Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847   1 MYRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEHHTCQ 80
Cdd:PRK09514   1 MYRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDPEHHTCQ 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847  81 ESKSIVQERLQDVEARIAELQTMQRSLQRLNDACCGTAHSSVYCSILEALEQGASGAKSG 140
Cdd:PRK09514  81 EVKGIVDEKLAEVEAKIAELQHMRRSLQRLNDACCGTAHSAVYCSILEALEQGASGVKSG 140

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847   1 MYRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEHHTCQ 80
Cdd:PRK09514   1 MYRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDPEHHTCQ 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847  81 ESKSIVQERLQDVEARIAELQTMQRSLQRLNDACCGTAHSSVYCSILEALEQGASGAKSG 140
Cdd:PRK09514  81 EVKGIVDEKLAEVEAKIAELQHMRRSLQRLNDACCGTAHSAVYCSILEALEQGASGVKSG 140

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 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEHHtCQE 81
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAP-CAE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 487139847  82 SKSIVQERLQDVEARIAELQTMQRSLQRLNDACCGTAhsSVYCSIL 127
Cdd:cd04770   80 VRALLEEKLAEVEAKIAELQALRAELAGLLSACDGDE--SVICPIL 123

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 487139847     2 YRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELL 68
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELL 67

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847   1 MYRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEHHTCQ 80
Cdd:PRK09514   1 MYRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDPEHHTCQ 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847  81 ESKSIVQERLQDVEARIAELQTMQRSLQRLNDACCGTAHSSVYCSILEALEQGASGAKSG 140
Cdd:PRK09514  81 EVKGIVDEKLAEVEAKIAELQHMRRSLQRLNDACCGTAHSAVYCSILEALEQGASGVKSG 140

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 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEHHtCQE 81
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAP-CAE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 487139847  82 SKSIVQERLQDVEARIAELQTMQRSLQRLNDACCGTAhsSVYCSIL 127
Cdd:cd04770   80 VRALLEEKLAEVEAKIAELQALRAELAGLLSACDGDE--SVICPIL 123

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 487139847   4 IGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPeHHTCQESK 83
Cdd:cd01108    3 IGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDP-SRASADVK 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 487139847  84 SIVQERLQDVEARIAELQTMQRSLQRLNDACCGTAHSSvyCSILEAL 130
Cdd:cd01108   82 ALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPD--CPILEGL 126

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEhHTCQE 81
Cdd:cd04784    1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPE-ASCAE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 487139847  82 SKSIVQERLQDVEARIAELQTMQRSLQRLNDaCCGTAHSSVYCSILEAL 130
Cdd:cd04784   80 VNALIDEHLAHVRARIAELQALEKQLQALRE-RCDGARTIEECGILQGL 127

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847    4 IGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEHHTCqESK 83
Cdd:TIGR02044   3 IGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSA-DVK 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 487139847   84 SIVQERLQDVEARIAELQTMQRSLQRLNDACCGTAHSSvyCSILEAL 130
Cdd:TIGR02044  82 ARTLEKVAEIERKISELQSMRDQLEALAQACPGDDSPD--CPIIENL 126

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847    3 RIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIrIDPEHhtCQES 82
Cdd:TIGR02051   1 TIGELAKAAGVNVETIRYYERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGL-VDGTH--CREM 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 487139847   83 KSIVQERLQDVEARIAELQTMQRSLQRLNDAcCGTAHSSVYCSILEAL 130
Cdd:TIGR02051  78 YELASRKLKSVQAKMADLLRIERLLEELLEQ-CPANKGNTSCPIIESL 124

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 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEvRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRidPEHHTCQE 81
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPE-RSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDAR--DEELSLAA 77

                         90       100
                 ....*....|....*....|...
gi 487139847  82 SKSIVQERLQDVEARIAELQTMQ 104
Cdd:cd00592   78 LLALLDEKLAELEEKIARLEALL 100

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEhHTCQE 81
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGD-STIPE 79

                         90       100       110
                 ....*....|....*....|....*....|.
gi 487139847  82 SKSIVQERLQDVEARIAELqtmQRSLQRLND 112
Cdd:cd01109   80 RLELLEEHREELEEQIAEL---QETLAYLDY 107

HTH-type transcriptional regulator CueR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847   4 IGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEHHTCqESK 83
Cdd:PRK10227   3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSA-DVK 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 487139847  84 SIVQERLQDVEARIAELQTMQRSLQRLNDACCGTahSSVYCSILEAL 130
Cdd:PRK10227  82 RRTLEKVAEIERHIEELQSMRDQLLALANACPGD--DSADCPIIENL 126

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 487139847    2 YRIGELAKLADVTPDTIRYYEKQQMMdHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELL 68
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLL-PPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

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 487139847   45 LQRLKFIRYARQLGFTLDSIRELLSIRIDPeHHTCQESKSIVQERLQDVEARIAELQTMQRSLQRL 110
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELLALYDDP-GPPCADVRALLREKLAELEARIAELQALRDELDAL 65

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 487139847   4 IGELAKLADVTPDTIRYYEKQQMMdHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRidPEHH--TCQE 81
Cdd:cd01110    4 VGEVAKRSGVAVSALHFYEQKGLI-ASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALATL--PEDRtpTKAD 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 487139847  82 SKSIVQERLQDVEARIAELQTMQRSLqrlnDAC--CG 116
Cdd:cd01110   81 WERLSRAWRDRLDERIAELQQLRDQL----DGCigCG 113

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 487139847   2 YRIGELAKLADVTPDTIRYYEKqqmMD----HEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLsiridpEHH 77
Cdd:cd01107    1 FTIGEFAKLSNLSIKALRYYDK---IGllkpAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEIL------DAD 71

                         90       100       110
                 ....*....|....*....|....*....|...
gi 487139847  78 TCQESKSIVQERLQDVEARIAELQTMQRSLQRL 110
Cdd:cd01107   72 NDDELRKLLREKLAELEAEIEELQRILRLLEDR 104

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 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSiriDPEHHTCQE 81
Cdd:cd04782    1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLD---NRNPDELIE 77

                         90       100
                 ....*....|....*....|...
gi 487139847  82 SksiVQERLQDVEARIAELQTMQ 104
Cdd:cd04782   78 L---LKKQEKEIKEEIEELQKIK 97

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 487139847   1 MYrIGELAKLADVTPDTIRYYEKQQMMdHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEHHTCQ 80
Cdd:cd04769    1 MY-IGELAQQTGVTIKAIRLYEEKGLL-PSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWP 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 487139847  81 ESKSIVQERLQDVEARIAELQTMQRSLQRLNDA 113
Cdd:cd04769   79 HLQQALEDKKQEIRAQITELQQLLARLDAFEAS 111

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 487139847   3 RIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPehhtcqeS 82
Cdd:cd04788    2 KIGELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFD-------P 74

                         90
                 ....*....|....*....
gi 487139847  83 KSIVQERLQDVEARIAELQ 101
Cdd:cd04788   75 LELLRRQLARLEEQLELAT 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 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 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEvRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLS--IRIDPEHHTC 79
Cdd:cd04779    1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPE-RSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEevQRSDKEQREV 79

                         90       100       110
                 ....*....|....*....|....*....|
gi 487139847  80 QESKSIVQERLQDVEARIAELQTMQRSLQR 109
Cdd:cd04779   80 AQEVQLVCDQIDGLEHRLKQLKPIASQTDR 109

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMdHEVRTEGGFRLYTENDLQRLKFIRYARQ-LGFTLDSIRELLSIRIDPEHHTCQ 80
Cdd:cd04774    1 YKVDEVAKRLGLTKRTLKYYEEIGLV-SPERSEGRYRLYSEEDLKRLERILRLREvLGFSLQEVTHFLERPLEPVDGGHR 79

                 ....*...
gi 487139847  81 ESKSIVQE 88
Cdd:cd04774   80 YSAESLRE 87

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 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLS 69
Cdd:cd01104    1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68

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 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEvRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELL 68
Cdd:cd04764    1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIP-RTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66

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 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELlsirIDPEHHT--C 79
Cdd:cd04773    1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATV----VEQLRHAggT 76

                         90
                 ....*....|....*..
gi 487139847  80 QESKSIVQERLQDVEAR 96
Cdd:cd04773   77 EALAAALEQRRVALTQR 93

Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which 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 N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSiRIDPEHHTCQE 81
Cdd:cd01111    1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCR-ALDAGDGKQPE 79

                         90       100
                 ....*....|....*....|....*.
gi 487139847  82 skSIVQERLQDVEARIAELQTMQRSL 107
Cdd:cd01111   80 --ACLAQLRQKIEVRRAALNALTTQL 103

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 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMdHEVRTEGGFRLYTENDLQRLKFI-RYARQLGFTLDSIRELLSIRidpehhtcq 80
Cdd:cd04766    2 YVISVAAELSGMHPQTLRLYERLGLL-SPSRTDGGTRRYSERDIERLRRIqRLTQELGVNLAGVKRILELE--------- 71

                         90       100
                 ....*....|....*....|....*
gi 487139847  81 esksivqERLQDVEARIAELQTMQR 105
Cdd:cd04766   72 -------EELAELRAELDELRARLR 89

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487139847   3 RIGELAKLADVTPDTIRYYekqqmMDHEV---RTEGGFRLYTENDLQRLKFIRYARQLGFTLDSIRELLSIRIDPEHHTC 79
Cdd:cd04777    2 KIGKFAKKNNITIDTVRHY-----IDLGLlipEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTH 76

                         90       100
                 ....*....|....*....|....*..
gi 487139847  80 QES---KSIVQERLQDVEARIAELQTM 103
Cdd:cd04777   77 EDQdyyKSFLKNKKDELEKEIEDLKKA 103

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 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 487139847   2 YRIGELAKLADVTPDTIRYYEKQQMMDHEVRTEGGFRLYTENDLQRLKFIRYARQ-LGFTLDSIRELLSIRID 73
Cdd:cd04780    1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQeGGLPISQIKEVLDAIAD 73

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.