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 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRERASSDV 80
Cdd:cd01108     1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2796344724  81 KALALSHIKELDDKIAELSAMRNLLQSLTIECHGDDRAECPILQGL 126
Cdd:cd01108    81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGL 126

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 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRERASSDV 80
Cdd:cd01108     1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2796344724  81 KALALSHIKELDDKIAELSAMRNLLQSLTIECHGDDRAECPILQGL 126
Cdd:cd01108    81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGL 126

HTH-type transcriptional regulator CueR;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRERASSDV 80
Cdd:PRK10227    1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2796344724  81 KALALSHIKELDDKIAELSAMRNLLQSLTIECHGDDRAECPILQGLEQPC 130
Cdd:PRK10227   81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLSGCC 130

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724    1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLW 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70

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 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRERASSDV 80
Cdd:cd01108     1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2796344724  81 KALALSHIKELDDKIAELSAMRNLLQSLTIECHGDDRAECPILQGL 126
Cdd:cd01108    81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGL 126

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 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRERASSDV 80
Cdd:cd04770     1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2796344724  81 KALALSHIKELDDKIAELSAMRNLLQSLTIECHGDDRAECPIL 123
Cdd:cd04770    81 RALLEEKLAEVEAKIAELQALRAELAGLLSACDGDESVICPIL 123

Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that 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 form 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 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRERASSDV 80
Cdd:cd04784     1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2796344724  81 KALALSHIKELDDKIAELSAMRNLLQSLTIECHGDDRA-ECPILQGL 126
Cdd:cd04784    81 NALIDEHLAHVRARIAELQALEKQLQALRERCDGARTIeECGILQGL 127

HTH-type transcriptional regulator CueR;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRERASSDV 80
Cdd:PRK10227    1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2796344724  81 KALALSHIKELDDKIAELSAMRNLLQSLTIECHGDDRAECPILQGLEQPC 130
Cdd:PRK10227   81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLSGCC 130

Zn(2+)-responsive transcriptional regulator;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   3 IGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRE-RASSDVK 81
Cdd:PRK09514    4 IGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDPEhHTCQEVK 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2796344724  82 ALALSHIKELDDKIAELSAMRNLLQSLTIECHG--DDRAECPILQGLEQpcvGASTKK 137
Cdd:PRK09514   84 GIVDEKLAEVEAKIAELQHMRRSLQRLNDACCGtaHSAVYCSILEALEQ---GASGVK 138

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 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIdQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWqDRERASSDV 80
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLL-PPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDAR-DEELSLAAL 78

                          90       100
                  ....*....|....*....|..
gi 2796344724  81 KALALSHIKELDDKIAELSAMR 102
Cdd:cd00592    79 LALLDEKLAELEEKIARLEALL 100

Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAgYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRERASSDV 80
Cdd:cd04769     1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSGN-YRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWPH 79

                          90
                  ....*....|....*....
gi 2796344724  81 KALALSHIK-ELDDKIAEL 98
Cdd:cd04769    80 LQQALEDKKqEIRAQITEL 98

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 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIdQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRE---RAS 77
Cdd:cd01282     1 MRIGELAARTGVSVRSLRYYEEQGLL-VPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLRGGEptfRPC 79

                          90       100
                  ....*....|....*....|....*....
gi 2796344724  78 SDVKALALSHIKELDDKIAELSAMRNLLQ 106
Cdd:cd01282    80 PDLLAVLRRELARIDRQIADLTRSRDRLD 108

Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. 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. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLslwqdrERASSDV 80
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELL------KDPSEDL 74

                          90       100
                  ....*....|....*....|....*...
gi 2796344724  81 KALALSHIKELDDKIAELSAMRNLLQSL 108
Cdd:cd01106    75 LEALREQKELLEEKKERLDKLIKTIDRT 102

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 2796344724   3 IGEAAKASGISAKMIRHYEGIGLIDQSHRSPA-GYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLslwqdRERASSDVK 81
Cdd:cd01107     3 IGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDtGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEIL-----DADNDDELR 77

                          90       100
                  ....*....|....*....|....*..
gi 2796344724  82 ALALSHIKELDDKIAELSAMRNLLQSL 108
Cdd:cd01107    78 KLLREKLAELEAEIEELQRILRLLEDR 104

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIdQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLL-SLWQDRERASSD 79
Cdd:cd01110     2 LSVGEVAKRSGVAVSALHFYEQKGLI-ASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALaTLPEDRTPTKAD 80

                          90       100
                  ....*....|....*....|....*...
gi 2796344724  80 VKALALSHIKELDDKIAELSAMRNLLQS 107
Cdd:cd01110    81 WERLSRAWRDRLDERIAELQQLRDQLDG 108

mercuric resistance operon transcriptional regulator MerR;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDR--ERASS 78
Cdd:PRK13752    8 LTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLEDGThcEEASS 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2796344724  79 dvkaLALSHIKELDDKIAELSAMRNLLQSLTIECHG-DDRAECPI---LQGLEQPCVGAST 135
Cdd:PRK13752   88 ----LAEHKLKDVREKMADLARMEAVLSELVCACHArKGNVSCPLiasLQGGAELAGSAMP 144

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 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDQSHRsPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQ--DRERASS 78
Cdd:cd04781     1 LDIAEVARQSGLPASTLRYYEEKGLIASIGR-RGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGkpPIDRQLL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2796344724  79 DVKALalshikELDDKIAELSAMRNLLQSlTIECHGDDRAECPILQGL 126
Cdd:cd04781    80 KAKAA------ELDQQIQRLQAMRELLRH-VAQCPAPSHLDCPTFQRL 120

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 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIdqshrSPA---GYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRERAS 77
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLL-----SPErrgQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNR 75

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2796344724  78 SDVKALalshIKELDDKIAELSAMRNLLQSLTIE 111
Cdd:cd04776    76 KQLEKM----LEKIEKRRAELEQQRRDIDAALAE 105

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2796344724   2 NIGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIY 39
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38

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 2796344724   3 IGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLslwqdrERASSDVKA 82
Cdd:cd04790     4 ISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLL------QQPGDDATD 77

                          90
                  ....*....|....*...
gi 2796344724  83 LALSHIKELDDKIAELSA 100
Cdd:cd04790    78 VLRRRLAELNREIQRLRQ 95

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIDqSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLSLWQDRerassdv 80
Cdd:cd04789     2 YTISELAEKAGISRSTLLYYEKLGLIT-GTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQGKLTR------- 73

                          90       100
                  ....*....|....*....|....*...
gi 2796344724  81 kALALSHIKELDDKIAELSAMRNLLQSL 108
Cdd:cd04789    74 -SLLLERLSSLAEQIARKQQARDLLAAL 100

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 2796344724   2 NIGEAAKASGISAKMIRHYEGIGLIdQSHRS-PAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLslwqDRERASSDV 80
Cdd:cd01105     3 GIGEVSKLTGVSPRQLRYWEEKGLI-KSIRSdGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKL----RRRRVQAEV 77

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   2 NIGEAAKASGISAKMIRHYE---GIGlidQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQLLS 68
Cdd:cd01104     2 TIGAVARLTGVSPDTLRAWErryGLP---APQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68

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
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2796344724   5 EAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYskNDLHTLSFvKSARSL 56
Cdd:cd04772     5 DLARAIGLSPQTVRNYESLGLIPPAERTANGYRIY--TDKHIAAL-RAYRAL 53

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   3 IGEAAKASGISAKMIRHYEGIGLIDQShRSPAGYRIYSKNDLHTLSFVKS-ARSLGFSLDQIKQLLSLWQDRERASSDVK 81
Cdd:cd04766     4 ISVAAELSGMHPQTLRLYERLGLLSPS-RTDGGTRRYSERDIERLRRIQRlTQELGVNLAGVKRILELEEELAELRAELD 82

                  ..
gi 2796344724  82 AL 83
Cdd:cd04766    83 EL 84

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIdQSHRSPAGYRiYSKNDLHTLSFVKSARSLGFSLDQIKQLLSL--------WQD 72
Cdd:cd04777     1 MKIGKFAKKNNITIDTVRHYIDLGLL-IPEKKGGQYF-FDEKCQDDLEFILELKGLGFSLIEIQKIFSYkrltksrtHED 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2796344724  73 RERassdVKALALSHIKELDDKIAELSAMRNLL 105
Cdd:cd04777    79 QDY----YKSFLKNKKDELEKEIEDLKKAIQKL 107

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
                  ....*....|....*....|....*....|....*....|....*..
gi 2796344724   1 MNIGEAAKASGISAKMIRHYEGIGLIdQSHRSPAGYRIYSKNDLHTL 47
Cdd:cd04762     1 LTTKEAAELLGVSPSTLRRWVKEGKL-KAIRTPGGHRRFPEEDLERL 46

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796344724   2 NIGEAAKASGISAKMIRHYEGIGLIDQSHRSpaGYRIYSKNDLHTLSFVKS-ARSLGFSLDQIKQLLSLW 70
Cdd:cd04767     3 PIGVVAELLNIHPETLRIWERHGLIKPARRN--GQRLYSNNDLKRLRFIKKlINEKGLNIAGVKQILSMY 70

N-terminal extended coiled-coil domain of Saccharomyces cerevisiae mitochondrial division protein 1 (Mdv1) and similar proteins; Mdv1, also known as mitochondrial fission 2 protein (FIS2), GAG3, or NET2, is involved in the mitochondrial fission machinery of the yeast Saccharomyces cerevisiae. Together with Fis1 and Dnm1, Mdv1 is an essential component of the machinery that mediates mitochondrial fission, a process crucial for mitochondrial maintenance and function. Mdv1 is an adapter protein that binds Fis1 and Dnm1 to form mitochondrial fission complexes, which facilitate the constriction and fission of the mitochondrial compartment during the late stages of mitochondrial division. Mdv1 works together with Caf4 to recruit Dnm1 to Fis1 on the mitochondrial outer membrane. Mdv1 protein has three domains: N-terminal extension, central coiled coil (CC), and C-terminal WD40 repeat region. The N-terminal extension binds to Fis1, while the CC domain facilitates dimerization of Mdv1 and is responsible for the recruitment of Dnm1 to the mitochondrial membrane. Both are included in this model. The C-terminal WD40 repeat region binds to Dnm1.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2796344724  68 SLWQDRERASSDV------KALALSHIKELDDKIAELSAMRNLL 105
Cdd:cd22881    35 TLPEEKEDINHKLdlleirKNLAASEIREIDNKIANLNSMRKIV 78

HTH-type transcriptional regulator MerD;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2796344724   3 IGEAAKASGISAKMIRHYEGIGLIDQSHRSPAGYRIYSKNDLHTLSFVKSARSLGFSLDQIKQL 66
Cdd:PRK13749    6 VSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARL 69