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 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREMTigSGDKQLLRNSL 84
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELL--KDPSEDLLEAL 78

                  ....*.
gi 1269842627  85 QIQKRL 90
Cdd:cd01106    79 REQKEL 84

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 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREMTigSGDKQLLRNSL 84
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELL--KDPSEDLLEAL 78

                  ....*.
gi 1269842627  85 QIQKRL 90
Cdd:cd01106    79 REQKEL 84

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1269842627    5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKEL 66

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPAtHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPP-RTERGRRYYTDEDVERLRLIKALLERGLSLKEIKEL 65

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 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREMTigSGDKQLLRNSL 84
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELL--KDPSEDLLEAL 78

                  ....*.
gi 1269842627  85 QIQKRL 90
Cdd:cd01106    79 REQKEL 84

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1269842627    5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKEL 66

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 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREMTIGSGDK---QLLR 81
Cdd:cd04768     1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEEltaMLLE 80

                          90
                  ....*....|
gi 1269842627  82 NSLQIQKRLA 91
Cdd:cd04768    81 KKQAIQQKID 90

Zn(2+)-responsive transcriptional regulator;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:PRK09514    2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIREL 67

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 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPA-THTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREmTIGSGDKQLLRNS 83
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAyVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKE-ILDADNDDELRKL 79

                  ....*.
gi 1269842627  84 LQIQKR 89
Cdd:cd01107    80 LREKLA 85

Zn(II)-responsive transcriptional regulator; This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Regulatory functions, DNA interactions]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:TIGR02043   2 FQIGELAKLCGVTSDTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKEL 67

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1269842627   8 GEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:cd01108     4 GEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIREL 66

Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators 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 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 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREMtIGSGDKQLLRNSL 84
Cdd:cd04782     1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDY-LDNRNPDELIELL 79

                  ....
gi 1269842627  85 QIQK 88
Cdd:cd04782    80 KKQE 83

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIRE 69
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKE 65

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIRE 69
Cdd:cd04783     1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAE 65

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1269842627   8 GEFAKKAHVSIRTIRYYDQKNLLKPatHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:cd04777     4 GKFAKKNNITIDTVRHYIDLGLLIP--EKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKI 64

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1269842627   8 GEFAKKAHVSIRTIRYYDQKNLLKPATHtKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREMTIGSG----DKQLLR 81
Cdd:cd04781     4 AEVARQSGLPASTLRYYEEKGLIASIGR-RGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGkppiDRQLLK 80

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1269842627   6 TSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLY 43
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1269842627   8 GEFAKKAHVSIRTIRYYDQKNLLKPaTHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:cd01282     4 GELAARTGVSVRSLRYYEEQGLLVP-ERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREF 65

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 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPaTHTKGGARLYTDQDFAKLQQILLLK-YLGFSLSDIREM 70
Cdd:cd04774     1 YKVDEVAKRLGLTKRTLKYYEEIGLVSP-ERSEGRYRLYSEEDLKRLERILRLReVLGFSLQEVTHF 66

mercuric resistance operon transcriptional regulator MerR;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1269842627   6 TSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:PRK13752    9 TIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAEL 73

Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, 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 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLkPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREMTIGSGDKQLLRNSL 84
Cdd:cd04775     2 YTIGQMSRKFGVSRSTLLYYESIGLI-PSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPHVQAILEERL 80

                  .
gi 1269842627  85 Q 85
Cdd:cd04775    81 Q 81

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 1269842627   5 YTSGEFAKKAHVSIRTIRYY-DQKNLLKPatHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:cd04764     1 YTIKEVSEIIGVKPHTLRYYeKEFNLYIP--RTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEI 65

HTH-type transcriptional regulator CueR;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1269842627   9 EFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREMTIGSGDKQllRNSLQIQK 88
Cdd:PRK10227    5 DVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQ--RHSADVKR 82

                  .
gi 1269842627  89 R 89
Cdd:PRK10227   83 R 83

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 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPAtHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIRE 69
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPE-RSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKD 64

Second 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 mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIRE 69
Cdd:cd04773     1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIAT 65

Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which 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 N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIRE--MTIGSGDKQLLRN 82
Cdd:cd01111     1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARlcRALDAGDGKQPEA 80

                          90
                  ....*....|..
gi 1269842627  83 SL-QIQKRLAVK 93
Cdd:cd01111    81 CLaQLRQKIEVR 92

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        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPATHTKGGARLYTDQDFAKL 51
Cdd:cd04772     1 YRTVDLARAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDKHIAAL 47

Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQKNLLKPAthTKGGARLYTDQDFAKLQQI-LLLKYLGFSLSDIREMT 71
Cdd:cd04767     2 YPIGVVAELLNIHPETLRIWERHGLIKPA--RRNGQRLYSNNDLKRLRFIkKLINEKGLNIAGVKQIL 67

Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, 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-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 1269842627   5 YTSGEFAKKAHVSIRTIRYYDQK-NLLKPaTHTKGGARLYTDQDFAKLQQILLLKYLGFSLSDIREM 70
Cdd:cd04763     1 YTIGEVALLTGIKPHVLRAWEREfGLLKP-QRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKL 66