Selected Cell
Cell:
Value:
6h results genes
12h results genes
24h results genes
DAVID 6h
DAVID 12h
DAVID 24h
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| Supplementary Table S2. List of down and upregulated genes comparing P. putida KT2440 cultures in solid vs liquid media at 6 hours of incubation. | |||||||||
| PP number | DAVID accession number | Symbol | Product | FoldChange | p.adj.Value | ||||
| PP_0008 | 1043484 | rnpA | ribonuclease P protein component | 4.96 | 0.00000815 | ||||
| PP_0009 | 1043485 | rpmH | 50S ribosomal protein L34 | 6.66 | 0.00000927 | ||||
| PP_0023 | 1043502 | NP_742193.1 | hypothetical protein | 2.23 | 0.00048457 | ||||
| PP_0068 | 1043549 | def-I | peptide deformylase | 4.73 | 0.00000000 | ||||
| PP_0089 | 1043570 | osmC | stress-induced peroxiredoxin | 4.11 | 0.00000014 | ||||
| PP_0115 | 1043606 | katE | hydroperoxidase | 3.21 | 0.00008868 | ||||
| PP_0135 | 1043635 | NP_742305.1 | hypothetical protein | 7.62 | 0.00000035 | ||||
| PP_0136 | 1043636 | NP_742306.1 | hypothetical protein | 3.41 | 0.00092760 | ||||
| PP_0157 | 1043670 | gcdR | gcdH transcriptional regulator | 2.54 | 0.00021027 | ||||
| PP_0161 | 1043684 | NP_742330.1 | putative transmembrane sensor | -23.00 | 0.00000000 | ||||
| PP_0162 | 1043685 | NP_742331.1 | ECF family RNA polymerase sigma-70 factor | -13.42 | 0.00000000 | ||||
| PP_0180 | 1043706 | NP_742349.1 | cytochrome c family protein | -2.92 | 0.00020427 | ||||
| PP_0213 | 1043755 | gabD-I | succinate-semialdehyde dehydrogenase | -2.23 | 0.00002239 | ||||
| PP_0214 | 1043757 | gabT | 5-aminovalerate aminotransferase DavT | -2.09 | 0.00075493 | ||||
| PP_0235 | 1043789 | NP_742403.1 | peroxidase | 4.03 | 0.00000000 | ||||
| PP_0236 | 1043798 | ssuE | NAD(P)H-dependent FMN reductase subunit | 4.28 | 0.00018864 | ||||
| PP_0270 | 1043866 | NP_742437.1 | sensor histidine kinase | -8.20 | 0.00000000 | ||||
| PP_0271 | 1043867 | gltR-I | two-component system response regulator | -9.78 | 0.00000000 | ||||
| PP_0339 | 1044044 | aceE | pyruvate dehydrogenase E1 component | 2.71 | 0.00000075 | ||||
| PP_0350 | 1044057 | NP_742517.1 | ferrichrome-iron receptor | -4.05 | 0.00026270 | ||||
| PP_0351 | 1044058 | NP_742518.1 | transmembrane sensor | -14.36 | 0.00000000 | ||||
| PP_0352 | 1044059 | NP_742519.1 | ECF family RNA polymerase sigma-70 factor | -12.51 | 0.00000000 | ||||
| PP_0369 | 1044078 | NP_742536.2 | diguanylate cyclase | -4.18 | 0.00003866 | ||||
| PP_0389 | 1044101 | rpsU | 30S ribosomal protein S21 | 4.44 | 0.00000228 | ||||
| PP_0404 | 1044119 | lptD | LPS-assembly protein LptD | 2.66 | 0.00003415 | ||||
| PP_0415 | 1044137 | rpe | ribulose-5-phosphate 3-epimerase | 3.02 | 0.00003245 | ||||
| PP_0418 | 1044141 | estP | esterase EstP | 2.16 | 0.00053502 | ||||
| PP_0440 | 1044182 | tufA | elongation factor Tu-A | 3.67 | 0.00000061 | ||||
| PP_0441 | 1044184 | secE | protein translocase subunit SecE | 3.02 | 0.00001712 | ||||
| PP_0445 | 1044188 | rplJ | 50S ribosomal protein L10 | 2.75 | 0.00000183 | ||||
| PP_0446 | 1044189 | rplL | 50S ribosomal protein L7/L12 | 2.20 | 0.00006480 | ||||
| PP_0449 | 1044192 | rpsL | 30S ribosomal protein S12 | 3.50 | 0.00000003 | ||||
| PP_0450 | 1044193 | rpsG | 30S ribosomal protein S7 | 2.41 | 0.00015258 | ||||
| PP_0451 | 1044195 | fusA | elongation factor G 1 | 2.63 | 0.00000036 | ||||
| PP_0452 | 1044196 | tufB | elongation factor Tu-B | 2.72 | 0.00000017 | ||||
| PP_0453 | 1044199 | rpsJ | 30S ribosomal protein S10 | 5.40 | 0.00000000 | ||||
| PP_0454 | 1044200 | rplC | 50S ribosomal protein L3 | 4.33 | 0.00000998 | ||||
| PP_0455 | 1044201 | rplD | 50S ribosomal protein L4 | 2.89 | 0.00025272 | ||||
| PP_0456 | 1044202 | rplW | 50S ribosomal protein L23 | 2.79 | 0.00055586 | ||||
| PP_0458 | 1044204 | rpsS | 30S ribosomal protein S19 | 2.27 | 0.00022455 | ||||
| PP_0459 | 1044206 | rplV | 50S ribosomal protein L22 | 2.37 | 0.00004627 | ||||
| PP_0460 | 1044209 | rpsC | 30S ribosomal protein S3 | 2.42 | 0.00023044 | ||||
| PP_0461 | 1044210 | rplP | 50S ribosomal protein L16 | 2.16 | 0.00059235 | ||||
| PP_0468 | 1044227 | rpsH | 30S ribosomal protein S8 | 3.53 | 0.00000025 | ||||
| PP_0469 | 1044228 | rplF | 50S ribosomal protein L6 | 2.69 | 0.00003449 | ||||
| PP_0476 | 1044241 | rpsM | 30S ribosomal protein S13 | 3.15 | 0.00001644 | ||||
| PP_0477 | 1044242 | rpsK | 30S ribosomal protein S11 | 2.27 | 0.00043908 | ||||
| PP_0478 | 1044244 | rpsD | 30S ribosomal protein S4 | 2.25 | 0.00033652 | ||||
| PP_0481 | 1044248 | katA | catalase | 45.36 | 0.00000000 | ||||
| PP_0482 | 1044249 | bfr-I | bacterioferritin | 4.56 | 0.00000000 | ||||
| PP_0486 | 1044256 | NP_742652.1 | GntR family transcriptional regulator | 4.88 | 0.00000002 | ||||
| PP_0513 | 1044288 | nrdR | DNA-binding transcriptional repressor NrdR | 4.90 | 0.00023149 | ||||
| PP_0516 | 1044291 | ribAB-I | bifunctional 3%2C4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II | 2.70 | 0.00000754 | ||||
| PP_0538 | 1044317 | ppa | inorganic pyrophosphatase | 2.61 | 0.00001116 | ||||
| PP_0552 | 1044336 | bdhA | 2%2C3-butanediol dehydrogenase | 5.09 | 0.00000000 | ||||
| PP_0553 | 1044339 | acoC | acetoin cleaving system dihydrolipoyllysine-residue acetyltransferase | 5.35 | 0.00000000 | ||||
| PP_0554 | 1044340 | acoB | acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit beta | 5.20 | 0.00000000 | ||||
| PP_0555 | 1044342 | acoA | acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit alpha | 4.86 | 0.00000000 | ||||
| PP_0556 | 1044343 | NP_742719.1 | acetoin catabolism protein | 2.42 | 0.00011583 | ||||
| PP_0558 | 1044345 | accC | acetyl-CoA carboxylase biotin carboxylase subunit | 2.35 | 0.00023044 | ||||
| PP_0559 | 1044346 | accB | acetyl-CoA carboxylase biotin carboxyl carrier subunit | 4.00 | 0.00000000 | ||||
| PP_0560 | 1044348 | aroQ-I | type II 3-dehydroquinate dehydratase | 4.05 | 0.00000008 | ||||
| PP_0563 | 1044352 | NP_742726.1 | two-component system response regulator | -3.18 | 0.00000004 | ||||
| PP_0570 | 1044360 | yfhM | lipoprotein | 2.97 | 0.00000037 | ||||
| PP_0600 | 1044414 | rpsT | 30S ribosomal protein S20 | 6.70 | 0.00002500 | ||||
| PP_0622 | 1044439 | bamD | outer membrane protein assembly factor BamD | 3.11 | 0.00033190 | ||||
| PP_0654 | 1044477 | mdh | malate dehydrogenase | -2.08 | 0.00038357 | ||||
| PP_0657 | 1044481 | NP_742818.1 | amino acid ABC transporter substrate-binding protein | 3.47 | 0.00037589 | ||||
| PP_0667 | 1044491 | NP_742828.1 | ECF family RNA polymerase sigma-70 factor | -10.98 | 0.00000000 | ||||
| PP_0668 | 1044492 | NP_742829.1 | transmembrane sensor | -20.06 | 0.00000000 | ||||
| PP_0674 | 1044500 | ettA | ADP/ATP ratio sensor/translation inhibitor | 3.43 | 0.00004606 | ||||
| PP_0685 | 1044511 | NP_742846.1 | hypothetical protein | -40.66 | 0.00000000 | ||||
| PP_0688 | 1044516 | rplU | 50S ribosomal protein L21 | 7.67 | 0.00000000 | ||||
| PP_0689 | 1044517 | rpmA | 50S ribosomal protein L27 | 4.12 | 0.00000805 | ||||
| PP_0700 | 1044530 | NP_742861.1 | transmembrane sensor | -14.06 | 0.00000000 | ||||
| PP_0703 | 1044534 | NP_742864.1 | transmembrane sensor | -15.24 | 0.00000000 | ||||
| PP_0704 | 1044535 | NP_742865.1 | ECF family RNA polymerase sigma-70 factor | -6.02 | 0.00000000 | ||||
| PP_0711 | 1044542 | ycaC-I | putative hydrolase | 3.59 | 0.00000000 | ||||
| PP_0723 | 1044555 | ispE | 4-diphosphocytidyl-2C-methyl-D-erythritol kinase | 5.81 | 0.00000000 | ||||
| PP_0732 | 1044565 | hemA | glutamyl-tRNA reductase | 3.11 | 0.00000591 | ||||
| PP_0737 | 1044570 | pagL-I | lipid A 3-O-deacylase | 2.24 | 0.00022052 | ||||
| PP_0786 | 1044626 | trxB | thioredoxin reductase | 24.22 | 0.00000000 | ||||
| PP_0812 | 1044661 | cyoA | cytochrome bo terminal oxidase subunit II | 6.62 | 0.00000000 | ||||
| PP_0817 | 1044669 | alaC | aminotransferase | 4.60 | 0.00000003 | ||||
| PP_0832 | 1044690 | queA | S-adenosylmethionine:tRNA ribosyltransferase-isomerase | 3.61 | 0.00022671 | ||||
| PP_0838 | 1044698 | suhB | bifunctional inositol monophosphatase/glycerol-2-phosphatase | 4.99 | 0.00000000 | ||||
| PP_0843 | 1044705 | iscU | iron-sulfur cluster assembly scaffold protein | -2.05 | 0.00082511 | ||||
| PP_0846 | 1044710 | hscA | DnaK-like molecular chaperone | -2.18 | 0.00012767 | ||||
| PP_0861 | 1044732 | NP_743022.2 | outer membrane ferric siderophore receptor | -3.37 | 0.00078766 | ||||
| PP_0863 | 1044737 | NP_743024.1 | hypothetical protein | -2.99 | 0.00001742 | ||||
| PP_0864 | 1044738 | speC | ornithine decarboxylase | 3.88 | 0.00018864 | ||||
| PP_0883 | 1044767 | opdP | glycine-glutamate dipeptide porin | 2.89 | 0.00000274 | ||||
| PP_0897 | 1044785 | NP_743058.1 | class 1 fumarate hydratase | 5.28 | 0.00000000 | ||||
| PP_0913 | 1044812 | NP_743074.1 | hypothetical protein | -5.88 | 0.00000000 | ||||
| PP_0915 | 1044816 | sodB | superoxide dismutase | 7.67 | 0.00000000 | ||||
| PP_0932 | 1044838 | gatC | aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C | 3.19 | 0.00000185 | ||||
| PP_0933 | 1044840 | mreB | cell wall structural actin-like protein MreB | 3.03 | 0.00027088 | ||||
| PP_0943 | 1044854 | NP_743104.1 | hypothetical protein | -88.09 | 0.00000000 |
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| Supplementary Table S3. List of down and upregulated genes comparing P. putida KT2440 cultures in solid vs liquid media at 12 hours of incubation. | |||||||||
| PP number | DAVID accession number | Symbol | Product | FoldChange | p.adj.Value | ||||
| PP_0008 | 1043484 | rnpA | ribonuclease P protein component | 11.45 | 0.0000001 | ||||
| PP_0009 | 1043485 | rpmH | 50S ribosomal protein L34 | 12.05 | 0.0000041 | ||||
| PP_0061 | 1043542 | glyQ | glycine-tRNA ligase subunit alpha | 4.34 | 0.0008186 | ||||
| PP_0068 | 1043549 | def-I | peptide deformylase | 11.51 | 0.0000000 | ||||
| PP_0085 | 1043566 | NP_742255.1 | hypothetical protein | 3.77 | 0.0000249 | ||||
| PP_0089 | 1043570 | osmC | stress-induced peroxiredoxin | 5.26 | 0.0001948 | ||||
| PP_0114 | 1043605 | metN | methionine ABC transporter ATP-binding protein | 6.48 | 0.0000013 | ||||
| PP_0154 | 1043665 | scpC | propionyl-CoA:succinate CoA transferase | 16.44 | 0.0000001 | ||||
| PP_0161 | 1043684 | NP_742330.1 | putative transmembrane sensor | -8.59 | 0.0000002 | ||||
| PP_0162 | 1043685 | NP_742331.1 | ECF family RNA polymerase sigma-70 factor | -8.27 | 0.0000003 | ||||
| PP_0168 | 1043692 | NP_742337.1 | putative surface adhesion protein | -5.01 | 0.0000009 | ||||
| PP_0202 | 1043730 | NP_742371.1 | CBS domain-containing protein | 4.84 | 0.0000020 | ||||
| PP_0204 | 1043733 | NP_742373.1 | GntR family transcriptional regulator | 8.67 | 0.0000002 | ||||
| PP_0224 | 1043769 | NP_742392.1 | DszC family monooxygenase | 21.91 | 0.0000000 | ||||
| PP_0233 | 1043786 | tauA | taurine ABC transporter substrate-binding protein | 12.16 | 0.0000000 | ||||
| PP_0234 | 1043787 | oprE | outer-membrane porin E | 5.19 | 0.0003797 | ||||
| PP_0235 | 1043789 | NP_742403.1 | peroxidase | 18.76 | 0.0000000 | ||||
| PP_0236 | 1043798 | ssuE | NAD(P)H-dependent FMN reductase subunit | 77.73 | 0.0000000 | ||||
| PP_0354 | 1044061 | NP_742521.1 | CBS domain-containing protein | 27.81 | 0.0000000 | ||||
| PP_0389 | 1044101 | rpsU | 30S ribosomal protein S21 | 11.07 | 0.0000000 | ||||
| PP_0425 | 1044153 | yhfA | hypothetical protein | 3.54 | 0.0008840 | ||||
| PP_0440 | 1044182 | tufA | elongation factor Tu-A | 3.73 | 0.0000746 | ||||
| PP_0441 | 1044184 | secE | protein translocase subunit SecE | 5.01 | 0.0000001 | ||||
| PP_0453 | 1044199 | rpsJ | 30S ribosomal protein S10 | 9.18 | 0.0000000 | ||||
| PP_0454 | 1044200 | rplC | 50S ribosomal protein L3 | 4.27 | 0.0002904 | ||||
| PP_0468 | 1044227 | rpsH | 30S ribosomal protein S8 | 6.02 | 0.0000000 | ||||
| PP_0469 | 1044228 | rplF | 50S ribosomal protein L6 | 3.89 | 0.0000802 | ||||
| PP_0481 | 1044248 | katA | catalase | 253.01 | 0.0000000 | ||||
| PP_0513 | 1044288 | nrdR | DNA-binding transcriptional repressor NrdR | 6.92 | 0.0007793 | ||||
| PP_0538 | 1044317 | ppa | inorganic pyrophosphatase | 5.67 | 0.0000001 | ||||
| PP_0553 | 1044339 | acoC | acetoin cleaving system dihydrolipoyllysine-residue acetyltransferase | 4.43 | 0.0006099 | ||||
| PP_0554 | 1044340 | acoB | acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit beta | 5.66 | 0.0001708 | ||||
| PP_0555 | 1044342 | acoA | acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit alpha | 5.10 | 0.0002365 | ||||
| PP_0556 | 1044343 | NP_742719.1 | acetoin catabolism protein | 9.33 | 0.0000072 | ||||
| PP_0560 | 1044348 | aroQ-I | type II 3-dehydroquinate dehydratase | 5.99 | 0.0000001 | ||||
| PP_0600 | 1044414 | rpsT | 30S ribosomal protein S20 | 17.64 | 0.0000000 | ||||
| PP_0622 | 1044439 | bamD | outer membrane protein assembly factor BamD | 7.10 | 0.0000102 | ||||
| PP_0657 | 1044481 | NP_742818.1 | amino acid ABC transporter substrate-binding protein | 14.18 | 0.0000000 | ||||
| PP_0685 | 1044511 | NP_742846.1 | hypothetical protein | -11.97 | 0.0000000 | ||||
| PP_0686 | 1044512 | yjdM | Zn-ribbon domain-containing protein | 5.21 | 0.0001873 | ||||
| PP_0688 | 1044516 | rplU | 50S ribosomal protein L21 | 10.18 | 0.0000000 | ||||
| PP_0689 | 1044517 | rpmA | 50S ribosomal protein L27 | 4.70 | 0.0000119 | ||||
| PP_0700 | 1044530 | NP_742861.1 | transmembrane sensor | -5.37 | 0.0000077 | ||||
| PP_0723 | 1044555 | ispE | 4-diphosphocytidyl-2C-methyl-D-erythritol kinase | 8.60 | 0.0000000 | ||||
| PP_0732 | 1044565 | hemA | glutamyl-tRNA reductase | 8.58 | 0.0000000 | ||||
| PP_0755 | 1044591 | NP_742916.1 | hypothetical protein | 7.57 | 0.0000300 | ||||
| PP_0765 | 1044601 | NP_742926.1 | hypothetical protein | -3.94 | 0.0000337 | ||||
| PP_0786 | 1044626 | trxB | thioredoxin reductase | 75.18 | 0.0000000 | ||||
| PP_0812 | 1044661 | cyoA | cytochrome bo terminal oxidase subunit II | 14.43 | 0.0000000 | ||||
| PP_0838 | 1044698 | suhB | bifunctional inositol monophosphatase/glycerol-2-phosphatase | 6.01 | 0.0000001 | ||||
| PP_0903 | 1044794 | NP_743064.1 | hypothetical protein | 4.17 | 0.0003324 | ||||
| PP_0913 | 1044812 | NP_743074.1 | hypothetical protein | -3.89 | 0.0001131 | ||||
| PP_0915 | 1044816 | sodB | superoxide dismutase | 3.87 | 0.0000259 | ||||
| PP_0932 | 1044838 | gatC | aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C | 5.50 | 0.0000094 | ||||
| PP_0941 | 1044851 | NP_743102.1 | ribosome associated protein | 4.69 | 0.0000742 | ||||
| PP_0943 | 1044854 | NP_743104.1 | hypothetical protein | -5.16 | 0.0005890 | ||||
| PP_0944 | 1044855 | fumC-I | class 2 fumarate hydratase | -13.15 | 0.0000001 | ||||
| PP_0945 | 1044858 | NP_743106.1 | hypothetical protein | -28.87 | 0.0000000 | ||||
| PP_0946 | 1044859 | sodA | superoxide dismutase | -10.26 | 0.0001087 | ||||
| PP_0993 | 1044920 | NP_743154.1 | hypothetical protein | -3.94 | 0.0001320 | ||||
| PP_1031 | 1044148 | guaB | IMP dehydrogenase and single strand DNA binding factor | 4.79 | 0.0000006 | ||||
| PP_1037 | 1044327 | purL | phosphoribosylformylglycinamidine synthase | 3.62 | 0.0001805 | ||||
| PP_1082 | 1045026 | bfr-II | bacterioferritin | 4.26 | 0.0000262 | ||||
| PP_1084 | 1045103 | tsaA | peroxiredoxin | 4.39 | 0.0000128 | ||||
| PP_1100 | 1045219 | dcd | deoxycytidine triphosphate deaminase | 3.42 | 0.0009570 | ||||
| PP_1111 | 1045223 | NP_743272.1 | synthetase | -4.60 | 0.0000048 | ||||
| PP_1112 | 1045233 | NP_743273.1 | membrane protein | -4.16 | 0.0007806 | ||||
| PP_1125 | 1045260 | NP_743286.1 | putative Helicase | 5.03 | 0.0001041 | ||||
| PP_1127 | 1045267 | estC | carboxylesterase | 5.36 | 0.0002039 | ||||
| PP_1144 | 1045464 | NP_743305.1 | membrane protein | -5.54 | 0.0000015 | ||||
| PP_1162 | 1045699 | gstA | glutathione S-transferase GstA | 9.40 | 0.0000000 | ||||
| PP_1212 | 1045969 | NP_743372.1 | hypothetical protein | 10.93 | 0.0000000 | ||||
| PP_1237 | 1046257 | dapA-I | 4-hydroxy-tetrahydrodipicolinate synthase | 7.65 | 0.0000001 | ||||
| PP_1289 | 1043300 | NP_743449.1 | DUF328 domain-containing protein | 47.35 | 0.0000000 | ||||
| PP_1303 | 1041607 | cysD | sulfate adenylyltransferase subunit 2 | 25.22 | 0.0000000 | ||||
| PP_1312 | 1041626 | zapE | nucleoside triphosphate hydrolase domain-containing protein | 9.19 | 0.0000000 | ||||
| PP_1315 | 1043891 | rplM | 50S ribosomal protein L13 | 6.41 | 0.0000000 | ||||
| PP_1373 | 1041750 | pitB | phosphate transporter | 9.22 | 0.0000000 | ||||
| PP_1424 | 1045860 | NP_743582.1 | DUF339 domain-containing protein | 5.33 | 0.0005890 | ||||
| PP_1431 | 1045850 | lepA | elongation factor 4 | 3.24 | 0.0005081 | ||||
| PP_1460 | 1045782 | NP_743618.1 | membrane protein | 5.18 | 0.0001371 | ||||
| PP_1462 | 1045775 | rpsP | 30S ribosomal protein S16 | 6.44 | 0.0000001 | ||||
| PP_1495 | 1045671 | prfB | peptide chain release factor 2 | 4.90 | 0.0001015 | ||||
| PP_1506 | 1045513 | adk | adenylate kinase | 13.09 | 0.0000000 | ||||
| PP_1607 | 1044925 | accA | acetyl-CoA carboxylase carboxyltransferase subunit alpha | 4.72 | 0.0000014 | ||||
| PP_1616 | 1044879 | frmA | glutathione-dependent formaldehyde dehydrogenase | 4.22 | 0.0000102 | ||||
| PP_1625 | 1044839 | fdxA | ferredoxin 1 | 10.33 | 0.0000037 | ||||
| PP_1638 | 1044791 | fpr-I | ferredoxin--NADP(+) reductase | 6.70 | 0.0000005 | ||||
| PP_1651 | 1044421 | NP_743808.2 | two-component system response regulator | -12.15 | 0.0000002 | ||||
| PP_1652 | 1044394 | pfeS-II | histidine kinase | -5.79 | 0.0000228 | ||||
| PP_1660 | 1044314 | NP_743817.1 | hypothetical protein | -3.93 | 0.0002427 | ||||
| PP_1665 | 1044224 | purM | phosphoribosylformylglycinamidine cyclo-ligase | 5.51 | 0.0000789 | ||||
| PP_1691 | 1043737 | NP_743848.1 | hypothetical protein | 5.98 | 0.0000655 | ||||
| PP_1702 | 1043631 | rdgC | recombination-associated protein RdgC | 4.76 | 0.0003045 | ||||
| PP_1714 | 1043498 | fklB-II | FKBP-type peptidyl-prolyl cis-trans isomerase | 7.34 | 0.0000000 | ||||
| PP_1742 | 1043433 | yjcH | inner membrane protein | 14.17 | 0.0000000 | ||||
| PP_1743 | 1043431 | actP-I | acetate permease | 7.12 | 0.0000744 | ||||
| PP_1795 | 1043308 | NP_743951.1 | hypothetical protein | 5.01 | 0.0000033 |
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| Supplementary Table S4. List of down and upregulated genes comparing P. putida KT2440 cultures in solid vs liquid media at 24 hours of incubation. | |||||||||
| PP number | DAVID accession number | Symbol | Product | FoldChange | p.adj.Value | ||||
| PP_0004 | 1043472 | trmF | tRNA uridine 5-carboxymethylaminomethyl modification protein | 2.42 | 0.00046481 | ||||
| PP_0007 | 1043483 | yidD | hypothetical protein | 5.99 | 0.00003606 | ||||
| PP_0008 | 1043484 | rnpA | ribonuclease P protein component | 10.56 | 0.00000000 | ||||
| PP_0009 | 1043485 | rpmH | 50S ribosomal protein L34 | 11.25 | 0.00000000 | ||||
| PP_0010 | 1043486 | dnaA | chromosomal replication initiator protein | 3.82 | 0.00001151 | ||||
| PP_0026 | 1043505 | NP_742196.1 | cobalt/cadmium/zinc exporter | 2.42 | 0.00036530 | ||||
| PP_0061 | 1043542 | glyQ | glycine-tRNA ligase subunit alpha | 4.19 | 0.00000049 | ||||
| PP_0067 | 1043548 | fmt | methionyl-tRNA formyltransferase | 10.22 | 0.00000000 | ||||
| PP_0068 | 1043549 | def-I | peptide deformylase | 6.94 | 0.00000000 | ||||
| PP_0085 | 1043566 | NP_742255.1 | hypothetical protein | 2.96 | 0.00003387 | ||||
| PP_0089 | 1043570 | osmC | stress-induced peroxiredoxin | 5.33 | 0.00000000 | ||||
| PP_0091 | 1043573 | NP_742261.1 | putative lipoprotein | -3.10 | 0.00000130 | ||||
| PP_0092 | 1043574 | NP_742262.1 | putative lipoprotein | 4.08 | 0.00000033 | ||||
| PP_0096 | 1043578 | prlC | oligopeptidase A | 3.89 | 0.00000000 | ||||
| PP_0113 | 1043604 | metI | ABC transporter permease | 2.91 | 0.00044632 | ||||
| PP_0114 | 1043605 | metN | methionine ABC transporter ATP-binding protein | 11.67 | 0.00000000 | ||||
| PP_0115 | 1043606 | katE | hydroperoxidase | 4.85 | 0.00000000 | ||||
| PP_0122 | 1043615 | NP_742292.1 | hypothetical protein | -2.65 | 0.00012208 | ||||
| PP_0144 | 1043652 | NP_742314.1 | insulinase family metalloprotease | 3.17 | 0.00040026 | ||||
| PP_0146 | 1043654 | ygdQ | transport protein | 3.00 | 0.00021471 | ||||
| PP_0147 | 1043655 | citN | citrate transporter | 6.87 | 0.00000000 | ||||
| PP_0148 | 1043656 | NP_742318.1 | hypothetical protein | -3.48 | 0.00000191 | ||||
| PP_0149 | 1043657 | NP_742319.1 | hypothetical protein | 2.67 | 0.00037369 | ||||
| PP_0156 | 1043668 | pntAA | pyridine nucleotide transhydrogenase subunit alpha | 3.20 | 0.00024838 | ||||
| PP_0161 | 1043684 | NP_742330.1 | putative transmembrane sensor | -4.25 | 0.00005944 | ||||
| PP_0168 | 1043692 | NP_742337.1 | putative surface adhesion protein | -3.90 | 0.00000000 | ||||
| PP_0169 | 1043693 | NP_742338.1 | TauD/TfdA family dioxygenase | 7.61 | 0.00000823 | ||||
| PP_0195 | 1043722 | NP_742364.1 | hypothetical protein | -3.12 | 0.00019026 | ||||
| PP_0196 | 1043723 | yheS | ABC transporter ATP-binding protein | 3.34 | 0.00013045 | ||||
| PP_0199 | 1043726 | qmcA | membrane protease family protein | -3.20 | 0.00000683 | ||||
| PP_0200 | 1043728 | nfeD | membrane bound peptidase NefD | -3.50 | 0.00000034 | ||||
| PP_0201 | 1043729 | NP_742370.1 | hypothetical protein | -2.82 | 0.00000603 | ||||
| PP_0202 | 1043730 | NP_742371.1 | CBS domain-containing protein | 7.70 | 0.00000000 | ||||
| PP_0203 | 1043732 | NP_742372.1 | dipeptidase | 2.58 | 0.00062307 | ||||
| PP_0204 | 1043733 | NP_742373.1 | GntR family transcriptional regulator | 11.38 | 0.00000000 | ||||
| PP_0215 | 1043758 | NP_742383.1 | two-component system response regulator | -2.16 | 0.00080612 | ||||
| PP_0216 | 1043759 | NP_742384.2 | sensory box/GGDEF family protein | 4.97 | 0.00000000 | ||||
| PP_0218 | 1043761 | NP_742386.1 | sensory box protein | 2.99 | 0.00013509 | ||||
| PP_0224 | 1043769 | NP_742392.1 | DszC family monooxygenase | 72.77 | 0.00000000 | ||||
| PP_0227 | 1043773 | fliY | cystine-binding protein | 2.74 | 0.00055104 | ||||
| PP_0233 | 1043786 | tauA | taurine ABC transporter substrate-binding protein | 33.06 | 0.00000000 | ||||
| PP_0234 | 1043787 | oprE | outer-membrane porin E | 5.20 | 0.00000015 | ||||
| PP_0235 | 1043789 | NP_742403.1 | peroxidase | 23.03 | 0.00000000 | ||||
| PP_0236 | 1043798 | ssuE | NAD(P)H-dependent FMN reductase subunit | 50.49 | 0.00000000 | ||||
| PP_0237 | 1043799 | ssuA | aliphatic sulfonatesABC transporter substrate-binding protein | 4.08 | 0.00022293 | ||||
| PP_0245 | 1043816 | yhgF | transcriptional accessory protein | 3.94 | 0.00015384 | ||||
| PP_0250 | 1043825 | hslR | heat shock protein Hsp15 | -2.99 | 0.00001677 | ||||
| PP_0257 | 1043838 | fdhD | protein sulfur transferase | 3.36 | 0.00000762 | ||||
| PP_0283 | 1043898 | aotP | arginine/ornithine ABC transporter ATP-binding protein AotP | 2.87 | 0.00013133 | ||||
| PP_0294 | 1043981 | cbcV | choline/betaine/carnitine ABC transporter ATP binding protein | -3.71 | 0.00000003 | ||||
| PP_0296 | 1043984 | cbcX | choline/betaine/carnitine ABC transporter substrate-binding protein | -2.41 | 0.00063327 | ||||
| PP_0298 | 1043988 | gbdR | AraC family transcriptional regulator | -2.81 | 0.00001865 | ||||
| PP_0308 | 1044001 | NP_742475.1 | dipeptidase | -2.76 | 0.00050783 | ||||
| PP_0310 | 1044003 | dgcA | dimethylglycine dehydrogenase subunit | -3.71 | 0.00000049 | ||||
| PP_0318 | 1044013 | NP_742485.1 | hypothetical protein | 6.77 | 0.00000000 | ||||
| PP_0325 | 1044023 | soxA | sarcosine oxidase subunit alpha | -3.14 | 0.00004049 | ||||
| PP_0327 | 1044026 | purU-I | formyltetrahydrofolate deformylase | -3.13 | 0.00020784 | ||||
| PP_0330 | 1044029 | NP_742497.2 | hypothetical protein | 3.14 | 0.00000688 | ||||
| PP_0339 | 1044044 | aceE | pyruvate dehydrogenase E1 component | 3.38 | 0.00000801 | ||||
| PP_0352 | 1044059 | NP_742519.1 | ECF family RNA polymerase sigma-70 factor | 2.66 | 0.00079287 | ||||
| PP_0389 | 1044101 | rpsU | 30S ribosomal protein S21 | 9.04 | 0.00000000 | ||||
| PP_0404 | 1044119 | lptD | LPS-assembly protein LptD | 3.43 | 0.00000058 | ||||
| PP_0405 | 1044120 | NP_742571.1 | hypothetical protein | -2.59 | 0.00045275 | ||||
| PP_0406 | 1044121 | NP_742572.1 | nucleotidyltransferase family protein | -3.59 | 0.00000284 | ||||
| PP_0407 | 1044124 | djlA | DnaJ-like protein DjlA | -4.04 | 0.00000002 | ||||
| PP_0415 | 1044137 | rpe | ribulose-5-phosphate 3-epimerase | 3.10 | 0.00002240 | ||||
| PP_0435 | 1044168 | NP_742601.1 | M23/M37 family peptidase | 2.49 | 0.00009781 | ||||
| PP_0440 | 1044182 | tufA | elongation factor Tu-A | 8.19 | 0.00000000 | ||||
| PP_0441 | 1044184 | secE | protein translocase subunit SecE | 5.62 | 0.00000000 | ||||
| PP_0442 | 1044185 | nusG | transcription antipausing factor NusG | 2.75 | 0.00006797 | ||||
| PP_0445 | 1044188 | rplJ | 50S ribosomal protein L10 | 2.55 | 0.00099181 | ||||
| PP_0449 | 1044192 | rpsL | 30S ribosomal protein S12 | 4.68 | 0.00000000 | ||||
| PP_0450 | 1044193 | rpsG | 30S ribosomal protein S7 | 3.55 | 0.00000075 | ||||
| PP_0453 | 1044199 | rpsJ | 30S ribosomal protein S10 | 7.83 | 0.00000000 | ||||
| PP_0454 | 1044200 | rplC | 50S ribosomal protein L3 | 7.88 | 0.00000000 | ||||
| PP_0468 | 1044227 | rpsH | 30S ribosomal protein S8 | 7.98 | 0.00000000 | ||||
| PP_0469 | 1044228 | rplF | 50S ribosomal protein L6 | 6.51 | 0.00000000 | ||||
| PP_0470 | 1044230 | rplR | 50S ribosomal protein L18 | 2.72 | 0.00040611 | ||||
| PP_0476 | 1044241 | rpsM | 30S ribosomal protein S13 | 7.59 | 0.00000000 | ||||
| PP_0477 | 1044242 | rpsK | 30S ribosomal protein S11 | 4.32 | 0.00000000 | ||||
| PP_0481 | 1044248 | katA | catalase | 593.45 | 0.00000000 | ||||
| PP_0482 | 1044249 | bfr-I | bacterioferritin | 2.41 | 0.00027373 | ||||
| PP_0486 | 1044256 | NP_742652.1 | GntR family transcriptional regulator | 4.17 | 0.00001714 | ||||
| PP_0500 | 1044272 | NP_742664.1 | dTDP-4-rhamnose reductase-like protein | 5.14 | 0.00000001 | ||||
| PP_0512 | 1044287 | NP_742675.2 | hypothetical protein | -4.31 | 0.00000001 | ||||
| PP_0513 | 1044288 | nrdR | DNA-binding transcriptional repressor NrdR | 5.11 | 0.00002502 | ||||
| PP_0516 | 1044291 | ribAB-I | bifunctional 3%2C4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II | 2.89 | 0.00011510 | ||||
| PP_0527 | 1044303 | dxs | 1-deoxyxylulose-5-phosphate synthase | 2.64 | 0.00015877 | ||||
| PP_0529 | 1044305 | xseB | exodeoxyribonuclease 7 small subunit | 5.26 | 0.00040704 | ||||
| PP_0536 | 1044315 | NP_742699.1 | hypothetical protein | -3.00 | 0.00005888 | ||||
| PP_0538 | 1044317 | ppa | inorganic pyrophosphatase | 5.04 | 0.00000002 | ||||
| PP_0545 | 1044329 | aldB-I | aldehyde dehydrogenase | -2.70 | 0.00019173 | ||||
| PP_0546 | 1044330 | NP_742709.2 | sigma-54 dependent transcriptional regulator | -3.20 | 0.00000084 | ||||
| PP_0550 | 1044334 | NP_742713.1 | hypothetical protein | -2.84 | 0.00000865 | ||||
| PP_0552 | 1044336 | bdhA | 2%2C3-butanediol dehydrogenase | 2.52 | 0.00027543 | ||||
| PP_0553 | 1044339 | acoC | acetoin cleaving system dihydrolipoyllysine-residue acetyltransferase | 6.93 | 0.00000000 | ||||
| PP_0554 | 1044340 | acoB | acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit beta | 6.24 | 0.00000012 | ||||
| PP_0555 | 1044342 | acoA | acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit alpha | 8.43 | 0.00000000 |
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| Supplementary Table S5. DAVID Functional analysis results for 6 hours comparison | ||||||||||
| Category | Term | Genes (DAVID accession numbers) | List Total | Pop Hits | Pop Total | Count | % | P-Value | Benjamini | -log10(PValue) |
| GOTERM_MF_DIRECT | GO:0003735 structural constituent of ribosome | 1044200, 1044517, 1044199, 1044204, 1044516, 1044227, 1044202, 1044228, 1044201, 1042258, 1044244, 1044241, 1044206, 1044242, 1044209, 1044192, 1044193, 1045775, 1043485, 1043991, 1043893, 1044189, 1044188, 1043891, 1044210, 1044101, 1044414, 1043837 | 323 | 54 | 3273 | 28 | 6 | 3.8E-14 | 9.1E-12 | 13.420216403383188 |
| GOTERM_BP_DIRECT | GO:0006412 translation | 1044200, 1044517, 1044199, 1044204, 1044516, 1044227, 1044202, 1044228, 1044201, 1042258, 1044244, 1044241, 1044206, 1044242, 1044209, 1044192, 1044193, 1045775, 1043485, 1043991, 1043549, 1043893, 1044189, 1044188, 1043891, 1044210, 1044838, 1044101, 1044414, 1043837 | 248 | 62 | 2269 | 30 | 6.5 | 3.9E-13 | 6.0E-11 | 12.4089353929735 |
| GOTERM_CC_DIRECT | GO:0005840 ribosome | 1044200, 1043991, 1044517, 1044199, 1043893, 1044189, 1044188, 1044516, 1043891, 1044227, 1044202, 1044228, 1044201, 1042258, 1044241, 1044242, 1044210, 1044101, 1044414, 1045775, 1043485, 1043837 | 218 | 42 | 2035 | 22 | 4.7 | 1.1E-10 | 3.5E-9 | 9.958607314841775 |
| KEGG_PATHWAY | ppu00190: Oxidative phosphorylation | 1042262, 1044317, 1044661, 1042266, 1042396, 1042277, 1042269, 1042285, 1041621, 1042273, 1042274, 1042283, 1042025, 1042426, 1045401, 1042014, 1042613, 1042016, 1042018, 1042421, 1041990, 1045265, 1042260, 1046071, 1042005 | 187 | 51 | 1575 | 25 | 5.4 | 1.8E-10 | 1.5E-8 | 9.744727494896694 |
| GOTERM_MF_DIRECT | GO:0019843 rRNA binding | 1044200, 1043991, 1043893, 1044204, 1044516, 1044227, 1044202, 1044228, 1044201, 1044244, 1044206, 1044241, 1044242, 1044210, 1044209, 1044192, 1044193, 1044414, 1043837 | 323 | 35 | 3273 | 19 | 4.1 | 4.5E-10 | 5.4E-8 | 9.346787486224656 |
| KEGG_PATHWAY | ppu00020: Citrate cycle (TCA cycle) | 1044044, 1044342, 1044340, 1042396, 1044785, 1044339, 1042406, 1042423, 1042414, 1042426, 1042413, 1042613, 1045338, 1042422, 1044855, 1042421, 1042391, 1044477 | 187 | 32 | 1575 | 18 | 3.9 | 9.7E-9 | 4.0E-7 | 8.013228265733755 |
| KEGG_PATHWAY | ppu01120: Microbial metabolism in diverse environments | 1044346, 1042253, 1044345, 1044342, 1046257, 1044340, 1042396, 1043939, 1042406, 1045402, 1042613, 1046926, 1042391, 1046726, 1042092, 1046807, 1046808, 1046845, 1042860, 1045004, 1042365, 1044785, 1042525, 1044339, 1046512, 1046613, 1046612, 1044855, 1044477, 1046812, 1044366, 1046818, 1041814, 1044137, 1045925, 1041590, 1044222, 1046507, 1044904, 1042423, 1042426, 1046180, 1042422, 1042421, 1043755, 1047015, 1045930, 1044044, 1041755, 1042490, 1044648, 1041851, 1044929, 1046932, 1042414, 1042413, 1045338, 1041608, 1041607, 1043023, 1047012 | 187 | 262 | 1575 | 61 | 13.1 | 1.4E-8 | 3.8E-7 | 7.853871964321761 |
| KEGG_PATHWAY | ppu03010: Ribosome | 1044200, 1044517, 1044199, 1044204, 1044516, 1044227, 1044202, 1044228, 1044201, 1042258, 1044244, 1044241, 1044206, 1044242, 1044209, 1044192, 1044193, 1045775, 1043485, 1043991, 1043893, 1044189, 1044188, 1043891, 1044210, 1044101, 1044414, 1043837 | 187 | 76 | 1575 | 28 | 6 | 2.5E-8 | 5.1E-7 | 7.602059991327962 |
| GOTERM_BP_DIRECT | GO:0006352 DNA-templated transcription, initiation | 1043685, 1042732, 1043876, 1041651, 1046334, 1044941, 1044059, 1042166, 1042476, 1045054, 1044535, 1042506, 1044491 | 248 | 21 | 2269 | 13 | 2.8 | 2.6E-7 | 2.0E-5 | 6.585026652029182 |
| GOTERM_MF_DIRECT | GO:0016987 sigma factor activity | 1043685, 1042732, 1043876, 1041651, 1046334, 1044941, 1044059, 1042166, 1042476, 1045054, 1044535, 1042506, 1044491 | 323 | 25 | 3273 | 13 | 2.8 | 1.1E-6 | 8.6E-5 | 5.958607314841775 |
| GOTERM_MF_DIRECT | GO:0046933 proton-transporting ATP synthase activity, rotational mechanism | 1042025, 1042014, 1042016, 1042018, 1045265, 1042005, 1046071 | 323 | 7 | 3273 | 7 | 1.5 | 5.6E-6 | 3.3E-4 | 5.251811972993799 |
| GOTERM_MF_DIRECT | GO:0008137 NADH dehydrogenase (ubiquinone) activity | 1042262, 1045401, 1042269, 1042285, 1041621, 1042260, 1042273, 1042283 | 323 | 10 | 3273 | 8 | 1.7 | 7.7E-6 | 3.7E-4 | 5.113509274827518 |
| GOTERM_BP_DIRECT | GO:0015986 ATP synthesis coupled proton transport | 1042025, 1042014, 1041990, 1042018, 1045265, 1042005, 1046071 | 248 | 7 | 2269 | 7 | 1.5 | 1.0E-5 | 5.1E-4 | 5 |
| KEGG_PATHWAY | ppu01130: Biosynthesis of antibiotics | 1044346, 1044345, 1044342, 1044340, 1046257, 1042396, 1045534, 1044248, 1044348, 1045533, 1042406, 1042613, 1042391, 1046726, 1042092, 1042860, 1045004, 1042365, 1044785, 1044339, 1044855, 1044477, 1044327, 1047007, 1045513, 1044137, 1041814, 1044224, 1041649, 1046542, 1046744, 1044904, 1042423, 1042426, 1042422, 1042421, 1044044, 1043224, 1044931, 1044932, 1041851, 1046932, 1042414, 1043606, 1042413, 1044738, 1045338, 1041607, 1043023, 1044555 | 187 | 235 | 1575 | 50 | 10.8 | 1.0E-5 | 1.7E-4 | 5 |
| KEGG_PATHWAY | ppu00364: Fluorobenzoate degradation | 1046812, 1046807, 1046808, 1046845, 1045930, 1046818, 1046512 | 187 | 7 | 1575 | 7 | 1.5 | 1.6E-5 | 2.2E-4 | 4.795880017344074 |
| KEGG_PATHWAY | ppu01200: Carbon metabolism | 1044346, 1042253, 1044345, 1044342, 1044340, 1042396, 1044137, 1041814, 1044248, 1042406, 1042423, 1044904, 1042426, 1042613, 1042422, 1042421, 1042391, 1044044, 1042860, 1045004, 1042490, 1042365, 1044785, 1044339, 1044929, 1043606, 1042414, 1042413, 1045338, 1043023, 1044855, 1044477 | 187 | 127 | 1575 | 32 | 6.9 | 2.6E-5 | 3.0E-4 | 4.585026652029182 |
| GOTERM_BP_DIRECT | GO:0006099 tricarboxylic acid cycle | 1042414, 1042423, 1042413, 1042426, 1042396, 1042613, 1045338, 1042422, 1044855, 1042421, 1044477 | 248 | 22 | 2269 | 11 | 2.4 | 3.9E-5 | 0.0015 | 4.4089353929735005 |
| KEGG_PATHWAY | ppu01100: Metabolic pathways | 1044346, 1042253, 1044345, 1044342, 1043982, 1046257, 1044340, 1044348, 1042402, 1042406, 1045402, 1045401, 1045604, 1046807, 1046808, 1042262, 1046845, 1045219, 1042860, 1045004, 1042266, 1042365, 1042269, 1042525, 1044339, 1044855, 1042260, 1046812, 1044366, 1046818, 1041702, 1041814, 1044137, 1045925, 1044224, 1044698, 1041590, 1044222, 1042423, 1042426, 1042422, 1042421, 1043755, 1045265, 1043757, 1044565, 1045930, 1044044, 1044291, 1041616, 1044930, 1043224, 1044148, 1041802, 1042490, 1044931, 1044932, 1044929, 1042414, 1044738, 1042413, 1046171, 1041608, 1041607, 1043023, 1041990, 1044555, 1043164, 1042396, 1043939, 1041621, 1045534, 1045533, 1042014, 1042613, 1043805, 1042016, 1046726, 1042018, 1042391, 1042092, 1044785, 1046512, 1042025, 1046613, 1046612, 1044477, 1044327, 1047007, 1045513, 1042277, 1042273, 1042274, 1041649, 1046542, 1046744, 1041844, 1043798, 1044904, 1042130, 1047015, 1044661, 1042285, 1042283, 1044838, 1041851, 1046932, 1045338, 1045133, 1045586, 1047012, 1046071, 1042005 | 187 | 755 | 1575 | 113 | 24.3 | 2.4E-4 | 0.0024 | 3.6197887582883936 |
| KEGG_PATHWAY | ppu00362: Benzoate degradation | 1046807, 1046812, 1046808, 1046845, 1045930, 1042860, 1041755, 1046818, 1043939, 1045925, 1046512, 1046932, 1046613, 1046612 | 187 | 39 | 1575 | 14 | 3 | 2.9E-4 | 0.0026 | 3.5376020021010435 |
| KEGG_PATHWAY | ppu01220: Degradation of aromatic compounds | 1046812, 1046807, 1046808, 1046845, 1045930, 1046818, 1046726, 1043939, 1045925, 1046512 | 187 | 22 | 1575 | 10 | 2.2 | 4.7E-4 | 0.0038 | 3.3279021420642825 |
| GOTERM_CC_DIRECT | GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1) | 1042025, 1042014, 1042016, 1042018, 1042005 | 218 | 5 | 2035 | 5 | 1.1 | 5.8E-4 | 0.0092 | 3.2365720064370627 |
| GOTERM_MF_DIRECT | GO:0000049 tRNA binding | 1044199, 1046544, 1041702, 1044241, 1044192, 1045214, 1044193, 1043484, 1044210 | 323 | 22 | 3273 | 9 | 1.9 | 7.5E-4 | 0.029 | 3.1249387366082995 |
| GOTERM_MF_DIRECT | GO:0048038 quinone binding | 1042262, 1042266, 1042277, 1042269, 1042285, 1041621, 1042260 | 323 | 14 | 3273 | 7 | 1.5 | 0.0013 | 0.044 | 2.886056647693163 |
| GOTERM_MF_DIRECT | GO:0004601 peroxidase activity | 1043789, 1045103, 1045608, 1046468, 1045549, 1043570 | 323 | 10 | 3273 | 6 | 1.3 | 0.0015 | 0.044 | 2.823908740944318 |
| GOTERM_CC_DIRECT | GO:0015935 small ribosomal subunit | 1044204, 1044244, 1044192, 1044193, 1044209 | 218 | 7 | 2035 | 5 | 1.1 | 0.0034 | 0.036 | 2.4685210829577446 |
| GOTERM_CC_DIRECT | GO:0045263 proton-transporting ATP synthase complex, coupling factor F(o) | 1042004, 1041990, 1045265, 1046071 | 218 | 4 | 2035 | 4 | 0.9 | 0.0044 | 0.035 | 2.356547323513812 |
| GOTERM_MF_DIRECT | GO:0051920 peroxiredoxin activity | 1043789, 1045103, 1045608, 1046468, 1045549 | 323 | 8 | 3273 | 5 | 1.1 | 0.0047 | 0.12 | 2.3279021420642825 |
| KEGG_PATHWAY | ppu00620: Pyruvate metabolism | 1044346, 1044345, 1044044, 1044342, 1042860, 1044340, 1044785, 1046419, 1044339, 1043023, 1044855, 1042391, 1044477 | 187 | 46 | 1575 | 13 | 2.8 | 0.0053 | 0.039 | 2.275724130399211 |
| GOTERM_MF_DIRECT | GO:0003746 translation elongation factor activity | 1045850, 1044182, 1043241, 1044195, 1044196 | 323 | 9 | 3273 | 5 | 1.1 | 0.0078 | 0.17 | 2.107905397309519 |
| GOTERM_MF_DIRECT | GO:0031177 phosphopantetheine binding | 1044150, 1042489, 1042600, 1042549 | 323 | 5 | 3273 | 4 | 0.9 | 0.0081 | 0.16 | 2.09151498112135 |
| GOTERM_BP_DIRECT | GO:0009058 biosynthetic process | 1046744, 1043224, 1041995, 1042489, 1044669, 1042513, 1043501 | 248 | 18 | 2269 | 7 | 1.5 | 0.0094 | 0.25 | 2.0268721464003012 |
| KEGG_PATHWAY | ppu01110: Biosynthesis of secondary metabolites | 1044346, 1042253, 1044345, 1044342, 1044340, 1046257, 1042396, 1045534, 1044248, 1044348, 1045533, 1042402, 1042406, 1042613, 1042391, 1046726, 1042092, 1042860, 1045004, 1042365, 1044785, 1044339, 1044855, 1044477, 1044327, 1047007, 1045513, 1044137, 1041814, 1044224, 1046542, 1044904, 1042423, 1042426, 1042422, 1042421, 1044565, 1044044, 1044291, 1043224, 1044148, 1044931, 1044932, 1041851, 1046932, 1043606, 1042414, 1042413, 1044738, 1045338, 1043023, 1044555 | 187 | 334 | 1575 | 52 | 11.2 | 0.019 | 0.12 | 1.721246399047171 |
| GOTERM_BP_DIRECT | GO:0042773 ATP synthesis coupled electron transport | 1042269, 1042285, 1042273, 1042283 | 248 | 6 | 2269 | 4 | 0.9 | 0.02 | 0.4 | 1.6989700043360185 |
| KEGG_PATHWAY | ppu00622: Xylene degradation | 1046807, 1046808, 1046845, 1046818 | 187 | 6 | 1575 | 4 | 0.9 | 0.025 | 0.15 | 1.6020599913279623 |
| GOTERM_MF_DIRECT | GO:0018623 benzoate 1,2-dioxygenase activity | 1046807, 1046808, 1046845 | 323 | 3 | 3273 | 3 | 0.6 | 0.027 | 0.42 | 1.5686362358410126 |
| GOTERM_MF_DIRECT | GO:0008177 succinate dehydrogenase (ubiquinone) activity | 1042426, 1042396, 1042421 | 323 | 3 | 3273 | 3 | 0.6 | 0.027 | 0.42 | 1.5686362358410126 |
| GOTERM_MF_DIRECT | GO:0046961 proton-transporting ATPase activity, rotational mechanism | 1042025, 1042014, 1042016 | 323 | 3 | 3273 | 3 | 0.6 | 0.027 | 0.42 | 1.5686362358410126 |
| GOTERM_CC_DIRECT | GO:0005623 cell | 1044249, 1042429, 1043789, 1045103, 1045608, 1045026, 1045609, 1042391 | 218 | 29 | 2035 | 8 | 1.7 | 0.029 | 0.17 | 1.5376020021010437 |
| GOTERM_BP_DIRECT | GO:0015991 ATP hydrolysis coupled proton transport | 1042014, 1041990, 1042005 | 248 | 3 | 2269 | 3 | 0.6 | 0.033 | 0.52 | 1.4814860601221123 |
| KEGG_PATHWAY | ppu00361: Chlorocyclohexane and chlorobenzene degradation | 1046812, 1045930, 1046512 | 187 | 3 | 1575 | 3 | 0.6 | 0.038 | 0.2 | 1.4202164033831897 |
| KEGG_PATHWAY | ppu00623: Toluene degradation | 1046812, 1045930, 1046512 | 187 | 3 | 1575 | 3 | 0.6 | 0.038 | 0.2 | 1.4202164033831897 |
| KEGG_PATHWAY | ppu00650: Butanoate metabolism | 1044336, 1046932, 1042860, 1047007, 1042426, 1042396, 1042613, 1042421, 1043755, 1043757 | 187 | 41 | 1575 | 10 | 2.2 | 0.045 | 0.22 | 1.346787486224656 |
| GOTERM_MF_DIRECT | GO:0008199 ferric iron binding | 1046812, 1044249, 1045930, 1045026 | 323 | 9 | 3273 | 4 | 0.9 | 0.051 | 0.62 | 1.2924298239020635 |
| GOTERM_MF_DIRECT | GO:0003989 acetyl-CoA carboxylase activity | 1044346, 1044345, 1043023 | 323 | 4 | 3273 | 3 | 0.6 | 0.051 | 0.59 | 1.2924298239020635 |
| KEGG_PATHWAY | ppu00350: Tyrosine metabolism | 1046171, 1041608, 1046726, 1041590, 1043755, 1044222 | 187 | 18 | 1575 | 6 | 1.3 | 0.052 | 0.24 | 1.2839966563652008 |
| GOTERM_BP_DIRECT | GO:0009072 aromatic amino acid family metabolic process | 1046171, 1041608, 1044222 | 248 | 4 | 2269 | 3 | 0.6 | 0.061 | 0.7 | 1.2146701649892329 |
| KEGG_PATHWAY | ppu00640: Propanoate metabolism | 1044346, 1044345, 1046932, 1042406, 1042860, 1042414, 1045338, 1043023 | 187 | 31 | 1575 | 8 | 1.7 | 0.064 | 0.27 | 1.1938200260161127 |
| KEGG_PATHWAY | ppu00310: Lysine degradation | 1046932, 1042860, 1042423, 1042413, 1043755, 1043757 | 187 | 20 | 1575 | 6 | 1.3 | 0.077 | 0.31 | 1.113509274827518 |
| KEGG_PATHWAY | ppu00010: Glycolysis / Gluconeogenesis | 1044044, 1044342, 1045004, 1044904, 1044340, 1042365, 1046726, 1042391, 1044339 | 187 | 40 | 1575 | 9 | 1.9 | 0.09 | 0.33 | 1.0457574905606752 |
| KEGG_PATHWAY | ppu03018: RNA degradation | 1042415, 1045958, 1044904, 1043228, 1043177 | 187 | 15 | 1575 | 5 | 1.1 | 0.091 | 0.32 | 1.0409586076789064 |
| GOTERM_MF_DIRECT | GO:0005506 iron ion binding | 1046807, 1046487, 1042262, 1041989, 1046803, 1042530, 1042277, 1041590, 1044732, 1044705, 1046507, 1044057 | 323 | 72 | 3273 | 12 | 2.6 | 0.091 | 0.78 | 1.0409586076789064 |
| GOTERM_MF_DIRECT | GO:0046872 metal ion binding | 1044327, 1044345, 1044137, 1041814, 1044248, 1042274, 1045402, 1042613, 1046180, 1046808, 1043549, 1043893, 1044370, 1045006, 1044148, 1042863, 1042269, 1045214, 1046419, 1044839, 1044816, 1043606, 1046171, 1045338, 1044859 | 323 | 185 | 3273 | 25 | 5.4 | 0.092 | 0.77 | 1.0362121726544447 |
| GOTERM_MF_DIRECT | GO:0051536 iron-sulfur cluster binding | 1046188, 1042462, 1042396, 1044705, 1042092 | 323 | 18 | 3273 | 5 | 1.1 | 0.093 | 0.75 | 1.0315170514460648 |
| GOTERM_BP_DIRECT | GO:0019545 arginine catabolic process to succinate | 1041844, 1043982, 1043805 | 248 | 5 | 2269 | 3 | 0.6 | 0.095 | 0.82 | 1.0222763947111522 |
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| Supplementary Table S6. DAVID functional analysis results for 12 hours comparison | ||||||||||
| Category | Term | Genes (DAVID accession numbers) | List Total | Pop Hits | Pop Total | Count | % | P-Value | Benjamini | -log10(PValue) |
| KEGG_PATHWAY | ppu02040: Flagellar assembly | 1042637, 1044605, 1041605, 1043101, 1041829, 1041827, 1042454, 1042481, 1045242, 1041836, 1045701, 1045714, 1041825, 1042471, 1042309, 1043820, 1044376, 1046146, 1041797, 1042947 | 103 | 35 | 1575 | 20 | 7.3 | 8.5E-15 | 4.7E-13 | 14.0705811 |
| GOTERM_CC_DIRECT | GO:0031514 motile cilium | 1042637, 1044605, 1041605, 1043101, 1041829, 1045204, 1041827, 1045202, 1042454, 1042481, 1045242, 1041836, 1045701, 1045714, 1041825, 1042471, 1044726, 1043820, 1046146, 1042947 | 139 | 37 | 2035 | 20 | 7.3 | 1.2E-13 | 3.0E-12 | 12.9208188 |
| GOTERM_BP_DIRECT | GO:0071973 bacterial-type flagellum-dependent cell motility | 1044605, 1041605, 1041829, 1042454, 1042481, 1041836, 1045714, 1041825, 1042471, 1042309, 1043820, 1044376, 1041797, 1042947 | 139 | 20 | 2269 | 14 | 5.1 | 4.8E-12 | 5.5E-10 | 11.3187588 |
| GOTERM_CC_DIRECT | GO:0005840 ribosome | 1044200, 1044517, 1044199, 1043893, 1043891, 1044516, 1044227, 1044228, 1042258, 1044101, 1044414, 1045775, 1043837, 1043485 | 139 | 42 | 2035 | 14 | 5.1 | 1.7E-6 | 2.2E-5 | 5.76955108 |
| GOTERM_MF_DIRECT | GO:0003735 structural constituent of ribosome | 1044200, 1044517, 1044199, 1043893, 1043891, 1044516, 1044227, 1044228, 1042258, 1044101, 1044414, 1045775, 1043837, 1043485 | 170 | 54 | 3273 | 14 | 5.1 | 2.0E-6 | 2.9E-4 | 5.69897 |
| GOTERM_BP_DIRECT | GO:0006412 translation | 1044200, 1043549, 1044517, 1044199, 1043893, 1044516, 1043891, 1044227, 1044228, 1042258, 1044838, 1044101, 1044414, 1045775, 1043837, 1043485 | 139 | 62 | 2269 | 16 | 5.8 | 2.1E-6 | 1.2E-4 | 5.67778071 |
| GOTERM_MF_DIRECT | GO:0003774 motor activity | 1042454, 1041836, 1045714, 1044376, 1041797, 1042947 | 170 | 7 | 3273 | 6 | 2.2 | 6.7E-6 | 4.8E-4 | 5.1739252 |
| GOTERM_CC_DIRECT | GO:0009425 bacterial-type flagellum basal body | 1041836, 1044605, 1045714, 1043101, 1041797, 1042947 | 139 | 11 | 2035 | 6 | 2.2 | 4.4E-4 | 0.0038 | 3.35654732 |
| GOTERM_MF_DIRECT | GO:0008556 potassium-transporting ATPase activity | 26969968, 1042357, 1042354, 1042353 | 170 | 4 | 3273 | 4 | 1.5 | 5.2E-4 | 0.025 | 3.28399666 |
| KEGG_PATHWAY | ppu03010: Ribosome | 1044200, 1044517, 1044199, 1043893, 1043891, 1044516, 1044227, 1044228, 1042258, 1044101, 1044414, 1045775, 1043837, 1043485 | 103 | 76 | 1575 | 14 | 5.1 | 8.1E-4 | 0.022 | 3.09151498 |
| GOTERM_MF_DIRECT | GO:0019843 rRNA binding | 1044200, 1046554, 1043893, 1044516, 1044227, 1044228, 1044414, 1043837 | 170 | 35 | 3273 | 8 | 2.9 | 0.0017 | 0.059 | 2.76955108 |
| GOTERM_MF_DIRECT | GO:0005524 ATP binding | 1045260, 1044327, 1046235, 1042357, 1044343, 1042354, 1045513, 1046544, 1041702, 1044224, 1041626, 1045202, 1044925, 1044288, 1042400, 1045877, 1046273, 1044394, 1045153, 1043228, 1043542, 1044838, 1046910, 1042415, 1043931, 1043605, 1041790, 1045154, 1042436, 1041607, 1046459, 1041972, 1045113, 1044555 | 170 | 405 | 3273 | 34 | 12.4 | 0.0042 | 0.11 | 2.37675071 |
| GOTERM_MF_DIRECT | GO:0005198 structural molecule activity | 1042481, 1042471, 1042309, 1041797 | 170 | 8 | 3273 | 4 | 1.5 | 0.0062 | 0.14 | 2.20760831 |
| GOTERM_BP_DIRECT | GO:0044781 bacterial-type flagellum organization | 1042637, 1043101, 1045204, 1041827 | 139 | 7 | 2269 | 4 | 1.5 | 0.0064 | 0.22 | 2.19382003 |
| GOTERM_MF_DIRECT | GO:0004601 peroxidase activity | 1043789, 1045103, 1045608, 1043570 | 170 | 10 | 3273 | 4 | 1.5 | 0.012 | 0.23 | 1.92081875 |
| GOTERM_CC_DIRECT | GO:0030694 bacterial-type flagellum basal body, rod | 1041825, 1041605, 1041829 | 139 | 3 | 2035 | 3 | 1.1 | 0.013 | 0.082 | 1.88605665 |
| KEGG_PATHWAY | ppu00020: Citrate cycle (TCA cycle) | 1043665, 1044342, 1044340, 1042422, 1044855, 1046547, 1044339 | 103 | 32 | 1575 | 7 | 2.6 | 0.015 | 0.24 | 1.82390874 |
| KEGG_PATHWAY | ppu01130: Biosynthesis of antibiotics | 1044327, 1044342, 1046257, 1044340, 1043224, 1045513, 1042365, 1044224, 1046547, 1044248, 1044348, 1041649, 1044339, 1046542, 1043665, 1044925, 1042436, 1042422, 1044855, 1041607, 1042159, 1044879, 1045317, 1044555 | 103 | 235 | 1575 | 24 | 8.8 | 0.022 | 0.27 | 1.65757732 |
| GOTERM_BP_DIRECT | GO:0006935 chemotaxis | 1041836, 1045714, 1045448, 1041629, 1043822, 1042947, 1043780 | 139 | 37 | 2269 | 7 | 2.6 | 0.022 | 0.47 | 1.65757732 |
| KEGG_PATHWAY | ppu00620: Pyruvate metabolism | 1043665, 1044925, 1044342, 1044340, 1042436, 1044855, 1046419, 1044339 | 103 | 46 | 1575 | 8 | 2.9 | 0.026 | 0.25 | 1.58502665 |
| GOTERM_BP_DIRECT | GO:0045454 cell redox homeostasis | 1042429, 1043789, 1045007, 1045103, 1045608, 1045609 | 139 | 30 | 2269 | 6 | 2.2 | 0.032 | 0.53 | 1.49485002 |
| GOTERM_MF_DIRECT | GO:0016987 sigma factor activity | 1043685, 1042166, 1045054, 1046334, 1044726 | 170 | 25 | 3273 | 5 | 1.8 | 0.037 | 0.49 | 1.43179828 |
| GOTERM_CC_DIRECT | GO:0005623 cell | 1042429, 1043789, 1045103, 1045608, 1045026, 1045609 | 139 | 29 | 2035 | 6 | 2.2 | 0.042 | 0.2 | 1.37675071 |
| GOTERM_BP_DIRECT | GO:0006189 'de novo' IMP biosynthetic process | 1044327, 1044224, 1042159, 1046542 | 139 | 14 | 2269 | 4 | 1.5 | 0.049 | 0.62 | 1.30980392 |
| GOTERM_MF_DIRECT | GO:0051920 peroxiredoxin activity | 1043789, 1045103, 1045608 | 170 | 8 | 3273 | 3 | 1.1 | 0.06 | 0.63 | 1.22184875 |
| KEGG_PATHWAY | ppu02030: Bacterial chemotaxis | 1041836, 1045714, 1045448, 1042670, 1043822, 1042947, 1043780 | 103 | 46 | 1575 | 7 | 2.6 | 0.072 | 0.5 | 1.1426675 |
| GOTERM_MF_DIRECT | GO:0003746 translation elongation factor activity | 1045850, 1044182, 1043241 | 170 | 9 | 3273 | 3 | 1.1 | 0.075 | 0.67 | 1.12493874 |
| GOTERM_BP_DIRECT | GO:0044780 bacterial-type flagellum assembly | 1042481, 1045242, 1042627 | 139 | 9 | 2269 | 3 | 1.1 | 0.1 | 0.82 | 1 |
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| Supplementary Table S7. DAVID functional analysis results for 24 hours comparison | ||||||||||
| Category | Term | Genes (DAVID accession numbers) | List Total | Pop Hits | Pop Total | Count | % | P-Value | Benjamini | -log10(PValue) |
| KEGG_PATHWAY | ppu02040: Flagellar assembly | 1044605, 1042637, 1043042, 1041605, 1043101, 1041829, 1041827, 1043501, 1042454, 1042481, 1045242, 1041836, 1045701, 1045714, 1041825, 1042471, 1042309, 1043820, 1044376, 1046146, 1041797, 1042947 | 269 | 35 | 1575 | 22 | 3 | 8.3E-9 | 8.0E-7 | 8.08092191 |
| GOTERM_CC_DIRECT | GO:0031514 motile cilium | 1042637, 1044605, 1043042, 1041605, 1043101, 1041829, 1045204, 1041827, 1045202, 1042454, 1042481, 1045242, 1041836, 1045701, 1045714, 1041825, 1042471, 1044726, 1043820, 1046146, 1042947 | 306 | 37 | 2035 | 21 | 2.9 | 2.6E-8 | 1.1E-6 | 7.58502665 |
| GOTERM_BP_DIRECT | GO:0071973 bacterial-type flagellum-dependent cell motility | 1044605, 1041605, 1041829, 1043501, 1042454, 1042481, 1041836, 1045714, 1041825, 1042471, 1042309, 1043820, 1044376, 1041797, 1042947 | 355 | 20 | 2269 | 15 | 2 | 6.3E-8 | 1.5E-5 | 7.20065945 |
| GOTERM_CC_DIRECT | GO:0005840 ribosome | 1044200, 1044517, 1044199, 1043893, 1044188, 1044516, 1043891, 1044227, 1044228, 1044230, 1042258, 1044241, 1041596, 1044242, 1044101, 1045770, 1042057, 1044414, 1045775, 1043485, 1043837 | 306 | 42 | 2035 | 21 | 2.9 | 4.0E-7 | 8.9E-6 | 6.39794001 |
| GOTERM_MF_DIRECT | GO:0003735 structural constituent of ribosome | 1044200, 1044517, 1044199, 1043893, 1044188, 1044516, 1043891, 1044227, 1044228, 1044230, 1042258, 1041596, 1044241, 1044242, 1044101, 1044192, 1044193, 1042057, 1044414, 1045775, 1043485, 1043837, 1045137 | 459 | 54 | 3273 | 23 | 3.1 | 1.0E-6 | 3.4E-4 | 6 |
| GOTERM_BP_DIRECT | GO:0006412 translation | 1044200, 1044517, 1044199, 1044516, 1044227, 1044228, 1042258, 1044241, 1041596, 1044242, 1044192, 1044193, 1042057, 1045775, 1043485, 1043549, 1043893, 1043891, 1044188, 1044230, 1044838, 1044835, 1044101, 1044414, 1043837, 1045137 | 355 | 62 | 2269 | 26 | 3.5 | 1.7E-6 | 2.1E-4 | 5.76955108 |
| GOTERM_CC_DIRECT | GO:0005737 cytoplasm | 1045634, 1045842, 1044343, 1042815, 1046257, 1044305, 1042359, 1044580, 1044776, 1041626, 1045671, 1045672, 1041726, 1045635, 1045845, 1043486, 1044726, 1042960, 1042055, 1043631, 1044722, 1042400, 1042723, 1045007, 1042365, 1044626, 1045214, 1043241, 1046554, 1045159, 1046556, 1042024, 1043356, 1045491, 1044327, 1043172, 1044366, 1041912, 1045513, 1046544, 1041702, 1044943, 1044224, 1044947, 1043278, 1045921, 1042427, 1044690, 1044749, 1041880, 1042422, 1046087, 1043073, 1044317, 1044930, 1043228, 1043542, 1042841, 1041658, 1043501, 1043472, 1045333, 1042185, 1045885, 1042381, 1042885, 1046100, 1045889, 1041992, 1045888, 1044182, 1045133, 1046075, 1045278, 1044553, 1043838, 1043780 | 306 | 345 | 2035 | 77 | 10.5 | 7.6E-5 | 0.0011 | 4.11918641 |
| KEGG_PATHWAY | ppu01130: Biosynthesis of antibiotics | 1044346, 1044345, 1044342, 1046257, 1044340, 1044303, 1043987, 1045534, 1044248, 1045080, 1044348, 1045533, 1044925, 1042613, 1042960, 1042391, 1044722, 1042159, 1041966, 1042365, 1044785, 1044234, 1044339, 1044914, 1045159, 1045317, 1044477, 1044327, 1043230, 1041911, 1047007, 1042276, 1045513, 1041814, 1044137, 1044224, 1046547, 1041646, 1046542, 1046744, 1043271, 1044904, 1042426, 1042422, 1045508, 1044044, 1043224, 1045333, 1046932, 1045885, 1043606, 1044870, 1046100, 1044738, 1045338, 1041607, 1043023, 1044879, 1044553, 1044555 | 269 | 235 | 1575 | 60 | 8.2 | 4.0E-4 | 0.019 | 3.39794001 |
| GOTERM_MF_DIRECT | GO:0019843 rRNA binding | 1044200, 1043893, 1044516, 1044227, 1044228, 1044230, 1044241, 1044242, 1046554, 1044192, 1044193, 1044414, 1042057, 1043837 | 459 | 35 | 3273 | 14 | 1.9 | 5.2E-4 | 0.083 | 3.28399666 |
| GOTERM_MF_DIRECT | GO:0003774 motor activity | 1042454, 1041836, 1045714, 1044376, 1041797, 1042947 | 459 | 7 | 3273 | 6 | 0.8 | 8.7E-4 | 0.092 | 3.06048075 |
| GOTERM_MF_DIRECT | GO:0000049 tRNA binding | 1044199, 1041701, 1045889, 1046544, 1041702, 1044241, 1044192, 1045214, 1044193, 1043484 | 459 | 22 | 3273 | 10 | 1.4 | 0.0017 | 0.14 | 2.76955108 |
| KEGG_PATHWAY | ppu01200: Carbon metabolism | 1044346, 1042253, 1044345, 1044342, 1041911, 1044340, 1041814, 1043987, 1044137, 1046547, 1044248, 1041646, 1045080, 1045894, 1044925, 1044904, 1042426, 1042613, 1042422, 1042391, 1044044, 1045045, 1042365, 1045046, 1044785, 1044339, 1044914, 1045885, 1043606, 1045719, 1045338, 1043023, 1044879, 1044553, 1044477 | 269 | 127 | 1575 | 35 | 4.8 | 0.0026 | 0.08 | 2.58502665 |
| GOTERM_MF_DIRECT | GO:0046872 metal ion binding | 1045634, 1044327, 1044345, 1044580, 1041814, 1044137, 1046547, 1044248, 1044918, 1041700, 1041726, 1042966, 1045402, 1045143, 1043652, 1042613, 1046180, 1045597, 1043549, 1043893, 1042681, 1045006, 1043578, 1044148, 1043263, 1045230, 1044787, 1045214, 1046419, 1045049, 1041698, 1044839, 1042002, 1044873, 1045865, 1044816, 1043606, 1044870, 1045338, 1046453 | 459 | 185 | 3273 | 40 | 5.4 | 0.0043 | 0.25 | 2.36653154 |
| KEGG_PATHWAY | ppu03010: Ribosome | 1044200, 1044517, 1044199, 1043893, 1044188, 1044516, 1043891, 1044227, 1044228, 1044230, 1042258, 1041596, 1044241, 1044242, 1044101, 1044192, 1044193, 1042057, 1044414, 1045775, 1043485, 1043837, 1045137 | 269 | 76 | 1575 | 23 | 3.1 | 0.0056 | 0.13 | 2.25181197 |
| KEGG_PATHWAY | ppu01110: Biosynthesis of secondary metabolites | 1044346, 1042253, 1044345, 1044342, 1046257, 1044340, 1044514, 1044303, 1044580, 1043987, 1044248, 1045534, 1045080, 1044348, 1045533, 1044925, 1045143, 1044583, 1042613, 1042960, 1042391, 1042113, 1044722, 1042159, 1041966, 1043422, 1045009, 1042365, 1044785, 1044234, 1045952, 1044339, 1044914, 1045159, 1045317, 1042120, 1044477, 1044329, 1044327, 1043230, 1047007, 1046895, 1045513, 1042276, 1041814, 1044137, 1044224, 1046547, 1041646, 1046542, 1044886, 1043271, 1044904, 1042426, 1042422, 1041981, 1044565, 1045508, 1044044, 1044291, 1043224, 1044148, 1042185, 1046932, 1045885, 1043606, 1044870, 1044738, 1045338, 1041992, 1043023, 1044879, 1044553, 1044555 | 269 | 334 | 1575 | 74 | 10.1 | 0.0059 | 0.11 | 2.22914799 |
| GOTERM_CC_DIRECT | GO:0005623 cell | 1044249, 1042429, 1043789, 1041936, 1045103, 1045608, 1044754, 1045609, 1042391, 1046746, 1046822 | 306 | 29 | 2035 | 11 | 1.5 | 0.007 | 0.074 | 2.15490196 |
| KEGG_PATHWAY | ppu00061: Fatty acid biosynthesis | 1044346, 1044925, 1044345, 1042381, 1045719, 1044943, 1043023, 1046532, 1043164 | 269 | 19 | 1575 | 9 | 1.2 | 0.0086 | 0.13 | 2.06550155 |
| GOTERM_MF_DIRECT | GO:0003989 acetyl-CoA carboxylase activity | 1044346, 1044925, 1044345, 1043023 | 459 | 4 | 3273 | 4 | 0.5 | 0.0098 | 0.42 | 2.00877392 |
| GOTERM_MF_DIRECT | GO:0008556 potassium-transporting ATPase activity | 26969968, 1042357, 1042354, 1042353 | 459 | 4 | 3273 | 4 | 0.5 | 0.0098 | 0.42 | 2.00877392 |
| KEGG_PATHWAY | ppu00020: Citrate cycle (TCA cycle) | 1044044, 1044342, 1044340, 1042426, 1042613, 1045338, 1042422, 1042391, 1046547, 1044785, 1044477, 1044339 | 269 | 32 | 1575 | 12 | 1.6 | 0.013 | 0.16 | 1.88605665 |
| GOTERM_BP_DIRECT | GO:0006633 fatty acid biosynthetic process | 1044346, 1044925, 1042381, 1046895, 1045719, 1044943, 1043023, 1046532 | 355 | 18 | 2269 | 8 | 1.1 | 0.014 | 0.69 | 1.85387196 |
| GOTERM_CC_DIRECT | GO:0009425 bacterial-type flagellum basal body | 1041836, 1044605, 1045714, 1043101, 1041797, 1042947 | 306 | 11 | 2035 | 6 | 0.8 | 0.016 | 0.13 | 1.79588002 |
| GOTERM_BP_DIRECT | GO:0009073 aromatic amino acid family biosynthetic process | 1043230, 1043271, 1045317, 1045534, 1045533, 1044348 | 355 | 12 | 2269 | 6 | 0.8 | 0.028 | 0.82 | 1.55284197 |
| GOTERM_BP_DIRECT | GO:0045454 cell redox homeostasis | 1042429, 1043789, 1045007, 1045103, 1045608, 1044754, 1045609, 1042391, 1046746, 1046822 | 355 | 30 | 2269 | 10 | 1.4 | 0.034 | 0.81 | 1.46852108 |
| KEGG_PATHWAY | ppu00620: Pyruvate metabolism | 1044346, 1044329, 1044345, 1044044, 1044342, 1044340, 1044785, 1046419, 1045080, 1044339, 1044925, 1043023, 1042391, 1044477 | 269 | 46 | 1575 | 14 | 1.9 | 0.037 | 0.37 | 1.43179828 |
| GOTERM_MF_DIRECT | GO:0050660 flavin adenine dinucleotide binding | 1046873, 1046280, 1045007, 1042864, 1041701, 1046955, 1046822, 1045081, 1043472, 1043769, 1042179, 1045609, 1042391, 1041966, 1046746 | 459 | 61 | 3273 | 15 | 2 | 0.038 | 0.85 | 1.4202164 |
| KEGG_PATHWAY | ppu00230: Purine metabolism | 1044327, 1042681, 1044930, 1043069, 1042276, 1045513, 1044148, 1046955, 1046956, 1041802, 1044224, 1044234, 1046542, 1045865, 1044583, 1041607, 1042159, 1046453, 1044553, 1044386 | 269 | 77 | 1575 | 20 | 2.7 | 0.051 | 0.43 | 1.29242982 |
| GOTERM_MF_DIRECT | GO:0033727 aldehyde dehydrogenase (FAD-independent) activity | 1046955, 1046956, 1046453 | 459 | 3 | 3273 | 3 | 0.4 | 0.053 | 0.9 | 1.27572413 |
| GOTERM_BP_DIRECT | GO:0006979 response to oxidative stress | 1045143, 1043606, 1045608, 1044248, 1044616, 1043570 | 355 | 14 | 2269 | 6 | 0.8 | 0.054 | 0.89 | 1.26760624 |
| GOTERM_BP_DIRECT | GO:0006189 'de novo' IMP biosynthetic process | 1044327, 1044026, 1044224, 1042159, 1044234, 1046542 | 355 | 14 | 2269 | 6 | 0.8 | 0.054 | 0.89 | 1.26760624 |
| KEGG_PATHWAY | ppu01212: Fatty acid metabolism | 1044346, 1044925, 1044345, 1046932, 1042381, 1045719, 1044943, 1043023, 1046532, 1045080, 1043164 | 269 | 35 | 1575 | 11 | 1.5 | 0.06 | 0.45 | 1.22184875 |
| GOTERM_CC_DIRECT | GO:0009317 acetyl-CoA carboxylase complex | 1044346, 1044925, 1043023 | 306 | 3 | 2035 | 3 | 0.4 | 0.061 | 0.37 | 1.21467016 |
| GOTERM_CC_DIRECT | GO:0030694 bacterial-type flagellum basal body, rod | 1041825, 1041605, 1041829 | 306 | 3 | 2035 | 3 | 0.4 | 0.061 | 0.37 | 1.21467016 |
| GOTERM_BP_DIRECT | GO:0042744 hydrogen peroxide catabolic process | 1045143, 1043606, 1044248 | 355 | 3 | 2269 | 3 | 0.4 | 0.065 | 0.9 | 1.18708664 |
| GOTERM_BP_DIRECT | GO:0000902 cell morphogenesis | 1043443, 1045333, 1044840 | 355 | 3 | 2269 | 3 | 0.4 | 0.065 | 0.9 | 1.18708664 |
| GOTERM_BP_DIRECT | GO:0044781 bacterial-type flagellum organization | 1042637, 1043101, 1045204, 1041827 | 355 | 7 | 2269 | 4 | 0.5 | 0.081 | 0.92 | 1.09151498 |
| KEGG_PATHWAY | ppu00500: Starch and sucrose metabolism | 1042139, 1046744, 1045885, 1042276, 1042130, 1042113, 1042120 | 269 | 19 | 1575 | 7 | 1 | 0.088 | 0.55 | 1.05551733 |
| GOTERM_MF_DIRECT | GO:0005198 structural molecule activity | 1042481, 1042471, 1042309, 1041797 | 459 | 8 | 3273 | 4 | 0.5 | 0.089 | 0.97 | 1.05060999 |
| GOTERM_MF_DIRECT | GO:0030976 thiamine pyrophosphate binding | 1045508, 1047007, 1044303, 1041966 | 459 | 8 | 3273 | 4 | 0.5 | 0.089 | 0.97 | 1.05060999 |
| GOTERM_MF_DIRECT | GO:0005524 ATP binding | 1045634, 1043885, 1044345, 1043981, 1042357, 1043843, 1044343, 1042815, 1042354, 1041626, 1044776, 1042512, 1045202, 1044918, 1041726, 1044925, 1044288, 1043444, 1043486, 1042307, 1042055, 1042400, 1045877, 1042993, 1044330, 1045214, 1043898, 1046910, 1045159, 1042335, 1043723, 1041972, 1043356, 1045113, 1045260, 1046235, 1044327, 1045263, 1044366, 1046544, 1045513, 1041702, 1044224, 1044984, 1045921, 1041946, 1043228, 1043542, 1043403, 1044500, 1041658, 1043501, 1044838, 1044874, 1044837, 1042415, 1043931, 1044835, 1043605, 1041790, 1045889, 1041607, 1043023, 1045133, 1046075, 1044553, 1044555 | 459 | 405 | 3273 | 67 | 9.1 | 0.09 | 0.96 | 1.04575749 |
| GOTERM_MF_DIRECT | GO:0043022 ribosome binding | 1046554, 1045850, 1045770 | 459 | 4 | 3273 | 3 | 0.4 | 0.097 | 0.95 | 1.01322827 |
| GOTERM_MF_DIRECT | GO:0015418 quaternary-ammonium-compound-transporting ATPase activity | 1043981, 1043984, 1043435 | 459 | 4 | 3273 | 3 | 0.4 | 0.097 | 0.95 | 1.01322827 |
| GOTERM_MF_DIRECT | GO:0004096 catalase activity | 1045143, 1043606, 1044248 | 459 | 4 | 3273 | 3 | 0.4 | 0.097 | 0.95 | 1.01322827 |
