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 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVKDgcilekinsdv 83
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL----------- 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2508160885  84 kSAQLSPSINKRIEILTKHLEKMEIKKRELEEVISTTKGKLDTYY 128
Cdd:cd01109    70 -RREGDSTIPERLELLEEHREELEEQIAELQETLAYLDYKIDYYE 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 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVKDgcilekinsdv 83
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL----------- 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2508160885  84 kSAQLSPSINKRIEILTKHLEKMEIKKRELEEVISTTKGKLDTYY 128
Cdd:cd01109    70 -RREGDSTIPERLELLEEHREELEEQIAELQETLAYLDYKIDYYE 113

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508160885   6 ISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVkdgcilekinsdvks 85
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELL--------------- 65

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2508160885  86 AQLSPSINKRIEILTKHLEKMEIKKRELEEVIST 119
Cdd:COG0789    66 DLLDDGEEEVRELLEEHLAELEAQIAELQALRAE 99

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 2508160885   6 ISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVKDGCILEKINSDVKS 85
Cdd:TIGR02044   3 IGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADVKA 82

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2508160885  86 AQLSpsinkRIEILTKHLEKMEIKKRELEEVISTTKG 122
Cdd:TIGR02044  83 RTLE-----KVAEIERKISELQSMRDQLEALAQACPG 114

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 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVKDgcilekinsdv 83
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL----------- 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2508160885  84 kSAQLSPSINKRIEILTKHLEKMEIKKRELEEVISTTKGKLDTYY 128
Cdd:cd01109    70 -RREGDSTIPERLELLEEHREELEEQIAELQETLAYLDYKIDYYE 113

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508160885   6 ISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVkdgcilekinsdvks 85
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELL--------------- 65

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2508160885  86 AQLSPSINKRIEILTKHLEKMEIKKRELEEVIST 119
Cdd:COG0789    66 DLLDDGEEEVRELLEEHLAELEAQIAELQALRAE 99

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 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLpPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEfvkdgcILEKINSDv 83
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLL-PPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRE------LLDARDEE- 72

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2508160885  84 ksaqlsPSINKRIEILTKHLEKMEIKKRELEEVI 117
Cdd:cd00592    73 ------LSLAALLALLDEKLAELEEKIARLEALL 100

Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508160885   6 ISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVKdgciL----EKINS 81
Cdd:cd01108     3 IGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLA----LwrdpSRASA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2508160885  82 DVKSAQLSpsinkRIEILTKHLEKMEIKKRELEEVISTTKG 122
Cdd:cd01108    79 DVKALALE-----HIAELERKIAELQAMRRTLQQLADSCHG 114

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPPKRKNsGRRFYTETDIQFMLFLKSLKETGMSLEDI 66
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTER-GRRYYTDEDVERLRLIKALLERGLSLKEI 62

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
                  ....*....|....*....|....*....|....*....|....*....|
gi 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLpPPKRKNSGRRFYTETDIQFMLFL 53
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLL-SPARTEGGYRLYSDADLERLRLI 49

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 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPPKR-KNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVKDgcilekinsd 82
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVdPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDA---------- 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2508160885  83 vksaqlsPSINKRIEILTKHLEKMEIKKRELEEVISTTKGKLDT 126
Cdd:cd01107    71 -------DNDDELRKLLREKLAELEAEIEELQRILRLLEDRLKQ 107

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINE 68
Cdd:cd04783     1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAE 65

Zn(2+)-responsive transcriptional regulator;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2508160885   3 LYSISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINE 68
Cdd:PRK09514    1 MYRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRE 66

Cd(II)/Pb(II)-responsive transcriptional regulator; This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal 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-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508160885   6 ISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEfvkdgcILEKINSDVKS 85
Cdd:TIGR02047   3 IGELAQKTGVSVETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQ------LLRYQDKPEKS 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2508160885  86 AQlspSINKRIEILTKHLEKMEIKKRELEEVISTTKGKLDTYYSI 130
Cdd:TIGR02047  77 CS---DVNALLDEHISHVRARIIKLQALIEQLVDLRGRCNGLCTV 118

Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVKDgcilekinsdv 83
Cdd:cd04782     1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN----------- 69

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2508160885  84 ksaqlsPSINKRIEILTKHLEKMEIKKRELEEV 116
Cdd:cd04782    70 ------RNPDELIELLKKQEKEIKEEIEELQKI 96

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 2508160885   3 LYSISKAAEKTSISSYTLRYYEKIGLLpPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINefvkdGCILEKINSD 82
Cdd:cd04775     1 MYTIGQMSRKFGVSRSTLLYYESIGLI-PSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIA-----GCLAQPHVQA 74

                          90
                  ....*....|....*..
gi 2508160885  83 VKSAQLSpSINKRIEIL 99
Cdd:cd04775    75 ILEERLQ-SLNREIQRL 90

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 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPpkRKNSGRRFYTETD-IQFMLFLKSlKETGMSLEDINEFVKdgciLEKINsD 82
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSP--ERRGQTRVYSRRDrARLKLILRG-KRLGFSLEEIRELLD----LYDPP-G 72

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2508160885  83 VKSAQLspsiNKRIEILTKHLEKMEIKKRELEEVI 117
Cdd:cd04776    73 GNRKQL----EKMLEKIEKRRAELEQQRRDIDAAL 103

Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators; Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the conserved, metal-binding cysteines seen in the MerR1 group.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2508160885  10 AEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVKDG 73
Cdd:cd04787     7 ANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHA 70

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 2508160885   4 YSISKAAEKTSISSYTLRYYEK-IGLLPPpkRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINE 68
Cdd:cd04764     1 YTIKEVSEIIGVKPHTLRYYEKeFNLYIP--RTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKE 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 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 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPpKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVKDGCILEKINSDV 83
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYYTNLGLLTP-ERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQRSDKEQREV 79

Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508160885   3 LYSISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVKD 72
Cdd:cd01105     1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRR 70

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 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLpPPKRKNSGRRFYTETDIQFMLFLKSLKET-GMSLEDINEFVK 71
Cdd:cd04774     1 YKVDEVAKRLGLTKRTLKYYEEIGLV-SPERSEGRYRLYSEEDLKRLERILRLREVlGFSLQEVTHFLE 68

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2508160885   3 LYSISKAAEKTSISSYTLRYYEKIGLLpPPKRKNSGRRFYTETDIQFMLFLKSL-KETGMSLEDI 66
Cdd:cd04766     1 VYVISVAAELSGMHPQTLRLYERLGLL-SPSRTDGGTRRYSERDIERLRRIQRLtQELGVNLAGV 64

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFV 70
Cdd:cd04773     1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVV 67

mercuric resistance operon transcriptional regulator MerR;

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2508160885   5 SISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINEFVK--DGCILEKINS 81
Cdd:PRK13752    9 TIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRleDGTHCEEASS 87

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPPKRKNSGRRFYTETDIQFMLFLKSLKET-GMSLEDINE 68
Cdd:cd04780     1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEgGLPISQIKE 66

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

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2508160885   5 SISKAAEKTSISSYTLRYYEKIGLLpPPKRKNSGRRFYTETDIQFMLFLKSLKETGMSLEDINE 68
Cdd:cd01110     3 SVGEVAKRSGVAVSALHFYEQKGLI-ASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAE 65

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.

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                  ....*....|....*....|....*....|....*....|....*
gi 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLpPPKRKNSGRRFYTETDIQ 48
Cdd:cd04762     1 LTTKEAAELLGVSPSTLRRWVKEGKL-KAIRTPGGHRRFPEEDLE 44

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2508160885   4 YSISKAAEKTSISSYTLRYYEKIGLLPPPKRKnsGR-RFYTETDIQFMLFLKSLKETGMSLEDINEFVK 71
Cdd:cd04778     2 YRIDDLARAAGTTVRNVRAYQDRGLLPPPRRR--GRvAIYNDSHLARLRLINQLLERGYTLAHIAELLA 68