TipAS antibiotic-recognition domain; This domain is found at the C-terminus of some MerR family transcription factors. The domain has an alpha-helical globin-like fold. The family includes Mta a central regulator of multidrug resistance in Bacillus subtilis.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279613  146 QDEQRAQA-WRELTEEVQTLMASGCPTDSPQAMRLATRWMERLEQDT-AGRPEFLTRLNEMHAAEPQMVEQTG-VTPAII 222
Cdd:pfam07739  28 EDWEEIQAeLEELFARLAAAMAAGVDPDSEEAQELAEEHRAWISRFWyDCSKEAHAGLGQMYVADERFTANYDkKGPGLA 107

                  ....*...
gi 490279613  223 AYITEAFA 230
Cdd:pfam07739 108 EFLRDAIE 115

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279613   5 VGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYL---DRQTLSLPELLT 81
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLdllDDGEEEVRELLE 80

                         90
                 ....*....|..
gi 490279613  82 QQIDMLNAQLRD 93
Cdd:COG0789   81 EHLAELEAQIAE 92

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490279613   4 QVGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLD 70
Cdd:PRK09514   3 RIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLS 69

Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue. [Regulatory functions, DNA interactions]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490279613    5 VGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYL 69
Cdd:TIGR02044   3 IGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELL 67

TipAS antibiotic-recognition domain; This domain is found at the C-terminus of some MerR family transcription factors. The domain has an alpha-helical globin-like fold. The family includes Mta a central regulator of multidrug resistance in Bacillus subtilis.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490279613  226 TEAFAESKlAIWARYLDEEEMAFTrqhyfdrlQEWPALVAKLHQACREGVAPDSASGQALARAWLELFQSYAGT 299
Cdd:pfam07739  12 TAAYKESN-ERTAGMSKEDWEEIQ--------AELEELFARLAAAMAAGVDPDSEEAQELAEEHRAWISRFWYD 76

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 490279613   4 QVGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLDRQTLSLPELLTQQ 83
Cdd:cd01106    2 TVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALREQ 81

                         90
                 ....*....|.
gi 490279613  84 IDMLNAQLRDV 94
Cdd:cd01106   82 KELLEEKKERL 92

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 490279613   4 QVGELAKRAGLTVRTLHHYEQTGLLTPsARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLD-----RQTLSLPE 78
Cdd:cd00592    2 TIGEVAKLLGVSVRTLRYYEEKGLLPP-ERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDardeeLSLAALLA 80

                         90
                 ....*....|....
gi 490279613  79 LLTQQIDMLNAQLR 92
Cdd:cd00592   81 LLDEKLAELEEKIA 94

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 490279613   4 QVGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYL---DRQTLSLPE-- 78
Cdd:cd04770    2 KIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLslrDDGAAPCAEvr 81

                         90
                 ....*....|....*.
gi 490279613  79 -LLTQQIDMLNAQLRD 93
Cdd:cd04770   82 aLLEEKLAEVEAKIAE 97

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 490279613   3 IQVGELAKRAGLTVRTLHHYEQTGLLTPSARSEA-GYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLDRQTLS-LPELL 80
Cdd:cd01107    1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDtGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDeLRKLL 80

                         90
                 ....*....|...
gi 490279613  81 TQQIDMLNAQLRD 93
Cdd:cd01107   81 REKLAELEAEIEE 93

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490279613   4 QVGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLD 70
Cdd:PRK09514   3 RIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLS 69

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 490279613   3 IQVGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLDRQTlslPELLtq 82
Cdd:cd04782    1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRN---PDEL-- 75

                         90
                 ....*....|..
gi 490279613  83 qIDMLNAQLRDV 94
Cdd:cd04782   76 -IELLKKQEKEI 86

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 490279613   5 VGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYL------DRQTLSLPE 78
Cdd:cd01108    3 IGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLalwrdpSRASADVKA 82

                         90
                 ....*....|....*
gi 490279613  79 LLTQQIDMLNAQLRD 93
Cdd:cd01108   83 LALEHIAELERKIAE 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 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 490279613   4 QVGELAKRAGLTVRTLHHYEQTGLLTPsARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLDRQTLSLPE----- 78
Cdd:cd04779    2 RIGQLAHLAGVSKRTIDYYTNLGLLTP-ERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQRSDKEqreva 80

                         90
                 ....*....|....*....
gi 490279613  79 ----LLTQQIDMLNAQLRD 93
Cdd:cd04779   81 qevqLVCDQIDGLEHRLKQ 99

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490279613   3 IQVGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLD 70
Cdd:cd04785    1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLA 68

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 490279613   5 VGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLDRQTLSLPELLTQQI 84
Cdd:cd04790    4 ISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDATDVLRRRL 83

                 ....
gi 490279613  85 DMLN 88
Cdd:cd04790   84 AELN 87

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490279613   5 VGELAKRAGLTVRTLHHYEQTGLLTPSARSEAgYRLYNLSAVQRLHMIKALAQAGLTLATIKD----YLDRQTLSLPEL 79
Cdd:cd04769    3 IGELAQQTGVTIKAIRLYEEKGLLPSPKRSGN-YRVYDAQHVECLRFIKEARQLGFTLAELKAifagHEGRAVLPWPHL 80

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490279613   2 LIQVGELAKRAGLTVRTLHHYEQTGLLtPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLDrqtlSLPE 78
Cdd:cd01110    1 ELSVGEVAKRSGVAVSALHFYEQKGLI-ASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA----TLPE 72

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 490279613   4 QVGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYL---DRQTLSLP--- 77
Cdd:cd04787    2 KVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILshaDQGESPCPmvr 81

                         90
                 ....*....|....*.
gi 490279613  78 ELLTQQIDMLNAQLRD 93
Cdd:cd04787   82 RLIEQRLAETERRIKE 97

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 490279613   5 VGELAKRAGLTVRTLHHYEQTGLLtPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLdrQTLSLPELLTQQI 84
Cdd:cd04775    4 IGQMSRKFGVSRSTLLYYESIGLI-PSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCL--AQPHVQAILEERL 80

                 ....*..
gi 490279613  85 DMLNAQL 91
Cdd:cd04775   81 QSLNREI 87

redox-sensitive transcriptional activator SoxR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279613   1 MLIQVGELAKRAGLTVRTLHHYEQTGLLTpSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLDrqtlSLPE-- 78
Cdd:PRK15002  10 ALLTPGEVAKRSGVAVSALHFYESKGLIT-SIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFG----VLPEgh 84

                         90
                 ....*....|....*.
gi 490279613  79 -LLTQQIDMLNAQLRD 93
Cdd:PRK15002  85 tLSAKEWKQLSSQWRE 100

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490279613   5 VGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIK 66
Cdd:cd01111    3 ISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELA 64

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 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 490279613   4 QVGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQ-AGLTLATIKDYLD 70
Cdd:cd04780    2 RMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQeGGLPISQIKEVLD 69

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 490279613   3 IQVGELAKRAGLTVRTLHHYEQTGLLTPSARsEAGYRLYNLSAVQRLHMIKALAQAGLTLATI--------KDYLDRQtl 74
Cdd:cd04781    1 LDIAEVARQSGLPASTLRYYEEKGLIASIGR-RGLRRQYDPQVLDRLALIALGRAAGFSLDEIqamlshdgKPPIDRQ-- 77

                         90
                 ....*....|....*....
gi 490279613  75 slpeLLTQQIDMLNAQLRD 93
Cdd:cd04781   78 ----LLKAKAAELDQQIQR 92

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490279613   5 VGELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIK 66
Cdd:cd01104    3 IGAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAA 64

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490279613   7 ELAKRAGLTVRTLHHYEQTGLLTPSARsEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYLD--RQTLSLPELL 80
Cdd:cd04778    6 DLARAAGTTVRNVRAYQDRGLLPPPRR-RGRVAIYNDSHLARLRLINQLLERGYTLAHIAELLAawEQGRDLGDVL 80

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
                 ....*....|....*....|....*....|....*.
gi 490279613   7 ELAKRAGLTVRTLHHYEQTGLLTPSARSEAGYRLYN 42
Cdd:cd04772    5 DLARAIGLSPQTVRNYESLGLIPPAERTANGYRIYT 40

Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator HspR and related proteins, 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 two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490279613   9 AKRAGLTVRTLHHYEQTGLLTPsARSEAGYRLYNLSAVQRLHMIKALAQA-GLTLATIKDYLD 70
Cdd:cd01279    8 AELLGIHPQTLRVYDRLGLVSP-ARTNGGGRRYSNNDLELLRQVQRLSQDeGFNLAGIKRIIE 69

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 490279613   5 VGELAKRAGLTVRTLHHYEQT-GLLTPsARSEAGYRLYNLSAVQRLHMIKALAQAGLTLATIKDYL 69
Cdd:cd04763    3 IGEVALLTGIKPHVLRAWEREfGLLKP-QRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67

TipAS antibiotic-recognition domain; This domain is found at the C-terminus of some MerR family transcription factors. The domain has an alpha-helical globin-like fold. The family includes Mta a central regulator of multidrug resistance in Bacillus subtilis.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490279613  226 TEAFAESKlAIWARYLDEEEMAFTrqhyfdrlQEWPALVAKLHQACREGVAPDSASGQALARAWLELFQSYAGT 299
Cdd:pfam07739  12 TAAYKESN-ERTAGMSKEDWEEIQ--------AELEELFARLAAAMAAGVDPDSEEAQELAEEHRAWISRFWYD 76