Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600309   4 LDIGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGMGAADGALRIDRAALA 83
Cdd:cd04781   1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDRQLLK 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 15600309  84 AKADELDRTIRRLAAMRDGLRHAAACPAREHMDCPTF 120
Cdd:cd04781  81 AKAAELDQQIQRLQAMRELLRHVAQCPAPSHLDCPTF 117

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600309   4 LDIGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGMGAADGALRIDRAALA 83
Cdd:cd04781   1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDRQLLK 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 15600309  84 AKADELDRTIRRLAAMRDGLRHAAACPAREHMDCPTF 120
Cdd:cd04781  81 AKAAELDQQIQRLQAMRELLRHVAQCPAPSHLDCPTF 117

Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue. [Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600309     4 LDIGEVARRSGVPASTLRYYEEKGLIASSGR-HGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGMGAadgaLRIDRAAL 82
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRsEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLN----LWNDPNRT 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 15600309    83 AA--------KADELDRTIRRLAAMRDGLRH-AAACPAREHMDCP 118
Cdd:TIGR02044  77 SAdvkartleKVAEIERKISELQSMRDQLEAlAQACPGDDSPDCP 121

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15600309      6 IGEVARRSGVPASTLRYYEEKGLIASSGR-HGLRRLFDAGVLERLALIGLGRAAGLSLDEIA 66
Cdd:smart00422   3 IGEVAKLAGVSVRTLRYYERIGLLPPPIRtEGGYRLYSDEDLERLRFIKRLKELGFSLEEIK 64

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600309   4 LDIGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGMGAADGALRIDRAALA 83
Cdd:cd04781   1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDRQLLK 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 15600309  84 AKADELDRTIRRLAAMRDGLRHAAACPAREHMDCPTF 120
Cdd:cd04781  81 AKAAELDQQIQRLQAMRELLRHVAQCPAPSHLDCPTF 117

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 15600309   6 IGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLDEIA---GMGAADGALRIDRAAL 82
Cdd:cd00592   3 IGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRellDARDEELSLAALLALL 82

                        90
                ....*....|....*...
gi 15600309  83 AAKADELDRTIRRLAAMR 100
Cdd:cd00592  83 DEKLAELEEKIARLEALL 100

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600309   6 IGEVARRSGVPASTLRYYEEKGLIASSGR-HGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGM-GAADGALRIDRAALA 83
Cdd:COG0789   1 IGEVARLTGVSVRTLRYYERIGLLPPPERtEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELlDLLDDGEEEVRELLE 80

                        90       100
                ....*....|....*....|
gi 15600309  84 AKADELDRTIRRLAAMRDGL 103
Cdd:COG0789  81 EHLAELEAQIAELQALRAEL 100

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 15600309   6 IGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGMGAADG------------ 73
Cdd:cd04769   3 IGELAQQTGVTIKAIRLYEEKGLLPSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEgravlpwphlqq 82

                        90       100       110
                ....*....|....*....|....*....|...
gi 15600309  74 ALRIDRAALAAKADELDRTIRRLAAMRDGLRHA 106
Cdd:cd04769  83 ALEDKKQEIRAQITELQQLLARLDAFEASLKDA 115

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 15600309   6 IGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLDEIAG----MGAADGALRID--- 78
Cdd:cd01282   3 IGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREflpcLRGGEPTFRPCpdl 82

                        90       100
                ....*....|....*....|....*..
gi 15600309  79 RAALAAKADELDRTIRRLAAMRDGLRH 105
Cdd:cd01282  83 LAVLRRELARIDRQIADLTRSRDRLDA 109

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 15600309   4 LDIGEVARRSGVPASTLRYYEEKGLIASSGR-HGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGM-GAADGALRIDRAA 81
Cdd:cd04783   1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRpEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELlELDDGTDCSEARE 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 15600309  82 LA-AKADELDRTIRRLAAMRDGLRH-AAACPAREHM-DCP 118
Cdd:cd04783  81 LAeQKLAEVDEKIADLQRMRASLQElVSQCAATKNNvSCP 120

redox-sensitive transcriptional activator SoxR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600309    7 GEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLdeiAGMGAADGALRiDRAALAAKA 86
Cdd:PRK15002  15 GEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPL---ATIGEAFGVLP-EGHTLSAKE 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 15600309   87 ---------DELDRTIRRLAAMRDGLRHAAACPAREHMDCP 118
Cdd:PRK15002  91 wkqlssqwrEELDRRIHTLVALRDELDGCIGCGCLSRSDCP 131

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 15600309   6 IGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGMGAAdgalRIDRAALAAK 85
Cdd:cd04775   4 IGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQ----PHVQAILEER 79

                        90
                ....*....|....*.
gi 15600309  86 ADELDRTIRRLAAMRD 101
Cdd:cd04775  80 LQSLNREIQRLRQQQQ 95

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        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600309   4 LDIGEVARRSGVPASTLRYYEEKGLIASSGR-HGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGM--------GAADGA 74
Cdd:cd04785   1 LSIGELARRTGVNVETIRYYESIGLLPEPARtAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALlalsdrpdRSCAEA 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 15600309  75 LRIDRAALAakadELDRTIRRLAAMRDGLRH-AAACPAREHMDCP 118
Cdd:cd04785  81 DAIARAHLA----DVRARIADLRRLEAELKRmVAACSGGRVADCR 121

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15600309     6 IGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGM 68
Cdd:pfam13411   3 ISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKEL 65

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 15600309   4 LDIGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALI 52
Cdd:cd04761   1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLRLI 49

Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. 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 15600309   6 IGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGMGAAdgalRIDRAALAAK 85
Cdd:cd04789   4 ISELAEKAGISRSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQG----KLTRSLLLER 79

                        90
                ....*....|....*...
gi 15600309  86 ADELDRTIRRLAAMRDGL 103
Cdd:cd04789  80 LSSLAEQIARKQQARDLL 97

Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively 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 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 15600309   6 IGEVARRSGVPASTLRYYEEKGLIASSGR-HGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGMgaADGALRIDRAALAA 84
Cdd:cd04788   3 IGELARRTGLSVRTLHHYDHIGLLSPSQRtEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRA--LDGPDFDPLELLRR 80

                        90
                ....*....|....*.
gi 15600309  85 KADELDRTIRRLAAMR 100
Cdd:cd04788  81 QLARLEEQLELATRLR 96

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 15600309   4 LDIGEVARRSGVPASTLRYYEEKGL-----IASSGrhglRRLFDAGVLERLALIGLGRAAGLSLDEIAGMGAADGALRid 78
Cdd:cd04768   1 LTIGEFAKLAGVSIRTLRHYDDIGLfkpakIAENG----YRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEEL-- 74

                        90       100
                ....*....|....*....|.
gi 15600309  79 RAALAAKADELDRTIRRLAAM 99
Cdd:cd04768  75 TAMLLEKKQAIQQKIDRLQQL 95

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
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15600309   6 IGEVARRSGVPASTLRYYEEKGLIAS--SGRHGlRRLFDAGVLERLALIGLGRAAGLSLDEIA 66
Cdd:cd01105   4 IGEVSKLTGVSPRQLRYWEEKGLIKSirSDGGG-QRKYSLADVDRLLVIKELLDEGFTLAAAV 65

Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15600309   4 LDIGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIGLGRAA-GLSLDEIAGM 68
Cdd:cd04774   1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLREVlGFSLQEVTHF 66

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15600309    46 LERLALIGLGRAAGLSLDEIAGM----GAADGALRIDRAALAAKADELDRTIRRLAAMRDGLRH 105
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELlalyDDPGPPCADVRALLREKLAELEARIAELQALRDELDA 64

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15600309   4 LDIGEVARRSGVPASTLRYYEEK-GLIASSGRHGLRRLFDAGVLERLALIGLGRAAGLSLDEIAGMGA 70
Cdd:cd01104   1 YTIGAVARLTGVSPDTLRAWERRyGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68

mercuric resistance operon transcriptional regulator MerR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600309    1 MRQLDIGEVARRSGVPASTLRYYEEKGLIASSGR--HGLRRLFDAGVlERLALIGLGRAAGLSLDEIAGMGAADGALRID 78
Cdd:PRK13752   5 LENLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKpyGSIRRYGEADV-TRVRFVKSAQRLGFSLDEIAELLRLEDGTHCE 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 15600309   79 RAALAA--KADELDRTIRRLAAMRDGLRH-AAACPARE-HMDCP 118
Cdd:PRK13752  84 EASSLAehKLKDVREKMADLARMEAVLSElVCACHARKgNVSCP 127

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15600309   6 IGEVARRSGVPASTLRYYEEKGLIASSGR-HGLRRLFDAGVLERLALI-GLGRAAGLSLDEIAGM 68
Cdd:cd04780   3 MSELSKRSGVSVATIKYYLREGLLPEGRRlAPNQAEYSEAHVERLRLIrALQQEGGLPISQIKEV 67

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 15600309   6 IGEVARRSGVPASTLRYYEEKGLIASSgRHGLRRLFDAGVLERLALIGLGRAAGLSLDEI---------AGMGAADGALR 76
Cdd:cd04777   3 IGKFAKKNNITIDTVRHYIDLGLLIPE-KKGGQYFFDEKCQDDLEFILELKGLGFSLIEIqkifsykrlTKSRTHEDQDY 81

                        90       100
                ....*....|....*....|....*..
gi 15600309  77 IdRAALAAKADELDRTIRRLAAMRDGL 103
Cdd:cd04777  82 Y-KSFLKNKKDELEKEIEDLKKAIQKL 107

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 15600309   6 IGEVARRSGVPASTLRYYEEKGLIASSGRHGLRRLFDAGVLERLALIG-LGRAAGLSL---DEIAgmgaadgALRIDRAA 81
Cdd:cd04766   4 ISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQrLTQELGVNLagvKRIL-------ELEEELAE 76

                        90
                ....*....|....
gi 15600309  82 LAAKADELDRTIRR 95
Cdd:cd04766  77 LRAELDELRARLRR 90