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Conserved domains on  [gi|1906460605|ref|WP_189227318|]
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MerR family transcriptional regulator [Saccharothrix coeruleofusca]

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) ...
 13-110 4.28e-33

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: 116.85  E-value: 4.28e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDPGNGYRRYRADQLPVARLVARLRMLDMPLATVARIVSA-PPDERAALLAAY 91
Cdd:cd01107     4 GEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDAdNDDELRKLLREK 83

                          90
                  ....*....|....*....
gi 1906460605  92 WDGVEQRVAAQRTLAAHLR 110
Cdd:cd01107    84 LAELEAEIEELQRILRLLE 102
BltR2 COG4978
GyrI-like small molecule binding domain [Signal transduction mechanisms];
133-270 1.79e-20

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


:

Pssm-ID: 444003  Cd Length: 144  Bit Score: 85.05  E-value: 1.79e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605 133 QVVLTEQRHVTPEQLPEWIAEATDRLEKAARAHGG-VAGASFVVYHGDvnEDSDGPAEVCVPIEADEAPADA-AARVEPE 210
Cdd:COG4978     9 QPVASIRATVPMDELGELIGEAFGELFAYLAENGIePAGPPFAIYHDT--DEDDVDVEVGVPVAGPLPGTGDiKVGTLPA 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1906460605 211 HREAYVRLTKAqvrYPQILSAYDAVAEWIKANGHEIAAAPREVYFAG-WGENGPDDAVCDV 270
Cdd:COG4978    87 GKAATATHRGP---YDTLDEAYEALLAWIEENGLEVAGPPREVYLTDpGNEPDPEEWVTEI 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) ...
 13-110 4.28e-33

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: 116.85  E-value: 4.28e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDPGNGYRRYRADQLPVARLVARLRMLDMPLATVARIVSA-PPDERAALLAAY 91
Cdd:cd01107     4 GEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDAdNDDELRKLLREK 83

                          90
                  ....*....|....*....
gi 1906460605  92 WDGVEQRVAAQRTLAAHLR 110
Cdd:cd01107    84 LAELEAEIEELQRILRLLE 102
BltR2 COG4978
GyrI-like small molecule binding domain [Signal transduction mechanisms];
133-270 1.79e-20

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


Pssm-ID: 444003  Cd Length: 144  Bit Score: 85.05  E-value: 1.79e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605 133 QVVLTEQRHVTPEQLPEWIAEATDRLEKAARAHGG-VAGASFVVYHGDvnEDSDGPAEVCVPIEADEAPADA-AARVEPE 210
Cdd:COG4978     9 QPVASIRATVPMDELGELIGEAFGELFAYLAENGIePAGPPFAIYHDT--DEDDVDVEVGVPVAGPLPGTGDiKVGTLPA 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1906460605 211 HREAYVRLTKAqvrYPQILSAYDAVAEWIKANGHEIAAAPREVYFAG-WGENGPDDAVCDV 270
Cdd:COG4978    87 GKAATATHRGP---YDTLDEAYEALLAWIEENGLEVAGPPREVYLTDpGNEPDPEEWVTEI 144
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
13-109 2.95e-17

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 74.94  E-value: 2.95e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDPGnGYRRYRADQLPVARLVARLRMLDMPLATVARIVSAPPD---ERAALLA 89
Cdd:COG0789     2 GEVARLTGVSVRTLRYYERIGLLPPPERTEG-GYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDgeeEVRELLE 80

                          90       100
                  ....*....|....*....|
gi 1906460605  90 AYWDGVEQRVAAQRTLAAHL 109
Cdd:COG0789    81 EHLAELEAQIAELQALRAEL 100
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
13-80 1.42e-11

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 58.69  E-value: 1.42e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1906460605   13 GEFARRSRLSLKALRLYDRLGLLVPARVDPGnGYRRYRADQLPVARLVARLRMLDMPLATVARIVSAP 80
Cdd:smart00422   4 GEVAKLAGVSVRTLRYYERIGLLPPPIRTEG-GYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
MerR_1 pfam13411
MerR HTH family regulatory protein;
13-76 2.93e-09

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 52.17  E-value: 2.93e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARvdPGNGYRRYRADQLPVARLVARLRMLDMPLATVARI 76
Cdd:pfam13411   4 SELARLLGVTPRTLRYWEREGLLPPPR--TERGRRYYTDEDVERLRLIKALLERGLSLKEIKEL 65
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 140-275 7.64e-09

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: 53.63  E-value: 7.64e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  140 RHVTP---EQLPEWIAEATDRLEKAARAHGGVAGASFVVYHGDVNEDSDG--PAEVCVPIEADEAPADAAARVE-PEHRE 213
Cdd:smart00871  16 RHRGPnedEKIPELWQRLIQWAKELGLLPVGNSGEPYGVYYDDPDDTPDGefRYDAGVEVSDEVEAPEGVETKTiPAGKY 95

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1906460605  214 AYVRLTKAqvRYPQILSAYDAVAEWIKANGHEIAAA---PREVYFAGWGENGPDDAVCDVAFPVR 275
Cdd:smart00871  96 AVFTHKGG--SYDEIQEAWEAIYGEWLPNSGYELRDagpDFEVYLNDPPDTDPEELVTEIYIPVK 158
PRK15002 PRK15002
redox-sensitive transcriptional activator SoxR;
5-92 1.49e-05

redox-sensitive transcriptional activator SoxR;


Pssm-ID: 184964  Cd Length: 154  Bit Score: 44.20  E-value: 1.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605   5 RVAELLGTGEFARRSRLSLKALRLYDRLGLLVPARvDPGNgYRRYRADQLPVARLVARLRMLDMPLATVARIVSAPPdER 84
Cdd:PRK15002    7 RIKALLTPGEVAKRSGVAVSALHFYESKGLITSIR-NSGN-QRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLP-EG 83


                  ....*...
gi 1906460605  85 AALLAAYW 92
Cdd:PRK15002   84 HTLSAKEW 91
 
Name Accession Description Interval E-value
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 13-110 4.28e-33

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: 116.85  E-value: 4.28e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDPGNGYRRYRADQLPVARLVARLRMLDMPLATVARIVSA-PPDERAALLAAY 91
Cdd:cd01107     4 GEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDAdNDDELRKLLREK 83

                          90
                  ....*....|....*....
gi 1906460605  92 WDGVEQRVAAQRTLAAHLR 110
Cdd:cd01107    84 LAELEAEIEELQRILRLLE 102
BltR2 COG4978
GyrI-like small molecule binding domain [Signal transduction mechanisms];
133-270 1.79e-20

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


Pssm-ID: 444003  Cd Length: 144  Bit Score: 85.05  E-value: 1.79e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605 133 QVVLTEQRHVTPEQLPEWIAEATDRLEKAARAHGG-VAGASFVVYHGDvnEDSDGPAEVCVPIEADEAPADA-AARVEPE 210
Cdd:COG4978     9 QPVASIRATVPMDELGELIGEAFGELFAYLAENGIePAGPPFAIYHDT--DEDDVDVEVGVPVAGPLPGTGDiKVGTLPA 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1906460605 211 HREAYVRLTKAqvrYPQILSAYDAVAEWIKANGHEIAAAPREVYFAG-WGENGPDDAVCDV 270
Cdd:COG4978    87 GKAATATHRGP---YDTLDEAYEALLAWIEENGLEVAGPPREVYLTDpGNEPDPEEWVTEI 144
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
13-109 2.95e-17

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 74.94  E-value: 2.95e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDPGnGYRRYRADQLPVARLVARLRMLDMPLATVARIVSAPPD---ERAALLA 89
Cdd:COG0789     2 GEVARLTGVSVRTLRYYERIGLLPPPERTEG-GYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDgeeEVRELLE 80

                          90       100
                  ....*....|....*....|
gi 1906460605  90 AYWDGVEQRVAAQRTLAAHL 109
Cdd:COG0789    81 EHLAELEAQIAELQALRAEL 100
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 12-110 4.21e-14

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: 66.74  E-value: 4.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  12 TGEFARRSRLSLKALRLYDRLGLLVPARVDpGNGYRRYRADQLPVARLVARLRMLDMPLATVARIVSAPPDERAALLAAY 91
Cdd:cd01106     3 VGEVAKLTGVSVRTLHYYDEIGLLKPSRRT-ENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALREQ 81

                          90
                  ....*....|....*....
gi 1906460605  92 WDGVEQRVAAQRTLAAHLR 110
Cdd:cd01106    82 KELLEEKKERLDKLIKTID 100
HTH_BltR cd04782
Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) ...
 12-88 1.63e-13

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: 64.94  E-value: 1.63e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1906460605  12 TGEFARRSRLSLKALRLYDRLGLLVPARVDPgNGYRRYRADQLPVARLVARLRMLDMPLATVARIVSAP-PDERAALL 88
Cdd:cd04782     3 TGEFAKLCGISKQTLFHYDKIGLFKPEIVKE-NGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRnPDELIELL 79
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 10-88 4.30e-13

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: 63.91  E-value: 4.30e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1906460605  10 LGTGEFARRSRLSLKALRLYDRLGLLVPARVDPgNGYRRYRADQLPVARLVARLRMLDMPLATVARIVSAPPDERAALL 88
Cdd:cd04768     1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAE-NGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAML 78
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 12-86 9.92e-13

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: 62.65  E-value: 9.92e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1906460605  12 TGEFARRSRLSLKALRLYDRLGLLVPARVDpgNGYRRYRADQLPVARLVARLRMLDMPLATVARIVSAPPDERAA 86
Cdd:cd00592     3 IGEVAKLLGVSVRTLRYYEEKGLLPPERSE--NGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSL 75
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
13-80 1.42e-11

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 58.69  E-value: 1.42e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1906460605   13 GEFARRSRLSLKALRLYDRLGLLVPARVDPGnGYRRYRADQLPVARLVARLRMLDMPLATVARIVSAP 80
Cdd:smart00422   4 GEVAKLAGVSVRTLRYYERIGLLPPPIRTEG-GYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 13-107 2.64e-09

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: 53.61  E-value: 2.64e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDpGNGYRRYRADQLPVARLVARLRMLDMPLATVARIVS------APPDERAA 86
Cdd:cd01109     4 KEVAEKTGLSADTLRYYEKEGLLPPVKRD-ENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAElrregdSTIPERLE 82

                          90       100
                  ....*....|....*....|..
gi 1906460605  87 LLAAYWDGVEQRVAA-QRTLAA 107
Cdd:cd01109    83 LLEEHREELEEQIAElQETLAY 104
MerR_1 pfam13411
MerR HTH family regulatory protein;
13-76 2.93e-09

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 52.17  E-value: 2.93e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARvdPGNGYRRYRADQLPVARLVARLRMLDMPLATVARI 76
Cdd:pfam13411   4 SELARLLGVTPRTLRYWEREGLLPPPR--TERGRRYYTDEDVERLRLIKALLERGLSLKEIKEL 65
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 140-275 7.64e-09

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: 53.63  E-value: 7.64e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  140 RHVTP---EQLPEWIAEATDRLEKAARAHGGVAGASFVVYHGDVNEDSDG--PAEVCVPIEADEAPADAAARVE-PEHRE 213
Cdd:smart00871  16 RHRGPnedEKIPELWQRLIQWAKELGLLPVGNSGEPYGVYYDDPDDTPDGefRYDAGVEVSDEVEAPEGVETKTiPAGKY 95

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1906460605  214 AYVRLTKAqvRYPQILSAYDAVAEWIKANGHEIAAA---PREVYFAGWGENGPDDAVCDVAFPVR 275
Cdd:smart00871  96 AVFTHKGG--SYDEIQEAWEAIYGEWLPNSGYELRDagpDFEVYLNDPPDTDPEELVTEIYIPVK 158
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 13-105 1.05e-08

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: 51.61  E-value: 1.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVP-ARVDpgNGYRRY-RADqlpVARL--VARLRMLDMPLATVARIVSAPPDERAALL 88
Cdd:cd04788     4 GELARRTGLSVRTLHHYDHIGLLSPsQRTE--GGHRLYdRAD---IRRLhqIIALRRLGFSLREIGRALDGPDFDPLELL 78

                          90
                  ....*....|....*..
gi 1906460605  89 AAYWDGVEQRVAAQRTL 105
Cdd:cd04788    79 RRQLARLEEQLELATRL 95
HTH_CadR-PbrR cd04784
Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; ...
 13-110 3.93e-08

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: 50.65  E-value: 3.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLL-VPARVDpgNGYRRYRADQLPVARLVARLRMLDMPLATVARIVS------APPDERA 85
Cdd:cd04784     4 GELAKKTGCSVETIRYYEKEGLLpAPARSA--NNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQlqddpeASCAEVN 81

                          90       100
                  ....*....|....*....|....*
gi 1906460605  86 ALLAAYWDGVEQRVAAQRTLAAHLR 110
Cdd:cd04784    82 ALIDEHLAHVRARIAELQALEKQLQ 106
MerR pfam00376
MerR family regulatory protein;
12-49 1.01e-07

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 47.03  E-value: 1.01e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1906460605  12 TGEFARRSRLSLKALRLYDRLGLLVPARvDPGNGYRRY 49
Cdd:pfam00376   2 IGEVAKLLGVSPRTLRYYEKIGLLPPPE-RTEGGYRRY 38
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 14-110 1.21e-07

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: 49.61  E-value: 1.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  14 EFARRSRLSLKALRLYDRLGLLVPARvDPGNGYRRYRADQLPVARLVARLRMLDMPLATVARIV-------SAPPDERaA 86
Cdd:cd04787     5 ELANAAGVTPDTVRFYTRIGLLRPTR-DPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILshadqgeSPCPMVR-R 82

                          90       100
                  ....*....|....*....|....
gi 1906460605  87 LLAAYWDGVEQRVaaQRTLAAHLR 110
Cdd:cd04787    83 LIEQRLAETERRI--KELLKLRDR 104
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 13-114 3.23e-07

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: 48.33  E-value: 3.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDPgNGYRRYRADQLPVARLVARLRMLDMPLATVARIVS------APPDERAA 86
Cdd:cd04770     4 GELAKAAGVSPDTIRYYERIGLLPPPQRSE-NGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSlrddgaAPCAEVRA 82

                          90       100
                  ....*....|....*....|....*...
gi 1906460605  87 LLAAYWDGVEQRVAAQRTLAAHLRVVLS 114
Cdd:cd04770    83 LLEEKLAEVEAKIAELQALRAELAGLLS 110
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 13-110 3.26e-07

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: 47.99  E-value: 3.26e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDpgNGYRRYRADQLPVARLVARLRMLDMPLATVARIV--------SAPPDER 84
Cdd:cd01282     4 GELAARTGVSVRSLRYYEEQGLLVPERSA--NGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLpclrggepTFRPCPD 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1906460605  85 A-ALLAAYWDGVEQRVAA----QRTLAAHLR 110
Cdd:cd01282    82 LlAVLRRELARIDRQIADltrsRDRLDAYLA 112
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 13-70 4.42e-07

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: 47.94  E-value: 4.42e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPA-RVDpgNGYRRYRADQLPVARLVARLRMLDMPL 70
Cdd:cd01108     4 GEAAKLTGLSAKMIRYYEEIGLIPPPsRSD--NGYRVYNQRDIEELRFIRRARDLGFSL 60
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 13-54 5.13e-07

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: 45.66  E-value: 5.13e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARvdPGNGYRRYRADQL 54
Cdd:cd04761     4 GELAKLTGVSPSTLRYYERIGLLSPAR--TEGGYRLYSDADL 43
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 13-109 7.06e-07

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: 46.97  E-value: 7.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARvDPGNGYRRYRADQLPVARLVARLRMLDMPLATVARIVSA-----PPDERAAL 87
Cdd:cd04773     4 GELAHLLGVPPSTLRHWEKEGLLSPDR-EPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQlrhagGTEALAAA 82

                          90       100
                  ....*....|....*....|..
gi 1906460605  88 LAAYWDGVEQRVAAQRTLAAHL 109
Cdd:cd04773    83 LEQRRVALTQRGRAMLDAAAAL 104
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 13-154 1.78e-06

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: 47.04  E-value: 1.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDPGNgYRRYRADQLPVARLVARLRMLDMPLATVARIVSAPPDERAALLaayw 92
Cdd:cd04790     5 SQLARQFGLSRSTLLYYERIGLLSPSARSESN-YRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDATDVL---- 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1906460605  93 dgvEQRVAA-----QRtLAAHLRVVLsggkGLLEMYEiaqrsvgrqvVLTEQRHVTPEQLPEWIAEA 154
Cdd:cd04790    80 ---RRRLAElnreiQR-LRQQQRAIA----TLLKQPT----------LLKEQRLVTKEKWVAILKAA 128
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
 13-102 2.56e-06

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: 45.43  E-value: 2.56e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDPgnGYRRYRADQLPVARLVARLRMLDMPLATVARIVSAPPDERAA---LLA 89
Cdd:cd04769     4 GELAQQTGVTIKAIRLYEEKGLLPSPKRSG--NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLpwpHLQ 81

                          90
                  ....*....|...
gi 1906460605  90 AYWDGVEQRVAAQ 102
Cdd:cd04769    82 QALEDKKQEIRAQ 94
PRK15002 PRK15002
redox-sensitive transcriptional activator SoxR;
5-92 1.49e-05

redox-sensitive transcriptional activator SoxR;


Pssm-ID: 184964  Cd Length: 154  Bit Score: 44.20  E-value: 1.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605   5 RVAELLGTGEFARRSRLSLKALRLYDRLGLLVPARvDPGNgYRRYRADQLPVARLVARLRMLDMPLATVARIVSAPPdER 84
Cdd:PRK15002    7 RIKALLTPGEVAKRSGVAVSALHFYESKGLITSIR-NSGN-QRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLP-EG 83


                  ....*...
gi 1906460605  85 AALLAAYW 92
Cdd:PRK15002   84 HTLSAKEW 91
HTH_HspR cd04766
Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) ...
 6-76 3.36e-05

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: 41.48  E-value: 3.36e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1906460605   6 VAELLGTGEfarrsrlslKALRLYDRLGLLVPARVDpGNGyRRYRADQLPVARLVARL-RMLDMPLATVARI 76
Cdd:cd04766     7 AAELSGMHP---------QTLRLYERLGLLSPSRTD-GGT-RRYSERDIERLRRIQRLtQELGVNLAGVKRI 67
HTH_SoxR cd01110
Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) ...
 9-101 3.82e-05

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: 42.57  E-value: 3.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605   9 LLGTGEFARRSRLSLKALRLYDRLGLLVPARvDPGNgYRRYRADQLpvaRLVARLRM---LDMPLATVARIVSAPPDERA 85
Cdd:cd01110     1 ELSVGEVAKRSGVAVSALHFYEQKGLIASWR-NAGN-QRRYPRDVL---RRIAFIKVaqrLGLSLAEIAEALATLPEDRT 75

                          90       100
                  ....*....|....*....|...
gi 1906460605  86 ------ALLAAYW-DGVEQRVAA 101
Cdd:cd01110    76 ptkadwERLSRAWrDRLDERIAE 98
HTH_MerR-like_sg7 cd04786
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 13-115 5.64e-04

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: 39.04  E-value: 5.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARvDPGNGYRRYRADQLPVARLVARLRMLDMPLATVARIVsaPPD----ERAALL 88
Cdd:cd04786     4 GELAKRSGMAASRIRFYEAEGLLSSVE-RSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLL--PADasnwQHDELL 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1906460605  89 AAYWDGVEQRVAAQRTLA---AHLRVVLSG 115
Cdd:cd04786    81 AALERKVADIEALEARLAqnkAQLLVLIDL 110
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 13-71 2.61e-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 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: 37.10  E-value: 2.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDpgNGYRRYRADQLPVARLVARLRMLDMPLA 71
Cdd:cd04779     4 GQLAHLAGVSKRTIDYYTNLGLLTPERSD--SNYRYYDETALDRLQLIEHLKGQRLSLA 60
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 10-78 3.56e-03

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.


Pssm-ID: 133379  Cd Length: 68  Bit Score: 35.29  E-value: 3.56e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1906460605  10 LGTGEFARRSRLSLKALRLYD-RLGLLVPARVDpgNGYRRYRADQLPVARLVARLRMLDMPLATVARIVS 78
Cdd:cd01104     1 YTIGAVARLTGVSPDTLRAWErRYGLPAPQRTD--GGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68
HTH_TioE_rpt1 cd04772
First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 12-58 6.57e-03

First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.


Pssm-ID: 133399  Cd Length: 99  Bit Score: 35.45  E-value: 6.57e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1906460605  12 TGEFARRSRLSLKALRLYDRLGLLVPARVDPgNGYRRY---RADQLPVAR 58
Cdd:cd04772     3 TVDLARAIGLSPQTVRNYESLGLIPPAERTA-NGYRIYtdkHIAALRAYR 51
HTH_YfmP cd04774
Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) ...
 13-84 8.04e-03

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.


Pssm-ID: 133401 [Multi-domain]  Cd Length: 96  Bit Score: 35.18  E-value: 8.04e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1906460605  13 GEFARRSRLSLKALRLYDRLGLLVPARVDpgNGYRRYRADQLPVARLVARLR-MLDMPLATVARIVSAPPDER 84
Cdd:cd04774     4 DEVAKRLGLTKRTLKYYEEIGLVSPERSE--GRYRLYSEEDLKRLERILRLReVLGFSLQEVTHFLERPLEPV 74
 
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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