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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755754716 125 LFLCIKKHNDDNTPLNLNFQSHPMLSKRERQVLELASIGMDYQSISEHLNITRKTVSHYMSNIRDKYG 192
Cdd:COG2771  104 LLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLG 171

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755754716 125 LFLCIKKHNDDNTPLNLNFQSHPMLSKRERQVLELASIGMDYQSISEHLNITRKTVSHYMSNIRDKYG 192
Cdd:COG2771  104 LLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLG 171

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 755754716 149 LSKRERQVLELASIGMDYQSISEHLNITRKTVSHYMSNIRDK 190
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRK 42

two component system response regulator;

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 755754716 146 HPMLSKRERQVLELASIGMDYQSISEHLNITRKTV-SHYMSNIR 188
Cdd:PRK15369 147 PPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVeTHRLNMMR 190

C-terminal (CT) toxin domain of the contact-dependent growth inhibition (CDI) system (CdiA-CT) of Burkholderia pseudomallei, and similar proteins; CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the C-terminal (CT) toxin domain of CdiA effector proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; this particular model contains the C-terminal (CT) domain of Burkholderia pseudomallei E479 CdiA. This CdiA-CT domain is a tRNAse that contains a core alpha/beta-fold that is characteristic of PD(D/E)XK superfamily nucleases. It is structurally similar to another CDI toxin domain from B. pseudomallei 1026b which is unrelated in sequence but has a similar nuclease domain, and shares similar fold and active-site architecture. The PD(D/E)XK superfamily includes most restriction endonucleases and other enzymes involved in DNA recombination and repair.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 755754716  29 GNKDKITTHLFSSF--DRFMNQLD--TNKGNIVIFDIDGIAKENQSIIFNKINNL 79
Cdd:cd20726   55 GTPIFPANFFDKQWawEKFQDQIIdhLEKADIVPLDLRGLTPENQAKVIEFVLSL 109

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755754716 125 LFLCIKKHNDDNTPLNLNFQSHPMLSKRERQVLELASIGMDYQSISEHLNITRKTVSHYMSNIRDKYG 192
Cdd:COG2771  104 LLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLG 171

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

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 755754716 148 MLSKRERQVLELASIGMDYQSISEHLNITRKTVSHYMSNIRDKYGYKR 195
Cdd:COG2197   69 LLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRN 116

Bacterial regulatory proteins, luxR family;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 755754716  149 LSKRERQVLELASIGMDYQSISEHLNITRKTVSHYMSNIRDKYG 192
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLN 46

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
                  ....*....|....*....|....*....|....*....|....
gi 755754716  148 MLSKRERQVLELASI-GMDYQSISEHLNITRKTVSHYMSNIRDK 190
Cdd:pfam08281  10 ELPPRQREVFLLRYLeGLSYAEIAELLGISEGTVKSRLSRARKK 53

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
                  ....*....|....*....|....*....|....*....|...
gi 755754716  149 LSKRERQVLELASI-GMDYQSISEHLNITRKTVSHYMSNIRDK 190
Cdd:TIGR02937 111 LPEREREVLVLRYLeGLSYKEIAEILGISVGTVKRRLKRARKK 153

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 755754716 149 LSKRERQVLELASI-GMDYQSISEHLNITRKTVSHYMSNIRDK 190
Cdd:cd06171   11 LPEREREVILLRFGeGLSYEEIAEILGISRSTVRQRLHRALKK 53

acid-sensing system DNA-binding response regulator EvgA;

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 755754716 149 LSKRERQVLELASIGMDYQSISEHLNITRKTVSHYMSNIRDKYGYK 194
Cdd:PRK09958 144 LSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECK 189

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

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 755754716 158 ELASIGMDYQSISEHLNITRKTVSHYMSNIRDKYG 192
Cdd:COG2909  132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLG 166

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 755754716  149 LSKRERQVLELASI-GMDYQSISEHLNITRKTVSHYMSNIRDK 190
Cdd:pfam04545   5 LPPRERQVLVLRYGeGLTLEEIGERLGISRERVRQIEKRALRK 47