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 923015758    1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQPCTAV 80
Cdd:TIGR02047   1 MKIGELAQKTGVSVETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKSCSDV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 923015758   81 NALLDDHISHVRSQITALQALEKQLVSLRASCNDDREVEACGVLAGI 127
Cdd:TIGR02047  81 NALLDEHISHVRARIIKLQALIEQLVDLRGRCNGLCTVEQCGVLQNL 127

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 923015758    1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQPCTAV 80
Cdd:TIGR02047   1 MKIGELAQKTGVSVETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKSCSDV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 923015758   81 NALLDDHISHVRSQITALQALEKQLVSLRASCNDDREVEACGVLAGI 127
Cdd:TIGR02047  81 NALLDEHISHVRARIIKLQALIEQLVDLRGRCNGLCTVEQCGVLQNL 127

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923015758   3 IGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQpctAVNA 82
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEE---EVRE 77

                         90       100
                 ....*....|....*....|...
gi 923015758  83 LLDDHISHVRSQITALQALEKQL 105
Cdd:COG0789   78 LLEEHLAELEAQIAELQALRAEL 100

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 923015758     1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHEL 66
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKEL 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 923015758    1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQPCTAV 80
Cdd:TIGR02047   1 MKIGELAQKTGVSVETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKSCSDV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 923015758   81 NALLDDHISHVRSQITALQALEKQLVSLRASCNDDREVEACGVLAGI 127
Cdd:TIGR02047  81 NALLDEHISHVRARIIKLQALIEQLVDLRGRCNGLCTVEQCGVLQNL 127

Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQPCTAV 80
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 923015758  81 NALLDDHISHVRSQITALQALEKQLVSLRASCNDDREVEaCGVL 124
Cdd:cd04770   81 RALLEEKLAEVEAKIAELQALRAELAGLLSACDGDESVI-CPIL 123

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 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQPCTAV 80
Cdd:cd01108    1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 923015758  81 NALLDDHISHVRSQITALQALEKQLVSLRASCNDDrEVEACGVLAGIS 128
Cdd:cd01108   81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGD-DRPDCPILEGLA 127

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923015758   3 IGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQpctAVNA 82
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEE---EVRE 77

                         90       100
                 ....*....|....*....|...
gi 923015758  83 LLDDHISHVRSQITALQALEKQL 105
Cdd:COG0789   78 LLEEHLAELEAQIAELQALRAEL 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 923015758    1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDP-HQPCTA 79
Cdd:TIGR02043   2 FQIGELAKLCGVTSDTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSIKLDAtEHSCAE 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 923015758   80 VNALLDDHISHVRSQITALQALEKQLVSLR-ASCNDDREVEACGVLAGI 127
Cdd:TIGR02043  82 VKAIVDAKLELVDEKINELTKIRRSLKKLSdACCGHTNDASHCSILEAL 130

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 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPdRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQpCTAV 80
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPE-RSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELS-LAAL 78

                         90       100
                 ....*....|....*....|..
gi 923015758  81 NALLDDHISHVRSQITALQALE 102
Cdd:cd00592   79 LALLDEKLAELEEKIARLEALL 100

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 923015758     1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHEL 66
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKEL 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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQPCTAV 80
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90
                 ....*....|....*....
gi 923015758  81 NALLDDHISHVRSQITALQ 99
Cdd:cd01109   81 LELLEEHREELEEQIAELQ 99

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQPCTAV 80
Cdd:cd04787    1 MKVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMV 80

                         90       100
                 ....*....|....*....|.
gi 923015758  81 NALLDDHISHVRSQITALQAL 101
Cdd:cd04787   81 RRLIEQRLAETERRIKELLKL 101

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLpPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPH---QPC 77
Cdd:cd01282    1 MRIGELAARTGVSVRSLRYYEEQGLL-VPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLRGGEptfRPC 79

                         90       100
                 ....*....|....*....|....*...
gi 923015758  78 TAVNALLDDHISHVRSQITALQALEKQL 105
Cdd:cd01282   80 PDLLAVLRRELARIDRQIADLTRSRDRL 107

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 923015758   3 IGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPhqpctaVNA 82
Cdd:cd04768    3 IGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEE------LTA 76

                         90       100
                 ....*....|....*....|
gi 923015758  83 LLDDHISHVRSQITALQALE 102
Cdd:cd04768   77 MLLEKKQAIQQKIDRLQQLE 96

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 923015758    2 RIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVY 39
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38

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 923015758   2 RIGQLAQLVGVETQTIRFYEQQGLLpPPDRQD--NGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDphqpcTA 79
Cdd:cd01107    2 TIGEFAKLSNLSIKALRYYDKIGLL-KPAYVDpdTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADND-----DE 75

                         90       100
                 ....*....|....*....|....*.
gi 923015758  80 VNALLDDHISHVRSQITALQALEKQL 105
Cdd:cd01107   76 LRKLLREKLAELEAEIEELQRILRLL 101

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 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLPPpdRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQPCTAV 80
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLLSP--ERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQL 78

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 923015758  81 NALLD---DHISHVRSQITALQALEKQLVSLRASC 112
Cdd:cd04776   79 EKMLEkieKRRAELEQQRRDIDAALAELDAAEERC 113

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 923015758   6 LAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHgegLAFIRRCRIL----GLSLAEVHeLQSYQDDPHQpctAVN 81
Cdd:cd04772    6 LARAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDKH---IAALRAYRALlpgyGYRVAQRI-MRAVHAGIVA---SAL 78

                         90
                 ....*....|....*....
gi 923015758  82 ALLDDHISHVRSQITALQA 100
Cdd:cd04772   79 ALVDAAHALLQRYRQQLDQ 97

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 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQdNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQDDPHQPCTAV 80
Cdd:cd04781    1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRR-GLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDRQLL 79

                         90       100
                 ....*....|....*....|....*
gi 923015758  81 NALLDDhishVRSQITALQALEKQL 105
Cdd:cd04781   80 KAKAAE----LDQQIQRLQAMRELL 100

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCR-ILGLSLAEVHEL 66
Cdd:cd04780    1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQqEGGLPISQIKEV 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 923015758   2 RIGQLAQLVGVETQTIRFYEQQGLLpPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQddphQPCTAVN 81
Cdd:cd04779    2 RIGQLAHLAGVSKRTIDYYTNLGLL-TPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEV----QRSDKEQ 76

                         90       100
                 ....*....|....*....|....
gi 923015758  82 ALLDDHISHVRSQITALQALEKQL 105
Cdd:cd04779   77 REVAQEVQLVCDQIDGLEHRLKQL 100

Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHEL 66
Cdd:cd04773    1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATV 66

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 923015758   3 IGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHEL-QSYQDDPHQPCTAVN 81
Cdd:cd01111    3 ISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLcRALDAGDGKQPEACL 82

                         90       100
                 ....*....|....*....|....*..
gi 923015758  82 ALLDDHISHVRSqitALQALEKQLVSL 108
Cdd:cd01111   83 AQLRQKIEVRRA---ALNALTTQLAEM 106

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 923015758   3 IGQLAQLVGVETQTIRFYEQQ-GLLPPPdRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQS 68
Cdd:cd04763    3 IGEVALLTGIKPHVLRAWEREfGLLKPQ-RSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLLS 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 923015758   3 IGQLAQLVGVETQTIRFYEQQGLLpPPDRQDNGYRVYTEKHGEGLAFIRR-CRILGLSLAEV 63
Cdd:cd04766    4 ISVAAELSGMHPQTLRLYERLGLL-SPSRTDGGTRRYSERDIERLRRIQRlTQELGVNLAGV 64

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 923015758   2 RIGQLAQLVGVETQTIRFYEQQGLLPPPdRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVhelQSYQDDPHQPctavn 81
Cdd:cd04775    3 TIGQMSRKFGVSRSTLLYYESIGLIPSA-RSEANYRLYSEADLSRLEKIVFLQAGGLPLEEI---AGCLAQPHVQ----- 73

                         90       100
                 ....*....|....*....|....*..
gi 923015758  82 ALLDDHISHVRSQITALQALEKQLVSL 108
Cdd:cd04775   74 AILEERLQSLNREIQRLRQQQQVLAAI 100

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923015758   1 MRIGQLAQLVGVETQTIRFYEQQGLLPPpdRQDNGYRVYTEKHGEGLAFIRRCRILGLSLAEVHELQSYQ 70
Cdd:cd04777    1 MKIGKFAKKNNITIDTVRHYIDLGLLIP--EKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYK 68

plasmid-partitioning protein SopA; Provisional

                         10        20        30
                 ....*....|....*....|....*....|....
gi 923015758   2 RIGQLAQLVGVETQTIRFYEQQGLLPPPDRQDNG 35
Cdd:PRK13705  41 RIGEAADLVGVSSQAIRDAEKAGRLPHPDMEMRG 74

Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 923015758   3 IGQLAQLVGVETQTIRFYEQQGLLPPpdRQDNGYRVYTEKHGEGLAFIRR-CRILGLSLAEVHELQS 68
Cdd:cd04767    4 IGVVAELLNIHPETLRIWERHGLIKP--ARRNGQRLYSNNDLKRLRFIKKlINEKGLNIAGVKQILS 68