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 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQK-SENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGHEGQELLPHLNK 80
Cdd:cd01106    1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRrTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                         90       100
                 ....*....|....*....|...
gi 489117279  81 QLQFLQQEREHLDTLISTLQKTI 103
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 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQK-SENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGHEGQELLPHLNK 80
Cdd:cd01106    1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRrTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                         90       100
                 ....*....|....*....|...
gi 489117279  81 QLQFLQQEREHLDTLISTLQKTI 103
Cdd:cd01106   81 QKELLEEKKERLDKLIKTIDRTL 103

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279     2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQK-SENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGHE 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIrTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489117279    2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELL 67
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

Hg(II)-responsive transcriptional regulator; This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Cellular processes, Detoxification, Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279    4 IKEAAQLSGVSVKTLHHYDKIGLLV-PQKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGHEG----QELLPHL 78
Cdd:TIGR02051   2 IGELAKAAGVNVETIRYYERKGLLPePDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLVDgthcREMYELA 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 489117279   79 NKQLQFLQQEREHLDTLISTLQKTIQAQKGERKMTT 114
Cdd:TIGR02051  82 SRKLKSVQAKMADLLRIERLLEELLEQCPANKGNTS 117

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 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQK-SENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGHEGQELLPHLNK 80
Cdd:cd01106    1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRrTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALRE 80

                         90       100
                 ....*....|....*....|...
gi 489117279  81 QLQFLQQEREHLDTLISTLQKTI 103
Cdd:cd01106   81 QKELLEEKKERLDKLIKTIDRTL 103

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279   4 IKEAAQLSGVSVKTLHHYDKIGLLVP-QKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELL---GHEGQELLPHLN 79
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPpERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLdllDDGEEEVRELLE 80

                         90       100
                 ....*....|....*....|
gi 489117279  80 KQLQFLQQEREHLDTLISTL 99
Cdd:COG0789   81 EHLAELEAQIAELQALRAEL 100

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 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQK-SENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGHEGQELLPHLNK 80
Cdd:cd04768    1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKiAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAMLLE 80

                         90
                 ....*....|....*.
gi 489117279  81 QLQFLQQEREHLDTLI 96
Cdd:cd04768   81 KKQAIQQKIDRLQQLE 96

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 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLL-VPQKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLG-HEGQEL----- 74
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLpPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSlRDDGAApcaev 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 489117279  75 -------LPHLNKQLQFLQQEREHLDTLIS 97
Cdd:cd04770   81 ralleekLAEVEAKIAELQALRAELAGLLS 110

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 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVP-QKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAEL--LGHEGQELLPhl 78
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPvKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYaeLRREGDSTIP-- 78

                         90       100
                 ....*....|....*....|....*..
gi 489117279  79 nKQLQFLQQEREHLDTLISTLQKTIQA 105
Cdd:cd01109   79 -ERLELLEEHREELEEQIAELQETLAY 104

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489117279   1 MYQIKEAAQLSGVSVKTLHHYDKIGLLVPQ-KSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELL 67
Cdd:PRK09514   1 MYRIGELAKLAEVTPDTLRFYEKQGLMDPEvRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELL 68

Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279   4 IKEAAQLSGVSVKTLHHYDKIGLLVP-QKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGhegqelL---PH-- 77
Cdd:cd01108    3 IGEAAKLTGLSAKMIRYYEEIGLIPPpSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLA------LwrdPSra 76

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489117279  78 -------LNKQLQFLQQEREHLDTLISTLQKTIQAQKG 108
Cdd:cd01108   77 sadvkalALEHIAELERKIAELQAMRRTLQQLADSCHG 114

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 489117279   1 MYQIKEAAQLSGVSVKTLHHYDKIGLLVPQ-KSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLG--HEGQEL--- 74
Cdd:cd04790    1 MLTISQLARQFGLSRSTLLYYERIGLLSPSaRSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQqpGDDATDvlr 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 489117279  75 --LPHLNKQLQFLQQEREHLDTLIStlQKTIqaqKGERKMTTQEKFV 119
Cdd:cd04790   81 rrLAELNREIQRLRQQQRAIATLLK--QPTL---LKEQRLVTKEKWV 122

Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQ-KSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGHEG-QELLPHLN 79
Cdd:cd04782    1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEiVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRNpDELIELLK 80

                         90
                 ....*....|....*.
gi 489117279  80 KQLQFLQQEREHLDTL 95
Cdd:cd04782   81 KQEKEIKEEIEELQKI 96

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLL-VPQKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELL 67
Cdd:cd04784    1 MKIGELAKKTGCSVETIRYYEKEGLLpAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLL 67

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 489117279   4 IKEAAQLSGVSVKTLHHYDKIGLL-VPQKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLG-------HEGQEL- 74
Cdd:cd04783    3 IGELAKAAGVNVETIRYYQRRGLLpEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLElddgtdcSEARELa 82

                         90       100
                 ....*....|....*....|....*..
gi 489117279  75 ---LPHLNKQLQFLQQEREHLDTLIST 98
Cdd:cd04783   83 eqkLAEVDEKIADLQRMRASLQELVSQ 109

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 489117279   1 MYQIKEAAQLSGVSVKTLHHYDKIGLLVPQKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGHEG-----QELL 75
Cdd:cd04775    1 MYTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPHvqailEERL 80

                         90       100
                 ....*....|....*....|.
gi 489117279  76 PHLNKQLQFLQQEREHLDTLI 96
Cdd:cd04775   81 QSLNREIQRLRQQQQVLAAIL 101

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 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQKSENGYRLYSEADLERLQIILFY-KYLGFSL---KKIAElLGHEGQELLPH 77
Cdd:cd04766    2 YVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLtQELGVNLagvKRILE-LEEELAELRAE 80

                         90
                 ....*....|.
gi 489117279  78 LNKQLQFLQQE 88
Cdd:cd04766   81 LDELRARLRRE 91

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 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQKsENGYRLYSEADLERLQIILFYKYLGFSLKKIAELL-------GHEGQ-- 72
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLLSPER-RGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLdlydppgGNRKQle 79

                         90       100
                 ....*....|....*....|....*..
gi 489117279  73 ELLPHLNKQLQFLQQEREHLDTLISTL 99
Cdd:cd04776   80 KMLEKIEKRRAELEQQRRDIDAALAEL 106

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQKSENGYRLYSEADLERLQIILFYK-YLGFSLKKIAELL 67
Cdd:cd04774    1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLReVLGFSLQEVTHFL 67

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279    4 IKEAAQLSGVSVKTLHHYDKIGLLVPQ-KSENGYRLYSEADLERLQIILFYKYLGFSLKKIAEL--LGHE---------- 70
Cdd:TIGR02044   3 IGQVAKLTGLSSKMIRYYEEKGLIPPPlRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELlnLWNDpnrtsadvka 82

                          90       100       110
                  ....*....|....*....|....*....|.
gi 489117279   71 -GQELLPHLNKQLQFLQQEREHLDTLISTLQ 100
Cdd:TIGR02044  83 rTLEKVAEIERKISELQSMRDQLEALAQACP 113

Second 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 mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279   4 IKEAAQLSGVSVKTLHHYDKIGLLVPQKS-ENGYRLYSEADLERLQIILFYKYLGFSLKKIAEL---LGHEG--QELLPH 77
Cdd:cd04773    3 IGELAHLLGVPPSTLRHWEKEGLLSPDREpETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVveqLRHAGgtEALAAA 82

                         90
                 ....*....|....*..
gi 489117279  78 LNKQLQFL-QQEREHLD 93
Cdd:cd04773   83 LEQRRVALtQRGRAMLD 99

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQKSENGYRLYSEADLERL 47
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERL 46

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 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLgHEGQELLP---HL 78
Cdd:cd04779    1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQL-EEVQRSDKeqrEV 79

                         90       100
                 ....*....|....*....|..
gi 489117279  79 NKQLQFLQQEREHLDTLISTLQ 100
Cdd:cd04779   80 AQEVQLVCDQIDGLEHRLKQLK 101

mercuric resistance operon transcriptional regulator MerR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279   8 AQLSGVSVKTLHHYDKIGLLV-PQKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLG-------HEGQELLPHLN 79
Cdd:PRK13752  14 AKAAGVNVETIRFYQRKGLLPePDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRledgthcEEASSLAEHKL 93

                         90       100
                 ....*....|....*....|....*....
gi 489117279  80 KQLQFLQQEREHLDTLISTLQKTIQAQKG 108
Cdd:PRK13752  94 KDVREKMADLARMEAVLSELVCACHARKG 122

redox-sensitive transcriptional activator SoxR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279   6 EAAQLSGVSVKTLHHYDKIGLLVPQKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLG--HEGQELLPHLNKQLQ 83
Cdd:PRK15002  16 EVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGvlPEGHTLSAKEWKQLS 95

                         90
                 ....*....|....*.
gi 489117279  84 flQQEREHLDTLISTL 99
Cdd:PRK15002  96 --SQWREELDRRIHTL 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 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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279   2 YQIKEAAQLSGVSVKTLHHYDKIGLLVPQK--SENGYRlYSEADLERLQIIlfyKYL----GFSLKKIAELLGHEGQELL 75
Cdd:cd04780    1 MRMSELSKRSGVSVATIKYYLREGLLPEGRrlAPNQAE-YSEAHVERLRLI---RALqqegGLPISQIKEVLDAIADASL 76

                 .
gi 489117279  76 P 76
Cdd:cd04780   77 P 77

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489117279   4 IKEAAQLSGVSVKTLHHYDKIGLLVPQKSENGYRLYSEADLERLQ 48
Cdd:COG2452    3 PGEAAELLGVSPKTLRRWEKEGKLPAIRTPGGHRRYPESEVERLE 47

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489117279   3 QIKEAAQLSGVSVKTLHHYDKIGLLVPQKsENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGH 69
Cdd:cd04777    2 KIGKFAKKNNITIDTVRHYIDLGLLIPEK-KGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSY 67

HTH-type transcriptional regulator MlrA;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489117279   1 MYQIKEAAQLSGVSVKTLHHYDK-IGLLVPQKSENGYRLYSEADLERLQIILFYKYLGFSLKKIAELLGHEGQEllphln 79
Cdd:PRK15043   3 LYTIGEVALLCDINPVTLRAWQRrYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNENVD------ 76

                         90       100
                 ....*....|....*....|..
gi 489117279  80 kqlqfLQQE-REHLDTLISTLQ 100
Cdd:PRK15043  77 -----VQNGwRDQQETLLTYLQ 93