Table 3 PhaR-activated genes associated with a PhaR-binding consensus sequence
Genes or orf | PhaR binding site | USDA110 RPKM | ΔphaR RPKM | Fold changea | Description |
|---|---|---|---|---|---|
phbB2 (bll0225) | TGCGCTGCACAC | 154.34 | 74.52 | 2.07 | acetoacetyl CoA reductase |
ragA (bll0304) | TGCGACGCCGCA | 8.95 | 2.29 | 3.91 | two-component response regulator |
blr0305 | TGCGACGCCGCA | 45.61 | 16.48 | 2.77 | unknown protein |
bll0805 | CGCAACGCACAA | 185.17 | 76.29 | 2.43 | hypothetical protein |
blr0806 | CGCAACGCACAA | 52.09 | 23.58 | 2.21 | hypothetical protein |
bll1416 | TGCGCGGCAGCA | 52.49 | 20.56 | 2.55 | unknown protein |
blr2204 | TGCAGTCCAGAA | 19.07 | 9.05 | 2.11 | transcriptional regulatory protein AraC family |
bll2446 | TTCGCCGCAGAA | 275.72 | 129.25 | 2.13 | hypothetical protein |
bsr2601 | TGCACCGCAGCC | 32.44 | 15.65 | 2.07 | unknown protein |
blr2810 | TGCATTGCGCAA | 15.88 | 7.35 | 2.16 | aldo/keto reductase |
bll2914 | TGCGCTGGAGAA | 25.07 | 9.61 | 2.61 | probable amidase |
bll3387 | TGCGCCGCAACA | 278.27 | 54.25 | 5.13 | unknown protein |
blr3795 | TGCATTGCAGCG | 40.09 | 19.03 | 2.11 | ABC transporter HlyB/MsbA family |
blr3904 | TGCAGTGCTGCA | 312.33 | 109.92 | 2.84 | probable iron transport protein |
blr4188 | CGCAGTGCAGCA | 28.85 | 12.98 | 2.22 | hypothetical protein |
bll4430 | TGCAGCGCAGCA | 104.34 | 38.21 | 2.73 | hypothetical protein |
bsr4431 | TGCAGCGCAGCA | 216.36 | 77.85 | 2.78 | hypothetical protein |
pdhA (bll4783) | TGCAGTGCGGCA | 249.67 | 111.10 | 2.25 | pyruvate dehydrogenase alpha subunit |
bll4833 | TGCGGCGCACCA | 530.73 | 140.09 | 3.79 | unknown protein |
bsr4834 | TGCGGCGCACCA | 168.95 | 52.96 | 3.19 | unknown protein |
blr4841 | TGCCGCGCACAA | 30.64 | 14.59 | 2.10 | unknown protein |
bll4952 | TGCATCGCACAA | 27.07 | 7.50 | 3.61 | NfeD protein homolog |
bll5160 | TGCGGCGCACAA | 106.54 | 46.40 | 2.30 | conserved hypothetical protein; putative alpha/beta-Hydrolases |
bsl5321 | CGCGGCGCAGCA | 415.34 | 205.51 | 2.02 | unknown protein |
bll5335 | TGCGCCGGACAA | 35.29 | 16.85 | 2.09 | putative thiolase |
blr5540 | TGCGGTGCCCAA | 231.26 | 58.07 | 3.98 | hypothetical protein |
bsl5717 | TGCGGCGCCCAA | 109.78 | 34.94 | 3.14 | hypothetical protein |
bll5961 | TGCGGTGCAACA | 12.66 | 4.23 | 2.99 | transcriptional regulatory protein Crp family |
blr5962 | TGCGGTGCAACA | 40.98 | 7.40 | 5.54 | ABC transporter ATP-binding protein |
bll6121 | TGCAGCGCACAA | 21.88 | 9.39 | 2.33 | probable sulfite oxidase |
bll6206 | CGCGCCGCACAA | 74.19 | 35.28 | 2.10 | hypothetical protein |
exaA (blr6207) | CGCGCCGCACAA | 93.32 | 23.85 | 3.91 | probable quinoprotein ethanol dehydrogenase precursor |
blr6443 | TGCAATGCAACA | 13.79 | 2.83 | 4.87 | ABC transporter permease protein |
blr6465 | CGCGATGCACAA | 39.03 | 14.29 | 2.73 | putative steroid monooxygenase |
bll6733 | TGCGACGAAGCA | 45.09 | 21.88 | 2.06 | putative amidase |
pqqA (bsr6735) | TGCAGTGCAACA | 156.84 | 40.03 | 3.92 | putative pyrroloquinoline quinone synthesis protein A |
blr6837 | CGCAGTGCAGCA | 34.10 | 7.30 | 4.67 | hypothetical protein |
blr6886 | CGCATTGCACAA | 57.55 | 25.47 | 2.26 | transcriptional regulatory protein MarR family |
bll7487 | TGCGGAGCACAA | 456.33 | 176.20 | 2.59 | unknown protein |
bll7511 | TGCAACGCAGAT | 167.13 | 62.44 | 2.68 | unknown protein |
bll7663 | TGCACCGCAGCA | 57.90 | 24.14 | 2.40 | unknown protein |
pckA (bll8141) | TGCGACGCACAA | 386.03 | 107.43 | 3.59 | phosphoenolpyruvate carboxykinase |