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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517293158   9 ITELTREFGVSTRTLRFYEDEGLIQPERR--GRTRLFRQADRRLIGEILRGRRIGFTIAEIREIIQVYKEPPGELGQLkl 86
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERteGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEEVREL-- 78

                         90       100
                 ....*....|....*....|....*.
gi 517293158  87 lmkrVDEKRDDLRQKRKDIDDTLAEL 112
Cdd:COG0789   79 ----LEEHLAELEAQIAELQALRAEL 100

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPERR--GRTRLFRQADRRLIGEILRGRRIGFTIAEIREIIQVYKEP 77
Cdd:PRK09514   2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRteGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDP 74

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517293158   9 ITELTREFGVSTRTLRFYEDEGLIQPERR--GRTRLFRQADRRLIGEILRGRRIGFTIAEIREIIQVYKEPPGELGQLkl 86
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERteGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEEVREL-- 78

                         90       100
                 ....*....|....*....|....*.
gi 517293158  87 lmkrVDEKRDDLRQKRKDIDDTLAEL 112
Cdd:COG0789   79 ----LEEHLAELEAQIAELQALRAEL 100

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 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPERR--GRTRLFRQADRRLIGEILRGRRIGFTIAEIREIIQVYKEPPGELGQL 84
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRdeNGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100
                 ....*....|....*....|....*....
gi 517293158  85 KLLMKrvdEKRDDLRQKRKDIDDTLAELD 113
Cdd:cd01109   81 LELLE---EHREELEEQIAELQETLAYLD 106

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517293158     7 YSITELTREFGVSTRTLRFYEDEGLIQPERR--GRTRLFRQADRRLIGEILRGRRIGFTIAEIREIIQVY 74
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRteGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70

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 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPERRGRT--RLFRQADRRLIGEILRGRRIGFTIAEIREIIqvyKEPPGELGQ- 83
Cdd:cd01106    1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENgyRLYTEEDLERLQQILFLKELGFSLKEIKELL---KDPSEDLLEa 77

                         90       100
                 ....*....|....*....|....*.
gi 517293158  84 LKLLMKRVDEKRDDLRQKRKDIDDTL 109
Cdd:cd01106   78 LREQKELLEEKKERLDKLIKTIDRTL 103

Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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 517293158   9 ITELTREFGVSTRTLRFYEDEGLI-QPERRGRTRLFRQADRRLIGEILRGRRIGFTIAEIREIIQVYKEPPGELGQlkLL 87
Cdd:cd04769    3 IGELAQQTGVTIKAIRLYEEKGLLpSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWP--HL 80

                         90       100
                 ....*....|....*....|....*....
gi 517293158  88 MKRVDEKRDDLRQKRKDIDDTLAELDSIE 116
Cdd:cd04769   81 QQALEDKKQEIRAQITELQQLLARLDAFE 109

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 517293158   9 ITELTREFGVSTRTLRFYEDEGLIQPERRGRT--RLFRQADRRLIGEILRGRRIGFTIAEIREIIQVYKEPPGELGQLKl 86
Cdd:cd01108    3 IGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNgyRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADVK- 81

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 517293158  87 lmKRVDEKRDDLRQKrkdiddtLAELDSIEETcLGRLAE 125
Cdd:cd01108   82 --ALALEHIAELERK-------IAELQAMRRT-LQQLAD 110

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. 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 517293158   8 SITELTREFGVSTRTLRFYEDEGLIQP-ERRGRTRLFRQADRRLIGEILRGRRIGFTIAEIREIIQVYKEPPgelgqlkl 86
Cdd:cd04781    2 DIAEVARQSGLPASTLRYYEEKGLIASiGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPP-------- 73

                         90       100       110
                 ....*....|....*....|....*....|..
gi 517293158  87 lmkrVDekRDDLRQKRKDIDDTLAELDSIEET 118
Cdd:cd04781   74 ----ID--RQLLKAKAAELDQQIQRLQAMREL 99

Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPERRGRT---RLFRQADRRLIGEILRGRRIGFTIAEIREIIQvyKEPPGELGQ 83
Cdd:cd01107    1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDtgyRYYSAEQLERLNRIKYLRDLGFPLEEIKEILD--ADNDDELRK 78

                         90       100       110
                 ....*....|....*....|....*....|
gi 517293158  84 -LKLLMKRVDEKRDDLRQKRKDIDDTLAEL 112
Cdd:cd01107   79 lLREKLAELEAEIEELQRILRLLEDRLKQI 108

Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. 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 predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPERR--GRTRLFRQADRRLIGEILRGRRIGFTIAEIREII 71
Cdd:cd04785    1 LSIGELARRTGVNVETIRYYESIGLLPEPARtaGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALL 67

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 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPERR-GRTRLFRQADRRLIGEI 54
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTeGGYRLYSDADLERLRLI 49

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPER-RGRTRLFRQADRRLIGEILRGRR-IGFTIAEIREIIQVYKEP 77
Cdd:cd04774    1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERsEGRYRLYSEEDLKRLERILRLREvLGFSLQEVTHFLERPLEP 73

HTH-type transcriptional regulator CueR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517293158   8 SITELTREFGVSTRTLRFYEDEGLIQPERRGRT--RLFRQADRRLIGEILRGRRIGFTIAEIREIIQVYKEPPGELGQLK 85
Cdd:PRK10227   2 NISDVAKITGLTSKAIRFYEEKGLVTPPMRSENgyRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADVK 81

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 517293158  86 llmKRVDEKRDDLRQKRKDIDDTLAELDSIEETCLG 121
Cdd:PRK10227  82 ---RRTLEKVAEIERHIEELQSMRDQLLALANACPG 114

Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators; Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that 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. This subgroup lacks one of the conserved, metal-binding cysteines seen in the MerR1 group.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 517293158  11 ELTREFGVSTRTLRFYEDEGLIQPERRGRT--RLFRQADRRLIGEILRGRRIGFTIAEIREII 71
Cdd:cd04787    5 ELANAAGVTPDTVRFYTRIGLLRPTRDPVNgyRLYSEKDLSRLRFILSARQLGFSLKDIKEIL 67

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 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPERR--GRTRLFRQADRRLIGEILRGRRIGFTIAEIREIIQvykEPPGELGQ- 83
Cdd:cd04790    2 LTISQLARQFGLSRSTLLYYERIGLLSPSARseSNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQ---QPGDDATDv 78

                         90       100
                 ....*....|....*....|..
gi 517293158  84 LKLLMKRVDEKRDDLRQKRKDI 105
Cdd:cd04790   79 LRRRLAELNREIQRLRQQQRAI 100

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517293158   7 YSITELTREFGVSTRTLRFYEDE--GLIQPERRGRTRLFRQADRRLIGEI---LRGRriGFTIAEIREIiqvykeppgeL 81
Cdd:cd04765    1 FSIGEVAEILGLPPHVLRYWETEfpQLKPVKRAGGRRYYRPKDVELLLLIkhlLYEK--GYTIEGAKQA----------L 68

                         90       100       110
                 ....*....|....*....|....*....|.
gi 517293158  82 GQLKLLMKRVDEKRDDLRQKRKDIDDTLAEL 112
Cdd:cd04765   69 KEDGAAAIREEEAEERLPSIRAELLDLRDQL 99

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 517293158   7 YSITELTREFGVSTRTLRFYEDEGLI-QPER-RGRTRLFRQADRRLIGEILRGRRIGFTIAEIREIIQVYKEPPGElgql 84
Cdd:cd04783    1 LTIGELAKAAGVNVETIRYYQRRGLLpEPPRpEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCS---- 76

                         90       100       110
                 ....*....|....*....|....*....|..
gi 517293158  85 kllmkrvdEKRDDLRQKRKDIDDTLAELDSIE 116
Cdd:cd04783   77 --------EARELAEQKLAEVDEKIADLQRMR 100

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), 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 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 517293158   9 ITELTREFGVSTRTLRFYEDEGLIQPERRGRTRLFRQADRRLIGEILRGRRIGFTIAEIREIIqVYKeppgelgQLKLLM 88
Cdd:cd04777    3 IGKFAKKNNITIDTVRHYIDLGLLIPEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIF-SYK-------RLTKSR 74

                         90       100       110
                 ....*....|....*....|....*....|...
gi 517293158  89 KRVD---------EKRDDLRQKRKDIDDTLAEL 112
Cdd:cd04777   75 THEDqdyyksflkNKKDELEKEIEDLKKAIQKL 107

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). 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. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 517293158   7 YSITELTREFGVSTRTLRFYEDE--GLIQPERRGRtRLFRQADRRLIGEILRGRRIGFTIAEIREIIQ 72
Cdd:cd04764    1 YTIKEVSEIIGVKPHTLRYYEKEfnLYIPRTENGR-RYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517293158   6 YYSITELTREFGVSTRTLRFYEDEGLIQPER-RGRTRLFRQADRRLIGEILR-GRRIGFTIAEIREIIQVYKEPPGELGQ 83
Cdd:cd04766    1 VYVISVAAELSGMHPQTLRLYERLGLLSPSRtDGGTRRYSERDIERLRRIQRlTQELGVNLAGVKRILELEEELAELRAE 80

                 ....*...
gi 517293158  84 LKLLMKRV 91
Cdd:cd04766   81 LDELRARL 88

First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.

                         10        20        30
                 ....*....|....*....|....*....|..
gi 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPERRG 38
Cdd:cd04772    1 YRTVDLARAIGLSPQTVRNYESLGLIPPAERT 32

Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), 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. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. 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. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 517293158   7 YSITELTREFGVSTRTLRFYEDE-GLIQPER-RGRTRLFRQADRRLIGEILRGRRIGFTIAEI 67
Cdd:cd01104    1 YTIGAVARLTGVSPDTLRAWERRyGLPAPQRtDGGHRLYSEADVARLRLIRRLTSEGVRISQA 63

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

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPERR-GRTRLFRQAD 47
Cdd:COG2452    1 LTPGEAAELLGVSPKTLRRWEKEGKLPAIRTpGGHRRYPESE 42

Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator HspR and related proteins, 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 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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517293158   7 YSITELTREFGVSTRTLRFYEDEGLIQPERR-GRTRLFRQADRRLIGEILR-GRRIGFTIAEIREIIQVY 74
Cdd:cd01279    2 YPISVAAELLGIHPQTLRVYDRLGLVSPARTnGGGRRYSNNDLELLRQVQRlSQDEGFNLAGIKRIIELY 71