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Table 1 Promoter motifs-based prediction of RpoE and RpoE2 regulon members in the genome of Shewanella oneidensis MR-1

From: An extracytoplasmic function sigma factor-dependent periplasmic glutathione peroxidase is involved in oxidative stress response of Shewanella oneidensis

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)