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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 555248975 158 LASILTAKEREIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINRTELVSR 215
Cdd:COG2197   66 LRRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLL 123

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 555248975 158 LASILTAKEREIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINRTELVSR 215
Cdd:COG2197   66 LRRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLL 123

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 555248975 162 LTAKEREIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINRTELV 213
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLV 52

Bacterial regulatory proteins, luxR family;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 555248975  160 SILTAKEREIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINRTELV 213
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELV 54

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
                  ....*....|....*....|....*....|....*..
gi 555248975  162 LTAKEREIVGMV-CEGASNKLIARQLNISLSTVKTHL 197
Cdd:TIGR02985 114 LPEQCREIFILSrFEGLSNKEIAEELGISVKTVEYHI 150

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 555248975 158 LASILTAKEREIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINRTELVSR 215
Cdd:COG2197   66 LRRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLL 123

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 555248975 162 LTAKEREIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINRTELV 213
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLV 52

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 555248975  88 ARHRHYYHEFMLPNHVCDMIEIFIRRGHRIIAGISLMRDIPFSSEERLRAQAVQPLLGLAIHDSLQEDNNLASILTAKER 167
Cdd:COG2771   54 LAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPRER 133

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 555248975 168 EIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINRTELVSR 215
Cdd:COG2771  134 EVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVAL 181

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 555248975 158 LASiLTAKEREIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINRTELV 213
Cdd:COG4566  135 LAS-LTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELV 189

two component system response regulator;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 555248975 147 AIHDSLQEDNNLASILTAKEREIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINRTELV 213
Cdd:PRK15369 135 AILALLNADDTNPPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELL 201

transcriptional regulator CsgD;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 555248975 155 DNNLASILTAKEREIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINRTELVS 214
Cdd:PRK10100 149 NSTESALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVS 208

nitrate/nitrite response regulator protein NarP;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 555248975 160 SILTAKEREIVGMVCEGASNKLIARQLNISLSTVKTHLRNIFAKTEVINR 209
Cdd:PRK10403 152 SVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSR 201

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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 555248975 112 RRGHRIIAGISLMRDIPFSSEERLRAQAVQPLLGLAIHDslqednnlasiLTAKEREIVGMVC-EGASNKLIARQLNISL 190
Cdd:COG1595   89 RRRELLDELAEELPDEAADPEEALEAEELLEALLAALER-----------LPPRQREVLVLRYlEGLSYAEIAEILGISE 157

                 ....*...
gi 555248975 191 STVKTHLR 198
Cdd:COG1595  158 GTVKSRLS 165

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
                  ....*....|....*....|....*....|....*..
gi 555248975  162 LTAKEREIVGMV-CEGASNKLIARQLNISLSTVKTHL 197
Cdd:TIGR02985 114 LPEQCREIFILSrFEGLSNKEIAEELGISVKTVEYHI 150