redox-sensitive transcriptional activator SoxR; SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species. [Cellular processes, Detoxification, Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131889    11 LLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKE 90
Cdd:TIGR01950   1 ELTVGELAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAVLPEGRTPTADD 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 16131889    91 WKQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCPLRNPGDRLGEEGTGARLLEDE 152
Cdd:TIGR01950  81 WARLSSQWREELDERIDQLNALRDQLDGCIGCGCLSLEDCPLRNPGDRLGEEGAGARLLEDE 142

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131889  15 GEVAKRSGVAVSALHFYESKGLITSI-RNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTlsakEWKQ 93
Cdd:COG0789   2 GEVARLTGVSVRTLRYYERIGLLPPPeRTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEE----EVRE 77

                        90       100
                ....*....|....*....|...
gi 16131889  94 LSSQWREELDRRIHTLVALRDEL 116
Cdd:COG0789  78 LLEEHLAELEAQIAELQALRAEL 100

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16131889    54 LRYVAIIKIAQRIGIPLATIGEAFgVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGC 119
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELL-ALYDDPGPPCADVRALLREKLAELEARIAELQALRDELDAL 65

redox-sensitive transcriptional activator SoxR; SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species. [Cellular processes, Detoxification, Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131889    11 LLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKE 90
Cdd:TIGR01950   1 ELTVGELAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAVLPEGRTPTADD 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 16131889    91 WKQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCPLRNPGDRLGEEGTGARLLEDE 152
Cdd:TIGR01950  81 WARLSSQWREELDERIDQLNALRDQLDGCIGCGCLSLEDCPLRNPGDRLGEEGAGARLLEDE 142

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 16131889  12 LTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSakEW 91
Cdd:cd00592   1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLA--AL 78

                        90       100
                ....*....|....*....|..
gi 16131889  92 KQLSSQWREELDRRIHTLVALR 113
Cdd:cd00592  79 LALLDEKLAELEEKIARLEALL 100

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 16131889  12 LTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFgvlpeGHTLSAKEW 91
Cdd:cd04781   1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAML-----SHDGKPPID 75

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 16131889  92 KQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCP 131
Cdd:cd04781  76 RQLLKAKAAELDQQIQRLQAMRELLRHVAQCPAPSHLDCP 115

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 16131889  15 GEVAKRSGVAVSALHFYESKGLITSI-RNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEaFGVLPEGHTLSAKEWKQ 93
Cdd:cd04770   4 GELAKAAGVSPDTIRYYERIGLLPPPqRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRE-LLSLRDDGAAPCAEVRA 82

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 16131889  94 LSSQWREELDRRIHTLVALRDELDGCIG-CGCLSRSDCPL 132
Cdd:cd04770  83 LLEEKLAEVEAKIAELQALRAELAGLLSaCDGDESVICPI 122

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 16131889  15 GEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTL--SAKEWK 92
Cdd:cd01282   4 GELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLRGGEPTfrPCPDLL 83

                        90       100
                ....*....|....*....|....*
gi 16131889  93 QLSSQWREELDRRIHTLVALRDELD 117
Cdd:cd01282  84 AVLRRELARIDRQIADLTRSRDRLD 108

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 16131889  15 GEVAKRSGVAVSALHFYESKGLIT-SIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGvLPEGHTLSAKEWKQ 93
Cdd:cd01108   4 GEAAKLTGLSAKMIRYYEEIGLIPpPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLA-LWRDPSRASADVKA 82

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 16131889  94 LSSQWREELDRRIHTLVALRDEL----DGCIGCgclSRSDCP 131
Cdd:cd01108  83 LALEHIAELERKIAELQAMRRTLqqlaDSCHGD---DRPDCP 121

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 16131889  12 LTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAII 60
Cdd:cd04761   1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLRLI 49

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131889  12 LTPGEVAKRSGVAVSALHFYESKGLIT-SIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGvLPEGHTLSAKE 90
Cdd:cd04785   1 LSIGELARRTGVNVETIRYYESIGLLPePARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLA-LSDRPDRSCAE 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 16131889  91 WKQLSSQWREELDRRIHTLVALRDELDGCI-GCGCLSRSDCPL 132
Cdd:cd04785  80 ADAIARAHLADVRARIADLRRLEAELKRMVaACSGGRVADCRI 122

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 16131889    13 TPGEVAKRSGVAVSALHFYESKGLI-TSIRNSGNQRRY 49
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLpPPERTEGGYRRY 38

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16131889    13 TPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAF 77
Cdd:pfam13411   2 TISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131889  12 LTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRY--KRDVLRYVAIIkIAQRIGIPLATIGEAFgvlpEGHTLSAK 89
Cdd:cd01106   1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLytEEDLERLQQIL-FLKELGFSLKEIKELL----KDPSEDLL 75

                        90       100
                ....*....|....*....|....*...
gi 16131889  90 EwkQLSSQwREELDRRIHTLVALRDELD 117
Cdd:cd01106  76 E--ALREQ-KELLEEKKERLDKLIKTID 100

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 16131889  11 LLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLAtigEAFGVLPEGHTLSAKE 90
Cdd:cd04775   1 MYTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLE---EIAGCLAQPHVQAILE 77

                        90       100       110
                ....*....|....*....|....*....|.
gi 16131889  91 wKQLSSqwreeLDRRIHTLVALRDELDGCIG 121
Cdd:cd04775  78 -ERLQS-----LNREIQRLRQQQQVLAAILG 102

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 16131889  12 LTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRY-VAIIKIAQRIGIPLATIGEAFgvlpegHTLSAKE 90
Cdd:cd04768   1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYqLQFILFLRELGFSLAEIKELL------DTEMEEL 74

                        90       100
                ....*....|....*....|..
gi 16131889  91 WKQLSSQwREELDRRIHTLVAL 112
Cdd:cd04768  75 TAMLLEK-KQAIQQKIDRLQQL 95

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 16131889  12 LTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRY-KRDVLRYVAIIKIAQRIGIPLATIGE 75
Cdd:cd04774   1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYsEEDLKRLERILRLREVLGFSLQEVTH 65

mercuric resistance operon transcriptional regulator MerR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131889   12 LTPGEVAKRSGVAVSALHFYESKGLITSI-RNSGNQRRY-KRDVLRyVAIIKIAQRIGIPLATIGEAFGVLPEGHtlsAK 89
Cdd:PRK13752   8 LTIGVFAKAAGVNVETIRFYQRKGLLPEPdKPYGSIRRYgEADVTR-VRFVKSAQRLGFSLDEIAELLRLEDGTH---CE 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 16131889   90 EWKQLSSQWREELDRRIHTLVALRDELDGCIgCGCLSRS---DCPL 132
Cdd:PRK13752  84 EASSLAEHKLKDVREKMADLARMEAVLSELV-CACHARKgnvSCPL 128

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16131889  11 LLTPGEVAKRSGVAVSALHFYESKGLIT-SIRNSGNQRRY-KRDVLRYVAIIKIaQRIGIPLATI 73
Cdd:cd04790   1 MLTISQLARQFGLSRSTLLYYERIGLLSpSARSESNYRLYgERDLERLEQICAY-RSAGVSLEDI 64

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131889  15 GEVAKRSGVAVSALHFYESKGLITS-IRNSGNQRRYKRDVLRYVAIIKIAQRI-GIPLATIGEAFGVLPE 82
Cdd:cd04780   4 SELSKRSGVSVATIKYYLREGLLPEgRRLAPNQAEYSEAHVERLRLIRALQQEgGLPISQIKEVLDAIAD 73

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
                ....*....|....*....|....*....|....*....|....*....|....*
gi 16131889  16 EVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPL 70
Cdd:cd04789   6 ELAEKAGISRSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSL 60

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 16131889  15 GEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATI----GEAFGVLPEGHTLsAKE 90
Cdd:cd04779   4 GQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIkdqlEEVQRSDKEQREV-AQE 82

                        90       100
                ....*....|....*....|....*...
gi 16131889  91 WKQLSSQwreeLDRRIHTLVALRDELDG 118
Cdd:cd04779  83 VQLVCDQ----IDGLEHRLKQLKPIASQ 106

Protein of unknown function (DUF2670); This bacterial family of proteins has no known function.

                          10        20
                  ....*....|....*....|....*.
gi 16131889   129 DCpLRNPGDRLGEEGTGARLLEDEQN 154
Cdd:pfam10875  93 DC-LSDPGEYKHEEGTGAKVLEDEIN 117

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.

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gi 16131889  12 LTPGEVAKRSGVAVSALHFYESK-GLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPlatIGEAFGVL 80
Cdd:cd01104   1 YTIGAVARLTGVSPDTLRAWERRyGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVR---ISQAAALA 67