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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDNPHRKSCEV 80
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2006089166  81 KALANTHIEFLSNKIKELEEMKTVLGAWSDACRGDDMPECPILQGL 126
Cdd:TIGR02044  81 KARTLEKVAEIERKISELQSMRDQLEALAQACPGDDSPDCPIIENL 126

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006089166   3 IGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDNPHRkscEVKA 82
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEE---EVRE 77

                          90       100
                  ....*....|....*....|...
gi 2006089166  83 LANTHIEFLSNKIKELEEMKTVL 105
Cdd:COG0789    78 LLEEHLAELEAQIAELQALRAEL 100

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLsNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELL 67
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLL-PPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDNPHRKSCEV 80
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2006089166  81 KALANTHIEFLSNKIKELEEMKTVLGAWSDACRGDDMPECPILQGL 126
Cdd:TIGR02044  81 KARTLEKVAEIERKISELQSMRDQLEALAQACPGDDSPDCPIIENL 126

Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDNPHRkSC-E 79
Cdd:cd04785     1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDRPDR-SCaE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2006089166  80 VKALANTHIEFLSNKIKELEEMKTVLGAWSDACRGDDMPECPILQGL 126
Cdd:cd04785    80 ADAIARAHLADVRARIADLRRLEAELKRMVAACSGGRVADCRIIEAL 126

Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDNPHRKscEV 80
Cdd:cd04783     1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCS--EA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2006089166  81 KALANTHIEFLSNKIKELEEMKTVLGAWSDAC-RGDDMPECPILQGL 126
Cdd:cd04783    79 RELAEQKLAEVDEKIADLQRMRASLQELVSQCaATKNNVSCPIIAAL 125

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006089166   3 IGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDNPHRkscEVKA 82
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEE---EVRE 77

                          90       100
                  ....*....|....*....|...
gi 2006089166  83 LANTHIEFLSNKIKELEEMKTVL 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 2006089166   3 IGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDNPHRKSC-EVK 81
Cdd:TIGR02043   4 IGELAKLCGVTSDTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSIKLDATEHSCaEVK 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2006089166  82 ALANTHIEFLSNKIKELEEMKTVLGAWSDACRG--DDMPECPILQGL 126
Cdd:TIGR02043  84 AIVDAKLELVDEKINELTKIRRSLKKLSDACCGhtNDASHCSILEAL 130

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006089166    1 MNIGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQ 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70

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 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLAlQDNPHRKscev 80
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLK-DPSEDLL---- 75

                          90       100
                  ....*....|....*....|....*
gi 2006089166  81 KALANtHIEFLSNKIKELEEMKTVL 105
Cdd:cd01106    76 EALRE-QKELLEEKKERLDKLIKTI 99

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 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTSRTSSgYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQD 71
Cdd:cd04769     1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSGN-YRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHE 70

Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively 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 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 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDnphrksCEV 80
Cdd:cd04788     1 WKIGELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPD------FDP 74

                          90       100
                  ....*....|....*....|..
gi 2006089166  81 KALANTHIEFLSNKIKELEEMK 102
Cdd:cd04788    75 LELLRRQLARLEEQLELATRLR 96

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLsNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELL 67
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLL-PPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSnTSRTSSGYRIYDNETLIRLKFI 50
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLLS-PARTEGGYRLYSDADLERLRLI 49

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELL 67
Cdd:cd04786     1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLL 67

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 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTsRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLA-LQDN--PHRKs 77
Cdd:cd01110     2 LSVGEVAKRSGVAVSALHFYEQKGLIASW-RNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALAtLPEDrtPTKA- 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2006089166  78 cEVKALANTHIEFLSNKIKELEEMKTVLgawsDACRGD---DMPECPIL 123
Cdd:cd01110    80 -DWERLSRAWRDRLDERIAELQQLRDQL----DGCIGCgclSLKKCPLY 123

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 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTSRTSSgyRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDNPHRKSCEV 80
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQT--RVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQL 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2006089166  81 KAL---ANTHIEFLSNKIKELEEMKTVLGAWSDACR 113
Cdd:cd04776    79 EKMlekIEKRRAELEQQRRDIDAALAELDAAEERCR 114

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 2006089166   3 IGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALqdnphrKSCEVKA 82
Cdd:cd04768     3 IGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDT------EMEELTA 76

                          90       100
                  ....*....|....*....|
gi 2006089166  83 LANTHIEFLSNKIKELEEMK 102
Cdd:cd04768    77 MLLEKKQAIQQKIDRLQQLE 96

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTsRTSSGYRIYDNETLIRLKFIAKARGV-GFSLAQIGELLALQDNP----HR 75
Cdd:cd04774     1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPE-RSEGRYRLYSEEDLKRLERILRLREVlGFSLQEVTHFLERPLEPvdggHR 79

                  ....*
gi 2006089166  76 KSCEV 80
Cdd:cd04774    80 YSAES 84

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 2006089166   8 KATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFI-AKARGVGFSLAQIGeLLALQDNPHRKScevKALANT 86
Cdd:cd04772     8 RAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDKHIAALRAYrALLPGYGYRVAQRI-MRAVHAGIVASA---LALVDA 83

                          90
                  ....*....|...
gi 2006089166  87 HIEFLSNKIKELE 99
Cdd:cd04772    84 AHALLQRYRQQLD 96

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 2006089166   3 IGQASKATGLSIKQIRDYEKLGLLSNTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDNPHRksceVKA 82
Cdd:cd04782     3 TGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRNPDEL----IEL 78

                          90       100
                  ....*....|....*....|
gi 2006089166  83 LANTHIEfLSNKIKELEEMK 102
Cdd:cd04782    79 LKKQEKE-IKEEIEELQKIK 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 2006089166   3 IGQASKATGLSIKQIRDYEKLGLLSNTsRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLAlqdNPHrksceVKA 82
Cdd:cd04775     4 IGQMSRKFGVSRSTLLYYESIGLIPSA-RSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLA---QPH-----VQA 74

                          90       100
                  ....*....|....*....|....*
gi 2006089166  83 LANTHIEFLSNKIKELEEMKTVLGA 107
Cdd:cd04775    75 ILEERLQSLNREIQRLRQQQQVLAA 99

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 2006089166   3 IGQASKATGLSIKQIRDYEKLGLLSnTSRTSSGYRIYDNETLIRLKFIAK-ARGVGFSLAQIGELLALQ 70
Cdd:cd04766     4 ISVAAELSGMHPQTLRLYERLGLLS-PSRTDGGTRRYSERDIERLRRIQRlTQELGVNLAGVKRILELE 71

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 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSNTsRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQDNPhrkscev 80
Cdd:cd04789     2 YTISELAEKAGISRSTLLYYEKLGLITGT-RNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQGKLTR------- 73

                          90       100
                  ....*....|....*....|....*....
gi 2006089166  81 kALANTHIEFLSNKIKELEEMKTVLGAWS 109
Cdd:cd04789    74 -SLLLERLSSLAEQIARKQQARDLLAALL 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 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 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLsnTSRTSSGYRIYDNETLIRLKFIAKARGVGFSLAQIGELLALQD----NPHRK 76
Cdd:cd04777     1 MKIGKFAKKNNITIDTVRHYIDLGLL--IPEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYKRltksRTHED 78

                          90       100
                  ....*....|....*....|....*....
gi 2006089166  77 SCEVKALANTHIEFLSNKIKELEEMKTVL 105
Cdd:cd04777    79 QDYYKSFLKNKKDELEKEIEDLKKAIQKL 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        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2006089166   1 MNIGQASKATGLSIKQIRDYEKLGLLSnTSRTSSGYRIYDNETLIRLKFI 50
Cdd:cd04762     1 LTTKEAAELLGVSPSTLRRWVKEGKLK-AIRTPGGHRRFPEEDLERLLGI 49

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2006089166   7 SKATGLSIKQIRDYEKLGLLSNTSRTS-SGyrIYDNETLIRLKFIAKARGVGFSLAQIGELLA 68
Cdd:cd04778     8 ARAAGTTVRNVRAYQDRGLLPPPRRRGrVA--IYNDSHLARLRLINQLLERGYTLAHIAELLA 68