TABLE 1.
Genes upregulated or downregulated in finR deletion mutant versus in wild-type P. putida KT2440a
| Gene IDb | Log2 fold change | P value | Gene name | Description |
|---|---|---|---|---|
| PP_0057 | −2.207 | 1.72E−39 | Major facilitator family transporter | |
| PP_0137 | 2.856 | 1.25E−103 | gltP | Glutamate/aspartate-proton DAACS transporter |
| PP_0596 | 3.701 | 0 | Omega-amino acid–pyruvate aminotransferase | |
| PP_0597 | 3.623 | 1.02E−290 | mmsA-I | Methylmalonate-semialdehyde dehydrogenase |
| PP_0614 | 2.447 | 2.58E−08 | Bifunctional N-carbamoyl-beta-alanine amidohydrolase/allantoin amidohydrolase | |
| PP_0615 | 3.250 | 5.79E−05 | ABC transporter ATP-binding protein | |
| PP_0616 | 3.154 | 2.77E−10 | ABC transporter ATP-binding protein | |
| PP_0617 | 4.385 | 3.32E−07 | Branched-chain amino acid ABC transporter permease | |
| PP_0618 | 4.646 | 3.32E−10 | Branched-chain amino acid ABC transporter permease | |
| PP_0619 | 3.991 | 1.39E−46 | Branched-chain amino acid ABC transporter substrate-binding protein | |
| PP_0620 | 5.553 | 3.63E−206 | GntR family transcriptional regulator | |
| PP_0817 | −2.297 | 5.46E−33 | alaC | Aminotransferase |
| PP_1039 | 4.143 | 0.0075892 | tatC-I | Sec-independent protein translocase protein |
| PP_1638 | −3.811 | 2.01E−149 | fpr-I | Ferredoxin-NADP+ reductase |
| PP_2034 | 3.046 | 8.06E−77 | Membrane protein | |
| PP_2035 | 3.295 | 2.17E−52 | benE-I | Benzoate transport protein |
| PP_2036 | 3.045 | 8.77E−101 | 4-Hydroxy-tetrahydrodipicolinate synthase | |
| PP_2037 | 2.091 | 3.92E−10 | Aldolase | |
| PP_2052 | 2.233 | 3.20E−14 | Bifunctional sugar-phosphatase/mannitol-1-phosphate 5-dehydrogenase | |
| PP_2397 | 4.002 | 3.31E−68 | EF hand domain-containing protein | |
| PP_2404 | 3.914 | 1.29E−18 | Hypothetical protein | |
| PP_2453 | 2.024 | 6.07E−148 | ansB | Glutaminase-asparaginase |
| PP_2454 | −2.195 | 2.45E−119 | rbsB | Ribose ABC transporter, periplasmic ribose-binding subunit |
| PP_3073 | −3.332 | 1.27E−84 | hbdH | 3-Hydroxybutyrate dehydrogenase |
| PP_3074 | −4.063 | 3.12E−164 | bhbP | d-Beta-hydroxybutyrate permease |
| PP_3191 | −2.213 | 4.57E−134 | Threonine ammonia-lyase/dehydratase | |
| PP_3589 | 2.618 | 1.16E−36 | sdaC | Serine:H+ symport permease |
| PP_3661 | 3.956 | 1.44E−90 | Membrane protein | |
| PP_3745 | −3.031 | 6.86E−37 | glcD | Glycolate oxidase FAD-linked subunit |
| PP_3940 | −2.455 | 3.63E−21 | nicT | Metabolite transport protein NicT |
| PP_3941 | −2.753 | 1.35E−33 | nicF | Maleamate amidohydrolase |
| PP_3942 | −2.414 | 5.88E−22 | nicE | Maleate isomerase |
| PP_3943 | −2.694 | 1.60E−16 | nicD | N-Formylmaleamate deformylase |
| PP_3944 | −3.601 | 2.45E−44 | nicC | 6-Hydroxynicotinate 3-monooxygenase |
| PP_3945 | −2.474 | 2.26E−58 | nicX | 2,5-Dihydroxypyridine 5,6-dioxygenase |
| PP_4232 | 2.120 | 1.93E−14 | Cytochrome c family protein | |
| PP_4233 | 2.640 | 1.50E−05 | Oxidoreductase small subunit | |
| PP_4434 | 3.476 | 1.57E−41 | dadA-I | d-Amino acid dehydrogenase small subunit |
| PP_4435 | 4.100 | 0 | Hypothetical protein | |
| PP_4548 | 2.585 | 6.57E−14 | Oxidoreductase | |
| PP_4625 | 3.054 | 4.80E−34 | cidB | Holin CidA anti-holin regulator |
| PP_4626 | 3.358 | 3.29E−12 | cidA | Murein hydrolase holin regulator |
| PP_4735 | 3.332 | 0.00E+00 | lldP | l-Lactate permease |
| PP_4736 | 3.441 | 4.45E−105 | lldD | l-Lactate dehydrogenase |
| PP_4737 | 4.059 | 1.27E−94 | dld2 | d-Lactate dehydrogenase |
| PP_5029 | 4.210 | 5.79E−145 | hutG | N-Formylglutamate deformylase |
| PP_5030 | 4.031 | 1.76E−213 | hutI | Imidazolonepropionase |
| PP_5031 | 3.454 | 3.46E−109 | proY | Proline (histidine) APC transporter |
| PP_5032 | 3.937 | 0 | hutH | Histidine ammonia-lyase |
| PP_5033 | 4.132 | 6.99E−245 | hutU | Urocanate hydratase |
| PP_5036 | 4.591 | 0 | hutF | Formiminoglutamate deiminase |
| PP_5073 | −3.290 | 6.77E−50 | Hypothetical protein | |
| PP_5269 | 4.310 | 0.00E+00 | dadX | Alanine racemase |
| PP_5270 | 3.167 | 0 | dadA-II | d-Amino acid:quinone oxidoreductase |
| PP_5338 | −2.377 | 1.80E−156 | aspA | Aspartate ammonia-lyase |
| PP_5549 | 2.424 | 1.95E−36 | Hypothetical protein |
a
Genes with log2 fold changes of >2 or <−2 are shown.
b
ID, identifier.