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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2319104423  13 VYSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLAE-GVNLAGARRIIQLEDDNHALRAT 91
Cdd:cd04766     1 VYVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQElGVNLAGVKRILELEEELAELRAE 80

                  ....*
gi 2319104423  92 LRLTR 96
Cdd:cd04766    81 LDELR 85

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 2319104423  13 VYSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLAE-GVNLAGARRIIQLEDDNHALRAT 91
Cdd:cd04766     1 VYVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQElGVNLAGVKRILELEEELAELRAE 80

                  ....*
gi 2319104423  92 LRLTR 96
Cdd:cd04766    81 LDELR 85

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRII 79
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

mercuric resistance operon transcriptional regulator MerR;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2319104423   1 MESGLETgrtrgvYSIAIAAELVGVGIQTLRLYESRGLL-DPARSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRII 79
Cdd:PRK13752    1 MENNLEN------LTIGVFAKAAGVNVETIRFYQRKGLLpEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELL 74

                          90
                  ....*....|..
gi 2319104423  80 QLEDDNHALRAT 91
Cdd:PRK13752   75 RLEDGTHCEEAS 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        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2319104423  13 VYSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLAE-GVNLAGARRIIQLEDDNHALRAT 91
Cdd:cd04766     1 VYVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQElGVNLAGVKRILELEEELAELRAE 80

                  ....*
gi 2319104423  92 LRLTR 96
Cdd:cd04766    81 LDELR 85

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 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIIQLEDDNHALRATLR 93
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLAALLA 80

                  .
gi 2319104423  94 L 94
Cdd:cd00592    81 L 81

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRII 79
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

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 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRV 62
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLRLI 49

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2319104423  14 YSIAIAAELVGVGIQTLRLYESR-GLLDPARSAGGTRRYSDADIDVLRRVVALLAEGVNLAgarRIIQLED 83
Cdd:cd01104     1 YTIGAVARLTGVSPDTLRAWERRyGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRIS---QAAALAL 68

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 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPAR-SAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIiqLEDDNHALRATL 92
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRrTENGYRLYTEEDLERLQQILFLKELGFSLKEIKEL--LKDPSEDLLEAL 78

                  ....
gi 2319104423  93 RLTR 96
Cdd:cd01106    79 REQK 82

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 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDP-ARSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIIQL 81
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPvKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL 69

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 2319104423  20 AELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIIQ-LEDDNHALRATLRLTRGI 98
Cdd:cd01282     7 AARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPcLRGGEPTFRPCPDLLAVL 86

                  ...
gi 2319104423  99 EHQ 101
Cdd:cd01282    87 RRE 89

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
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVAL 65
Cdd:cd04774     1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRL 52

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
                  ....*....|....*....|....*....|....*....|....*...
gi 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLD-PARSAGGTRRYSDADIDVLR 60
Cdd:cd04785     1 LSIGELARRTGVNVETIRYYESIGLLPePARTAGGYRLYGAAHVERLR 48

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 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIIQ 80
Cdd:cd04764     1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPRTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 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
                  ....*....|....*....|....*....|....*....|....*.
gi 2319104423  16 IAIAAELVGVGIQTLRLYESRGLLDPA-RSAGGTRRYSDADIDVLR 60
Cdd:cd01108     3 IGEAAKLTGLSAKMIRYYEEIGLIPPPsRSDNGYRVYNQRDIEELR 48

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLA 67
Cdd:COG2452     1 LTPGEAAELLGVSPKTLRRWEKEGKLPAIRTPGGHRRYPESEVERLERRTVIYA 54

HTH-type transcriptional regulator MlrA;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2319104423  13 VYSIAIAAELVGVGIQTLRLYESR-GLLDPARSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIIQLED 83
Cdd:PRK15043    3 LYTIGEVALLCDINPVTLRAWQRRyGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNEN 74

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 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPAR--SAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIIQlEDDNHALRAT 91
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYvdPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILD-ADNDDELRKL 79

                  ..
gi 2319104423  92 LR 93
Cdd:cd01107    80 LR 81

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 2319104423  16 IAIAAELVGVGIQTLRLYESRGLL-DPARSAGGTRRYSDADIDVL---RRVVALlaeGVNLAGARRIIQLEDD 84
Cdd:cd04784     3 IGELAKKTGCSVETIRYYEKEGLLpAPARSANNYRLYDEEHLERLlfiRRCRSL---DMSLDEIRTLLQLQDD 72

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 2319104423  16 IAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIIQLEDDN------HALR 89
Cdd:cd04769     3 IGELAQQTGVTIKAIRLYEEKGLLPSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRavlpwpHLQQ 82

                          90
                  ....*....|..
gi 2319104423  90 ATLRLTRGIEHQ 101
Cdd:cd04769    83 ALEDKKQEIRAQ 94

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVL 59
Cdd:cd04762     1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERL 46

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 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPARsAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIIQLEDDNHALRATLR 93
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSPER-RGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLE 79

                  ....*....
gi 2319104423  94 LT-RGIEHQ 101
Cdd:cd04776    80 KMlEKIEKR 88

redox-sensitive transcriptional activator SoxR;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2319104423  20 AELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDadiDVLRRVVAL-LAE--GVNLAGARRIIQLEDDNHALRA 90
Cdd:PRK15002   18 AKRSGVAVSALHFYESKGLITSIRNSGNQRRYKR---DVLRYVAIIkIAQriGIPLATIGEAFGVLPEGHTLSA 88

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). 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 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDPARSAGGTRRYSDADIDVLRRVVALLAEGVNLAG 74
Cdd:cd04778     2 YRIDDLARAAGTTVRNVRAYQDRGLLPPPRRRGRVAIYNDSHLARLRLINQLLERGYTLAH 62

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2319104423  20 AELVGVGIQTLRLYESRGLLDPA-RSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIIQLEDDNHAL 88
Cdd:cd04782     7 AKLCGISKQTLFHYDKIGLFKPEiVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRNPDELI 76

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 2319104423  14 YSIAIAAELVGVGIQTLRLYESRGLLDP-ARSAGGTRRYSDADIDVLRRVVALLAEGVNLAGARRIIQLED--DNHALRA 90
Cdd:cd01111     1 YSISQLALDAGVSVHIVRDYLLRGLLHPvARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDagDGKQPEA 80

                          90
                  ....*....|..
gi 2319104423  91 TLRLTRG-IEHQ 101
Cdd:cd01111    81 CLAQLRQkIEVR 92