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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488408620    3 FNNVYHQFNKYIHYLLNKYHI-RYNYDEYYQLMLIRLWQLTNQYNASlnSNFSTFIIFRLNYYLIDLFRKEQPKQSVEIS 81
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGdDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488408620   82 ILNPSSSKLPIY---ILNDFNLIMQEAWKHLTRQEQQWLIL-QISGYKQYEIAQHMHVSLSSVKNYKRNARQKLQR 153
Cdd:TIGR02937  81 LEELLDSDPSPEeelEQEEEREALREALEKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156

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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488408620    3 FNNVYHQFNKYIHYLLNKYHI-RYNYDEYYQLMLIRLWQLTNQYNASlnSNFSTFIIFRLNYYLIDLFRKEQPKQSVEIS 81
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGdDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488408620   82 ILNPSSSKLPIY---ILNDFNLIMQEAWKHLTRQEQQWLIL-QISGYKQYEIAQHMHVSLSSVKNYKRNARQKLQR 153
Cdd:TIGR02937  81 LEELLDSDPSPEeelEQEEEREALREALEKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156

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

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 488408620 109 LTRQEQQWLILQISGYKQYEIAQHMHVSLSSVKNYKRNARQKLQ 152
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLG 113

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 488408620 109 LTRQEQQWLILQISGYKQYEIAQHMHVSLSSVKNYKRNARQKL 151
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43

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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488408620    3 FNNVYHQFNKYIHYLLNKYHI-RYNYDEYYQLMLIRLWQLTNQYNASlnSNFSTFIIFRLNYYLIDLFRKEQPKQSVEIS 81
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGdDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488408620   82 ILNPSSSKLPIY---ILNDFNLIMQEAWKHLTRQEQQWLIL-QISGYKQYEIAQHMHVSLSSVKNYKRNARQKLQR 153
Cdd:TIGR02937  81 LEELLDSDPSPEeelEQEEEREALREALEKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156

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

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 488408620 109 LTRQEQQWLILQISGYKQYEIAQHMHVSLSSVKNYKRNARQKLQ 152
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLG 113

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 488408620   108 HLTRQEQQWLILQISGYKQYEIAQHMHVSLSSVKNYKRNARQKL 151
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46

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 488408620 109 LTRQEQQWLILQISGYKQYEIAQHMHVSLSSVKNYKRNARQKL 151
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 488408620  100 LIMQEAWKHLTRQEQQWLIL-QISGYKQYEIAQHMHVSLSSVKNYKRNARQKL 151
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLrYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488408620  99 NLIMQEAWKHLTRQEQQWLIL-QISGYKQYEIAQHMHVSLSSVKNYKRNARQKLQ 152
Cdd:cd06171    1 RERLEEALDKLPEREREVILLrFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55

RNA polymerase sigma factor SigX; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488408620  27 YDEYYQLMLIRL-WQLTNQYNA----------------SLNSNFSTFIIFRLNYYLIDLFRKEQPKQSVEI-----SILN 84
Cdd:PRK09639   9 FEQYYPDVVQQIfYIVKDRTQAedlaqevflrlyrsdfKGIENEKGWLIKSARNVAYNYLRSEKRRRARILgefqwQEVD 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488408620  85 PSSSKLPIYILNDFNLIMQEAWKHLTRQEQQWLILQISGYKQYEIAQHMHVSLSSVKNYKRNARQKL 151
Cdd:PRK09639  89 NEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKF 155

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488408620   14 IHYLLNKYHIRYNYDEYYQLMLIRLWQLTNQYNASLNSNFSTFIIFRLNYYLIDLFRKEQ 73
Cdd:pfam04542  10 YSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69