Table 2. Transcription factors and other regulators affected in the absence of PamR.
| gene | Effect3 | Exp. Diff. | TR & Mod 1 | Functional category 2 | Function |
|---|---|---|---|---|---|
| ypoP | + | 3,00 | TF* | U | similar to transcriptional regulator (MarR family) |
| yopO | + | 4,12 | TF* | Prophages & mobile gen. elemts | similar to transcriptional regulator (Xre family) |
| yonR | + | 5,29 | TF* | Prophages & mobile gen. elemts | similar to transcriptional regulator (Xre family) |
| yobD | + | 3,69 | TF* | U | similar to transcriptional regulator (Xre family) |
| ykvN | + | 2,64 | TF* | U | unknown; MarR family transcription regulator |
| ydfL | + | 3,30 | TF* | U | unknown; similar to multidrux efflux transporter regulator of MreR family |
| ydeB | + | 3,26 | TF* | U | unknown; putative transcriptional regulator |
| yceK | + | 2,56 | TF* | U | unknown; putative transcriptional regulator |
| ybzH | + | 3,84 | TF* | Prophages & mobile gen. elemts | unknown; putative transcriptional regulator |
| xre | + | 3,83 | TF | Prophages & mobile gen. elemts | regulation of PBSX prophage gene expression |
| tnrA | + | 2,45 | TF | Metabolism | control of nitrogen assimilation (MerR family) |
| sknR | + | 3,04 | TF | Prophages & mobile gen. elemts | repression of yqaF operon of the skin element (Xre family) |
| sinR | + | 2,76 | TF | Lifestyle | regulator of post-exponential-phase responses genes, and biofilm formation |
| ntdR | + | 3,73 | TF | Lifestyle | activator of ntdABC-glcP operon (LacI family) |
| mntR | + | 2,77 | TF | Cellular processes | regulation of manganese transport (DtxR family) |
| mgsR | + | 2,86 | TF | Stress response | regulator of a subset of the SigB stress regulon; oxidative stress protection |
| lrpB | + | 3,51 | TF | Metabolism | metabolism of glycine; Repression of glyA transcription and KinB-dependent spo. |
| lrpA | + | 5,26 | TF | Metabolism | metabolism of glycine; Repression of glyA transcription and KinB-dependent spo. |
| immR | + | 3,86 | TF | Prophages & mobile gen. elemts | Control of transfer of the mobile genetic element ICEBs1 |
| comK | + | 2,74 | TF | Lifestyle | master regulator for competence |
| abrB | + | 4,34 | TF | Lifestyle | tansition state regulator |
| sigX | + | 3,07 | TF | Stress response | resistance to cationic antimicrobial peptides; RNA polymerase ECF-type σ factor |
| pyrR | + | 3,56 | R | Metabolism | transcriptional antiterminator of the pyr operon |
| kre | + | 3,31 | R | Lifestyle | inhibitor of competence; ComK repressor |
| yydG | + | 4,50 | R | Stress response | control of LiaR-LiaS activity; oxidoreductase |
| yisI | + | 4,16 | R | Lifestyle | inhibition of phosphorelay; Spo0A-P phosphatase |
| sda | + | 2,68 | R | Lifestyle | checkpoint coupling replication and sporulation; inhibitor of Spo0A phosphorelay |
| rapI | + | 2,96 | R | Prophages & mobile gen. elemts | control of ICEBs1, ImmR antagonist; response regulator aspartate phosphatase |
| phrE | + | 3,48 | R | Lifestyle | Regulator of RapE phosphatase |
| immA | + | 3,40 | R | Prophages & mobile gen. elemts | control of ImmR activity; site-specific protease |
| degR | + | 3,58 | R | Metabolism | control of DegU; Positive effector of DegU-phosphate stability |
| yhcF | - | 3,26 | TF* | U | unknown; putative transcription factor (GntR family) |
| thrR | - | 2,75 | TF | Metabolism | control of threonine biosynthesis |
| spoVT | - | 2,37 | TF | Lifestyle | regulation of forespore gene expression |
| sigF | - | 2,56 | TF | Lifestyle | RNA polymerase forespore-specific (early) sigma factor SigF |
| ycbM | - | 2,71 | R* | U | predicted two-component sensor kinase |
| yhcY | - | 2,13 | R | U | two component sensor kinase |
| yesM | - | 4,38 | R | U | two-component sensor kinase |
| psdS | - | 2,41 | R | Stress response | two-component sensor kinase, response to lipid II-binding lantibiotics |
| crh | - | 2,43 | R | Metabolism | CcpA cofactor |
1 "TF" stands for transcriptional factor,
* indicates its function is putative, based on sequence similarity,
R stands for other Regulatory function
2 "U" stands for unknown
3 +/- impact of ΔpamR on expression of the gene