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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASADV 80
Cdd:cd01108    1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 518281673  81 KALTLKHVADLEVRIAELGAMRDTLRALADACSGDDRPDCPILSDMA 127
Cdd:cd01108   81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGLA 127

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASADV 80
Cdd:cd01108    1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 518281673  81 KALTLKHVADLEVRIAELGAMRDTLRALADACSGDDRPDCPILSDMA 127
Cdd:cd01108   81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGLA 127

HTH-type transcriptional regulator CueR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASADV 80
Cdd:PRK10227   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 518281673  81 KALTLKHVADLEVRIAELGAMRDTLRALADACSGDDRPDCPILSDMAraggedcPACH 138
Cdd:PRK10227  81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLS-------GCCH 131

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518281673     1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLW 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASADV 80
Cdd:cd01108    1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 518281673  81 KALTLKHVADLEVRIAELGAMRDTLRALADACSGDDRPDCPILSDMA 127
Cdd:cd01108   81 KALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPDCPILEGLA 127

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASADV 80
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 518281673  81 KALTLKHVADLEVRIAELGAMRDTLRALADACSGDDRPDCPIL 123
Cdd:cd04770   81 RALLEEKLAEVEAKIAELQALRAELAGLLSACDGDESVICPIL 123

HTH-type transcriptional regulator CueR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASADV 80
Cdd:PRK10227   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 518281673  81 KALTLKHVADLEVRIAELGAMRDTLRALADACSGDDRPDCPILSDMAraggedcPACH 138
Cdd:PRK10227  81 KRRTLEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENLS-------GCCH 131

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLwhDRARASADV 80
Cdd:cd04783    1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLEL--DDGTDCSEA 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 518281673  81 KALTLKHVADLEVRIAELGAMRDTLRALADAC-SGDDRPDCPIL 123
Cdd:cd04783   79 RELAEQKLAEVDEKIADLQRMRASLQELVSQCaATKNNVSCPII 122

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518281673   3 IGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARasaDVKA 82
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEE---EVRE 77

                         90       100
                 ....*....|....*....|...
gi 518281673  83 LTLKHVADLEVRIAELGAMRDTL 105
Cdd:COG0789   78 LLEEHLAELEAQIAELQALRAEL 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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVdAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWhDRARASADV 80
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLL-PPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDAR-DEELSLAAL 78

                         90       100
                 ....*....|....*....|..
gi 518281673  81 KALTLKHVADLEVRIAELGAMR 102
Cdd:cd00592   79 LALLDEKLAELEEKIARLEALL 100

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSeGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASADV 80
Cdd:cd04769    1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRS-GNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWPH 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 518281673  81 KALTLKHV-ADLEVRIAELGAMRDTLRALADA 111
Cdd:cd04769   80 LQQALEDKkQEIRAQITELQQLLARLDAFEAS 111

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 518281673   44 VHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASADVKALTLKHVADLEVRIAELGAMRDTLRAL 108
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELLALYDDPGPPCADVRALLREKLAELEARIAELQALRDELDAL 65

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSlwhdraRASADV 80
Cdd:cd01106    1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLK------DPSEDL 74

                         90       100
                 ....*....|....*....|....*...
gi 518281673  81 KALTLKHVADLEVRIAELGAMRDTLRAL 108
Cdd:cd01106   75 LEALREQKELLEEKKERLDKLIKTIDRT 102

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVdAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLL---SLWHDRARAS 77
Cdd:cd01282    1 MRIGELAARTGVSVRSLRYYEEQGLL-VPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLpclRGGEPTFRPC 79

                         90       100       110
                 ....*....|....*....|....*....|
gi 518281673  78 ADVKALTLKHVADLEVRIAELGAMRDTLRA 107
Cdd:cd01282   80 PDLLAVLRRELARIDRQIADLTRSRDRLDA 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 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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRsEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLslwHDRARASADV 80
Cdd:cd04781    1 LDIAEVARQSGLPASTLRYYEEKGLIASIGR-RGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAML---SHDGKPPIDR 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 518281673  81 KALTLKhVADLEVRIAELGAMRDTLRALAdACSGDDRPDCPI 122
Cdd:cd04781   77 QLLKAK-AAELDQQIQRLQAMRELLRHVA-QCPAPSHLDCPT 116

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASADV 80
Cdd:cd04786    1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPADASNWQHDELL 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 518281673  81 KALTLKhVADLEVRIAELGAMRDTLRALADACSGddRPD 119
Cdd:cd04786   81 AALERK-VADIEALEARLAQNKAQLLVLIDLIES--KPD 116

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVdAPPRSEGGYRRYdERSVhtLR---FVRRARNLGFSLDEIRGLL-SLWHDRARA 76
Cdd:cd01110    2 LSVGEVAKRSGVAVSALHFYEQKGLI-ASWRNAGNQRRY-PRDV--LRriaFIKVAQRLGLSLAEIAEALaTLPEDRTPT 77

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 518281673  77 SADVKALTLKHVADLEVRIAELGAMRDTLralaDACSG 114
Cdd:cd01110   78 KADWERLSRAWRDRLDERIAELQQLRDQL----DGCIG 111

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDapPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASADV 80
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLLS--PERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQL 78

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 518281673  81 KAL---TLKHVADLEVRIAELGAMRDTLRALADAC 112
Cdd:cd04776   79 EKMlekIEKRRAELEQQRRDIDAALAELDAAEERC 113

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVdAPPRSEGGYRRYDERSVHTLRFVRRARN-LGFSLDEIRGLLSL 69
Cdd:cd04774    1 YKVDEVAKRLGLTKRTLKYYEEIGLV-SPERSEGRYRLYSEEDLKRLERILRLREvLGFSLQEVTHFLER 69

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 518281673   3 IGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLwhdraRASADVKA 82
Cdd:cd04782    3 TGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN-----RNPDELIE 77

                         90       100
                 ....*....|....*....|
gi 518281673  83 LTLKHVADLEVRIAELGAMR 102
Cdd:cd04782   78 LLKKQEKEIKEEIEELQKIK 97

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 518281673   3 IGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLslwhdrARASADVKA 82
Cdd:cd04790    4 ISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLL------QQPGDDATD 77

                         90       100
                 ....*....|....*....|....*..
gi 518281673  83 LTLKHVADLEVriaELGAMRDTLRALA 109
Cdd:cd04790   78 VLRRRLAELNR---EIQRLRQQQRAIA 101

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVdAPPRSEG-GYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLSLWHDRARASAD 79
Cdd:cd04773    1 MTIGELAHLLGVPPSTLRHWEKEGLL-SPDREPEtGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTEAL 79

                         90
                 ....*....|
gi 518281673  80 VKALTLKHVA 89
Cdd:cd04773   80 AAALEQRRVA 89

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 518281673   3 IGEAAEASGVSAKMIRHYESIGLVDaPPRSEGGYRRYDERSVHTLRFVRR-ARNLGFSLDEIRGLLSLWHDRARASADVK 81
Cdd:cd04766    4 ISVAAELSGMHPQTLRLYERLGLLS-PSRTDGGTRRYSERDIERLRRIQRlTQELGVNLAGVKRILELEEELAELRAELD 82

                 ..
gi 518281673  82 AL 83
Cdd:cd04766   83 EL 84

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 518281673   2 NIGEAAEASGVSAKMIRHYES-IGLVdAPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLS 68
Cdd:cd01104    2 TIGAVARLTGVSPDTLRAWERrYGLP-APQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVdaPPRSEGGYRRYDERSVHTLRFVRRARNLGFSLDEIRGLLS 68
Cdd:cd04777    1 MKIGKFAKKNNITIDTVRHYIDLGLL--IPEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFS 66

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518281673   3 IGEAAEASGVSAKMIRHYESIGLVdAPPRSEGGYRRYDERSVHTLRFVRR-ARNLGFSLDEIRGLLSLWhdrarasadvk 81
Cdd:cd01279    4 ISVAAELLGIHPQTLRVYDRLGLV-SPARTNGGGRRYSNNDLELLRQVQRlSQDEGFNLAGIKRIIELY----------- 71

                         90       100
                 ....*....|....*....|....*.
gi 518281673  82 altlKHVADLEVRIAELGAMRDTLRA 107
Cdd:cd01279   72 ----PQVLLLQCRSCEHATELIGCAK 93

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVRR-ARNLGFSLDEIRGLLS 68
Cdd:cd04780    1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRAlQQEGGLPISQIKEVLD 69

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
                 ....*....|....*....|....*....|....*....|....*..
gi 518281673   5 EAAEASGVSAKMIRHYESIGLVDAPPRSEGGYRRYDERSVHTLRFVR 51
Cdd:cd04772    5 DLARAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDKHIAALRAYR 51

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 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDApPRSEGGYRRYDERSVHTL 47
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLKA-IRTPGGHRRFPEEDLERL 46

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

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 518281673   1 MNIGEAAEASGVSAKMIRHYESIGLVDApPRSEGGYRRYDERSV 44
Cdd:COG2452    1 LTPGEAAELLGVSPKTLRRWEKEGKLPA-IRTPGGHRRYPESEV 43