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
               ....*....|....*....|....*....|....*....|....*....|....
1P4W_A      35 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNY 88
Cdd:cd06170  1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54

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

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
1P4W_A       35 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYL 89
Cdd:COG2197  70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLA 124

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
1P4W_A         34 RLSPKESEVLRLFA-EGFLVTEIAKKLNRSIKTISSQKKSAMMKL 77
Cdd:TIGR02937 110 KLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154

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
               ....*....|....*....|....*....|....*....|....*....|....
1P4W_A      35 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNY 88
Cdd:cd06170  1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54

DNA-binding transcriptional activator BglJ; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
1P4W_A        35 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLN 87
Cdd:PRK11475 135 LSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGLLD 187

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

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
1P4W_A       34 RLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYL 89
Cdd:COG2771 127 GLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALA 182

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];

                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*....
1P4W_A      33 KRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDN 81
Cdd:COG5905 11 SLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRN 59

transcriptional regulator UhpA;

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
1P4W_A        11 GSY-TPESVAKLlekisAGGYGDKrLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIAL 85
Cdd:PRK10360 119 GCYlTPDIAIKL-----ASGRQDP-LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
1P4W_A         34 RLSPKESEVLRLFA-EGFLVTEIAKKLNRSIKTISSQKKSAMMKL 77
Cdd:TIGR02937 110 KLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
1P4W_A       34 RLSPKESEVLRL-FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 77
Cdd:COG1595 127 RLPPRQREVLVLrYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171

fimbriae biosynthesis transcriptional regulator FimW;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
1P4W_A        33 KRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYL 89
Cdd:PRK15201 132 RHFSVTERHLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQFLKYI 188

response regulator; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
1P4W_A        33 KRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIAL 85
Cdd:PRK09483 147 ASLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVEL 199

acid-sensing system DNA-binding response regulator EvgA;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1P4W_A        12 SYTPESvaklLEKISAGGYGDKR----LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLN 87
Cdd:PRK09958 121 CYFPFS----LNRFVGSLTSDQQkldsLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYT 196

                 .
1P4W_A        88 Y 88
Cdd:PRK09958 197 F 197

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
1P4W_A       33 KRLSPKESEVLRL-FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 77
Cdd:COG1191 185 EQLPERERLVLSLyYFEELTLKEIAEVLGVSESRVSRLHKKALARL 230

RNA polymerase sporulation sigma factor SigH;

                         10        20        30
                 ....*....|....*....|....*....|..
1P4W_A        35 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTI 66
Cdd:PRK08295 156 LSELEKEVLELYLDGKSYQEIAEELNRHVKSI 187