Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDL-EMEELFAFY 84
Cdd:cd01107   1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDAdNDDELRKLL 80

                        90       100
                ....*....|....*....|....*...
gi 50812267  85 TEQERQIREKLDFLSALEQTISLVKKRM 112
Cdd:cd01107  81 REKLAELEAEIEELQRILRLLEDRLKQI 108

Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDL-EMEELFAFY 84
Cdd:cd01107   1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDAdNDDELRKLL 80

                        90       100
                ....*....|....*....|....*...
gi 50812267  85 TEQERQIREKLDFLSALEQTISLVKKRM 112
Cdd:cd01107  81 REKLAELEAEIEELQRILRLLEDRLKQI 108

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50812267   8 IGEVSKLANVSIKALRYYDKIDLFKPAYVDpDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEM---EELFAFY 84
Cdd:COG0789   1 IGEVARLTGVSVRTLRYYERIGLLPPPERT-EGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDdgeEEVRELL 79

                        90       100
                ....*....|....*....|.
gi 50812267  85 TEQERQIREKLDFLSALEQTI 105
Cdd:COG0789  80 EEHLAELEAQIAELQALRAEL 100

GyrI-like small molecule binding domain; This family contains the small molecule binding domain of a number of different bacterial transcription activators. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50812267   123 EVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGF-TNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQIS 201
Cdd:pfam06445   1 EVEIVELPAFRVAGLRHRGPYNEEGIGALWEELCAWASENGLSpAPSPLIGVSYDDPEVTEDEELRYDAGVAVPIPVEGP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 50812267   202 sitPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQ--LTVVSDVYELIIPIHYSPkKQEEYRVEMKIRI 276
Cdd:pfam06445  81 ---EGVEELELPGGEYAVFRHKGPYDDLQETYAKIYGEWLPESgyERRDGPSFEIYLNDPREV-PEEELKTEIYIPV 153

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50812267    6 YSIGEVSKLANVSIKALRYYDKIDLFKPAyVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEME 78
Cdd:PRK09514   2 YRIGELAKLAEVTPDTLRFYEKQGLMDPE-VRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLD 73

Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDL-EMEELFAFY 84
Cdd:cd01107   1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDAdNDDELRKLL 80

                        90       100
                ....*....|....*....|....*...
gi 50812267  85 TEQERQIREKLDFLSALEQTISLVKKRM 112
Cdd:cd01107  81 REKLAELEAEIEELQRILRLLEDRLKQI 108

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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAYVDpDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYT 85
Cdd:cd01106   1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRT-ENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALR 79

                        90       100
                ....*....|....*....|
gi 50812267  86 EQERQIREKLDFLSALEQTI 105
Cdd:cd01106  80 EQKELLEEKKERLDKLIKTI 99

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 50812267      6 YSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDtSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLE 76
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEG-GYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70

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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAYVDpDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKK-AQDLEMEELFAFY 84
Cdd:cd04782   1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVK-ENGYRYYTLEQFEQLDIILLLKELGISLKEIKDyLDNRNPDELIELL 79

                        90
                ....*....|....*...
gi 50812267  85 TEQERQIREKLDFLSALE 102
Cdd:cd04782  80 KKQEKEIKEEIEELQKIK 97

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        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAyvDPDTSYRYYTDSQLIHLDLI 56
Cdd:cd04761   1 YTIGELAKLTGVSPSTLRYYERIGLLSPA--RTEGGYRLYSDADLERLRLI 49

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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAyVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEME------E 79
Cdd:cd04770   1 MKIGELAKAAGVSPDTIRYYERIGLLPPP-QRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDgaapcaE 79

                        90       100
                ....*....|....*....|....*..
gi 50812267  80 LFAFYTEQERQIREKLDFLSALEQTIS 106
Cdd:cd04770  80 VRALLEEKLAEVEAKIAELQALRAELA 106

Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50812267   8 IGEVSKLANVSIKALRYYDKIDLFKPAYvDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQ 87
Cdd:cd04788   3 IGELARRTGLSVRTLHHYDHIGLLSPSQ-RTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLELLRRQ 81

                        90
                ....*....|....
gi 50812267  88 ERQIREKLDFLSAL 101
Cdd:cd04788  82 LARLEEQLELATRL 95

GyrI-like small molecule binding domain [Signal transduction mechanisms];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50812267 147 VLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEmtyrHIFTPVltnKQISSITPDMEITTIPKGRYACIAYNFSP 226
Cdd:COG4978  26 LIGEAFGELFAYLAENGIEPAGPPFAIYHDTDEDDVDV----EVGVPV---AGPLPGTGDIKVGTLPAGKAATATHRGPY 98

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 50812267 227 EHYFLNLQKLIKYIADRQLTVVSDVYELIIPIHYSPKKQEEYRVEM 272
Cdd:COG4978  99 DTLDEAYEALLAWIEENGLEVAGPPREVYLTDPGNEPDPEEWVTEI 144

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 50812267   8 IGEVSKLANVSIKALRYYDKIDLFKPAyVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKkaqdlemeELFAFYTEQ 87
Cdd:cd01108   3 IGEAAKLTGLSAKMIRYYEEIGLIPPP-SRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIR--------ELLALWRDP 73

                ....*.
gi 50812267  88 ERQIRE 93
Cdd:cd01108  74 SRASAD 79

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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAyvDPDTSYRYYTDSQLIHLDLIkslkyigtpleEMKKAQDLEMEELFAFYT 85
Cdd:cd04779   1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPE--RSDSNYRYYDETALDRLQLI-----------EHLKGQRLSLAEIKDQLE 67

                        90       100
                ....*....|....*....|....*....
gi 50812267  86 EQERQIREKldflSALEQTISLVKKRMKR 114
Cdd:cd04779  68 EVQRSDKEQ----REVAQEVQLVCDQIDG 92

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAYvDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKA 72
Cdd:cd04773   1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDR-EPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATV 66

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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAyVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKK--------AQDLEM 77
Cdd:cd04790   2 LTISQLARQFGLSRSTLLYYERIGLLSPS-ARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSllqqpgddATDVLR 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 50812267  78 EELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPE 145
Cdd:cd04790  81 RRLAELNREIQRLRQQQRAIATLLKQPTLLKEQRLVTKEKWVAILKAAGMDEADMRRWHIEFEKMEPE 148

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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFkPAYVDPdTSYRYYTDSQLIHLDLIKSLKYIGTPLEEM-----KKAQDLEMEEL 80
Cdd:cd04775   2 YTIGQMSRKFGVSRSTLLYYESIGLI-PSARSE-ANYRLYSEADLSRLEKIVFLQAGGLPLEEIagclaQPHVQAILEER 79

                        90       100
                ....*....|....*....|.
gi 50812267  81 FAFYTEQERQIREKLDFLSAL 101
Cdd:cd04775  80 LQSLNREIQRLRQQQQVLAAI 100

Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators; Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the conserved, metal-binding cysteines seen in the MerR1 group.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50812267  10 EVSKLANVSIKALRYYDKIDLFKPAYvDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKkaQDLEMEE---------- 79
Cdd:cd04787   5 ELANAAGVTPDTVRFYTRIGLLRPTR-DPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIK--EILSHADqgespcpmvr 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 50812267  80 -LFA-FYTEQERQIREkldfLSALEQtislvkkRMKRQME 117
Cdd:cd04787  82 rLIEqRLAETERRIKE----LLKLRD-------RMQQAVS 110

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFkpAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEE--LFAF 83
Cdd:cd04789   2 YTISELAEKAGISRSTLLYYEKLGLI--TGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQGKLTRslLLER 79

                        90       100
                ....*....|....*....|.
gi 50812267  84 YTEQERQIREKL---DFLSAL 101
Cdd:cd04789  80 LSSLAEQIARKQqarDLLAAL 100

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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFKPAYvdpDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMK------------KAQ 73
Cdd:cd04776   1 YTISELAREFDVTPRTLRFYEDKGLLSPER---RGQTRVYSRRDRARLKLILRGKRLGFSLEEIRelldlydppggnRKQ 77

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 50812267  74 DLEMEELFAFYTEQ-ERQIREKLDFLSALEQTISLVKKR 111
Cdd:cd04776  78 LEKMLEKIEKRRAElEQQRRDIDAALAELDAAEERCRER 116

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 50812267   6 YSIGEVSKLANVSIKALRYYDKIDLFkpayVDPD---TSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLE----ME 78
Cdd:cd04783   1 LTIGELAKAAGVNVETIRYYQRRGLL----PEPPrpeGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDdgtdCS 76

                        90       100       110
                ....*....|....*....|....*....|...
gi 50812267  79 ELFAFYTEQERQIREKLDFLSALEQTISLVKKR 111
Cdd:cd04783  77 EARELAEQKLAEVDEKIADLQRMRASLQELVSQ 109

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 50812267   5 YYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTsyRYYTDSQLIHLDLIKSL-KYIGTPLEEMKKAQDLEME 78
Cdd:cd04766   1 VYVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGT--RRYSERDIERLRRIQRLtQELGVNLAGVKRILELEEE 73

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 50812267   6 YSIGEVSKLANVSIKALRYYDK-IDLFKPAyvdPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKA 72
Cdd:cd04764   1 YTIKEVSEIIGVKPHTLRYYEKeFNLYIPR---TENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEI 65