Table 11

Summary of predicted regulatory sites in δ-proteobacteria

Regulator

Regulon

Consensus

Genomes

BirA

Biotin biosynthesis

TTGTAAACC-[N_14/15]-GGTTTACAA

DD, DV, GM, GS, DA, DP

RFN riboswitch

Riboflavin biosynthesis

see Additional data files

DP

THI riboswitch

Thiamin biosynthesis

see Additional data files

DD, DV, GM, GS, DA, DP

B12 riboswitch

Cobalamin biosynthsis and transport

see Additional data files

DD, DV, GM, GS, DA, DP

S-box riboswitch

Methionine biosynthesis

see Additional data files

GM, GS, DA

LysX

Lysine biosynthesis and transport

GTgGTaCTnnnnAGTACCAC

DD, DV

Fur

Iron uptake and metabolism

GATAATGATnATCATTATC

DD, DV, GM, GS, DA

NikR

Nickel uptake and metabolism

GTGTTAC-[N_13/14]-GTAACAC

DD, DV, GM, GS, DA, DP

Zur

Zinc uptake

ATGCAACnnnGTTGCAT

DD, DV

TAAATCGTAATnATTACGATTTA

GS

ModE

Molybdate uptake and metabolism

cgGTCACg-[N₁₄]-cGTGACCg

DD, DV

atCGnTATATA-[N₆]-TATATAnCGat

GS

PerR

Peroxide stress response

AwnAGnAAtngTTnCTnwT

DD, DV

TtnCgnnTTnAAnncGnAA

DA, GS

AatTGnnATnnnATnnCAatt

GM, GS-2

GtTAATgATnATcATTAaC

DP

GgnnTTGnCAAnncC

DA-2

HrcA

Heat-shock response

TTAGCACTC-[N₉]-GAGTGCTAA

DD, DV, GM, GS, DA

Sigma-32

Heat-shock response

CTTGAAA-[N_11/16]-CCCCAT

DD, DV, GM, GS, DA, DP

CooA

CO dehydrogenase

TGTCGGCnnGCCGACA

DD, DV

HcpR

Sulfate reduction and energy metabolism (prismanes)

TTGTGAnnnnnnTCACAA

DD, DV

atTTGAccnnggTCAAat

DA, DP

DV (Desulfovibrio vulgaris); DD (Desulfovibrio desulfuricans G20); GM (Geobacter metallireducens); GS (Geobacter sulfurreducens PCA); DA (Desulfuromonas species); DP (Desulfotalea psychrophila). Lower case letters represent positions that do not conform to the consensus sequence.

Rodionov et al. Genome Biology 2004 5:R90   doi:10.1186/gb-2004-5-11-r90