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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERRGRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKEPPGELGQLKL 86
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEK 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 740757822  87 LMTRLDEKRNDLRQKRKDIDDTLTELDNVEEACLTRLA 124
Cdd:cd04776   81 MLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERLA 118

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERRGRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKEPPGELGQLKL 86
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEK 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 740757822  87 LMTRLDEKRNDLRQKRKDIDDTLTELDNVEEACLTRLA 124
Cdd:cd04776   81 MLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERLA 118

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740757822     7 YSITELTREFGVSTRTLRFYEDEGLIHPERR--GRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVY 74
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRteGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERR--GRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKEP 77
Cdd:PRK09514   2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRteGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDP 74

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERRGRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKEPPGELGQLKL 86
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEK 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 740757822  87 LMTRLDEKRNDLRQKRKDIDDTLTELDNVEEACLTRLA 124
Cdd:cd04776   81 MLEKIEKRRAELEQQRRDIDAALAELDAAEERCRERLA 118

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERR-GRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYkeppGELGQLK 85
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSeNGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDAR----DEELSLA 76

                         90
                 ....*....|....*..
gi 740757822  86 LLMTRLDEKRNDLRQKR 102
Cdd:cd00592   77 ALLALLDEKLAELEEKI 93

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERR--GRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKEPPGELGQL 84
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRdeNGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 740757822  85 KLLmtrLDEKRNDLRQKRKDIDDTLTELDN 114
Cdd:cd01109   81 LEL---LEEHREELEEQIAELQETLAYLDY 107

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERRGRT--RLFRATDRRLIQEILRGRRIGFTIAEIREIIQvykeppgelGQL 84
Cdd:cd01106    1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENgyRLYTEEDLERLQQILFLKELGFSLKEIKELLK---------DPS 71

                         90       100       110
                 ....*....|....*....|....*....|..
gi 740757822  85 KLLMTRLDEKRNDLRQKRKDIDDTLTELDNVE 116
Cdd:cd01106   72 EDLLEALREQKELLEEKKERLDKLIKTIDRTL 103

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERR--GRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKEP 77
Cdd:PRK09514   2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRteGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDP 74

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 740757822   9 ITELTREFGVSTRTLRFYEDEGLIHPERRGRT-RLFRATDRRLIQEILRGRRIGFTIAEIREIIqvykePPGELGQLKLL 87
Cdd:cd01282    3 IGELAARTGVSVRSLRYYEEQGLLVPERSANGyRDYDEAAVDRVRQIRRLLAAGLTLEEIREFL-----PCLRGGEPTFR 77

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 740757822  88 MTrlDEKRNDLRQKRKDIDDTLTELDNVEEACLTRLA 124
Cdd:cd01282   78 PC--PDLLAVLRRELARIDRQIADLTRSRDRLDAYLA 112

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERRGRT---RLFRATDRRLIQEILRGRRIGFTIAEIREIIQvyKEPPGELGQ 83
Cdd:cd01107    1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDtgyRYYSAEQLERLNRIKYLRDLGFPLEEIKEILD--ADNDDELRK 78

                         90       100       110
                 ....*....|....*....|....*....|.
gi 740757822  84 LkllmtrLDEKRNDLRQKRKDIDDTLTELDN 114
Cdd:cd01107   79 L------LREKLAELEAEIEELQRILRLLED 103

Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 740757822   8 SITELTREFGVSTRTLRFYEDEGLIHPER-RGRTRLFRATDRRLIQEILRGRRIGFTIAEIRE 69
Cdd:cd01110    3 SVGEVAKRSGVAVSALHFYEQKGLIASWRnAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAE 65

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 740757822  11 ELTREFGVSTRTLRFYEDEGLIHPERRGRT--RLFRATDRRLIQEILRGRRIGFTIAEIREII 71
Cdd:cd04787    5 ELANAAGVTPDTVRFYTRIGLLRPTRDPVNgyRLYSEKDLSRLRFILSARQLGFSLKDIKEIL 67

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPER--RGRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKEPPG 79
Cdd:cd01105    2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRsdGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRVQAE 76

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLI-HPERR-GRTRLFRATDRRLIQEILRGRRIGFTIAEIREII 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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERR-GRTRLFRATDRRLIQEI 54
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTeGGYRLYSDADLERLRLI 49

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 740757822   9 ITELTREFGVSTRTLRFYEDEGLIHPERR--GRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKEP 77
Cdd:cd04784    3 IGELAKKTGCSVETIRYYEKEGLLPAPARsaNNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDP 73

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERRGRTRLFRATD-------RRLIQEilrgrrIGFTIAEIREIIQVY 74
Cdd:cd04767    2 YPIGVVAELLNIHPETLRIWERHGLIKPARRNGQRLYSNNDlkrlrfiKKLINE------KGLNIAGVKQILSMY 70

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERR--GRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQvykEPPGELGQ- 83
Cdd:cd04790    2 LTISQLARQFGLSRSTLLYYERIGLLSPSARseSNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQ---QPGDDATDv 78

                         90       100
                 ....*....|....*....|..
gi 740757822  84 LKLLMTRLDEKRNDLRQKRKDI 105
Cdd:cd04790   79 LRRRLAELNREIQRLRQQQRAI 100

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 740757822   6 YYSITELTREFGVSTRTLRFYEDEGLIHPER-RGRTRLFRATDRRLIQEILR-GRRIGFTIAEIREIIQVYKEPPGELGQ 83
Cdd:cd04766    1 VYVISVAAELSGMHPQTLRLYERLGLLSPSRtDGGTRRYSERDIERLRRIQRlTQELGVNLAGVKRILELEEELAELRAE 80

                 ....*...
gi 740757822  84 LKLLMTRL 91
Cdd:cd04766   81 LDELRARL 88

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIH-PER-RGRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKEPPG----E 80
Cdd:cd04783    1 LTIGELAKAAGVNVETIRYYQRRGLLPePPRpEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCsearE 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 740757822  81 LGQLKLlmTRLDEKRNDLRQKRkdidDTLTEL 112
Cdd:cd04783   81 LAEQKL--AEVDEKIADLQRMR----ASLQEL 106

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERRGRT--RLFRATDRRLIQEILRGRRIGFTIAEIREIIQVyKEPPGELGQL 84
Cdd:cd04782    1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENgyRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN-RNPDELIELL 79

                         90
                 ....*....|....*.
gi 740757822  85 KLLMTRLDEKRNDLRQ 100
Cdd:cd04782   80 KKQEKEIKEEIEELQK 95

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERRGRTRLFRATDRRLIQeilrgrrigFTIAeiREIIQVYKEPPGELGQLKL 86
Cdd:cd04772    1 YRTVDLARAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDKHIAA---------LRAY--RALLPGYGYRVAQRIMRAV 69

                         90       100
                 ....*....|....*....|....*....
gi 740757822  87 LMTRLDEKRNDLRQKRKDIDDTLTELDNV 115
Cdd:cd04772   70 HAGIVASALALVDAAHALLQRYRQQLDQE 98

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 740757822   9 ITELTREFGVSTRTLRFYEDEGLIHPERRGRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIqVYKEPPGELGQLKLLM 88
Cdd:cd04777    3 IGKFAKKNNITIDTVRHYIDLGLLIPEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIF-SYKRLTKSRTHEDQDY 81

                         90       100
                 ....*....|....*....|....*.
gi 740757822  89 TR--LDEKRNDLRQKRKDIDDTLTEL 112
Cdd:cd04777   82 YKsfLKNKKDELEKEIEDLKKAIQKL 107

redox-sensitive transcriptional activator SoxR;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 740757822  11 ELTREFGVSTRTLRFYEDEGLIHPERR-GRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKE 76
Cdd:PRK15002  16 EVAKRSGVAVSALHFYESKGLITSIRNsGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPE 82

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 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERR-GRTRLFRATDRRLIQEILRGRRIGFTIAEIREIIQVYKEPpgelGQLK 85
Cdd:cd04775    2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARSeANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPHVQ----AILE 77

                         90
                 ....*....|....*..
gi 740757822  86 LLMTRLDEKRNDLRQKR 102
Cdd:cd04775   78 ERLQSLNREIQRLRQQQ 94

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine 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 740757822   9 ITELTREFGVSTRTLRFYEDEGLIHPERRGRT--RLFRATDRRLIQEILRGRRIGFTIAEIREIIqvykepPGELGQLkl 86
Cdd:cd04786    3 IGELAKRSGMAASRIRFYEAEGLLSSVERSANgyRDYPPETVWVLEIISSAQQAGFSLDEIRQLL------PADASNW-- 74

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 740757822  87 lmtRLDEKRNDLRQKRKDIddtlteldnveEACLTRLAE 125
Cdd:cd04786   75 ---QHDELLAALERKVADI-----------EALEARLAQ 99

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHPERR-GRTRLFRATDRRLIQEILR-GRRIGFTIAEIREIIQVYKEPPGELGQL 84
Cdd:cd01279    2 YPISVAAELLGIHPQTLRVYDRLGLVSPARTnGGGRRYSNNDLELLRQVQRlSQDEGFNLAGIKRIIELYPQVLLLQCRS 81

                         90
                 ....*....|....*..
gi 740757822  85 KLLMTRLDEKRNDLRQK 101
Cdd:cd01279   82 CEHATELIGCAKPCRKE 98

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 740757822   7 YSITELTREFGVSTRTLRFYEDEGLIHP-ERRGRTRLFRATDR----RLIQEILRGRriGFTIAEIREIIQVYKE 76
Cdd:cd04780    1 MRMSELSKRSGVSVATIKYYLREGLLPEgRRLAPNQAEYSEAHverlRLIRALQQEG--GLPISQIKEVLDAIAD 73