C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446835703 136 LSPQEEKVLAMWTEGTSNKEIAYALGIHGKTVYTYKRNIRMKLHMDNRY 184
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRT 49

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446835703 136 LSPQEEKVLAMWTEGTSNKEIAYALGIHGKTVYTYKRNIRMKLHMDNRY 184
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRT 49

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446835703   1 MLKILVIDRCHFTRTGMEAWLNHTDVLSsslLVSGMNNLILAKEHILQWKPHLVIADLygflndALPEqpinaffaacrM 80
Cdd:COG2197    1 MIRVLIVDDHPLVREGLRALLEAEPDIE---VVGEAADGEEALELLEELRPDVVLLDI------RMPG-----------M 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446835703  81 TPLvllqsgnmpyrpqyashavlskhtplhELAQRIkgalythplqeapesatplLSPQEEKVLAMWTEGTSNKEIAYAL 160
Cdd:COG2197   61 DGL---------------------------EALRRL-------------------LTPREREVLRLLAEGLSNKEIAERL 94

                        170       180
                 ....*....|....*....|...
gi 446835703 161 GIHGKTVYTYKRNIRMKLHMDNR 183
Cdd:COG2197   95 GISERTVKTHVSNILRKLGVRNR 117

DNA-binding transcriptional regulator, CsgD family [Transcription];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446835703 132 ATPLLSPQEEKVLAMWTEGTSNKEIAYALGIHGKTVYTYKRNIRMKLHMDNR 183
Cdd:COG2771  124 RAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSR 175

transcriptional regulator RcsA;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446835703   5 LVIDRCHFTRTGMEAWLNHTDVLSSSllVSGMNNLILAKEHILQWKPHLVIADLYGFLND--------ALPEQPINAFFa 76
Cdd:PRK15411   4 IIMDLCSYTRLGLTGYLLSRGVKKRE--INDIETVDDLAIACDSLRPSVVFINEDCFIHDasnsqrikQIINQHPNTLF- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446835703  77 acrmtpLVLLQSGNM---PYRPQYASHAVLSKHTPLHELAQRIKGALYthplQEAPESA----TPL-LSPQEEKVLAMWT 148
Cdd:PRK15411  81 ------IVFMAIANIhfdEYLLVRKNLLISSKSIKPESLDDLLGDILK----KETTITSflnlPTLsLSRTESSMLRMWM 150

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 446835703 149 EGTSNKEIAYALGIHGKTVYTYKRNIRMKLHMDNR 183
Cdd:PRK15411 151 AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNK 185

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446835703 136 LSPQEEKVLAMWTEGTSNKEIAYALGIHGKTVYTYKRNIRMKLHMDNRY 184
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRT 49

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446835703   1 MLKILVIDRCHFTRTGMEAWLNHTDVLSsslLVSGMNNLILAKEHILQWKPHLVIADLygflndALPEqpinaffaacrM 80
Cdd:COG2197    1 MIRVLIVDDHPLVREGLRALLEAEPDIE---VVGEAADGEEALELLEELRPDVVLLDI------RMPG-----------M 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446835703  81 TPLvllqsgnmpyrpqyashavlskhtplhELAQRIkgalythplqeapesatplLSPQEEKVLAMWTEGTSNKEIAYAL 160
Cdd:COG2197   61 DGL---------------------------EALRRL-------------------LTPREREVLRLLAEGLSNKEIAERL 94

                        170       180
                 ....*....|....*....|...
gi 446835703 161 GIHGKTVYTYKRNIRMKLHMDNR 183
Cdd:COG2197   95 GISERTVKTHVSNILRKLGVRNR 117

DNA-binding transcriptional regulator, CsgD family [Transcription];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446835703 132 ATPLLSPQEEKVLAMWTEGTSNKEIAYALGIHGKTVYTYKRNIRMKLHMDNR 183
Cdd:COG2771  124 RAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSR 175

two component system response regulator;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446835703 123 HPLQEAPESATPLLSPQEEKVLAMWTEGTSNKEIAYALGIHGKTVYTYKRNIRMKLHMDN 182
Cdd:PRK15369 137 LALLNADDTNPPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHK 196

response regulator FixJ; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 446835703 136 LSPQEEKVLAMWTEGTSNKEIAYALGIHGKTVYTYKRNIRMKLHMDN 182
Cdd:PRK09390 142 LSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGS 188

nitrate/nitrite response regulator protein NarP;

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446835703 113 AQRIKGALYTHPLQEAPESATPLLSPQEEKVLAMWTEGTSNKEIAYALGIHGKTVYTYKRNIRMKLHMDNR 183
Cdd:PRK10403 131 SERVNQYLREREMFGAEEDPFSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSR 201

RNA polymerase sporulation sigma factor SigH;

                         10        20        30
                 ....*....|....*....|....*....|...
gi 446835703 135 LLSPQEEKVLAMWTEGTSNKEIAYALGIHGKTV 167
Cdd:PRK08295 155 LLSELEKEVLELYLDGKSYQEIAEELNRHVKSI 187

acid-sensing system DNA-binding response regulator EvgA;

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 446835703 136 LSPQEEKVLAMWTEGTSNKEIAYALGIHGKTVYTYKRNIRMKL 178
Cdd:PRK09958 144 LSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKL 186