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Conserved domains on  [gi|1154143883|ref|WP_078519009|]
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MerR family transcriptional regulator [Streptomyces sp. Tu6071]

Protein Classification

MerR family transcriptional regulator( domain architecture ID 10099992)

MerR family transcriptional regulator containing an N-terminal MerR family helix-turn-helix (HTH) DNA-binding domain and specific effector binding regions

CATH:  3.20.80.10|1.20.5.490|1.10.1660.10
Gene Ontology:  GO:0006355|GO:0003677|GO:0003700
PubMed:  17302809|12829265|15808743|35130613
SCOP:  3000062|3000158

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 5-112 1.23e-42

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.


:

Pssm-ID: 133382 [Multi-domain]  Cd Length: 108  Bit Score: 141.50  E-value: 1.23e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEVSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGARNALI 84
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLL 80

                          90       100
                  ....*....|....*....|....*...
gi 1154143883  85 ARHLRRLEDQLARTHDAVTSLRDLLEHP 112
Cdd:cd01107    81 REKLAELEAEIEELQRILRLLEDRLKQI 108
BltR2 COG4978
GyrI-like small molecule binding domain [Signal transduction mechanisms];
118-264 9.27e-34

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


:

Pssm-ID: 444003  Cd Length: 144  Bit Score: 119.72  E-value: 9.27e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883 118 ITHRRLPARRVAAVTADdLPVADIGAWYHGALGELFATLASQGLPPSGPAGGVYDDAlfTLEHGRATVYVPVATEPRAAG 197
Cdd:COG4978     1 VEVKELPAQPVASIRAT-VPMDELGELIGEAFGELFAYLAENGIEPAGPPFAIYHDT--DEDDVDVEVGVPVAGPLPGTG 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1154143883 198 RVRMTELPPAELAVITHEGPETGIDRAYGTLATYVTRHALAVAGPIHEFYPVTFHDTPDPSHWRTEI 264
Cdd:COG4978    78 DIKVGTLPAGKAATATHRGPYDTLDEAYEALLAWIEENGLEVAGPPREVYLTDPGNEPDPEEWVTEI 144
 
Name Accession Description Interval E-value
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 5-112 1.23e-42

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.


Pssm-ID: 133382 [Multi-domain]  Cd Length: 108  Bit Score: 141.50  E-value: 1.23e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEVSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGARNALI 84
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLL 80

                          90       100
                  ....*....|....*....|....*...
gi 1154143883  85 ARHLRRLEDQLARTHDAVTSLRDLLEHP 112
Cdd:cd01107    81 REKLAELEAEIEELQRILRLLEDRLKQI 108
BltR2 COG4978
GyrI-like small molecule binding domain [Signal transduction mechanisms];
118-264 9.27e-34

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


Pssm-ID: 444003  Cd Length: 144  Bit Score: 119.72  E-value: 9.27e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883 118 ITHRRLPARRVAAVTADdLPVADIGAWYHGALGELFATLASQGLPPSGPAGGVYDDAlfTLEHGRATVYVPVATEPRAAG 197
Cdd:COG4978     1 VEVKELPAQPVASIRAT-VPMDELGELIGEAFGELFAYLAENGIEPAGPPFAIYHDT--DEDDVDVEVGVPVAGPLPGTG 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1154143883 198 RVRMTELPPAELAVITHEGPETGIDRAYGTLATYVTRHALAVAGPIHEFYPVTFHDTPDPSHWRTEI 264
Cdd:COG4978    78 DIKVGTLPAGKAATATHRGPYDTLDEAYEALLAWIEENGLEVAGPPREVYLTDPGNEPDPEEWVTEI 144
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
7-97 1.33e-24

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 94.59  E-value: 1.33e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   7 IGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPG--ARNALI 84
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTE-GGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGeeEVRELL 79

                          90
                  ....*....|...
gi 1154143883  85 ARHLRRLEDQLAR 97
Cdd:COG0789    80 EEHLAELEAQIAE 92
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 121-268 6.56e-16

Bacterial transcription activator, effector binding domain; This domain is found in the probable effector binding domain of a number of different bacterial transcription activators.and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.


Pssm-ID: 214874 [Multi-domain]  Cd Length: 158  Bit Score: 73.28  E-value: 6.56e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883  121 RRLPARRVAAVTAddlpvadIGAWYHGALGELFATL----ASQGLPPSGPAG---GVYDDALFTLEHGRATVY--VPVAT 191
Cdd:smart00871   5 VELPAFKVAGLRH-------RGPNEDEKIPELWQRLiqwaKELGLLPVGNSGepyGVYYDDPDDTPDGEFRYDagVEVSD 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883  192 EPRAAGRVRMTELPPAELAVITHEG-PETGIDRAYGTLATYV---TRHALAVAGPIHEFYPVTFHDTpDPSHWRTEIGWP 267
Cdd:smart00871  78 EVEAPEGVETKTIPAGKYAVFTHKGgSYDEIQEAWEAIYGEWlpnSGYELRDAGPDFEVYLNDPPDT-DPEELVTEIYIP 156


                   .
gi 1154143883  268 V 268
Cdd:smart00871 157 V 157
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
5-75 1.21e-15

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 69.86  E-value: 1.21e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1154143883    5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTP 75
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTE-GGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
MerR_1 pfam13411
MerR HTH family regulatory protein;
6-72 6.20e-13

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 62.19  E-value: 6.20e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1154143883   6 SIGDFARATHLSVKALRHYHEQGLLEPAATDevSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREIL 72
Cdd:pfam13411   2 TISELARLLGVTPRTLRYWEREGLLPPPRTE--RGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
GyrI-like pfam06445
GyrI-like small molecule binding domain; This family contains the small molecule binding ...
 121-268 9.26e-13

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.


Pssm-ID: 428947  Cd Length: 153  Bit Score: 64.35  E-value: 9.26e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883 121 RRLPARRVAAVTAD-DLPVADIGAwyhgALGELFATLASQGLPP-SGPAGGVYDDALFTLEHGRATVYVPVATEPRAAGR 198
Cdd:pfam06445   5 VELPAFRVAGLRHRgPYNEEGIGA----LWEELCAWASENGLSPaPSPLIGVSYDDPEVTEDEELRYDAGVAVPIPVEGP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1154143883 199 VRM--TELPPAELAVITHEGPETGIDRAYGTL-ATYVTRHALAVA-GPIHEFYPVTFHDTPDPShWRTEIGWPV 268
Cdd:pfam06445  81 EGVeeLELPGGEYAVFRHKGPYDDLQETYAKIyGEWLPESGYERRdGPSFEIYLNDPREVPEEE-LKTEIYIPV 153
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
7-72 1.71e-06

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 46.50  E-value: 1.71e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1154143883   7 IGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRY---DLAQIptaQIIHRFRDLDMPLADIREIL 72
Cdd:PRK09514    4 IGELAKLAEVTPDTLRFYEKQGLMDPEVRTE-GGYRLYteqDLQRL---RFIRRAKQLGFTLEEIRELL 68
 
Name Accession Description Interval E-value
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 5-112 1.23e-42

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.


Pssm-ID: 133382 [Multi-domain]  Cd Length: 108  Bit Score: 141.50  E-value: 1.23e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEVSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGARNALI 84
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLL 80

                          90       100
                  ....*....|....*....|....*...
gi 1154143883  85 ARHLRRLEDQLARTHDAVTSLRDLLEHP 112
Cdd:cd01107    81 REKLAELEAEIEELQRILRLLEDRLKQI 108
BltR2 COG4978
GyrI-like small molecule binding domain [Signal transduction mechanisms];
118-264 9.27e-34

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


Pssm-ID: 444003  Cd Length: 144  Bit Score: 119.72  E-value: 9.27e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883 118 ITHRRLPARRVAAVTADdLPVADIGAWYHGALGELFATLASQGLPPSGPAGGVYDDAlfTLEHGRATVYVPVATEPRAAG 197
Cdd:COG4978     1 VEVKELPAQPVASIRAT-VPMDELGELIGEAFGELFAYLAENGIEPAGPPFAIYHDT--DEDDVDVEVGVPVAGPLPGTG 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1154143883 198 RVRMTELPPAELAVITHEGPETGIDRAYGTLATYVTRHALAVAGPIHEFYPVTFHDTPDPSHWRTEI 264
Cdd:COG4978    78 DIKVGTLPAGKAATATHRGPYDTLDEAYEALLAWIEENGLEVAGPPREVYLTDPGNEPDPEEWVTEI 144
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 5-109 3.58e-25

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.


Pssm-ID: 133381 [Multi-domain]  Cd Length: 103  Bit Score: 96.02  E-value: 3.58e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGARNALi 84
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTE-NGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEAL- 78

                          90       100
                  ....*....|....*....|....*
gi 1154143883  85 ARHLRRLEDQLARTHDAVTSLRDLL 109
Cdd:cd01106    79 REQKELLEEKKERLDKLIKTIDRTL 103
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
7-97 1.33e-24

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 94.59  E-value: 1.33e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   7 IGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPG--ARNALI 84
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTE-GGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGeeEVRELL 79

                          90
                  ....*....|...
gi 1154143883  85 ARHLRRLEDQLAR 97
Cdd:COG0789    80 EEHLAELEAQIAE 92
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 5-97 5.42e-23

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.


Pssm-ID: 133378 [Multi-domain]  Cd Length: 100  Bit Score: 90.38  E-value: 5.42e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDevSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREIL----RTPDPGAR 80
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSE--NGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLdardEELSLAAL 78

                          90
                  ....*....|....*..
gi 1154143883  81 NALIARHLRRLEDQLAR 97
Cdd:cd00592    79 LALLDEKLAELEEKIAR 95
HTH_CadR-PbrR cd04784
Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; ...
 7-120 2.49e-18

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.


Pssm-ID: 133411  Cd Length: 127  Bit Score: 78.77  E-value: 2.49e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   7 IGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGAR-----N 81
Cdd:cd04784     3 IGELAKKTGCSVETIRYYEKEGLLPAPARSA-NNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEAscaevN 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1154143883  82 ALIARHLRRLEDQLARTHDAVTSLRDLLEHPEAAGAITH 120
Cdd:cd04784    82 ALIDEHLAHVRARIAELQALEKQLQALRERCDGARTIEE 120
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 5-111 5.32e-17

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.


Pssm-ID: 133383 [Multi-domain]  Cd Length: 127  Bit Score: 75.29  E-value: 5.32e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREIL---RTPDPGARN 81
Cdd:cd01108     1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSD-NGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLalwRDPSRASAD 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1154143883  82 --ALIARHLRRLEDQLARTHDAVTSLRDLLEH 111
Cdd:cd01108    80 vkALALEHIAELERKIAELQAMRRTLQQLADS 111
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 5-97 9.09e-17

Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133396 [Multi-domain]  Cd Length: 96  Bit Score: 73.54  E-value: 9.09e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPgARNALI 84
Cdd:cd04768     1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAE-NGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEME-ELTAML 78

                          90
                  ....*....|...
gi 1154143883  85 ARHLRRLEDQLAR 97
Cdd:cd04768    79 LEKKQAIQQKIDR 91
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 121-268 6.56e-16

Bacterial transcription activator, effector binding domain; This domain is found in the probable effector binding domain of a number of different bacterial transcription activators.and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.


Pssm-ID: 214874 [Multi-domain]  Cd Length: 158  Bit Score: 73.28  E-value: 6.56e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883  121 RRLPARRVAAVTAddlpvadIGAWYHGALGELFATL----ASQGLPPSGPAG---GVYDDALFTLEHGRATVY--VPVAT 191
Cdd:smart00871   5 VELPAFKVAGLRH-------RGPNEDEKIPELWQRLiqwaKELGLLPVGNSGepyGVYYDDPDDTPDGEFRYDagVEVSD 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883  192 EPRAAGRVRMTELPPAELAVITHEG-PETGIDRAYGTLATYV---TRHALAVAGPIHEFYPVTFHDTpDPSHWRTEIGWP 267
Cdd:smart00871  78 EVEAPEGVETKTIPAGKYAVFTHKGgSYDEIQEAWEAIYGEWlpnSGYELRDAGPDFEVYLNDPPDT-DPEELVTEIYIP 156


                   .
gi 1154143883  268 V 268
Cdd:smart00871 157 V 157
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 5-98 9.71e-16

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.


Pssm-ID: 133415 [Multi-domain]  Cd Length: 96  Bit Score: 70.87  E-value: 9.71e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGARnALI 84
Cdd:cd04788     1 WKIGELARRTGLSVRTLHHYDHIGLLSPSQRTE-GGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFDPL-ELL 78

                          90
                  ....*....|....
gi 1154143883  85 ARHLRRLEDQLART 98
Cdd:cd04788    79 RRQLARLEEQLELA 92
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 5-111 1.19e-15

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.


Pssm-ID: 133384 [Multi-domain]  Cd Length: 113  Bit Score: 70.95  E-value: 1.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPG-----A 79
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDE-NGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGdstipE 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1154143883  80 RNALIARHLRRLEDQLARTHDAvtslRDLLEH 111
Cdd:cd01109    80 RLELLEEHREELEEQIAELQET----LAYLDY 107
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
5-75 1.21e-15

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 69.86  E-value: 1.21e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1154143883    5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTP 75
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTE-GGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
HTH_BltR cd04782
Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) ...
 5-97 2.70e-15

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.


Pssm-ID: 133409 [Multi-domain]  Cd Length: 97  Bit Score: 69.57  E-value: 2.70e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGARNALI 84
Cdd:cd04782     1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKE-NGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRNPDELIELL 79

                          90
                  ....*....|...
gi 1154143883  85 ARHLRRLEDQLAR 97
Cdd:cd04782    80 KKQEKEIKEEIEE 92
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 7-107 6.78e-15

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.


Pssm-ID: 133398 [Multi-domain]  Cd Length: 123  Bit Score: 69.51  E-value: 6.78e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   7 IGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGAR-----N 81
Cdd:cd04770     3 IGELAKAAGVSPDTIRYYERIGLLPPPQRSE-NGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAApcaevR 81

                          90       100
                  ....*....|....*....|....*....
gi 1154143883  82 ALIARHLRRLE---DQLARTHDAVTSLRD 107
Cdd:cd04770    82 ALLEEKLAEVEakiAELQALRAELAGLLS 110
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-111 1.17e-14

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.


Pssm-ID: 133388  Cd Length: 112  Bit Score: 68.40  E-value: 1.17e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   7 IGDFARATHLSVKALRHYHEQGLLEPAATDevSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREIL---RTPDPGAR--N 81
Cdd:cd01282     3 IGELAARTGVSVRSLRYYEEQGLLVPERSA--NGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLpclRGGEPTFRpcP 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1154143883  82 ALIARHLRRLeDQLARTHDAVTSLRDLLEH 111
Cdd:cd01282    81 DLLAVLRREL-ARIDRQIADLTRSRDRLDA 109
MerR_1 pfam13411
MerR HTH family regulatory protein;
6-72 6.20e-13

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 62.19  E-value: 6.20e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1154143883   6 SIGDFARATHLSVKALRHYHEQGLLEPAATDevSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREIL 72
Cdd:pfam13411   2 TISELARLLGVTPRTLRYWEREGLLPPPRTE--RGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
GyrI-like pfam06445
GyrI-like small molecule binding domain; This family contains the small molecule binding ...
 121-268 9.26e-13

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.


Pssm-ID: 428947  Cd Length: 153  Bit Score: 64.35  E-value: 9.26e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883 121 RRLPARRVAAVTAD-DLPVADIGAwyhgALGELFATLASQGLPP-SGPAGGVYDDALFTLEHGRATVYVPVATEPRAAGR 198
Cdd:pfam06445   5 VELPAFRVAGLRHRgPYNEEGIGA----LWEELCAWASENGLSPaPSPLIGVSYDDPEVTEDEELRYDAGVAVPIPVEGP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1154143883 199 VRM--TELPPAELAVITHEGPETGIDRAYGTL-ATYVTRHALAVA-GPIHEFYPVTFHDTPDPShWRTEIGWPV 268
Cdd:pfam06445  81 EGVeeLELPGGEYAVFRHKGPYDDLQETYAKIyGEWLPESGYERRdGPSFEIYLNDPREVPEEE-LKTEIYIPV 153
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
 5-107 6.07e-12

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.


Pssm-ID: 133397 [Multi-domain]  Cd Length: 116  Bit Score: 61.23  E-value: 6.07e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvsGYRRYDLAQIPTAQIIHRFRDLDMPLADIREIL-------RTPDP 77
Cdd:cd04769     1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSG--NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFaghegraVLPWP 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1154143883  78 GARNAL------IARHLRRLEDQLARTHDAVTSLRD 107
Cdd:cd04769    79 HLQQALedkkqeIRAQITELQQLLARLDAFEASLKD 114
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
 5-97 2.77e-11

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


Pssm-ID: 133412 [Multi-domain]  Cd Length: 126  Bit Score: 59.48  E-value: 2.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLL-EPAATDevSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILR-TPDP----G 78
Cdd:cd04785     1 LSIGELARRTGVNVETIRYYESIGLLpEPARTA--GGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLAlSDRPdrscA 78

                          90
                  ....*....|....*....
gi 1154143883  79 ARNALIARHLRRLEDQLAR 97
Cdd:cd04785    79 EADAIARAHLADVRARIAD 97
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 5-55 1.18e-09

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.


Pssm-ID: 133389 [Multi-domain]  Cd Length: 49  Bit Score: 52.98  E-value: 1.18e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDevSGYRRYDLAQIPTAQII 55
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTE--GGYRLYSDADLERLRLI 49
MerR pfam00376
MerR family regulatory protein;
6-44 1.35e-09

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 52.42  E-value: 1.35e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1154143883   6 SIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRY 44
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTE-GGYRRY 38
HTH_MerR1 cd04783
Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix ...
 5-120 2.53e-09

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.


Pssm-ID: 133410 [Multi-domain]  Cd Length: 126  Bit Score: 54.15  E-value: 2.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLL-EPAATDevSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGARNA- 82
Cdd:cd04783     1 LTIGELAKAAGVNVETIRYYQRRGLLpEPPRPE--GGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCSEa 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1154143883  83 --LIARHLRRLEDQLARTHDAVTSLRDLLEHPEAAGAITH 120
Cdd:cd04783    79 reLAEQKLAEVDEKIADLQRMRASLQELVSQCAATKNNVS 118
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 5-115 7.12e-09

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.


Pssm-ID: 133403  Cd Length: 118  Bit Score: 52.53  E-value: 7.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEVSGYRRYDLAQIptaQIIHRFRDLDMPLADIREILRTPDPGARNA-- 82
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARL---KLILRGKRLGFSLEEIRELLDLYDPPGGNRkq 77

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1154143883  83 ------LIARHLRRLEDQLARTHDAVTSLRDLLEHPEAA 115
Cdd:cd04776    78 lekmleKIEKRRAELEQQRRDIDAALAELDAAEERCRER 116
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-109 1.15e-08

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.


Pssm-ID: 133406 [Multi-domain]  Cd Length: 134  Bit Score: 52.51  E-value: 1.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   7 IGDFARATHLSVKALRHYHEQGLLEPAATDevSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREIL--RTPDPGARNALI 84
Cdd:cd04779     3 IGQLAHLAGVSKRTIDYYTNLGLLTPERSD--SNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLeeVQRSDKEQREVA 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1154143883  85 ------ARHLRRLEDQLARTHDAVTSLRDLL 109
Cdd:cd04779    81 qevqlvCDQIDGLEHRLKQLKPIASQTDRAQ 111
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 5-109 2.50e-08

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.


Pssm-ID: 133400  Cd Length: 108  Bit Score: 50.82  E-value: 2.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAaTDEVSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRT----PDPGAR 80
Cdd:cd04773     1 MTIGELAHLLGVPPSTLRHWEKEGLLSPD-REPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQlrhaGGTEAL 79

                          90       100
                  ....*....|....*....|....*....
gi 1154143883  81 NALIARHLRRLEDQLARTHDAVTSLRDLL 109
Cdd:cd04773    80 AAALEQRRVALTQRGRAMLDAAAALAAYL 108
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 4-113 2.52e-08

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.


Pssm-ID: 133417 [Multi-domain]  Cd Length: 172  Bit Score: 52.43  E-value: 2.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   4 LLSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGArNAL 83
Cdd:cd04790     1 MLTISQLARQFGLSRSTLLYYERIGLLSPSARSE-SNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDA-TDV 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 1154143883  84 IARHLRRLEDQLARTHDAVTSLRDLLEHPE 113
Cdd:cd04790    79 LRRRLAELNREIQRLRQQQRAIATLLKQPT 108
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 13-99 2.81e-08

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.


Pssm-ID: 133414 [Multi-domain]  Cd Length: 133  Bit Score: 51.53  E-value: 2.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883  13 ATHLSVKA--LRHYHEQGLLEPAaTDEVSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILR------TPDPGARnALI 84
Cdd:cd04787     7 ANAAGVTPdtVRFYTRIGLLRPT-RDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILShadqgeSPCPMVR-RLI 84

                          90
                  ....*....|....*
gi 1154143883  85 ARHLRRLEDQLARTH 99
Cdd:cd04787    85 EQRLAETERRIKELL 99
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 4-73 5.11e-08

Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. 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.


Pssm-ID: 133380  Cd Length: 88  Bit Score: 49.54  E-value: 5.11e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   4 LLSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILR 73
Cdd:cd01105     1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDG-GGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLR 69
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
106-268 1.02e-06

DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];


Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 49.09  E-value: 1.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883 106 RDLLEHPEAAGAITHRRLPARRVAAVTAddlpvadIGAW--YHGALGELFATLASQGLPP--SGPAGGVYDDALFT-LEH 180
Cdd:COG3449   123 PLDPPRLEPMMDVEIKELPPRRVAYLRH-------RGPYeeIGEAFERLIAWAKARGLLPpdSRTIGIYYDDPDITpPEK 195

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883 181 GRATVYVPVATEPRAAGRVRMTELPPAELAVITHEGPETGIDRAYGTL-ATYVTRHALAVA-GPIHEFYPVTFHDTPdPS 258
Cdd:COG3449   196 LRYDACVTVPEDVALPGGVEVKTIPGGRYAVLRHKGPYEDLGAAWDWLyGEWLPASGYELRdRPCFEIYLNDPRETP-EG 274

                         170
                  ....*....|
gi 1154143883 259 HWRTEIGWPV 268
Cdd:COG3449   275 ELITDIYLPL 284
HTH_SoxR cd01110
Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) ...
 4-110 1.60e-06

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.


Pssm-ID: 133385 [Multi-domain]  Cd Length: 139  Bit Score: 46.42  E-value: 1.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   4 LLSIGDFARATHLSVKALRHYHEQGLLepAATDEVSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRT-PD---PGA 79
Cdd:cd01110     1 ELSVGEVAKRSGVAVSALHFYEQKGLI--ASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALATlPEdrtPTK 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1154143883  80 RN-ALIARHLR-RLEDQLARthdaVTSLRDLLE 110
Cdd:cd01110    79 ADwERLSRAWRdRLDERIAE----LQQLRDQLD 107
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
7-72 1.71e-06

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 46.50  E-value: 1.71e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1154143883   7 IGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRY---DLAQIptaQIIHRFRDLDMPLADIREIL 72
Cdd:PRK09514    4 IGELAKLAEVTPDTLRFYEKQGLMDPEVRTE-GGYRLYteqDLQRL---RFIRRAKQLGFTLEEIRELL 68
PRK10227 PRK10227
HTH-type transcriptional regulator CueR;
5-109 4.12e-06

HTH-type transcriptional regulator CueR;


Pssm-ID: 182320  Cd Length: 135  Bit Score: 45.41  E-value: 4.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRT-PDPGARNAL 83
Cdd:PRK10227    1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSE-NGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLfNDPQRHSAD 79

                          90       100
                  ....*....|....*....|....*...
gi 1154143883  84 IARhlRRLED--QLARTHDAVTSLRDLL 109
Cdd:PRK10227   80 VKR--RTLEKvaEIERHIEELQSMRDQL 105
MerR-DNA-bind pfam09278
MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in ...
 53-108 5.04e-06

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.


Pssm-ID: 462739  Cd Length: 65  Bit Score: 43.26  E-value: 5.04e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1154143883  53 QIIHRFRDLDMPLADIREIL-----RTPDPGARNALIARHLRRLEDQLARTHDAVTSLRDL 108
Cdd:pfam09278   5 AFIRRARRLGFSLEEIRELLalyddPGPPCADVRALLREKLAELEARIAELQALRDELDAL 65
HTH_MerR-like_sg6 cd04781
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 5-111 6.26e-06

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.


Pssm-ID: 133408  Cd Length: 120  Bit Score: 44.58  E-value: 6.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDevSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGA--RNA 82
Cdd:cd04781     1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRR--GLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPidRQL 78

                          90       100
                  ....*....|....*....|....*....
gi 1154143883  83 LIARhlrrlEDQLARTHDAVTSLRDLLEH 111
Cdd:cd04781    79 LKAK-----AAELDQQIQRLQAMRELLRH 102
PRK15002 PRK15002
redox-sensitive transcriptional activator SoxR;
4-126 3.02e-05

redox-sensitive transcriptional activator SoxR;


Pssm-ID: 184964  Cd Length: 154  Bit Score: 43.04  E-value: 3.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   4 LLSIGDFARATHLSVKALRHYHEQGLLEpaATDEVSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGarNAL 83
Cdd:PRK15002   11 LLTPGEVAKRSGVAVSALHFYESKGLIT--SIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEG--HTL 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1154143883  84 IARHLRRLEDQ----LARTHDAVTSLRDLLEHPEAAGAITHRRLPAR 126
Cdd:PRK15002   87 SAKEWKQLSSQwreeLDRRIHTLVALRDELDGCIGCGCLSRSDCPLR 133
PRK13752 PRK13752
mercuric resistance operon transcriptional regulator MerR;
3-76 5.49e-05

mercuric resistance operon transcriptional regulator MerR;


Pssm-ID: 184302  Cd Length: 144  Bit Score: 42.20  E-value: 5.49e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1154143883   3 ELLSIGDFARATHLSVKALRHYHEQGLLePAATDEVSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPD 76
Cdd:PRK13752    6 ENLTIGVFAKAAGVNVETIRFYQRKGLL-PEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLED 78
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
121-256 4.10e-04

DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];


Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 41.00  E-value: 4.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883 121 RRLPARRVAAVTADDLPVADIGAWYHGALGELFATLASQGLPPSGPAGGVYDDAlftlEHGRATVYVPVATEPRAAGRVR 200
Cdd:COG3449    61 LLRRRLLAALALLLLSSSAIIAAAAAASGYSSSASFRRFFRAFGGSSRSRRRRA----KAKLLALPPLDPPRLEPMMDVE 136

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1154143883 201 MTELPPAELAVITHEGPETGIDRAYGTLATYVTRHALavAGPIHEFYPVtFHDTPD 256
Cdd:COG3449   137 IKELPPRRVAYLRHRGPYEEIGEAFERLIAWAKARGL--LPPDSRTIGI-YYDDPD 189
HTH_HspR cd04766
Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) ...
 20-97 4.93e-04

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.


Pssm-ID: 133394 [Multi-domain]  Cd Length: 91  Bit Score: 38.40  E-value: 4.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883  20 ALRHYHEQGLLEPAATDevSGYRRY---DLAQIPTAQiiHRFRDLDMPLADIREILRTPdpgARNALIARHLRRLEDQLA 96
Cdd:cd04766    17 TLRLYERLGLLSPSRTD--GGTRRYserDIERLRRIQ--RLTQELGVNLAGVKRILELE---EELAELRAELDELRARLR 89


                  .
gi 1154143883  97 R 97
Cdd:cd04766    90 R 90
HTH_MerR-like_sg7 cd04786
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 5-131 1.72e-03

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.


Pssm-ID: 133413 [Multi-domain]  Cd Length: 131  Bit Score: 37.88  E-value: 1.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEpAATDEVSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGARNALI 84
Cdd:cd04786     1 MKIGELAKRSGMAASRIRFYEAEGLLS-SVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPADASNWQHDEL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1154143883  85 ARHLRR-------LEDQLARTHDAVTSLRDLLEHPEAAGAITHRrlpARRVAAV 131
Cdd:cd04786    80 LAALERkvadieaLEARLAQNKAQLLVLIDLIESKPDEMDCADN---ARRVMAR 130
HTH_MerR-like_sg1 cd04777
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-72 3.58e-03

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.


Pssm-ID: 133404 [Multi-domain]  Cd Length: 107  Bit Score: 36.24  E-value: 3.58e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1154143883   7 IGDFARATHLSVKALRHYHEQGLLEPaatDEVSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREIL 72
Cdd:cd04777     3 IGKFAKKNNITIDTVRHYIDLGLLIP---EKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIF 65
HTH_MerD cd01111
Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) ...
 5-91 3.61e-03

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.


Pssm-ID: 133386  Cd Length: 107  Bit Score: 36.21  E-value: 3.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1154143883   5 LSIGDFARATHLSVKALRHYHEQGLLEPAATDEvSGYRRYDLAQIPTAQIIHRFRDLDMPLADIREILRTPDPGARNALI 84
Cdd:cd01111     1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARTE-GGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDAGDGKQPE 79


                  ....*....
gi 1154143883  85 A--RHLRRL 91
Cdd:cd01111    80 AclAQLRQK 88
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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