HTH-type transcriptional regulator MlrA;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065    1 MALYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVDVQNG 80
Cdd:PRK15043   1 MALYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVDVQNG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065   81 WRDQQETLLTYLQSGNLHSLRTWIKERGQDYPAQTLTTHLFIPLRRRLQCQQPTLQALLAILDGVLINYIAICLASARKK 160
Cdd:PRK15043  81 WRDQQETLLTYLQSGNLHSLRTWIKERGQDYPAQTLTTHLFIPLRRRLQCQQPTLQALLAILDGVLINYIAICLASARKK 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065  161 QGKDALVVGWNIQDTTRLWLEGWIASQQGWRIDVLAHSLNQLRPELFEGRTLLVWCGENRTSAQQQQLTSWQEQGHDIFP 240
Cdd:PRK15043 161 QGKDALVVGWNIHDTTRLWLEGWIASQQGWRIDVLAHSLNQLRPELFEGRTLLVWCGENRTSAQQQQLTSWQEQGHDIFP 240

                 ...
gi 16130065  241 LGI 243
Cdd:PRK15043 241 LGI 243

HTH-type transcriptional regulator MlrA;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065    1 MALYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVDVQNG 80
Cdd:PRK15043   1 MALYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVDVQNG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065   81 WRDQQETLLTYLQSGNLHSLRTWIKERGQDYPAQTLTTHLFIPLRRRLQCQQPTLQALLAILDGVLINYIAICLASARKK 160
Cdd:PRK15043  81 WRDQQETLLTYLQSGNLHSLRTWIKERGQDYPAQTLTTHLFIPLRRRLQCQQPTLQALLAILDGVLINYIAICLASARKK 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065  161 QGKDALVVGWNIQDTTRLWLEGWIASQQGWRIDVLAHSLNQLRPELFEGRTLLVWCGENRTSAQQQQLTSWQEQGHDIFP 240
Cdd:PRK15043 161 QGKDALVVGWNIHDTTRLWLEGWIASQQGWRIDVLAHSLNQLRPELFEGRTLLVWCGENRTSAQQQQLTSWQEQGHDIFP 240

                 ...
gi 16130065  241 LGI 243
Cdd:PRK15043 241 LGI 243

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16130065      4 YTIGEVALLCDINPVTLRAWQRrYGLLKPQ-RTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLL 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYER-IGLLPPPiRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELL 67

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065   6 IGEVALLCDINPVTLRAWQRrYGLLKP-QRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNEN 74
Cdd:COG0789   1 IGEVARLTGVSVRTLRYYER-IGLLPPpERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLD 69

HTH-type transcriptional regulator MlrA;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065    1 MALYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVDVQNG 80
Cdd:PRK15043   1 MALYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVDVQNG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065   81 WRDQQETLLTYLQSGNLHSLRTWIKERGQDYPAQTLTTHLFIPLRRRLQCQQPTLQALLAILDGVLINYIAICLASARKK 160
Cdd:PRK15043  81 WRDQQETLLTYLQSGNLHSLRTWIKERGQDYPAQTLTTHLFIPLRRRLQCQQPTLQALLAILDGVLINYIAICLASARKK 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065  161 QGKDALVVGWNIQDTTRLWLEGWIASQQGWRIDVLAHSLNQLRPELFEGRTLLVWCGENRTSAQQQQLTSWQEQGHDIFP 240
Cdd:PRK15043 161 QGKDALVVGWNIHDTTRLWLEGWIASQQGWRIDVLAHSLNQLRPELFEGRTLLVWCGENRTSAQQQQLTSWQEQGHDIFP 240

                 ...
gi 16130065  241 LGI 243
Cdd:PRK15043 241 LGI 243

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 16130065   4 YTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLS 71
Cdd:cd01104   1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68

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 16130065   4 YTIGEVALLCDINPVTLRAWQRRyGLLKPQRTDGGHRLFNDADIDRIREI 53
Cdd:cd04761   1 YTIGELAKLTGVSPSTLRYYERI-GLLSPARTEGGYRLYSDADLERLRLI 49

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16130065   4 YTIGEVALLCDINPVTLRAWQRRyGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVDVQN 79
Cdd:cd00592   1 YTIGEVAKLLGVSVRTLRYYEEK-GLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSL 75

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 16130065   3 LYTIGEVALLCDINPVTLRAWQRRyGLLKPQRTDGGHRLFNDADIDRIREIKRWIDN-GVQVSKVKMLL 70
Cdd:cd04766   1 VYVISVAAELSGMHPQTLRLYERL-GLLSPSRTDGGTRRYSERDIERLRRIQRLTQElGVNLAGVKRIL 68

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 16130065   3 LYTIGEVALLCDINPVTLRAWQRRyGLLKPQRTDGGH-RLFNDADIDRIREIKRWIDNGVQVSKVK 67
Cdd:cd01105   1 VIGIGEVSKLTGVSPRQLRYWEEK-GLIKSIRSDGGGqRKYSLADVDRLLVIKELLDEGFTLAAAV 65

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
                ....*....|....*....|....*....|....*....|....*....|...
gi 16130065   4 YTIGEVALLCDINPVTLRAWQRRyGLL-KPQRTDGGHRLFNDADIDRIREIKR 55
Cdd:cd04783   1 LTIGELAKAAGVNVETIRYYQRR-GLLpEPPRPEGGYRRYPEETVTRLRFIKR 52

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16130065   4 YTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWI-DNGVQVSKVKMLLSNE 73
Cdd:cd04765   1 FSIGEVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLyEKGYTIEGAKQALKED 71

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

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 16130065   4 YTIGEVALLCDINPVTLRAWQRRyGLLKPQRTDGGHRLFNDADIDRIREI 53
Cdd:cd04762   1 LTTKEAAELLGVSPSTLRRWVKE-GKLKAIRTPGGHRRFPEEDLERLLGI 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16130065   6 IGEVALLCDINPVTLRAWQRRyGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLL 70
Cdd:cd01282   3 IGELAARTGVSVRSLRYYEEQ-GLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFL 66

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16130065   4 YTIGEVALLCDINPVTLRAWQRRyGLLKP-QRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVK 67
Cdd:cd01109   1 YTIKEVAEKTGLSADTLRYYEKE-GLLPPvKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIK 64

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

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 16130065   4 YTIGEVALLCDINPVTLRAWQRRyGLLKPQRTDGGHRLFNDADIDRIREIKR 55
Cdd:cd04774   1 YKVDEVAKRLGLTKRTLKYYEEI-GLVSPERSEGRYRLYSEEDLKRLERILR 51

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16130065   4 YTIGEVALLCDINPVTLrawqRRY---GLLKPQRTDG--GHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVD 76
Cdd:cd01107   1 FTIGEFAKLSNLSIKAL----RYYdkiGLLKPAYVDPdtGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDD 74

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16130065   3 LYTIGEVALLCDINPVTLRAWQRRyGLLKPQ-RTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVDVQ 78
Cdd:cd04790   1 MLTISQLARQFGLSRSTLLYYERI-GLLSPSaRSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDAT 76

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
                ....*....|....*....|....*....|....*....|....*....
gi 16130065   4 YTIGEVALLCDINPVTLRAWQRRyGLLKPQRTDG-GHRLFNDADIDRIR 51
Cdd:cd04773   1 MTIGELAHLLGVPPSTLRHWEKE-GLLSPDREPEtGYRVYDPSDVRDAR 48

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16130065   3 LYTIGEVALLCDINPVTLRAWQRRyGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLL 70
Cdd:cd04775   1 MYTIGQMSRKFGVSRSTLLYYESI-GLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCL 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 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 16130065   4 YTIGEVALLCDINPVTLRAWQRrYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSN-ENVDVQNGWR 82
Cdd:cd04779   1 YRIGQLAHLAGVSKRTIDYYTN-LGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEvQRSDKEQREV 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16130065  83 DQQETLLTYLQSGNLHSLrtwikERGQDYPAQTlTTHLFIPLRRRLQCQQPTL-QALLAIL 142
Cdd:cd04779  80 AQEVQLVCDQIDGLEHRL-----KQLKPIASQT-DRAQRMKMTKELSQQVLTLiQSLTLLL 134

Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130065   4 YTIGEVALLCDINPVTLRAWQRRyGLLKP-QRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVDVQNGWR 82
Cdd:cd01111   1 YSISQLALDAGVSVHIVRDYLLR-GLLHPvARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDAGDGKQPE 79

                ....*...
gi 16130065  83 DQQETLLT 90
Cdd:cd01111  80 ACLAQLRQ 87

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

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 16130065   5 TIGEVALLCDINPVTLRAWQRRyGLLKPQRTDGGHRLFNDADIDRIREIK 54
Cdd:cd01110   3 SVGEVAKRSGVAVSALHFYEQK-GLIASWRNAGNQRRYPRDVLRRIAFIK 51