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        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495777508 154 LTHSERKVLRLLGKGWGINQIATLLKKSNKTISAQKNSAMRRLSLRSNADMYAWINS 210
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495777508 154 LTHSERKVLRLLGKGWGINQIATLLKKSNKTISAQKNSAMRRLSLRSNADMYAWINS 210
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495777508 154 LTHSERKVLRLLGKGWGINQIATLLKKSNKTISAQKNSAMRRLSLRSNADMYAW 207
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLL 123

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495777508  41 LQELTLLQLRRADVIIADISGEYRNPRGALEEYYGLLNQYRDIHWIFLVSRPLYPIAVELLMRPESTLLSDMEPIEGVVN 120
Cdd:COG2771   11 LALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLAL 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495777508 121 AIRAGSERAERISQTLLTPEPQSTENENEHVIA----LTHSERKVLRLLGKGWGINQIATLLKKSNKTISAQKNSAMRRL 196
Cdd:COG2771   91 LALLAALLARLAALLLALALAALLLAALARLLArapgLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170

                        170
                 ....*....|..
gi 495777508 197 SLRSNADMYAWI 208
Cdd:COG2771  171 GVSSRAELVALA 182

DNA-binding protein, Tfx family; PSI-BLAST starting with one member of this family converges with significant hits only to other members of the family, which is restricted to the Archaea. Homology is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter. [Regulatory functions, DNA interactions]

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 495777508  154 LTHSERKVLRLLGKGWGINQIATLLKKSNKTISAQKNSAMRRLSLRSNA-DMYAWINS 210
Cdd:TIGR00721   7 LTERQIKVLELREKGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTlDFVKFIKS 64

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495777508 154 LTHSERKVLRLLGKGWGINQIATLLKKSNKTISAQKNSAMRRLSLRSNADMYAWINS 210
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495777508 154 LTHSERKVLRLLGKGWGINQIATLLKKSNKTISAQKNSAMRRLSLRSNADMYAW 207
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLL 123

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495777508  41 LQELTLLQLRRADVIIADISGEYRNPRGALEEYYGLLNQYRDIHWIFLVSRPLYPIAVELLMRPESTLLSDMEPIEGVVN 120
Cdd:COG2771   11 LALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLAL 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495777508 121 AIRAGSERAERISQTLLTPEPQSTENENEHVIA----LTHSERKVLRLLGKGWGINQIATLLKKSNKTISAQKNSAMRRL 196
Cdd:COG2771   91 LALLAALLARLAALLLALALAALLLAALARLLArapgLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170

                        170
                 ....*....|..
gi 495777508 197 SLRSNADMYAWI 208
Cdd:COG2771  171 GVSSRAELVALA 182

transcriptional regulator RcsB; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495777508 154 LTHSERKVLRLLGKGWGINQIATLLKKSNKTISAQKNSAMRRLSLRSNADMYAWINS 210
Cdd:PRK10840 151 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSS 207

transcriptional regulator NarL; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495777508 108 LLSDMEPiEGVVNAIR---AG----SERAERISQTLLTPEPQSTENENEhviALTHSERKVLRLLGKGWGINQIATLLKK 180
Cdd:PRK10651 107 LLKDMEP-EDLLKALQqaaAGemvlSEALTPVLAASLRANRATTERDVN---QLTPRERDILKLIAQGLPNKMIARRLDI 182

                         90       100       110
                 ....*....|....*....|....*....|....
gi 495777508 181 SNKTISAQKNSAMRRLSLRSNADMYAWINSTQGM 214
Cdd:PRK10651 183 TESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF 216

fimbriae biosynthesis transcriptional regulator FimZ;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495777508 150 HVIALTHSERKVLRLLGKGWGINQIATLLKKSNKTISAQKNSAMRRLSLRS 200
Cdd:PRK09935 146 TDTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHS 196