redox-sensitive transcriptional activator SoxR; SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species. [Cellular processes, Detoxification, Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAELAKLPADRVPSRRDW 81
Cdd:TIGR01950   2 LTVGELAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAVLPEGRTPTADDW 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2083980810  82 SRLSSAWAKRIDQRIAELQRLRSGLGECIGCGCLSIDRCRLANPADVAGRKGPGARY 138
Cdd:TIGR01950  82 ARLSSQWREELDERIDQLNALRDQLDGCIGCGCLSLEDCPLRNPGDRLGEEGAGARL 138

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   4 ITEVSRRSGVASSALRFYEERGLI-ASERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAELAKLPADrvpsRRDWS 82
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLpPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDG----EEEVR 76

                          90       100
                  ....*....|....*....|....
gi 2083980810  83 RLSSAWAKRIDQRIAELQRLRSGL 106
Cdd:COG0789    77 ELLEEHLAELEAQIAELQALRAEL 100

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2083980810   3 TITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEI 63
Cdd:pfam13411   2 TISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEI 62

redox-sensitive transcriptional activator SoxR; SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species. [Cellular processes, Detoxification, Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAELAKLPADRVPSRRDW 81
Cdd:TIGR01950   2 LTVGELAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAVLPEGRTPTADDW 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2083980810  82 SRLSSAWAKRIDQRIAELQRLRSGLGECIGCGCLSIDRCRLANPADVAGRKGPGARY 138
Cdd:TIGR01950  82 ARLSSQWREELDERIDQLNALRDQLDGCIGCGCLSLEDCPLRNPGDRLGEEGAGARL 138

Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAELAKLPADrvPSRRDW 81
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEE--LSLAAL 78

                          90       100
                  ....*....|....*....|..
gi 2083980810  82 SRLSSAWAKRIDQRIAELQRLR 103
Cdd:cd00592    79 LALLDEKLAELEEKIARLEALL 100

Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLI-ASERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIgAELAKLPADRVPSRRD 80
Cdd:cd04770     1 MKIGELAKAAGVSPDTIRYYERIGLLpPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEI-RELLSLRDDGAAPCAE 79

                          90       100
                  ....*....|....*....|....*.
gi 2083980810  81 WSRLSSAWAKRIDQRIAELQRLRSGL 106
Cdd:cd04770    80 VRALLEEKLAEVEAKIAELQALRAEL 105

Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIAS-ERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAELAklpADRVPSRRD 80
Cdd:cd04783     1 LTIGELAKAAGVNVETIRYYQRRGLLPEpPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLE---LDDGTDCSE 77

                          90       100
                  ....*....|....*....|....*.
gi 2083980810  81 WSRLSSAWAKRIDQRIAELQRLRSGL 106
Cdd:cd04783    78 ARELAEQKLAEVDEKIADLQRMRASL 103

Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLI-ASERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGaELAKLPADRVPSRRD 80
Cdd:cd01108     1 MNIGEAAKLTGLSAKMIRYYEEIGLIpPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIR-ELLALWRDPSRASAD 79

                          90       100
                  ....*....|....*....|....*...
gi 2083980810  81 WSRLSSAWAKRIDQRIAELQRLRSGLGE 108
Cdd:cd01108    80 VKALALEHIAELERKIAELQAMRRTLQQ 107

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAELAKLPADRVPSRRDW 81
Cdd:cd01282     1 MRIGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLRGGEPTFRPCP 80

                          90       100
                  ....*....|....*....|....*..
gi 2083980810  82 SRLSSAWAKR--IDQRIAELQRLRSGL 106
Cdd:cd01282    81 DLLAVLRRELarIDRQIADLTRSRDRL 107

Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIAS-ERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIG--AELAKLPADRVPSR 78
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPvKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKeyAELRREGDSTIPER 80

                          90       100
                  ....*....|....*....|...
gi 2083980810  79 RdwsRLSSAWAKRIDQRIAELQR 101
Cdd:cd01109    81 L---ELLEEHREELEEQIAELQE 100

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2083980810   3 TITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEI 63
Cdd:pfam13411   2 TISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEI 62

Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFI 50
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLRLI 49

Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIA-SERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAELAKLPADRVPSRRD 80
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKpSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                          90       100
                  ....*....|....*....|..
gi 2083980810  81 WSRLSSAWAKRIDQRIAELQRL 102
Cdd:cd01106    81 QKELLEEKKERLDKLIKTIDRT 102

Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   4 ITEVSRRSGVASSALRFYEERGLIA-SERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAELaklpADRVPSRRDWS 82
Cdd:cd04788     3 IGELARRTGLSVRTLHHYDHIGLLSpSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRAL----DGPDFDPLELL 78

                          90       100
                  ....*....|....*....|.
gi 2083980810  83 RLSSAwakRIDQRIAELQRLR 103
Cdd:cd04788    79 RRQLA---RLEEQLELATRLR 96

Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASERAGsGHRRYHRSALRRIAFIVFAQRIGLTLEEIGA--ELAKLPADRVPSRR 79
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSPERRG-QTRVYSRRDRARLKLILRGKRLGFSLEEIREllDLYDPPGGNRKQLE 79

                          90       100
                  ....*....|....*....|....
gi 2083980810  80 dwsrlssAWAKRIDQRIAELQRLR 103
Cdd:cd04776    80 -------KMLEKIEKRRAELEQQR 96

Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASER-AGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAELAKLPADRVPSRRD 80
Cdd:cd04768     1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKiAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAMLLE 80

                          90       100
                  ....*....|....*....|..
gi 2083980810  81 WSRlssawakRIDQRIAELQRL 102
Cdd:cd04768    81 KKQ-------AIQQKIDRLQQL 95

Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASER-AGSGHRRYHRSALRRIAFIVFAQRIGLTLEEI 63
Cdd:cd01105     2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRsDGGGQRKYSLADVDRLLVIKELLDEGFTLAAA 64

mercuric resistance operon transcriptional regulator MerR;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASERAGSGH-RRYHRSALRRIAFIVFAQRIGLTLEEIgAELAKLpaDRVPSRRD 80
Cdd:PRK13752    8 LTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSiRRYGEADVTRVRFVKSAQRLGFSLDEI-AELLRL--EDGTHCEE 84

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2083980810  81 WSRLSSAWAKRIDQRIAELQRLRSGLGECIgCGC 114
Cdd:PRK13752   85 ASSLAEHKLKDVREKMADLARMEAVLSELV-CAC 117

Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFIVFAQR-IGLTLEEI 63
Cdd:cd04774     1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLREvLGFSLQEV 63

Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2083980810   1 MLTITEVSRRSGVASSALRFYEERGLIA-SERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAELAKLPADRvpsrr 79
Cdd:cd04790     1 MLTISQLARQFGLSRSTLLYYERIGLLSpSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDA----- 75

                          90       100
                  ....*....|....*....|....*
gi 2083980810  80 dwsrlSSAWAKRIDQRIAELQRLRS 104
Cdd:cd04790    76 -----TDVLRRRLAELNREIQRLRQ 95

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2083980810   4 ITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFIVFAQRIGLTLEEIGAEL 67
Cdd:cd04779     3 IGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQL 66

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFI 50
Cdd:cd04762     1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERLLGI 49

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2083980810   2 LTITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRR 46
Cdd:COG2452     1 LTPGEAAELLGVSPKTLRRWEKEGKLPAIRTPGGHRRYPESEVER 45

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

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gi 2083980810   3 TITEVSRRSGVASSALRFYEER-GLIASERAGSGHRRYHRS---ALRRIAFIVFAQriGLTLEEIGAELAKLPADRVP 76
Cdd:cd04765     2 SIGEVAEILGLPPHVLRYWETEfPQLKPVKRAGGRRYYRPKdveLLLLIKHLLYEK--GYTIEGAKQALKEDGAAAIR 77

Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

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gi 2083980810   3 TITEVSRRSGVASSALRFYEERGLIASERAGSGHRRYHRSALRRIAFIVF-AQRIGLTLEEI 63
Cdd:cd04766     3 VISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRlTQELGVNLAGV 64