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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLI-YPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRYDGDDTIKER 81
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLpPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 698935304  82 LELLEEQMDRLNIEKRKIEENIIHLNKKISIYK 114
Cdd:cd01109   81 LELLEEHREELEEQIAELQETLAYLDYKIDYYE 113

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLI-YPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRYDGDDTIKER 81
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLpPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 698935304  82 LELLEEQMDRLNIEKRKIEENIIHLNKKISIYK 114
Cdd:cd01109   81 LELLEEHREELEEQIAELQETLAYLDYKIDYYE 113

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 698935304     3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQ-RDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQ 65
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPiRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIK 64

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQ-RDEANKRVYSEKDIEWLKFIIRLKEI 57
Cdd:PRK09514   2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEvRTEGGYRLYTEQDLQRLRFIRRAKQL 57

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLI-YPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRYDGDDTIKER 81
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLpPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 698935304  82 LELLEEQMDRLNIEKRKIEENIIHLNKKISIYK 114
Cdd:cd01109   81 LELLEEHREELEEQIAELQETLAYLDYKIDYYE 113

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 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRYDGDD------ 76
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSlaalla 80

                         90
                 ....*....|....*..
gi 698935304  77 TIKERLELLEEQMDRLN 93
Cdd:cd00592   81 LLDEKLAELEEKIARLE 97

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 698935304   5 IGEFSEKIGLSIDTLRYYEKLGLI-YPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRYDGD-------D 76
Cdd:cd04770    3 IGELAKAAGVSPDTIRYYERIGLLpPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAapcaevrA 82

                         90
                 ....*....|....*..
gi 698935304  77 TIKERLELLEEQMDRLN 93
Cdd:cd04770   83 LLEEKLAEVEAKIAELQ 99

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 698935304    3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQ 65
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIK 63

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 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRYDgDDTIKERL 82
Cdd:cd04775    2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPHV-QAILEERL 80

                         90
                 ....*....|
gi 698935304  83 ELLEEQMDRL 92
Cdd:cd04775   81 QSLNREIQRL 90

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
                 ....*....|....*....|....*....|....*....|....*....
gi 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQRDEANKRVYSEKDIEWLKFI 51
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLRLI 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 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698935304   5 IGEFSEKIGLSIDTLRYYEKLGLIYPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRYDGD--------- 75
Cdd:cd01282    3 IGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLRGGEptfrpcpdl 82

                         90
                 ....*....|....*...
gi 698935304  76 -DTIKERLELLEEQMDRL 92
Cdd:cd01282   83 lAVLRRELARIDRQIADL 100

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 698935304   5 IGEFSEKIGLSIDTLRYYEKLGLIYP-QRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQ-YYSKLRYDGDDTIKERL 82
Cdd:cd04788    3 IGELARRTGLSVRTLHHYDHIGLLSPsQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGrALDGPDFDPLELLRRQL 82

                         90
                 ....*....|
gi 698935304  83 ELLEEQMDRL 92
Cdd:cd04788   83 ARLEEQLELA 92

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 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQ-RDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRYDG-DDTIKE 80
Cdd:cd04790    2 LTISQLARQFGLSRSTLLYYERIGLLSPSaRSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDaTDVLRR 81

                         90
                 ....*....|....*....
gi 698935304  81 RLELLEEQMDRLNIEKRKI 99
Cdd:cd04790   82 RLAELNREIQRLRQQQRAI 100

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQRDEANKRVYSEKDIEWLKFIIRLKE---INMP-IKQIqyyskLRydgddtI 78
Cdd:cd04766    2 YVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQelgVNLAgVKRI-----LE------L 70

                         90
                 ....*....|....
gi 698935304  79 KERLELLEEQMDRL 92
Cdd:cd04766   71 EEELAELRAELDEL 84

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 698935304   5 IGEFSEKIGLSIDTLRYYEKLGLI-YPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQ 65
Cdd:cd04785    3 IGELARRTGVNVETIRYYESIGLLpEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIR 64

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 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRYDgDDTIKERL 82
Cdd:cd04789    2 YTISELAEKAGISRSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQGKLT-RSLLLERL 80

                         90
                 ....*....|
gi 698935304  83 ELLEEQMDRL 92
Cdd:cd04789   81 SSLAEQIARK 90

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 698935304   5 IGEFSEKIGLSIDTLRYYEKLGLI-YPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRyDGDDTIK---- 79
Cdd:cd04783    3 IGELAKAAGVNVETIRYYQRRGLLpEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELD-DGTDCSEarel 81

                         90
                 ....*....|....*
gi 698935304  80 --ERLELLEEQMDRL 92
Cdd:cd04783   82 aeQKLAEVDEKIADL 96

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 698935304    5 IGEFSEKIGLSIDTLRYYEKLGLIY-PQRDEANKRVY 40
Cdd:pfam00376   2 IGEVAKLLGVSPRTLRYYEKIGLLPpPERTEGGYRRY 38

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 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQR-DEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQYYSKLRY-DGDDTIKE 80
Cdd:cd04768    1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKiAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMeELTAMLLE 80

                         90
                 ....*....|..
gi 698935304  81 RLELLEEQMDRL 92
Cdd:cd04768   81 KKQAIQQKIDRL 92

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
                 ....*....|....*....|....*....|....*....|....*....|..
gi 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQRDEANKRVYSEKDIEWLKFIIRL 54
Cdd:cd01279    2 YPISVAAELLGIHPQTLRVYDRLGLVSPARTNGGGRRYSNNDLELLRQVQRL 53

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 698935304   3 YYIGEFSEKIGLSIDTLRYYEKLGLIYPQRDEAnKRVYSEKDIEWLKFIIRL 54
Cdd:cd04767    2 YPIGVVAELLNIHPETLRIWERHGLIKPARRNG-QRLYSNNDLKRLRFIKKL 52

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 698935304   5 IGEFSEKIGLSIDTLRYYEKLGLIYPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQI 64
Cdd:cd01110    4 VGEVAKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEI 63

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 698935304   5 IGEFSEKIGLSIDTLRYYEKLGLIYP-QRDEANKRVYSEKDIEWLKFIIRLKEI-NMPIKQI 64
Cdd:cd04780    3 MSELSKRSGVSVATIKYYLREGLLPEgRRLAPNQAEYSEAHVERLRLIRALQQEgGLPISQI 64

redox-sensitive transcriptional activator SoxR;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 698935304   6 GEFSEKIGLSIDTLRYYEKLGLIYPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQI 64
Cdd:PRK15002  15 GEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATI 73

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.

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gi 698935304   3 YYIGEFSEKIGLSIDTLRYYEK-LGLIYPQRDEANKRVYSEKDIEWLKFIIRLKEINMPIKQIQ 65
Cdd:cd04763    1 YTIGEVALLTGIKPHVLRAWEReFGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVK 64

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 698935304   3 YYIGEFSEKIGLSIDTLRYYEK-LGLIYPQRDEANKRVYSEKDIEWLKFIIRL 54
Cdd:cd04765    1 FSIGEVAEILGLPPHVLRYWETeFPQLKPVKRAGGRRYYRPKDVELLLLIKHL 53