HTH-type transcriptional regulator CueR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128471    1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80
Cdd:PRK10227   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 16128471   81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLSGCCHHRAG 135
Cdd:PRK10227  81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLSGCCHHRAG 135

HTH-type transcriptional regulator CueR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128471    1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80
Cdd:PRK10227   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 16128471   81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLSGCCHHRAG 135
Cdd:PRK10227  81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLSGCCHHRAG 135

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 16128471   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80
Cdd:cd01108   1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 16128471  81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLS 127
Cdd:cd01108  81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGLA 127

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128471      1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNL 69
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLEL 69

HTH-type transcriptional regulator CueR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128471    1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80
Cdd:PRK10227   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 16128471   81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLSGCCHHRAG 135
Cdd:PRK10227  81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLSGCCHHRAG 135

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 16128471   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80
Cdd:cd01108   1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 16128471  81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLS 127
Cdd:cd01108  81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGLA 127

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 16128471   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80
Cdd:cd04785   1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCAEA 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 16128471  81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENL 126
Cdd:cd04785  81 DAIARAHLADVRARIADLRRLEAELKRMVAACSGGRVADCRIIEAL 126

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128471   3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQrhsADVKR 82
Cdd:COG0789   1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGE---EEVRE 77

                        90       100
                ....*....|....*....|...
gi 16128471  83 RTLEKVAEIERHIEELQSMRDQL 105
Cdd:COG0789  78 LLEEHLAELEAQIAELQALRAEL 100

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 16128471   1 MNISDVAKITGLTSKAIRFYEEKGLVtPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNlfNDPQRHSADV 80
Cdd:cd00592   1 YTIGEVAKLLGVSVRTLRYYEEKGLL-PPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLD--ARDEELSLAA 77

                        90       100
                ....*....|....*....|...
gi 16128471  81 KRRTL-EKVAEIERHIEELQSMR 102
Cdd:cd00592  78 LLALLdEKLAELEEKIARLEALL 100

Zn(II)-responsive transcriptional regulator; This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc 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-Cys-X(8-9)-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 16128471     3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHS-ADVK 81
Cdd:TIGR02043   4 IGELAKLCGVTSDTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSIKLDATEHScAEVK 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 16128471    82 RRTLEKVAEIERHIEELQSMRDQLLALANACPG--DDSADCPIIENL 126
Cdd:TIGR02043  84 AIVDAKLELVDEKINELTKIRRSLKKLSDACCGhtNDASHCSILEAL 130

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 16128471   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENgYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80
Cdd:cd04769   1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSGN-YRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWPH 79

                        90       100
                ....*....|....*....|....*....
gi 16128471  81 KRRTLE-KVAEIERHIEELQSMRDQLLAL 108
Cdd:cd04769  80 LQQALEdKKQEIRAQITELQQLLARLDAF 108

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 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 16128471   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRsENGYRTYTQQHLNELTLLRQARQVGFNLEESGElvnLFNDPQRHSADv 80
Cdd:cd04781   1 LDIAEVARQSGLPASTLRYYEEKGLIASIGR-RGLRRQYDPQVLDRLALIALGRAAGFSLDEIQA---MLSHDGKPPID- 75

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 16128471  81 KRRTLEKVAEIERHIEELQSMRDqLLALANACPGDDSADCPI 122
Cdd:cd04781  76 RQLLKAKAAELDQQIQRLQAMRE-LLRHVAQCPAPSHLDCPT 116

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 16128471   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFND-----PQR 75
Cdd:cd01109   1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREgdstiPER 80

                        90       100
                ....*....|....*....|....*.
gi 16128471  76 HS--ADVKRRTLEKVAEIERHIEELQ 99
Cdd:cd01109  81 LEllEEHREELEEQIAELQETLAYLD 106

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 16128471    44 LNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADVKRRTLEKVAEIERHIEELQSMRDQLLAL 108
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELLALYDDPGPPCADVRALLREKLAELEARIAELQALRDELDAL 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        50
                ....*....|....*....|....*....|....*....|....*....|
gi 16128471   1 MNISDVAKITGLTSKAIRFYEEKGLVtPPMRSENGYRTYTQQHLNELTLL 50
Cdd:cd04761   1 YTIGELAKLTGVSPSTLRYYERIGLL-SPARTEGGYRLYSDADLERLRLI 49

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 16128471   3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLfNDPQRHSADVKr 82
Cdd:cd04782   3 TGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN-RNPDELIELLK- 80

                        90       100
                ....*....|....*....|
gi 16128471  83 rtlEKVAEIERHIEELQSMR 102
Cdd:cd04782  81 ---KQEKEIKEEIEELQKIK 97

First 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 contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128471   4 SDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQArQVGFNLEESGELVNLFndpqrHSADVKrr 83
Cdd:cd04772   4 VDLARAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDKHIAALRAYRAL-LPGYGYRVAQRIMRAV-----HAGIVA-- 75

                        90       100
                ....*....|....*....|..
gi 16128471  84 tlEKVAEIERHIEELQSMRDQL 105
Cdd:cd04772  76 --SALALVDAAHALLQRYRQQL 95

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 16128471   3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLfndpqrHSADVKR 82
Cdd:cd04768   3 IGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDT------EMEELTA 76

                        90
                ....*....|....*....
gi 16128471  83 RTLEKVAEIERHIEELQSM 101
Cdd:cd04768  77 MLLEKKQAIQQKIDRLQQL 95

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 16128471     2 NISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTY 39
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128471   2 NISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVnlfnDPQRHSADVK 81
Cdd:cd01105   3 GIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKL----RRRRVQAEVR 78

                ..
gi 16128471  82 RR 83
Cdd:cd01105  79 RR 80

Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128471   3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQrhsADVKR 82
Cdd:cd04790   4 ISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDA---TDVLR 80

                        90       100
                ....*....|....*....|....*.
gi 16128471  83 RTLekvAEIERHIEELQSMRDQLLAL 108
Cdd:cd04790  81 RRL---AELNREIQRLRQQQRAIATL 103

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 16128471   3 ISDVAKITGLTSKAIRFYEEKGLVtPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNlfndpQRHsadVKR 82
Cdd:cd04775   4 IGQMSRKFGVSRSTLLYYESIGLI-PSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLA-----QPH---VQA 74

                        90       100
                ....*....|....*....|....*.
gi 16128471  83 RTLEKVAEIERHIEELQSMRDQLLAL 108
Cdd:cd04775  75 ILEERLQSLNREIQRLRQQQQVLAAI 100

mercuric resistance operon transcriptional regulator MerR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128471    1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLfnDPQRHSADV 80
Cdd:PRK13752   8 LTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRL--EDGTHCEEA 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 16128471   81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPG-DDSADCPIIENLSG 128
Cdd:PRK13752  86 SSLAEHKLKDVREKMADLARMEAVLSELVCACHArKGNVSCPLIASLQG 134

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 16128471   3 ISDVAKITGLTSKAIRFYEEK-GLVTPpmRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVN 68
Cdd:cd04764   3 IKEVSEIIGVKPHTLRYYEKEfNLYIP--RTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67

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
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 16128471   2 NISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGF 58
Cdd:cd01104   2 TIGAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGV 58

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 16128471   3 ISDVAKITGLTSKAIRFYEEKGLVTPpMRSENGYRTYTQQHLNELTLLRQARQVGFNLEE-SGELVNLFN--DPQRHSAD 79
Cdd:cd04779   3 IGQLAHLAGVSKRTIDYYTNLGLLTP-ERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEiKDQLEEVQRsdKEQREVAQ 81

                        90       100
                ....*....|....*....|....*...
gi 16128471  80 VKRRTLEKVAEIERHIEELQSMRDQLLA 107
Cdd:cd04779  82 EVQLVCDQIDGLEHRLKQLKPIASQTDR 109

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128471   3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQ-----------ARQVgfnLEESGELVNlfn 71
Cdd:cd04765   3 IGEVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHllyekgytiegAKQA---LKEDGAAAI--- 76

                        90       100       110
                ....*....|....*....|....*....|....
gi 16128471  72 dpqrhSADVKRRTLEKVAeierhiEELQSMRDQL 105
Cdd:cd04765  77 -----REEEAEERLPSIR------AELLDLRDQL 99

Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 16128471   3 ISDVAKITGLTSKAIRFYE-EKGLVTPPmRSENGYRTYTQQHLN 45
Cdd:cd04763   3 IGEVALLTGIKPHVLRAWErEFGLLKPQ-RSDGGHRLFNDADID 45

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
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 16128471   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGF 58
Cdd:cd04780   1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGG 58

HTH-type transcriptional regulator MerD;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128471    3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADVKR 82
Cdd:PRK13749   6 VSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAADGDEAAAQL 85

                         90       100
                 ....*....|....*....|....*.
gi 16128471   83 RTLEKVaeIERHIEELQSMRDQLLAL 108
Cdd:PRK13749  86 AVLRQL--VERRREALADLEVQLATM 109