Table 1.
Promoter motifs-based prediction of RpoE and RpoE2 regulon members in the genome of Shewanella oneidensis MR-1
| Gene identity | Putative RpoE-dependent promoter sequence | Gene name | Functions | Other genes in the operon |
|---|---|---|---|---|
| SO_0516 | GAACTTATGTTTAAAATGACTGTCAGA | Hypothetical protein | ||
| SO_1065 | GAACTTGCTCCTAAAGTTGGTGTCTCT | fkpA | FKBP-type peptidyl prolyl cis-trans isomerase | |
| SO_1342 | GAACTTTTTCAAAGTACGCGAGTCTAC | rpoE | RNA polymerase sigma 24 factor | rseA(SO_1343)-rseB(SO_1344)-rseC(SO_1345) |
| SO_1476 | GAACTAAAACCCGCGGCTTAGGTCGAA | bamE | Outer membrane protein (OMP) assembly complex subunit E | |
| SO_1492 | GAACTTCTCTTCACACCTCGCCACTAT | ppiA | Peptidyl prolyl cis-trans isomerase A | |
| SO_1636 | GAACCTTTAGATTTTTTCAAAGTCGGA | rseP | Membrane associated zinc metalloprotease | bamA(SO_1637)-skp(SO_1638)- lpxD(SO_1639)-fabZ(SO_1640)- lpxA(SO_1641)-lpxB(SO_1642)- rnhB(SO_1643) |
| SO_1880 | GAACTTTCTGAGCAATGTCATGGTCTGT | bamC | OMP assembly complex subunit C | |
| SO_3309 | GAACTCAAAGGCGACTTCTTTGTTCGT | bamB | OMP assembly complex subunit B | |
| SO_3580 | GAACCGTACCCGCGTTTTGGGGTCCAA | bamD | OMP assembly complex subunit D | SO_3581 |
| SO_3636 | CAACTTTCCCCGTCGATACTTGTCCAG | lptD | Lipopolysaccharide (LPS) transporter subunit D | surA(SO_3637)-pdxA(SO_3638)-ksgA(SO_3639) |
| SO_3637 | GAACCTCAACAAGGACTGAGAGTCCAA | surA | LPS assembly protein | pdxA(SO_3638)-ksgA(SO_3639) |
| SO_3942 | GAACTTTTTCAATGAGGTGCGTGTCCGA | degQ | Periplasmic serine protease | |
| SO_3958 | GAACTGCTATCGATCTACAATGTCACC | lptC | LPS transporter (LPT) subunit C | lptA(SO_3959)-lptB(SO_3960) |
| SO_3959 | GAACTCGATCTCAACACTATGATAATG | lptA | LPS transporter subunit A | lptB(SO_3960) |
| SO_4562 | GAACTTTAGCGTGTAAAATCACTCTATG | Conserved hypothetical protein | ||
| SO_4583 | GAACTTTTGTTCACTTGCAATGTCTAT | rpoH | RNA polymerase sigma 32 factor | |
| RpoE2-dependent promoter sequence | ||||
| SO_1986 | TGATCCATTATTCAAAGGGCCACGTATT | rpoE2 | ECF RNA polymerase | chrR (SO_1985, anti-sigma factor) |
| SO_1987 | TGATCAAATTCTGATGATGGTACGTAAT | Lon | Lon domain protease | |
| SO_3349 | TGATCCCTATCGTAGCAAGTTACGTAAT | pgpD | Periplasmic glutathione peroxidase | hemH2 (SO_3348, ferrochelatase) |
| SO_3386 | TGATCCTTGTACAAGAATGGTCCGTAAT | ybgA | Photoreactivation-associated inner membrane protein | phrB (SO_3384, deoxyribo-dipyrimidine photolyase) cfa (SO_3379, cyclopropane fatty acid synthase) |
| SO_4169 | TGATCCTCACAGTGCTGCTATCCGTAAC | phr | Deoxyribodipyrimidine photolyase-related protein | SO_4170 (CsgA short chain dehydrogenase/reductase) |