Selected Cell
Cell:
Value:
6h results genes
12h results genes
24h results genes
DAVID 6h
DAVID 12h
DAVID 24h
A
B
C
D
E
F
G
H
I
J
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
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PP_3788 | 1046461 | NP_745918.1 | non-ribosomal peptide synthetase | 5.59 | 0.00000000 | ||||
PP_3789 | 1046416 | NP_745919.1 | efflux transporter | 3.86 | 0.00000563 | ||||
PP_3797 | 1046569 | NP_745927.1 | membrane protein | -3.90 | 0.00044808 | ||||
PP_3799 | 1046555 | NP_745929.1 | hypothetical protein | -3.46 | 0.00015445 | ||||
PP_3821 | 1046744 | galU | UTP-glucose-1-phosphate uridylyltransferase | 2.10 | 0.00037589 | ||||
PP_3839 | 1046726 | adhP | alcohol dehydrogenase | 2.15 | 0.00009133 | ||||
PP_3923 | 1046642 | NP_746053.1 | phosphoglycerate mutase | 2.39 | 0.00000622 | ||||
PP_3924 | 1046641 | NP_746054.1 | hypothetical protein | 2.69 | 0.00009717 | ||||
PP_3928 | 1046637 | NP_746058.1 | hypothetical protein | 6.48 | 0.00013553 | ||||
PP_3951 | 1046613 | pcaI | 3-oxoadipate CoA-transferase subunit A | -13.17 | 0.00000000 | ||||
PP_3952 | 1046612 | pcaJ | 3-oxoadipate CoA-transferase subunit A | -16.45 | 0.00000000 | ||||
PP_3954 | 1046610 | NP_746084.1 | substrate-binding protein | 2.03 | 0.00041521 | ||||
PP_4014 | 1046544 | mnmA | tRNA 2-thiouridine(34) synthase MnmA | 2.77 | 0.00001723 | ||||
PP_4016 | 1046542 | purB | adenylosuccinate lyase | 4.96 | 0.00000040 | ||||
PP_4020 | 1046536 | NP_746150.1 | oxidoreductase | -3.54 | 0.00000020 | ||||
PP_4021 | 1046534 | cpo | non-heme chloroperoxidase | 3.58 | 0.00000000 | ||||
PP_4037 | 1042092 | pydX | NADP-dependent dihydropyrimidine dehydrogenase subunit | 2.65 | 0.00000313 | ||||
PP_4054 | 1042129 | NP_746180.1 | hypothetical protein | 2.64 | 0.00029399 | ||||
PP_4059 | 1042130 | treSB | bifunctional trehalose synthase B/maltokinase | 2.74 | 0.00000083 | ||||
PP_4060 | 1042139 | glgE | alpha-1%2C4-glucan:maltose-1-phosphate maltosyltransferase | 3.82 | 0.00000000 | ||||
PP_4070 | 1042166 | NP_746196.1 | hypothetical protein | -12.12 | 0.00000000 | ||||
PP_4116 | 1042253 | aceA | isocitrate lyase | 4.34 | 0.00000000 | ||||
PP_4119 | 1041621 | nuoA | NADH-quinone oxidoreductase subunit A | 2.80 | 0.00000002 | ||||
PP_4120 | 1042262 | nuoB | NADH-quinone oxidoreductase subunit B | 2.06 | 0.00072698 | ||||
PP_4121 | 1042260 | nuoC | NADH-quinone oxidoreductase subunit C/D | 3.47 | 0.00000000 | ||||
PP_4122 | 1042274 | nuoE | NADH-quinone oxidoreductasesubunit E | 3.33 | 0.00014674 | ||||
PP_4123 | 1045401 | nuoF | NADH-quinone oxidoreductase subunit F | 4.02 | 0.00000000 | ||||
PP_4124 | 1042269 | nuoG | NADH-quinone oxidoreductase subunit G | 4.76 | 0.00000000 | ||||
PP_4125 | 1042266 | nuoH | NADH-quinone oxidoreductase subunit H | 3.05 | 0.00051646 | ||||
PP_4126 | 1042277 | nuoI | NADH-quinone oxidoreductase subunit I | 3.72 | 0.00000910 | ||||
PP_4129 | 1042283 | nuoL | NADH-quinone oxidoreductase subunit L | 2.98 | 0.00004606 | ||||
PP_4130 | 1042273 | nuoM | NADH-quinone oxidoreductase subunit M | 3.69 | 0.00000000 | ||||
PP_4131 | 1042285 | nuoN | NADH-quinone oxidoreductase subunit N | 3.91 | 0.00002966 | ||||
PP_4138 | 1042299 | chrR | chromate reductase | 2.05 | 0.00020122 | ||||
PP_4145 | 1042314 | mltD | membrane-bound lytic murein transglycosylase D | 4.94 | 0.00000000 | ||||
PP_4185 | 1042406 | sucD | succinyl-CoA synthetase subunit alpha | 3.34 | 0.00000014 | -5.70 | 0.00000004 | ||
PP_4186 | 1042414 | sucC | bifunctional succinyl-CoA synthetase subunit beta/glutaryl-CoA synthetase subunit beta | 3.72 | 0.00000000 | -23.23 | 0.00000000 | ||
PP_4187 | 1042391 | lpdG | dihydrolipoyl dehydrogenase | 4.18 | 0.00000000 | -11.46 | 0.00000000 | ||
PP_4188 | 1042423 | sucB | 2-oxoglutarate dehydrogenase dihydrolipoyltranssuccinylase subunit | 3.16 | 0.00000000 | -10.92 | 0.00000000 | ||
PP_4189 | 1042413 | sucA | 2-oxoglutarate dehydrogenase subunit E1 | 2.73 | 0.00000012 | -3.03 | 0.00056977 | ||
PP_4190 | 1042396 | sdhB | succinate dehydrogenase iron-sulfur subunit | 2.37 | 0.00014013 | -3.11 | 0.00002231 | ||
PP_4191 | 1042421 | sdhA | succinate dehydrogenase flavoprotein subunit | 2.29 | 0.00015288 | 5.75 | 0.00000000 | ||
PP_4192 | 1042613 | sdhD | succinate dehydrogenase hydrophobic membrane anchor subunit | 3.55 | 0.00007093 | 3.64 | 0.00000490 | ||
PP_4193 | 1042426 | sdhC | succinate dehydrogenase membrane b-556 subunit | 3.81 | 0.00000024 | 7.32 | 0.00000000 | ||
PP_4194 | 1042422 | gltA | citrate synthase | 4.83 | 0.00000002 | 4.00 | 0.00000259 | ||
PP_4202 | 1042448 | etfB | electron transfer flavoprotein subunit beta | 2.21 | 0.00005086 | 4.12 | 0.00000645 | ||
PP_4203 | 1042462 | NP_746320.1 | ubiquinone oxidoreductase electron transfer flavoprotein | 3.41 | 0.00000045 | 5.91 | 0.00000000 | ||
PP_4208 | 1042476 | NP_746325.1 | ECF family RNA polymerase sigma-70 factor | -3.53 | 0.00000005 | 6.79 | 0.00000000 | ||
PP_4217 | 1042530 | fpvA | TonB-dependent outer membrane ferripyoverdine receptor FpvA | -24.69 | 0.00000000 | 2.82 | 0.00009866 | ||
PP_4219 | 1042489 | pvdD | non-ribosomal peptide synthetase | -2.54 | 0.00046535 | 3.23 | 0.00001219 | ||
PP_4221 | 1042549 | pvdI | non-ribosomal peptide synthetase | -4.27 | 0.00008013 | -4.30 | 0.00002753 | ||
PP_4243 | 1042600 | pvdL | non-ribosomal peptide synthetase | -2.41 | 0.00091419 | 7.61 | 0.00000003 | ||
PP_4244 | 1041651 | pvdS | alternative sigma factor | -4.38 | 0.00000000 | -3.10 | 0.00008974 | ||
PP_4286 | 1041762 | puuE | allantoinase | -3.13 | 0.00000017 | -3.07 | 0.00000667 | ||
PP_4287 | 1043742 | pucL | 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase | -3.16 | 0.00000383 | 3.44 | 0.00059759 | ||
PP_4288 | 1041802 | allA | ureidoglycolate lyase | -3.53 | 0.00000002 | 2.96 | 0.00015680 | ||
PP_4289 | 1041777 | NP_746405.1 | membrane protein | -2.86 | 0.00000383 | -2.65 | 0.00053645 | ||
PP_4309 | 1043128 | NP_746425.1 | NCS1 family transporter | -3.39 | 0.00000005 | -3.76 | 0.00000246 | ||
PP_4310 | 1044648 | NP_746426.1 | hydantoin racemase | -3.19 | 0.00026650 | -5.50 | 0.00000000 | ||
PP_4314 | 1041791 | NP_746430.1 | hypothetical protein | 2.54 | 0.00002500 | -3.99 | 0.00000123 | ||
PP_4331 | 1044707 | NP_746446.1 | hypothetical protein | -2.25 | 0.00024678 | 4.81 | 0.00000099 | ||
PP_4352 | 1042653 | flhB | flagellin export apparatus substrate specificity protein | -2.27 | 0.00010038 | 6.12 | 0.00025364 | ||
PP_4365 | 1046205 | fliJ | flagellar protein FliJ | -3.03 | 0.00005228 | -4.17 | 0.00000010 | ||
PP_4366 | 1043501 | fliI | flagellum-specific ATP synthase | -2.65 | 0.00000117 | -4.16 | 0.00000004 | ||
PP_4387 | 1043250 | NP_746501.1 | hypothetical protein | -2.66 | 0.00039430 | -4.99 | 0.00000000 | ||
PP_4388 | 1044605 | flgE | flagellar hook protein FlgE | -2.11 | 0.00085102 | -4.06 | 0.00000000 | ||
PP_4468 | 1044276 | NP_746579.1 | Cro/CI family transcriptional regulator | 3.22 | 0.00001162 | -2.66 | 0.00080544 | ||
PP_4478 | 1043982 | astD | N-succinylglutamate 5-semialdehyde dehydrogenase | -5.22 | 0.00000000 | -3.17 | 0.00060012 | ||
PP_4479 | 1041844 | astA-I | arginine N-succinyltransferase subunit beta | -4.29 | 0.00000000 | -2.53 | 0.00039851 | ||
PP_4480 | 1043805 | astA-II | arginine N-succinyltransferase subunit alpha | -2.77 | 0.00000188 | -2.64 | 0.00045546 | ||
PP_4481 | 1041851 | astC | acetylornithine aminotransferase | -2.92 | 0.00000038 | -4.35 | 0.00000000 | ||
PP_4531 | 1046254 | NP_746641.1 | hypothetical protein | 4.23 | 0.00000571 | -5.50 | 0.00000000 | ||
PP_4561 | 1046343 | csbD | stress response protein | 3.06 | 0.00004068 | -4.84 | 0.00000000 | ||
PP_4604 | 1046163 | NP_746713.1 | DMT superfamily permease | 4.05 | 0.00000045 | -4.31 | 0.00000000 | ||
PP_4611 | 1042506 | NP_746720.1 | ECF family RNA polymerase sigma-70 factor | -5.96 | 0.00000019 | 3.96 | 0.00000047 | ||
PP_4618 | 1042694 | NP_746727.1 | hypothetical protein | -2.19 | 0.00057972 | -4.75 | 0.00000003 | ||
PP_4619 | 1041608 | hmgC | maleylacetoacetate isomerase | -2.53 | 0.00009245 | -5.76 | 0.00000000 | ||
PP_4620 | 1044222 | hmgB | fumarylacetoacetase | -2.54 | 0.00003658 | -3.34 | 0.00000092 | ||
PP_4621 | 1041590 | hmgA | homogentisate 1%2C2-dioxygenase | -3.89 | 0.00000000 | -7.23 | 0.00000000 | ||
PP_4643 | 1042015 | NP_746752.1 | xanthine/uracil permease family protein | -2.59 | 0.00006417 | -5.58 | 0.00000000 | ||
PP_4663 | 1045216 | NP_746772.1 | transmembrane protein | 11.34 | 0.00000010 | -5.82 | 0.00000000 | ||
PP_4688 | 1045897 | NP_746797.1 | heme/hemin ABC transporter permease | -3.20 | 0.00027658 | -4.67 | 0.00000000 | ||
PP_4704 | 1042000 | NP_746813.1 | hypothetical protein | -2.35 | 0.00003645 | -3.73 | 0.00000000 | ||
PP_4707 | 1041940 | NP_746816.1 | OsmY-like protein | 12.32 | 0.00000000 | -2.71 | 0.00014109 | ||
PP_4708 | 1045958 | pnp | polyribonucleotide nucleotidyltransferase | 2.74 | 0.00000102 | -9.44 | 0.00000000 | ||
PP_4709 | 1043991 | rpsO | 30S ribosomal protein S15 | 2.69 | 0.00000418 | -4.22 | 0.00000001 | ||
PP_4713 | 1042024 | nusA | transcription termination/antitermination factor L | 2.84 | 0.00002147 | 4.48 | 0.00000000 | ||
PP_4714 | 1041880 | rimP | ribosome maturation factor | 5.58 | 0.00000000 | -6.34 | 0.00000000 | ||
PP_4715 | 1042365 | tpiA | triose phosphate isomerase | 3.97 | 0.00000212 | -4.96 | 0.00000000 | ||
PP_4738 | 1042279 | NP_746846.1 | hypothetical protein | 3.83 | 0.00000795 | -5.09 | 0.00000000 | ||
PP_4788 | 1046266 | ybeY | endoribonuclease YbeY | -2.34 | 0.00000481 | -8.95 | 0.00000000 | ||
PP_4789 | 1042537 | corC | Co(2+)/Mg(2+)efflux heat shock protein | -2.65 | 0.00000127 | -8.93 | 0.00000000 | ||
PP_4794 | 1042400 | leuS | leucine--tRNA ligase | 2.44 | 0.00017539 | -6.08 | 0.00000000 | ||
PP_4821 | 1045805 | NP_746926.1 | Fis-like DNA-binding protein | 2.97 | 0.00013758 | -6.64 | 0.00000000 | ||
PP_4855 | 1042822 | NP_746960.1 | osmotically-inducible lipoprotein OsmE | 4.48 | 0.00000235 | -15.85 | 0.00000000 | ||
PP_4877 | 1043837 | rpsF | 30S ribosomal protein S6 | 2.88 | 0.00000262 | -16.06 | 0.00000000 | ||
PP_4881 | 1044370 | NP_746985.1 | iron ABC transporter substrate-binding protein | -2.71 | 0.00000022 | -15.03 | 0.00000000 | ||
PP_4882 | 1042290 | NP_746986.1 | iron ABC transporter permease | -4.56 | 0.00000000 | -11.30 | 0.00000000 | ||
PP_4888 | 1041629 | NP_746991.2 | methyl-accepting chemotaxis transducer | -4.45 | 0.00000000 | -9.29 | 0.00000000 | ||
PP_4922 | 1041616 | thiC | phosphomethylpyrimidine synthase | 3.80 | 0.00000535 | -5.33 | 0.00000000 |
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
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90
91
92
93
94
95
96
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100
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 |
A
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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 |