
Protein synthesis
HD1591 / Conserved hypothetical protein / 2.93 / 0.17
HD1927 / rpmE2 / 50S ribosomal protein L31 type B / 2.87 / 0.07
HD1357 / Conserved possible translation initiation factor / 2.04 / 0.13
HD1978 / rplV / 50S ribosomal protein L22 / 1.93 / 0.13
HD1975 / rpmC / 50S ribosomal protein L29 / 1.87 / 0.13
HD1974 / rpsQ / 30S ribosomal protein S17 / 1.79 / 0.09
HD1982 / rplD / 50S ribosomal protein L4 / 1.64 / 0.13
HD1461 / infB / Translation initiation factor IF-2 / 1.61 / 0.09
HD0351 / prfC / Peptide chain release factor 3 / 1.59 / 0.07
HD1983 / rplC / 50S ribosomal protein L3 / 1.54 / 0.13
HD1962 / rplR / 50S ribosomal protein L18 / 1.50 / 0.08
HD1967 / rplX / 50S ribosomal protein L24 / 1.46 / 0.05
HD1961 / rpsE / 30S ribosomal protein S5 / 1.46 / 0.12
HD1459 / truB / tRNA pseudouridine synthase B / 1.43 / 0.09
HD1968 / rplN / 50S ribosomal protein L14 / 1.41 / 0.07
HD1963 / rplF / 50S ribosomal protein L6 / 1.40 / 0.08
HD1966 / rplE / 50S ribosomal protein L5 / 1.37 / 0.09
HD1964 / rpsH / 30S ribosomal protein S8 / 1.32 / 0.09
HD1965 / rpsN / 30S ribosomal protein S14 / 1.30 / 0.10
HD1589 / nlpI / Lipoprotein NlpI homolog / 1.26 / 0.12
HD1803 / thrS / Threonyl-tRNA synthetase / 1.24 / 0.07
HD1179 / ksgA / Dimethyladenosine transferase / 1.18 / 0.13
HD0270 / Putative tRNA/rRNA methyltransferase / 1.11 / 0.07
HD1249 / rplY / 50S ribosomal protein L25 / 1.09 / 0.12
HD0584 / Conserved hypothetical protein / -1.07 / 0.07
HD1368 / tgt / Queuine tRNA-ribosyltransferase / -1.15 / 0.13
HD0577 / selD / Selenide, water dikinase / -1.19 / 0.09
HD0645 / rluC / Ribosomal large subunit pseudouridine synthase C / -1.20 / 0.11
Purines, pyrimidines, nucleosides, and nucleotides
HD0889 / deoD / Purine nucleoside phosphorylase / 1.79 / 0.09
HD1356 / pyrF / Orotidine 5`-phosphate decarboxylase / 1.75 / 0.09
HD0826 / adk / Adenylate kinase / 1.48 / 0.08
HD0888 / deoC / Deoxyribose-phosphate aldolase / 1.37 / 0.02
HD1731 / nrdA / Ribonucleoside-diphosphate reductase, alpha chain / 1.29 / 0.08
HD1807 / purA / Adenylosuccinate synthetase / 1.20 / 0.06
HD1473 / tdk / Thymidine kinase / 1.10 / 0.06
HD1005 / thyA / Thymidylate synthase / -1.10 / 0.23
HD1503 / guaB / Inosine-5-monophosphate dehydrogenase / -2.06 / 0.08
HD0233 / carB / Carbamoyl-phosphate synthase, large subunit / -4.06 / 0.11
HD0235 / carA / Carbamoyl-phosphate synthase, small subunit / -4.44 / 0.14
Regulatory functions
HD1591 / Conserved hypothetical protein / 2.93 / 0.17
HD0357 / Probable carbon starvation protein A / 2.54 / 0.10
HD1470 / cpxA / Sensor kinase CpxA / 2.16 / 0.09
HD1462 / nusA / Transcription termination-antitermination factor nusA, N utilization substance protein A / 1.57 / 0.06
HD1648 / glpR / Glycerol-3-phosphate regulon repressor / 1.26 / 0.07
HD1589 / nlpI / Lipoprotein NlpI homolog / 1.26 / 0.12
HD1469 / cpxR / Transcriptional regulatory protein CpxR / 1.13 / 0.05
HD1605 / era / GTP-binding protein era homolog / 1.06 / 0.08
HD0545 / lexA / Probable LexA repressor / -1.00 / 0.16
HD0111 / Mu-like phage C protein, possible positive regulator of late transcription / -1.07 / 0.16
HD1028 / gcvA / Glycine cleavage system transcriptional activator / -1.34 / 0.15
Transcription
HD0876 / Conserved probable ribonuclease / 1.75 / 0.08
HD0876 / Conserved probable ribonuclease / 1.75 / 0.08
HD1460 / rbfA / Ribosome binding factor A / 1.59 / 0.08
HD1462 / nusA / Transcription termination-antitermination factor nusA, N utilization substance protein A / 1.57 / 0.06
HD1876 / rpoC / RNA polymerase beta subunit / 1.53 / 0.05
HD0604 / pcnB / PolyA polymerase / 1.27 / 0.07
HD1606 / rnc / Ribonuclease III / 1.14 / 0.05
HD1923 / rpoZ / RNA polymerase omega subunit / 1.03 / 0.10
HD1935 / holB / DNA polymerase III delta subunit / -1.11 / 0.08
HD1172 / rpoE / RNA polymerase sigma-E factor / -1.12 / 0.13
HD0667 / holC / DNA polymerase III chi subunit / -1.63 / 0.07
Transport and binding proteins
HD0384 / nqrF / Na+-translocating NADH-ubiquinone oxidoreductase, subunit F / 2.75 / 0.08
HD0382 / nqrD / Na+-translocating NADH-ubiquinone oxidoreductase, subunit D / 2.68 / 0.07
HD0383 / nqrE / Na+-translocating NADH-ubiquinone oxidoreductase, subunit E / 2.52 / 0.10
HD0381 / nqrC / Na+-translocating NADH-ubiquinone oxidoreductase, subunit C / 2.46 / 0.11
HD0648 / tnaB / Tryptophan-specific transport protein / 2.22 / 0.12
HD1109 / Putative oxalate/formate antiporter / 2.15 / 0.13
HD0380 / nqrB / NADH dehydrogenase / 2.09 / 0.12
HD0766 / manZ / Mannose-specific phosphotransferase system IID component / 1.87 / 0.10
HD0646 / Conserved hypothetical protein / 1.85 / 0.12
HD0709 / brnQ / Branched-chain amino acid carrier protein / 1.85 / 0.07
HD0767 / manY / Mannose-specific phosphotransferase system IIC component / 1.77 / 0.09
HD1143 / sdaC / Serine transporter / 1.75 / 0.09
HD0379 / nqrA / Na+-translocating NADH-ubiquinone oxidoreductase, subunit A / 1.57 / 0.08
HD0401 / rnfG / Electron transport complex protein RnfG / 1.49 / 0.10
HD1150 / glpT / Glycerol 3-phosphate transporter / 1.38 / 0.06
HD1146 / glpF / Glycerol uptake facilitator protein / 1.37 / 0.09
HD1756 / Putative xanthine/uracil permease / 1.22 / 0.07
HD0994 / potD1 / Spermidine/putrescine-binding periplasmic protein (SPBP) / 1.15 / 0.13
HD0312 / dppB / Dipeptide transport system permease protein / 1.15 / 0.19
HD0313 / dppC / Dipeptide transport system permease protein / 1.12 / 0.11
HD1728 / nhaB / Na+/H+ antiporter protein / 1.11 / 0.06
HD0768 / manX / Mannose-specific phosphotransferase IIAB component / 1.01 / 0.10
HD1632 / Conserved hypothetical protein / -1.14 / 0.12
HD0025 / dcuB1 / Anaerobic C4-dicarboxylate transporter / -1.15 / 0.20
HD0998 / uraA / Uracil permease / -3.40 / 0.16
Unclassified
HD0647 / Conserved hypothetical protein / 2.65 / 0.19
HD0045 / momp / Major outer membrane protein / 2.39 / 0.05
HD1513 / Putative RND efflux membrane fusion protein / 1.72 / 0.09
HD1298 / tadG / Tight adherence protein G / 1.69 / 0.07
HD1190 / Hypothetical outer membrane protein / 1.56 / 0.05
HD1299 / tadF / Tight adherence protein F / 1.52 / 0.05
HD1771 / djlA / DnaJ-like protein DjlA / 1.44 / 0.06
HD1219 / Conserved hypothetical protein / 1.43 / 0.10
HD0404 / lpxM / Lipid A acyltransferase / 1.42 / 0.08
HD1300 / tadE / Tight adherence protein E / 1.38 / 0.11
HD0284 / fimD / Probable periplasmic fimbrial chaperone / 1.37 / 0.10
HD1463 / Conserved hypothetical protein / 1.35 / 0.04
HD1191 / D15 / Outer membrane protein D-15 / 1.32 / 0.05
HD0283 / fimC / Probable fimbrial outer membrane usher protein / 1.32 / 0.30
HD0445 / Possible ADP-heptose--lipooligosaccharide heptosyltransferase I / 1.29 / 0.08
HD1815 / Putative sulfite reductase / 1.26 / 0.20
HD0472 / lgtB / Lipooligosaccharide galactosyltransferase II / 1.10 / 0.09
HD0886 / lsgF / Putative lipooligosaccharide galactosyltransferase / 1.10 / 0.06
HD0589 / Conserved hypothetical protein / 1.06 / 0.06
HD0800 / Conserved hypothetical protein / 1.06 / 0.08
HD1861 / Conserved hypothetical protein / -1.01 / 0.13
HD1827 / Conserved hypothetical protein / -1.07 / 0.08
HD1828 / Conserved hypothetical protein / -1.07 / 0.10
HD0904 / cdtC / Cytolethal distending toxin protein C / -1.08 / 0.12
HD0903 / cdtB / Cytolethal distending toxin protein B / -1.13 / 0.10
HD1312 / flp1 / flp operon protein Flp1 / -1.87 / 0.14
HD1311 / flp2 / flp operon protein Flp2 / -1.94 / 0.18
HD1310 / flp3 / flp operon protein Flp3 / -2.12 / 0.19
Unknown function
HD0387 / Conserved hypothetical protein / 2.14 / 0.17
HD0558 / Conserved hypothetical protein / 1.29 / 0.06
HD1589 / nlpI / Lipoprotein NlpI homolog / 1.26 / 0.12
HD1089 / Conserved hypothetical protein / 1.21 / 0.03
HD0400 / rnfD / Putative Na-translocating NADH-quinone reductase / 1.20 / 0.09
HD1770 / Putative nitrogen regulator protein / 1.14 / 0.12
HD0040 / yidC / 60 kD inner-membrane protein / 1.07 / 0.11
HD1212 / smpA / Small protein A / -1.02 / 0.08
HD1308 / flp operon protein C / -1.14 / 0.07
HD1141 / Conserved hypothetical protein / -1.26 / 0.07
HD0376 / Conserved hypothetical protein / -1.34 / 0.10
HD1309 / flp operon protein B / -1.69 / 0.12
HD0740 / hflX / GTP-binding protein HflX / -1.88 / 0.06
Hypothetical proteins
HD1434 / Hypothetical protein / 2.81 / 0.06
HD1622 / Conserved hypothetical protein / 2.13 / 0.12
HD1343 / Hypothetical protein / 2.10 / 0.09
HD1926 / rpmJ1 / 50S ribosomal protein L36 / 1.93 / 0.09
HD1471 / Conserved hypothetical protein / 1.82 / 0.06
HD0352 / Hypothetical protein / 1.52 / 0.08
HD1354 / Conserved hypothetical protein / 1.39 / 0.11
HD1151 / Hypothetical protein / 1.37 / 0.04
HD1086 / Conserved hypothetical protein / 1.26 / 0.04
HD1011 / Hypothetical protein / 1.13 / 0.09
HD2014 / Hypothetical protein / 1.10 / 0.13
HD1410 / Conserved hypothetical protein / 1.03 / 0.10
HD0108 / Hypothetical protein / -1.00 / 0.14
HD0146 / Hypothetical protein / -1.01 / 0.16
HD0161 / Hypothetical protein / -1.02 / 0.07
HD1634 / Hypothetical protein / -1.02 / 0.26
HD0606 / Hypothetical protein / -1.05 / 0.08
HD0137 / Hypothetical protein / -1.06 / 0.25
HD1892 / Conserved hypothetical protein / -1.07 / 0.06
HD1211 / Hypothetical protein / -1.10 / 0.30
HD0488 / Conserved hypothetical protein / -1.13 / 0.20
HD1856 / Hypothetical protein / -1.13 / 0.15
HD0942 / Hypothetical protein / -1.15 / 0.19
HD1746 / Hypothetical protein / -1.16 / 0.25
HD1364 / Hypothetical protein / -1.17 / 0.24
HD0022 / Hypothetical protein / -1.18 / 0.23
HD1520 / Conserved hypothetical protein / -1.19 / 0.18
HD0097 / Conserved hypothetical protein / -1.21 / 0.19
HD2037 / Hypothetical protein / -1.21 / 0.21
HD1615 / Hypothetical protein / -1.25 / 0.11
HD0600 / Conserved hypothetical protein / -1.31 / 0.12
HD0526 / Hypothetical protein / -1.32 / 0.13
HD0972 / Hypothetical protein / -1.34 / 0.25
HD0047 / Hypothetical protein not likely / -1.36 / 0.11
HD0096 / Hypothetical protein / -1.37 / 0.21
HD0107 / Conserved hypothetical protein / -1.39 / 0.08
HD1519 / Hypothetical protein / -1.42 / 0.25
HD0048 / Hypothetical protein / -1.45 / 0.16
HD1572 / Hypothetical protein / -1.51 / 0.27
HD1515 / Conserved hypothetical protein / -1.56 / 0.19
HD1432 / Conserved hypothetical protein / -1.64 / 0.08
HD0925 / Hypothetical protein / -1.73 / 0.14
HD0997 / Hypothetical protein / -2.21 / 0.09
HD0805 / Conserved hypothetical protein / -2.39 / 0.36

a The table does not include ORFs described as encoding hypothetical or conserved hypothetical proteins.

b Median log2 ratio of expression levels from comparisons of 35000HPhfq::catto 35000HP in three independent experiments (P 0.05).

cGenes were classified into functional categories based on the role classification available in the comprehensive microbial resource database.

1