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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIMDNPSFDLTSALES 82
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                          90       100
                  ....*....|....*....|...
gi 1084523956  83 HKEALKERIVRMERLIRTVDNTL 105
Cdd:cd01106    81 QKELLEEKKERLDKLIKTIDRTL 103

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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIMDNPSFDLTSALES 82
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                          90       100
                  ....*....|....*....|...
gi 1084523956  83 HKEALKERIVRMERLIRTVDNTL 105
Cdd:cd01106    81 QKELLEEKKERLDKLIKTIDRTL 103

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 1084523956 131 YALEAEKMY-DPEIVRASNRIWKSYSAEKKTQILEEGNKVYTDILAKMHLG--AESDEVQACVERWRRHMDYFWT-PSLK 206
Cdd:pfam07739   1 YEKEARERWgDTAAYKESNERTAGMSKEDWEEIQAELEELFARLAAAMAAGvdPDSEEAQELAEEHRAWISRFWYdCSKE 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1084523956 207 QLVGLAEGYNNHPGFKANFDKIDPRLAGFMLQAVNVY 243
Cdd:pfam07739  81 AHAGLGQMYVADERFTANYDKKGPGLAEFLRDAIEAY 117

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPtSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIM 69
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPP-PRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIMDNPSFDLTSALES 82
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                          90       100
                  ....*....|....*....|...
gi 1084523956  83 HKEALKERIVRMERLIRTVDNTL 105
Cdd:cd01106    81 QKELLEEKKERLDKLIKTIDRTL 103

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084523956   5 VKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIM---DNPSFDLTSALE 81
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLdllDDGEEEVRELLE 80

                          90       100
                  ....*....|....*....|
gi 1084523956  82 SHKEALKERIVRMERLIRTV 101
Cdd:COG0789    81 EHLAELEAQIAELQALRAEL 100

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPtSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIMDNPSFD-----LT 77
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLPP-ERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEElslaaLL 79

                          90       100
                  ....*....|....*....|.
gi 1084523956  78 SALESHKEALKERIVRMERLI 98
Cdd:cd00592    80 ALLDEKLAELEEKIARLEALL 100

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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIMDNPSFDLTSALES 82
Cdd:cd04790     2 LTISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDATDVLRR 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1084523956  83 HKEALKERIVRMERLIRTVDNTLSH--LKGQKDMTDKQLFSA------FTDDEQEKYALEAEKM 138
Cdd:cd04790    82 RLAELNREIQRLRQQQRAIATLLKQptLLKEQRLVTKEKWVAilkaagMDEADMRRWHIEFEKM 145

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1084523956    3 YTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIMD 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLE 68

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 1084523956   5 VKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIM---DNPSFDLTSA-- 79
Cdd:cd04784     3 IGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLqlqDDPEASCAEVna 82

                          90       100
                  ....*....|....*....|..
gi 1084523956  80 -LESHKEALKERIVRMERLIRT 100
Cdd:cd04784    83 lIDEHLAHVRARIAELQALEKQ 104

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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIM---DNPSF---DL 76
Cdd:cd04770     1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLslrDDGAApcaEV 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1084523956  77 TSALESHKEALKERIVRMERLIRTVDNTLSH 107
Cdd:cd04770    81 RALLEEKLAEVEAKIAELQALRAELAGLLSA 111

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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPTsLGSNGYRYYGEEALIKLQQI 52
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLLSPA-RTEGGYRLYSDADLERLRLI 49

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 1084523956   4 TVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIMdNPSFDLTSALESH 83
Cdd:cd04787     2 KVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEIL-SHADQGESPCPMV 80

                          90
                  ....*....|....*.
gi 1084523956  84 KEALKERIVRMERLIR 99
Cdd:cd04787    81 RRLIEQRLAETERRIK 96

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 1084523956   7 QLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIM---DNPSFDLTSAL--- 80
Cdd:cd04785     5 ELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLalsDRPDRSCAEADaia 84

                          90
                  ....*....|....*..
gi 1084523956  81 ESHKEALKERIVRMERL 97
Cdd:cd04785    85 RAHLADVRARIADLRRL 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 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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNgYRYYGEEALIKLQQILFYRELELSLDGIRRIMDN--PSFDLTSAL 80
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSN-YRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEvqRSDKEQREV 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1084523956  81 ESHKEALKERIVRME-RLIRTVDNTLSHLKGQKDMTDKQL 119
Cdd:cd04779    80 AQEVQLVCDQIDGLEhRLKQLKPIASQTDRAQRMKMTKEL 119

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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILkPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIMDNPSfdLTSALES 82
Cdd:cd04775     2 YTIGQMSRKFGVSRSTLLYYESIGLI-PSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPH--VQAILEE 78

                          90
                  ....*....|...
gi 1084523956  83 HKEALKERIVRME 95
Cdd:cd04775    79 RLQSLNREIQRLR 91

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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIR---RIMDNPSFDLTSA 79
Cdd:cd04783     1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAellELDDGTDCSEARE 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1084523956  80 LESHK-EALKERIVRMERlIRTVdntLSHLKGQ 111
Cdd:cd04783    81 LAEQKlAEVDEKIADLQR-MRAS---LQELVSQ 109

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 1084523956   4 TVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNgYRYYGEEALIKLQQILFYRELELSLDGIRRIMD------NPSFDLT 77
Cdd:cd01110     3 SVGEVAKRSGVAVSALHFYEQKGLIASWRNAGN-QRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALAtlpedrTPTKADW 81

                          90       100
                  ....*....|....*....|.
gi 1084523956  78 SALESH-KEALKERIVRMERL 97
Cdd:cd01110    82 ERLSRAwRDRLDERIAELQQL 102

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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEaliKLQQILFYRELeLSLDGIR---RIM-DNPSFDLTS 78
Cdd:cd04772     1 YRTVDLARAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDK---HIAALRAYRAL-LPGYGYRvaqRIMrAVHAGIVAS 76

                          90
                  ....*....|....*.
gi 1084523956  79 AL----ESHKEALKER 90
Cdd:cd04772    77 ALalvdAAHALLQRYR 92

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1084523956   2 GYTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRIMD 70
Cdd:cd01105     1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLR 69

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 1084523956   3 YTVKQLSRLAGVSVRTLHYYDEISILKPTSLGSNGYRYYGEEALIKLQQILFYRELELSLDGIRR 67
Cdd:cd01111     1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELAR 65

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084523956   4 TVKQLSRLAGVSVRTLHYYDEISILKPTSlGSNGYRYYGEEALIKLQQILFYRELELSLDGIRRImdnpsFDLTSALESH 83
Cdd:cd04781     2 DIAEVARQSGLPASTLRYYEEKGLIASIG-RRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAM-----LSHDGKPPID 75

                          90
                  ....*....|....*.
gi 1084523956  84 KEALKERIVRMERLIR 99
Cdd:cd04781    76 RQLLKAKAAELDQQIQ 91

MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084523956  49 LQQILFYRELELSLDGIRRIMD------NPSFDLTSALESHKEALKERIVRMERLIRTVD 102
Cdd:pfam09278   4 LAFIRRARRLGFSLEEIRELLAlyddpgPPCADVRALLREKLAELEARIAELQALRDELD 63