helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 510828766    9 KPLLTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVKGRSQAVV 64
Cdd:smart00421  1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVR 56

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 510828766 12 LTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVKGRSQAVVELLR 68
Cdd:cd06170   1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 510828766   12 LTKREREVFEL-LVQDKTTKEIASDLFISEKTVRNHISNAMQKL 54
Cdd:TIGR02985 114 LPEQCREIFILsRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 510828766  11 LLTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMG 70
Cdd:COG2197   69 LLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLG 128

Bacterial regulatory proteins, luxR family;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 510828766  12 LTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVKGRSQAVV 64
Cdd:pfam00196  3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVR 55

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 510828766 12 LTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVKGRSQAVVELLR 68
Cdd:cd06170   1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 510828766  21 ELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELE 73
Cdd:COG2909  132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGLLA 184

transcriptional regulator UhpA;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 510828766  12 LTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVKGRsqavVELLR 68
Cdd:PRK10360 138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSND----VELAR 190

nitrate/nitrite response regulator protein NarP;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 510828766  11 LLTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVKGRSQAVVELL 67
Cdd:PRK10403 153 VLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFL 209

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 510828766   12 LTKREREVFEL-LVQDKTTKEIASDLFISEKTVRNHISNAMQKL 54
Cdd:TIGR02985 114 LPEQCREIFILsRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157

response regulator FixJ; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 510828766  12 LTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVKGRSqavvELLRM 69
Cdd:PRK09390 142 LSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLS----ELVRM 195

HTH-type transcriptional regulator MalT;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 510828766  12 LTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVKGRSQAVV---ELLRM 69
Cdd:PRK04841 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQhaqDLLKM 899

fimbriae biosynthesis transcriptional regulator FimZ;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 510828766  12 LTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVkgrsQAVVELL 67
Cdd:PRK09935 150 LSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGL----HSIVELI 201

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 510828766  12 LTKREREVFEL-LVQDKTTKEIASDLFISEKTVRNHISNAMQKL 54
Cdd:pfam04545  5 LPPRERQVLVLrYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48

acid-sensing system DNA-binding response regulator EvgA;

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 510828766  12 LTKREREVFELLVQDKTTKEIASDLFISEKTVRNHISNAMQKLGVK 57
Cdd:PRK09958 144 LSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECK 189

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 510828766 12 LTKREREVFEL-LVQDKTTKEIASDLFISEKTVRNHISNAMQKL 54
Cdd:cd06171  11 LPEREREVILLrFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54

RNA polymerase sigma factor; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 510828766  12 LTKREREVFELL-VQDKTTKEIASDLFISEKTVRNHISNAMQKL 54
Cdd:PRK11924 126 LPVKQREVFLLRyVEGLSYREIAEILGVPVGTVKSRLRRARQLL 169