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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIP-ARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRYQGNSTIDER 81
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPvKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489665925  82 LQLLFTQKNRLTAQRQEIDAHIAFLENKIATYY 114
Cdd:cd01109   81 LELLEEHREELEEQIAELQETLAYLDYKIDYYE 113

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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIP-ARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRYQGNSTIDER 81
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPvKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489665925  82 LQLLFTQKNRLTAQRQEIDAHIAFLENKIATYY 114
Cdd:cd01109   81 LELLEEHREELEEQIAELQETLAYLDYKIDYYE 113

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489665925     3 YPIGKFSKMVSLSIDTLRYYEKERLIIPA-RDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLR 71
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPiRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIPA-RDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIK 65
Cdd:PRK09514   2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEvRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIR 65

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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIP-ARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRYQGNSTIDER 81
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPvKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489665925  82 LQLLFTQKNRLTAQRQEIDAHIAFLENKIATYY 114
Cdd:cd01109   81 LELLEEHREELEEQIAELQETLAYLDYKIDYYE 113

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489665925   5 IGKFSKMVSLSIDTLRYYEKERLIIPA-RDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRYQGNstiDERLQ 83
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPeRTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGE---EEVRE 77

                         90       100
                 ....*....|....*....|...
gi 489665925  84 LLFTQKNRLTAQRQEIDAHIAFL 106
Cdd:COG0789   78 LLEEHLAELEAQIAELQALRAEL 100

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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLI-IPARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRYQGNSTIder 81
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLpPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPC--- 77

                         90       100
                 ....*....|....*....|....*..
gi 489665925  82 lqllfTQKNRLTAQR-QEIDAHIAFLE 107
Cdd:cd04770   78 -----AEVRALLEEKlAEVEAKIAELQ 99

Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIPAR--DQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARlryqgNSTIDE 80
Cdd:cd01107    1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYvdPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILD-----ADNDDE 75

                         90       100       110
                 ....*....|....*....|....*....|..
gi 489665925  81 RLQLLFTQKNRLTAQRQEIDAHIAFLENKIAT 112
Cdd:cd01107   76 LRKLLREKLAELEAEIEELQRILRLLEDRLKQ 107

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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIPARDQNNRRTYSEADQRWIAFI 51
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLRLI 49

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 489665925   5 IGKFSKMVSLSIDTLRYYEKERLIIPARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTY----------------A 68
Cdd:cd01282    3 IGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFlpclrggeptfrpcpdL 82

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489665925  69 RLRYQgnstidERLQLLFTQKNRLTAQRQEIDAHIA 104
Cdd:cd01282   83 LAVLR------RELARIDRQIADLTRSRDRLDAYLA 112

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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIPARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRYQgNSTIDERL 82
Cdd:cd04775    2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPHV-QAILEERL 80

                         90
                 ....*....|....*....
gi 489665925  83 QLLFTQKNRLTAQRQEIDA 101
Cdd:cd04775   81 QSLNREIQRLRQQQQVLAA 99

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 489665925   5 IGKFSKMVSLSIDTLRYYEKERLIIPARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRYQGNSTIDERLQL 84
Cdd:cd04769    3 IGELAQQTGVTIKAIRLYEEKGLLPSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWPHLQQ 82

                         90       100
                 ....*....|....*....|....*...
gi 489665925  85 LFTQKnrltaqRQEIDAHIAFLENKIAT 112
Cdd:cd04769   83 ALEDK------KQEIRAQITELQQLLAR 104

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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIPAR-DQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRYqgnstider 81
Cdd:cd04768    1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKiAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEM--------- 71

                         90       100
                 ....*....|....*....|....*.
gi 489665925  82 lqllFTQKNRLTAQRQEIDAHIAFLE 107
Cdd:cd04768   72 ----EELTAMLLEKKQAIQQKIDRLQ 93

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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIPARDqNNRRTYSEADQRWIAFIKRL-KATGMPIKEIKTY 67
Cdd:cd04767    2 YPIGVVAELLNIHPETLRIWERHGLIKPARR-NGQRLYSNNDLKRLRFIKKLiNEKGLNIAGVKQI 66

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489665925   5 IGKFSKMVSLSIDTLRYYEKERLIIPARD-QNNRRTYSEADQRWIAFIKRLKATGMPIKEIKT-YARLRYQGNS-----T 77
Cdd:cd04773    3 IGELAHLLGVPPSTLRHWEKEGLLSPDREpETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATvVEQLRHAGGTealaaA 82

                         90
                 ....*....|....
gi 489665925  78 IDERLQLLfTQKNR 91
Cdd:cd04773   83 LEQRRVAL-TQRGR 95

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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIPA-RDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKT-YARLRYQGNSTIDE 80
Cdd:cd04790    2 LTISQLARQFGLSRSTLLYYERIGLLSPSaRSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSlLQQPGDDATDVLRR 81

                         90
                 ....*....|....*....
gi 489665925  81 RLQLLFTQKNRLTAQRQEI 99
Cdd:cd04790   82 RLAELNREIQRLRQQQRAI 100

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489665925  10 KMVSLSIDTLRYYEKERLIIPARD-QNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRYQGNSTIdERLQLLFTQ 88
Cdd:cd04787    8 NAAGVTPDTVRFYTRIGLLRPTRDpVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGESPC-PMVRRLIEQ 86

                         90
                 ....*....|..
gi 489665925  89 knRLTAQRQEID 100
Cdd:cd04787   87 --RLAETERRIK 96

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 489665925   5 IGKFSKMVSLSIDTLRYYEKERLII-PARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRyQGNSTIDERlq 83
Cdd:cd04783    3 IGELAKAAGVNVETIRYYQRRGLLPePPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELD-DGTDCSEAR-- 79

                         90       100
                 ....*....|....*....|....*
gi 489665925  84 llftqknRLTAQR-QEIDAHIAFLE 107
Cdd:cd04783   80 -------ELAEQKlAEVDEKIADLQ 97

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 489665925  18 TLRYYEKERLIIPARDqNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLrYQGNSTIDERLQLLF----TQKNRLT 93
Cdd:cd04776   16 TLRFYEDKGLLSPERR-GQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL-YDPPGGNRKQLEKMLekieKRRAELE 93

                         90
                 ....*....|....*
gi 489665925  94 AQRQEIDAHIAFLEN 108
Cdd:cd04776   94 QQRRDIDAALAELDA 108

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIPARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARLRYQGNSTIDER- 81
Cdd:cd04779    1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQRSDKEQREVa 80

                         90
                 ....*....|....*.
gi 489665925  82 --LQLLFTQKNRLTAQ 95
Cdd:cd04779   81 qeVQLVCDQIDGLEHR 96

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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKE-RLIIPARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIK 65
Cdd:cd04763    1 YTIGEVALLTGIKPHVLRAWEREfGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVK 64

MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 489665925   46 RWIAFIKRLKATGMPIKEIKTYARLRYQGNSTIDERLQLLFTQKNRLTAQRQEIDA 101
Cdd:pfam09278   2 RRLAFIRRARRLGFSLEEIRELLALYDDPGPPCADVRALLREKLAELEARIAELQA 57

redox-sensitive transcriptional activator SoxR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489665925   6 GKFSKMVSLSIDTLRYYEKERLIIPARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEI---------------KTYARL 70
Cdd:PRK15002  15 GEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIgeafgvlpeghtlsaKEWKQL 94

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489665925  71 RYQGNSTIDERLQllftqknRLTAQRQEIDAHI 103
Cdd:PRK15002  95 SSQWREELDRRIH-------TLVALRDELDGCI 120

mercuric resistance operon transcriptional regulator MerR;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489665925   5 IGKFSKMVSLSIDTLRYYEKERLII-PARDQNNRRTYSEADQRWIAFIKRLKATGMPIKEIKTYARL 70
Cdd:PRK13752  10 IGVFAKAAGVNVETIRFYQRKGLLPePDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRL 76

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 489665925   3 YPIGKFSKMVSLSIDTLRYYEKERLIIPARDQNNRRTYSEADQRWIAFIKRL-KATGMPIKEIKTYARLrYQGNSTIDER 81
Cdd:cd01279    2 YPISVAAELLGIHPQTLRVYDRLGLVSPARTNGGGRRYSNNDLELLRQVQRLsQDEGFNLAGIKRIIEL-YPQVLLLQCR 80

                         90
                 ....*....|....*...
gi 489665925  82 LQLLFTQKNRL-TAQRQE 98
Cdd:cd01279   81 SCEHATELIGCaKPCRKE 98

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489665925   3 YPIGKFSKMVSLSIDTLRYYEKE-RLIIPARDQNNRRTYSEADQRWIAFIKRL-KATGMPIKEIKtyARLRYQGNSTIDE 80
Cdd:cd04765    1 FSIGEVAEILGLPPHVLRYWETEfPQLKPVKRAGGRRYYRPKDVELLLLIKHLlYEKGYTIEGAK--QALKEDGAAAIRE 78