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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 801449663  12 MSIGAVLDLLrpdfpDVTISKIRFLEAEGLVTPRRASSGYRRFTAYDCARLRFILTAQRdHYLPLKVIRAQLDAQPDGE 90
Cdd:cd00592    1 YTIGEVAKLL-----GVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRE-LGLSLKEIRELLDARDEEL 73

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 801449663  12 MSIGAVLDLLrpdfpDVTISKIRFLEAEGLVTPRRASSGYRRFTAYDCARLRFILTAQRdHYLPLKVIRAQLDAQPDGE 90
Cdd:cd00592    1 YTIGEVAKLL-----GVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRE-LGLSLKEIRELLDARDEEL 73

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 801449663  14 IGAVLDLLrpdfpDVTISKIRFLEAEGLVTP-RRASSGYRRFTAYDCARLRFILTAqRDHYLPLKVIRAQLDAQPDGE 90
Cdd:COG0789    1 IGEVARLT-----GVSVRTLRYYERIGLLPPpERTEGGYRLYSEEDVERLRFIRRL-RELGFSLAEIRELLDLLDDGE 72

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 801449663  27 DVTISKIRFLEAEGLVTP-RRASSGYRRFTAYDCARLRFILTAQR 70
Cdd:PRK09514  12 EVTPDTLRFYEKQGLMDPeVRTEGGYRLYTEQDLQRLRFIRRAKQ 56

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 801449663  12 MSIGAVLDLLrpdfpDVTISKIRFLEAEGLVTPRRASSGYRRFTAYDCARLRFILTAQRdHYLPLKVIRAQLDAQPDGE 90
Cdd:cd00592    1 YTIGEVAKLL-----GVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRE-LGLSLKEIRELLDARDEEL 73

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 801449663  14 IGAVLDLLrpdfpDVTISKIRFLEAEGLVTP-RRASSGYRRFTAYDCARLRFILTAqRDHYLPLKVIRAQLDAQPDGE 90
Cdd:COG0789    1 IGEVARLT-----GVSVRTLRYYERIGLLPPpERTEGGYRLYSEEDVERLRFIRRL-RELGFSLAEIRELLDLLDDGE 72

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 801449663   12 MSIGAVLDLLRpdfpdVTISKIRFLEAEGLVTPRRASSGYRRFTAYDCARLRFILtAQRDHYLPLKVIR 80
Cdd:pfam13411   1 YTISELARLLG-----VTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIK-ALLERGLSLKEIK 63

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 801449663  12 MSIGAVLDLLrpdfpDVTISKIRFLEAEGLVT-PRRASSGYRRFTAYDCARLRFILTAQrDHYLPLKVIRAQLDAQPDGE 90
Cdd:cd04770    1 MKIGELAKAA-----GVSPDTIRYYERIGLLPpPQRSENGYRLYGEADLARLRFIRRAQ-ALGFSLAEIRELLSLRDDGA 74

                 ..
gi 801449663  91 LP 92
Cdd:cd04770   75 AP 76

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
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 801449663  12 MSIGAVLDLLrpdfpDVTISKIRFLEAEGLVTP-RRASSGYRRFTAYDCARLRFIL 66
Cdd:cd01109    1 YTIKEVAEKT-----GLSADTLRYYEKEGLLPPvKRDENGIRDFTEEDLEWLEFIK 51

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 801449663  27 DVTISKIRFLEAEGLVT-PRRASSGYRRFTAYDCARLRFILTAqRDHYLPLKVIRAQLDAQPDGE 90
Cdd:cd04785   11 GVNVETIRYYESIGLLPePARTAGGYRLYGAAHVERLRFIRRA-RDLGFSLEEIRALLALSDRPD 74

Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that 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 form 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 801449663  27 DVTISKIRFLEAEGLV-TPRRASSGYRRFTAYDCARLRFILTAqRDHYLPLKVIRAQLDAQPDGE 90
Cdd:cd04784   11 GCSVETIRYYEKEGLLpAPARSANNYRLYDEEHLERLLFIRRC-RSLDMSLDEIRTLLQLQDDPE 74

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 801449663  12 MSIGAVLDLlrpdfPDVTISKIRFLEAEGLVTP-RRASSGYRRFTAYDCARLRFILTAqRDHYLPLKVIRAQLD 84
Cdd:cd01108    1 MNIGEAAKL-----TGLSAKMIRYYEEIGLIPPpSRSDNGYRVYNQRDIEELRFIRRA-RDLGFSLEEIRELLA 68

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 801449663  28 VTISKIRFLEAEGLVTPRRASSGYRRFTAYDCARLRFILTAQRDHyLPLKVIRAQLDAQPDGELPPFGSPYVLPRL 103
Cdd:cd01282   12 VSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAG-LTLEEIREFLPCLRGGEPTFRPCPDLLAVL 86

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
                 ....*....|....*....|....*....|....*...
gi 801449663  34 RFLEAEGLVTPRRASSGYRRFTAYDCARLRFILTAQRD 71
Cdd:cd04766   19 RLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQE 56

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
                 ....*....|....*....|....*....|....*....|....*
gi 801449663  27 DVTISKIRFLEAEGLVTPRRAssGYRR-FTAYDCARLRFILTAQR 70
Cdd:cd04776   11 DVTPRTLRFYEDKGLLSPERR--GQTRvYSRRDRARLKLILRGKR 53

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
                 ....*....|....*....|....*....|....*....|..
gi 801449663  28 VTISKIRFLEAEGLVTPRRASSGYRRFTAYDCARLRFILTAQ 69
Cdd:cd04774   12 LTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLR 53

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 801449663  28 VTISKIRFLEAEGLVTP-RRASSGYRRFTAYDCARLRFILTAQRDHYLPL--KVIRAQ 82
Cdd:cd04772   12 LSPQTVRNYESLGLIPPaERTANGYRIYTDKHIAALRAYRALLPGYGYRVaqRIMRAV 69