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 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIINQPSFDQMVALEE 82
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                          90       100
                  ....*....|....*....|...
gi 1678045263  83 HYDKLMHKRNRLDTMLSTIEKTI 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 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIINQPSFDQMVALEE 82
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                          90       100
                  ....*....|....*....|...
gi 1678045263  83 HYDKLMHKRNRLDTMLSTIEKTI 105
Cdd:cd01106    81 QKELLEEKKERLDKLIKTIDRTL 103

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678045263   5 ISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIINQPSFDQMV---ALE 81
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEEvreLLE 80

                          90       100
                  ....*....|....*....|
gi 1678045263  82 EHYDKLMHKRNRLDTMLSTI 101
Cdd:COG0789    81 EHLAELEAQIAELQALRAEL 100

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHdINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTII 69
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPP-RTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

Zn(2+)-responsive transcriptional regulator;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEI 65
Cdd:PRK09514    2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEI 64

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 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIINQPSFDQMVALEE 82
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                          90       100
                  ....*....|....*....|...
gi 1678045263  83 HYDKLMHKRNRLDTMLSTIEKTI 105
Cdd:cd01106    81 QKELLEEKKERLDKLIKTIDRTL 103

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678045263   5 ISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIINQPSFDQMV---ALE 81
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEEvreLLE 80

                          90       100
                  ....*....|....*....|
gi 1678045263  82 EHYDKLMHKRNRLDTMLSTI 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 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPhDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIINqpSFDQMVALEE 82
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLPP-ERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLD--ARDEELSLAA 77

                          90       100
                  ....*....|....*....|...
gi 1678045263  83 HYDKLMHKRNRLDTMLSTIEKTI 105
Cdd:cd00592    78 LLALLDEKLAELEEKIARLEALL 100

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1678045263    3 YTISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIIN 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLE 68

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 1678045263   5 ISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIINQPSFDQMVALEEHY 84
Cdd:cd04788     3 IGELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLELLRRQL 82

                  ...
gi 1678045263  85 DKL 87
Cdd:cd04788    83 ARL 85

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHdINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTII 69
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPP-RTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

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 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIIN-----QPSFDQM 77
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAElrregDSTIPER 80

                          90       100
                  ....*....|....*....|....*....
gi 1678045263  78 VA-LEEHYDKLMHKRNRLDTMLSTIEKTI 105
Cdd:cd01109    81 LElLEEHREELEEQIAELQETLAYLDYKI 109

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 1678045263   5 ISNLANLSGVSTRTLRYYDEIGLLKPHDiNASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTII---------NQPSFD 75
Cdd:cd01282     3 IGELAARTGVSVRSLRYYEEQGLLVPER-SANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLpclrggeptFRPCPD 81

                          90       100
                  ....*....|....*....|....*....
gi 1678045263  76 QMVALEehydklmHKRNRLDTMLSTIEKT 104
Cdd:cd01282    82 LLAVLR-------RELARIDRQIADLTRS 103

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1678045263   4 TISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIY 41
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38

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 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLkPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIINQPS-----FDQM 77
Cdd:cd04775     2 YTIGQMSRKFGVSRSTLLYYESIGLI-PSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPHvqailEERL 80

                          90       100
                  ....*....|....*....|.
gi 1678045263  78 VALEEHYDKLMHKRNRLDTML 98
Cdd:cd04775    81 QSLNREIQRLRQQQQVLAAIL 101

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 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHDINASgyRIYTQNEVDLLQQIIFYRELDVPLKEINTII--------NQPSF 74
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQT--RVYSRRDRARLKLILRGKRLGFSLEEIRELLdlydppggNRKQL 78

                          90       100
                  ....*....|....*....|....*
gi 1678045263  75 DQMVA-LEEHYDKLMHKRNRLDTML 98
Cdd:cd04776    79 EKMLEkIEKRRAELEQQRRDIDAAL 103

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 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPhDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIIN--QPSFD----- 75
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYYTNLGLLTP-ERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEevQRSDKeqrev 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1678045263  76 --QMVALEEHYDKLMHKRNRLDTMLSTIEKTISSK 108
Cdd:cd04779    80 aqEVQLVCDQIDGLEHRLKQLKPIASQTDRAQRMK 114

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1678045263   4 TISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIINQ 71
Cdd:cd04787     2 KVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSH 69

HTH-type transcriptional regulator CueR;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678045263   5 ISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQ---NEVDLLQQIifyRELDVPLKEINTIIN----------- 70
Cdd:PRK10227    3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQqhlNELTLLRQA---RQVGFNLEESGELVNlfndpqrhsad 79

                          90       100
                  ....*....|....*....|....*.
gi 1678045263  71 --QPSFDQMVALEEHYDKLMHKRNRL 94
Cdd:PRK10227   80 vkRRTLEKVAEIERHIEELQSMRDQL 105

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678045263   4 TISNLANLSGVSTRTLRYYDEIGLLKPhdINASG-YRIYTQNEVDLLQQIIFYRELDVPLKEINTIInQPSFDQMVALEE 82
Cdd:cd04769     2 YIGELAQQTGVTIKAIRLYEEKGLLPS--PKRSGnYRVYDAQHVECLRFIKEARQLGFTLAELKAIF-AGHEGRAVLPWP 78

                          90       100
                  ....*....|....*....|...
gi 1678045263  83 HYDKLMH-KRNRLDTMLSTIEKT 104
Cdd:cd04769    79 HLQQALEdKKQEIRAQITELQQL 101

First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDllqQIIFYREL 58
Cdd:cd04772     1 YRTVDLARAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDKHIA---ALRAYRAL 53

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
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRE 57
Cdd:cd01105     2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLD 56

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1678045263   3 YTISNLANLSGVSTRTLRYYDE-IGLLKPHDiNASGYRIYTQNEVDLLQQIIFYRELDVPLKEI 65
Cdd:cd01104     1 YTIGAVARLTGVSPDTLRAWERrYGLPAPQR-TDGGHRLYSEADVARLRLIRRLTSEGVRISQA 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 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 1678045263   5 ISNLANLSGVSTRTLRYYDEIGLLKPHDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTII 69
Cdd:cd04786     3 IGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLL 67

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). 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. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1678045263   3 YTISNLANLSGVSTRTLRYY-DEIGLLKPHDINasGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIIN 70
Cdd:cd04764     1 YTIKEVSEIIGVKPHTLRYYeKEFNLYIPRTEN--GRRYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678045263   4 TISNLANLSGVSTRTLRYYDEIGLLKPhDINASGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIINQPSFDQMvaleeh 83
Cdd:cd04781     2 DIAEVARQSGLPASTLRYYEEKGLIAS-IGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPI------ 74

                          90       100
                  ....*....|....*....|..
gi 1678045263  84 ydklmhKRNRLDTMLSTIEKTI 105
Cdd:cd04781    75 ------DRQLLKAKAAELDQQI 90

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
                  ....*....|....*....|....*....
gi 1678045263   2 EYTISNLANLSGVSTRTLRYYDEIGLLKP 30
Cdd:cd04778     1 EYRIDDLARAAGTTVRNVRAYQDRGLLPP 29

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 1678045263   5 ISNLANLSGVSTRTLRYYDEIGLLKPHDINasGYRIYTQNEVDLLQQIIFYRELDVPLKEINTIInqpSFDQMVALEEHY 84
Cdd:cd04777     3 IGKFAKKNNITIDTVRHYIDLGLLIPEKKG--GQYFFDEKCQDDLEFILELKGLGFSLIEIQKIF---SYKRLTKSRTHE 77

                          90       100
                  ....*....|....*....|....*..
gi 1678045263  85 DK------LMHKRNRLDTMLSTIEKTI 105
Cdd:cd04777    78 DQdyyksfLKNKKDELEKEIEDLKKAI 104

Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1678045263   2 EYTISNLANLSGVSTRTLRYYDEIGLLKPHDiNASGYRIYTQnevDLLQQIIFYR---ELDVPLKEI 65
Cdd:cd01110     1 ELSVGEVAKRSGVAVSALHFYEQKGLIASWR-NAGNQRRYPR---DVLRRIAFIKvaqRLGLSLAEI 63

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 1678045263   3 YTISNLANLSGVSTRTLRYYDEIGLLKPHDINasGYRIYTQNEVDLLQQIIF 54
Cdd:cd04767     2 YPIGVVAELLNIHPETLRIWERHGLIKPARRN--GQRLYSNNDLKRLRFIKK 51