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Conserved domains on  [gi|1027832820|ref|WP_063730262|]
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MerR family transcriptional regulator [Lactiplantibacillus plantarum]

Protein Classification

MerR family transcriptional regulator( domain architecture ID 10100010)

MerR family transcriptional regulator is one of a group of transcriptional regulators with a conserved N-terminal helix-turn-helix (HTH) DNA binding motif and a specific effector binding region

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 2.36e-41

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: 138.03  E-value: 2.36e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPHSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSKLTSML 84
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLL 80

                          90       100
                  ....*....|....*....|....*...
gi 1027832820  85 TTQQQQVEAQLRLLTAVQQRINTRLAQI 112
Cdd:cd01107    81 REKLAELEAEIEELQRILRLLEDRLKQI 108
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 124-270 1.08e-07

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: 50.17  E-value: 1.08e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820  124 ECVTLPERAMVALRQPYRPQD-DIELVIAKLRAQTGATNEIFLGKVALML-----DQQAIQAGHFDRYAGICLLFEPGDT 197
Cdd:smart00871   3 RIVELPAFKVAGLRHRGPNEDeKIPELWQRLIQWAKELGLLPVGNSGEPYgvyydDPDDTPDGEFRYDAGVEVSDEVEAP 82

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1027832820  198 VPPHQEHLAAGSYAQRIFHG-THLDAPMQYRQLLADCRARGWHV---AGTAIETALIDYGITDqVAQSVTQIQLPIK 270
Cdd:smart00871  83 EGVETKTIPAGKYAVFTHKGgSYDEIQEAWEAIYGEWLPNSGYElrdAGPDFEVYLNDPPDTD-PEELVTEIYIPVK 158
 
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 2.36e-41

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: 138.03  E-value: 2.36e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPHSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSKLTSML 84
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLL 80

                          90       100
                  ....*....|....*....|....*...
gi 1027832820  85 TTQQQQVEAQLRLLTAVQQRINTRLAQI 112
Cdd:cd01107    81 REKLAELEAEIEELQRILRLLEDRLKQI 108
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
7-105 3.80e-23

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 90.74  E-value: 3.80e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   7 IGQLAQLFDIPVATLRYYDEIGLLTPARVNPhSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARE--LSKLTSML 84
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTE-GGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDdgEEEVRELL 79

                          90       100
                  ....*....|....*....|.
gi 1027832820  85 TTQQQQVEAQLRLLTAVQQRI 105
Cdd:COG0789    80 EEHLAELEAQIAELQALRAEL 100
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
5-72 9.84e-16

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 69.86  E-value: 9.84e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1027832820    5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPhSHYRYYGTPQFERLSTIKYLRALGLPLATIADFF 72
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTE-GGYRLYSDEDLERLRFIKRLKELGFSLEEIKELL 67
MerR_1 pfam13411
MerR HTH family regulatory protein;
5-70 4.32e-13

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 62.57  E-value: 4.32e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPhsHYRYYGTPQFERLSTIKYLRALGLPLATIAD 70
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTER--GRRYYTDEDVERLRLIKALLERGLSLKEIKE 64
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
5-106 5.80e-12

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 61.91  E-value: 5.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNpHSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVAR-ELSKLT-- 81
Cdd:PRK09514    2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRT-EGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRlDPEHHTcq 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1027832820  82 ---SMLTTQQQQVEAQLRLLTAVQ---QRIN 106
Cdd:PRK09514   81 evkGIVDEKLAEVEAKIAELQHMRrslQRLN 111
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 124-270 1.08e-07

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: 50.17  E-value: 1.08e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820  124 ECVTLPERAMVALRQPYRPQD-DIELVIAKLRAQTGATNEIFLGKVALML-----DQQAIQAGHFDRYAGICLLFEPGDT 197
Cdd:smart00871   3 RIVELPAFKVAGLRHRGPNEDeKIPELWQRLIQWAKELGLLPVGNSGEPYgvyydDPDDTPDGEFRYDAGVEVSDEVEAP 82

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1027832820  198 VPPHQEHLAAGSYAQRIFHG-THLDAPMQYRQLLADCRARGWHV---AGTAIETALIDYGITDqVAQSVTQIQLPIK 270
Cdd:smart00871  83 EGVETKTIPAGKYAVFTHKGgSYDEIQEAWEAIYGEWLPNSGYElrdAGPDFEVYLNDPPDTD-PEELVTEIYIPVK 158
GyrI-like pfam06445
GyrI-like small molecule binding domain; This family contains the small molecule binding ...
 126-269 5.32e-05

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: 42.40  E-value: 5.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820 126 VTLPERAMVALRQPYRPQD-DIELVIAKLRAQTGATNEIFLGKVA--LMLDQQAIQAGHFDRYAgICLLFEPGDTVPP-- 200
Cdd:pfam06445   5 VELPAFRVAGLRHRGPYNEeGIGALWEELCAWASENGLSPAPSPLigVSYDDPEVTEDEELRYD-AGVAVPIPVEGPEgv 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1027832820 201 HQEHLAAGSYAQRIFHGTHLDAPMQYRQLLADC-RARGW-HVAGTAIETALIDYGITDQvAQSVTQIQLPI 269
Cdd:pfam06445  84 EELELPGGEYAVFRHKGPYDDLQETYAKIYGEWlPESGYeRRDGPSFEIYLNDPREVPE-EELKTEIYIPV 153
 
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 2.36e-41

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: 138.03  E-value: 2.36e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPHSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSKLTSML 84
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLL 80

                          90       100
                  ....*....|....*....|....*...
gi 1027832820  85 TTQQQQVEAQLRLLTAVQQRINTRLAQI 112
Cdd:cd01107    81 REKLAELEAEIEELQRILRLLEDRLKQI 108
HTH_BltR cd04782
Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) ...
 5-102 9.32e-24

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: 91.91  E-value: 9.32e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPArVNPHSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSKLTSML 84
Cdd:cd04782     1 FTTGEFAKLCGISKQTLFHYDKIGLFKPE-IVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRNPDELIELL 79

                          90
                  ....*....|....*...
gi 1027832820  85 TTQQQQVEAQLRLLTAVQ 102
Cdd:cd04782    80 KKQEKEIKEEIEELQKIK 97
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
7-105 3.80e-23

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 90.74  E-value: 3.80e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   7 IGQLAQLFDIPVATLRYYDEIGLLTPARVNPhSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARE--LSKLTSML 84
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTE-GGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDdgEEEVRELL 79

                          90       100
                  ....*....|....*....|.
gi 1027832820  85 TTQQQQVEAQLRLLTAVQQRI 105
Cdd:COG0789    80 EEHLAELEAQIAELQALRAEL 100
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 5-116 5.58e-23

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: 90.24  E-value: 5.58e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPhSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSKLTSMl 84
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTE-NGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEAL- 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1027832820  85 ttqqqqvEAQLRLLTAVQQRINTRLAQIKTAQ 116
Cdd:cd01106    79 -------REQKELLEEKKERLDKLIKTIDRTL 103
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 5-102 8.39e-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: 89.61  E-value: 8.39e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNphSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVAR----ELSKL 80
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSE--NGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARdeelSLAAL 78

                          90       100
                  ....*....|....*....|..
gi 1027832820  81 TSMLTTQQQQVEAQLRLLTAVQ 102
Cdd:cd00592    79 LALLDEKLAELEEKIARLEALL 100
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 5-102 3.09e-22

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: 88.18  E-value: 3.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPHShYRYYGTPQFERLSTIKYLRALGLPLATIADfFVARELSKLTSML 84
Cdd:cd04768     1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENG-YRYYSYAQLYQLQFILFLRELGFSLAEIKE-LLDTEMEELTAML 78

                          90
                  ....*....|....*...
gi 1027832820  85 TTQQQQVEAQLRLLTAVQ 102
Cdd:cd04768    79 LEKKQAIQQKIDRLQQLE 96
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 5-110 8.27e-19

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: 79.42  E-value: 8.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNpHSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSKLT--- 81
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRD-ENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTipe 79

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1027832820  82 --SMLTTQQQQVEAQLRLLTAVQQRINTRLA 110
Cdd:cd01109    80 rlELLEEHREELEEQIAELQETLAYLDYKID 110
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 7-110 2.20e-16

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: 73.37  E-value: 2.20e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   7 IGQLAQLFDIPVATLRYYDEIGLLTPARVNPhSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSKLTS---- 82
Cdd:cd04770     3 IGELAKAAGVSPDTIRYYERIGLLPPPQRSE-NGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCaevr 81

                          90       100
                  ....*....|....*....|....*....
gi 1027832820  83 -MLTTQQQQVEAQLRLLTAVQQRINTRLA 110
Cdd:cd04770    82 aLLEEKLAEVEAKIAELQALRAELAGLLS 110
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
5-72 9.84e-16

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 69.86  E-value: 9.84e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1027832820    5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPhSHYRYYGTPQFERLSTIKYLRALGLPLATIADFF 72
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTE-GGYRLYSDEDLERLRFIKRLKELGFSLEEIKELL 67
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 5-111 2.57e-14

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: 69.00  E-value: 2.57e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPhSHYRYYGTPQFERLSTIKYLRALGLPLATIADfFVARELSKLTSML 84
Cdd:cd04790     2 LTISQLARQFGLSRSTLLYYERIGLLSPSARSE-SNYRLYGERDLERLEQICAYRSAGVSLEDIRS-LLQQPGDDATDVL 79

                          90       100
                  ....*....|....*....|....*..
gi 1027832820  85 TTQQQQVEAQLRLLTAVQQRINTRLAQ 111
Cdd:cd04790    80 RRRLAELNREIQRLRQQQRAIATLLKQ 106
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 7-101 2.85e-13

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: 64.32  E-value: 2.85e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   7 IGQLAQLFDIPVATLRYYDEIGLLTPARvNPHSHYRYYGTPQFERLSTIKYLRALGLPLATIADfFVARELSKLTSMLTT 86
Cdd:cd04788     3 IGELARRTGLSVRTLHHYDHIGLLSPSQ-RTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGR-ALDGPDFDPLELLRR 80

                          90
                  ....*....|....*
gi 1027832820  87 QQQQVEAQLRLLTAV 101
Cdd:cd04788    81 QLARLEEQLELATRL 95
MerR_1 pfam13411
MerR HTH family regulatory protein;
5-70 4.32e-13

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 62.57  E-value: 4.32e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPhsHYRYYGTPQFERLSTIKYLRALGLPLATIAD 70
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTER--GRRYYTDEDVERLRLIKALLERGLSLKEIKE 64
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
 7-116 6.72e-13

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: 63.54  E-value: 6.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   7 IGQLAQLFDIPVATLRYYDEIGLLTPARVNPhsHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARE------LSKL 80
Cdd:cd04769     3 IGELAQQTGVTIKAIRLYEEKGLLPSPKRSG--NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEgravlpWPHL 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1027832820  81 TSMLTTQQQQVEAQLRLLTAVQQRINTRLAQIKTAQ 116
Cdd:cd04769    81 QQALEDKKQEIRAQITELQQLLARLDAFEASLKDAL 116
HTH_CadR-PbrR cd04784
Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; ...
 7-125 8.30e-13

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: 63.74  E-value: 8.30e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   7 IGQLAQLFDIPVATLRYYDEIGLL-TPARVNphSHYRYYGTPQFERLSTIKYLRALGLPLATIadffvaRELSKLTS--- 82
Cdd:cd04784     3 IGELAKKTGCSVETIRYYEKEGLLpAPARSA--NNYRLYDEEHLERLLFIRRCRSLDMSLDEI------RTLLQLQDdpe 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1027832820  83 --------MLTTQQQQVEAQLRLLTAVQQrintRLAQIKTAQSANFDVTEC 125
Cdd:cd04784    75 ascaevnaLIDEHLAHVRARIAELQALEK----QLQALRERCDGARTIEEC 121
HTH_MerR-like_sg6 cd04781
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 6-106 9.30e-13

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: 63.46  E-value: 9.30e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   6 SIGQLAQLFDIPVATLRYYDEIGLLTParVNPHSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSKLT-SML 84
Cdd:cd04781     2 DIAEVARQSGLPASTLRYYEEKGLIAS--IGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDrQLL 79

                          90       100
                  ....*....|....*....|..
gi 1027832820  85 TTQQQQVEAQLRLLTAVQQRIN 106
Cdd:cd04781    80 KAKAAELDQQIQRLQAMRELLR 101
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
5-106 5.80e-12

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 61.91  E-value: 5.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNpHSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVAR-ELSKLT-- 81
Cdd:PRK09514    2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRT-EGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRlDPEHHTcq 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1027832820  82 ---SMLTTQQQQVEAQLRLLTAVQ---QRIN 106
Cdd:PRK09514   81 evkGIVDEKLAEVEAKIAELQHMRrslQRLN 111
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-110 1.00e-11

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: 60.31  E-value: 1.00e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   7 IGQLAQLFDIPVATLRYYDEIGLLTPARVNphSHYRYYGTPQFERLSTIKYLRALGLPLATIADFF--------VARELS 78
Cdd:cd01282     3 IGELAARTGVSVRSLRYYEEQGLLVPERSA--NGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLpclrggepTFRPCP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1027832820  79 KLTSMLTTQQQQVEAQLRLLTAVQQRINTRLA 110
Cdd:cd01282    81 DLLAVLRRELARIDRQIADLTRSRDRLDAYLA 112
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 5-115 5.67e-11

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: 58.31  E-value: 5.67e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPHshyRYYGTPQFERLSTIKYLRALGLPLATIadffvaRELSKLTSML 84
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQT---RVYSRRDRARLKLILRGKRLGFSLEEI------RELLDLYDPP 71

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1027832820  85 TTQQQQVEAQLRLLTAVQQRINTRLAQIKTA 115
Cdd:cd04776    72 GGNRKQLEKMLEKIEKRRAELEQQRRDIDAA 102
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 5-52 1.15e-10

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: 55.68  E-value: 1.15e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNphSHYRYYGTPQFERL 52
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTE--GGYRLYSDADLERL 46
MerR pfam00376
MerR family regulatory protein;
6-44 2.50e-10

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 54.35  E-value: 2.50e-10
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1027832820   6 SIGQLAQLFDIPVATLRYYDEIGLLTPARvNPHSHYRYY 44
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPE-RTEGGYRRY 38
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
 5-114 3.10e-10

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: 56.79  E-value: 3.10e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLT-PARVNphSHYRYYGTPQFERLSTIKYLRALGLPLATIadffvaRELSKLTSM 83
Cdd:cd04785     1 LSIGELARRTGVNVETIRYYESIGLLPePARTA--GGYRLYGAAHVERLRFIRRARDLGFSLEEI------RALLALSDR 72

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1027832820  84 LTTQQQQVEAQLRL-LTAVQQRInTRLAQIKT 114
Cdd:cd04785    73 PDRSCAEADAIARAhLADVRARI-ADLRRLEA 103
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 5-113 4.76e-10

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: 56.36  E-value: 4.76e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNphSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSKLTsml 84
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSD--SNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQRSDKE--- 75

                          90       100
                  ....*....|....*....|....*....
gi 1027832820  85 ttqQQQVEAQLRLLTAVQQRINTRLAQIK 113
Cdd:cd04779    76 ---QREVAQEVQLVCDQIDGLEHRLKQLK 101
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 9-104 1.80e-09

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: 54.62  E-value: 1.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   9 QLAQLFDIPVATLRYYDEIGLLTPARvNPHSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSK----LTSML 84
Cdd:cd04787     5 ELANAAGVTPDTVRFYTRIGLLRPTR-DPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGEspcpMVRRL 83

                          90       100
                  ....*....|....*....|.
gi 1027832820  85 TTQQ-QQVEAQLRLLTAVQQR 104
Cdd:cd04787    84 IEQRlAETERRIKELLKLRDR 104
HTH_Cfa-like cd04775
Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative ...
 5-101 4.54e-09

Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133402 [Multi-domain]  Cd Length: 102  Bit Score: 52.93  E-value: 4.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARvNPhSHYRYYGTPQFERLSTIKYLRALGLPLATIADFFVAR----ELSKL 80
Cdd:cd04775     2 YTIGQMSRKFGVSRSTLLYYESIGLIPSAR-SE-ANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPhvqaILEER 79

                          90       100
                  ....*....|....*....|.
gi 1027832820  81 TSMLTTQQQQVEAQLRLLTAV 101
Cdd:cd04775    80 LQSLNREIQRLRQQQQVLAAI 100
HTH_MerR1 cd04783
Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix ...
 5-115 3.94e-08

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: 50.69  E-value: 3.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLL-TPARvnPHSHYRYYGTPQFERLSTIKYLRALGLPLATIAdffvarELSKLTSM 83
Cdd:cd04783     1 LTIGELAKAAGVNVETIRYYQRRGLLpEPPR--PEGGYRRYPEETVTRLRFIKRAQELGFTLDEIA------ELLELDDG 72

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1027832820  84 LTTQQQQVEAQLRlLTAVQQRINtRLAQIKTA 115
Cdd:cd04783    73 TDCSEARELAEQK-LAEVDEKIA-DLQRMRAS 102
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 6-69 5.01e-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: 50.05  E-value: 5.01e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1027832820   6 SIGQLAQLFDIPVATLRYYDEIGLLTPARvNPHSHYRYYGTPQFERLSTIKYLRALGLPLATIA 69
Cdd:cd04773     2 TIGELAHLLGVPPSTLRHWEKEGLLSPDR-EPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIA 64
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 124-270 1.08e-07

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: 50.17  E-value: 1.08e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820  124 ECVTLPERAMVALRQPYRPQD-DIELVIAKLRAQTGATNEIFLGKVALML-----DQQAIQAGHFDRYAGICLLFEPGDT 197
Cdd:smart00871   3 RIVELPAFKVAGLRHRGPNEDeKIPELWQRLIQWAKELGLLPVGNSGEPYgvyydDPDDTPDGEFRYDAGVEVSDEVEAP 82

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1027832820  198 VPPHQEHLAAGSYAQRIFHG-THLDAPMQYRQLLADCRARGWHV---AGTAIETALIDYGITDqVAQSVTQIQLPIK 270
Cdd:smart00871  83 EGVETKTIPAGKYAVFTHKGgSYDEIQEAWEAIYGEWLPNSGYElrdAGPDFEVYLNDPPDTD-PEELVTEIYIPVK 158
HTH_MerR-like_sg1 cd04777
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-105 1.43e-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 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: 48.56  E-value: 1.43e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   7 IGQLAQLFDIPVATLRYYDEIGLLTPARVNphSHYrYYGTPQFERLSTIKYLRALGLPLATIADFFVARELSKLT----- 81
Cdd:cd04777     3 IGKFAKKNNITIDTVRHYIDLGLLIPEKKG--GQY-FFDEKCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRthedq 79

                          90       100
                  ....*....|....*....|....*...
gi 1027832820  82 ----SMLTTQQQQVEAQLRLLTAVQQRI 105
Cdd:cd04777    80 dyykSFLKNKKDELEKEIEDLKKAIQKL 107
HTH_SoxR cd01110
Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) ...
 6-113 2.45e-07

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: 48.73  E-value: 2.45e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   6 SIGQLAQLFDIPVATLRYYDEIGLLTPARvNPHSHyRYYGTPQFERLSTIKYLRALGLPLATIADffvarELSKLTSMLT 85
Cdd:cd01110     3 SVGEVAKRSGVAVSALHFYEQKGLIASWR-NAGNQ-RRYPRDVLRRIAFIKVAQRLGLSLAEIAE-----ALATLPEDRT 75

                          90       100
                  ....*....|....*....|....*...
gi 1027832820  86 TQQQQVEaqlRLLTAVQQRINTRLAQIK 113
Cdd:cd01110    76 PTKADWE---RLSRAWRDRLDERIAELQ 100
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 7-71 3.15e-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: 48.33  E-value: 3.15e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1027832820   7 IGQLAQLFDIPVATLRYYDEIGLLTPArVNPHSHYRYYGTPQFERLSTIKYLRALGLPLATIADF 71
Cdd:cd01108     3 IGEAAKLTGLSAKMIRYYEEIGLIPPP-SRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIREL 66
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 5-84 1.33e-06

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: 45.30  E-value: 1.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPHSHyRYYGTPQFERLSTIKYLRALGLPLATIADffVARELSKLTSML 84
Cdd:cd01105     2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQ-RKYSLADVDRLLVIKELLDEGFTLAAAVE--KLRRRRVQAEVR 78
HTH_YfmP cd04774
Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) ...
 5-71 7.32e-06

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: 43.65  E-value: 7.32e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNphSHYRYYGTPQFERLSTIKYLRA-LGLPLATIADF 71
Cdd:cd04774     1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERSE--GRYRLYSEEDLKRLERILRLREvLGFSLQEVTHF 66
HTH_HspR cd04766
Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) ...
 5-104 8.26e-06

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: 43.41  E-value: 8.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPHShyRYYGTPQFERLSTIKYL-RALGLPLATIADFFVARElskltsm 83
Cdd:cd04766     2 YVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGT--RRYSERDIERLRRIQRLtQELGVNLAGVKRILELEE------- 72

                          90       100
                  ....*....|....*....|.
gi 1027832820  84 lttQQQQVEAQLRLLTAVQQR 104
Cdd:cd04766    73 ---ELAELRAELDELRARLRR 90
HTH_MerR-like_sg5 cd04780
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 7-72 1.19e-05

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


Pssm-ID: 133407  Cd Length: 95  Bit Score: 43.08  E-value: 1.19e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1027832820   7 IGQLAQLFDIPVATLRYYDEIGLLTPA-RVNPHSHyrYYGTPQFERLSTIKYLR-ALGLPLATIADFF 72
Cdd:cd04780     3 MSELSKRSGVSVATIKYYLREGLLPEGrRLAPNQA--EYSEAHVERLRLIRALQqEGGLPISQIKEVL 68
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 5-69 1.86e-05

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: 41.84  E-value: 1.86e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDE-IGLLTPARVNphSHYRYYGTPQFERLSTIKYLRALGLPLATIA 69
Cdd:cd01104     1 YTIGAVARLTGVSPDTLRAWERrYGLPAPQRTD--GGHRLYSEADVARLRLIRRLTSEGVRISQAA 64
GyrI-like pfam06445
GyrI-like small molecule binding domain; This family contains the small molecule binding ...
 126-269 5.32e-05

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: 42.40  E-value: 5.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820 126 VTLPERAMVALRQPYRPQD-DIELVIAKLRAQTGATNEIFLGKVA--LMLDQQAIQAGHFDRYAgICLLFEPGDTVPP-- 200
Cdd:pfam06445   5 VELPAFRVAGLRHRGPYNEeGIGALWEELCAWASENGLSPAPSPLigVSYDDPEVTEDEELRYD-AGVAVPIPVEGPEgv 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1027832820 201 HQEHLAAGSYAQRIFHGTHLDAPMQYRQLLADC-RARGW-HVAGTAIETALIDYGITDQvAQSVTQIQLPI 269
Cdd:pfam06445  84 EELELPGGEYAVFRHKGPYDDLQETYAKIYGEWlPESGYeRRDGPSFEIYLNDPREVPE-EELKTEIYIPV 153
HTH_Cfa cd04789
Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative ...
 5-65 2.01e-04

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


Pssm-ID: 133416  Cd Length: 102  Bit Score: 39.78  E-value: 2.01e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARvNPHShYRYYGTPQFERLSTIKYLRALGLPL 65
Cdd:cd04789     2 YTISELAEKAGISRSTLLYYEKLGLITGTR-NANG-YRLYPDSDLQRLLLIQQLQAGGLSL 60
HTH_HspR-like_MBC cd04767
Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative ...
 5-58 4.52e-04

Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). 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: 133395  Cd Length: 120  Bit Score: 39.02  E-value: 4.52e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLTPARVNPHshyRYYGTPQFERLSTIKYL 58
Cdd:cd04767     2 YPIGVVAELLNIHPETLRIWERHGLIKPARRNGQ---RLYSNNDLKRLRFIKKL 52
PRK15002 PRK15002
redox-sensitive transcriptional activator SoxR;
8-106 1.35e-03

redox-sensitive transcriptional activator SoxR;


Pssm-ID: 184964  Cd Length: 154  Bit Score: 38.42  E-value: 1.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1027832820   8 GQLAQLFDIPVATLRYYDEIGLLTPARVNphSHYRYYGTPQFERLSTIKYLRALGLPLATIADFF-VARELSKLTS---- 82
Cdd:PRK15002   15 GEVAKRSGVAVSALHFYESKGLITSIRNS--GNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFgVLPEGHTLSAkewk 92

                          90       100
                  ....*....|....*....|....*
gi 1027832820  83 MLTTQ-QQQVEAQLRLLTAVQQRIN 106
Cdd:PRK15002   93 QLSSQwREELDRRIHTLVALRDELD 117
HTH_MlrA-like cd04763
Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix ...
 5-68 2.83e-03

Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, 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-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: 133391  Cd Length: 68  Bit Score: 35.59  E-value: 2.83e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYD-EIGLLTPARVNphSHYRYYGTPQFERLSTIKYLRALGLPLATI 68
Cdd:cd04763     1 YTIGEVALLTGIKPHVLRAWErEFGLLKPQRSD--GGHRLFNDADIDRILEIKRWIDNGVQVSKV 63
PRK13752 PRK13752
mercuric resistance operon transcriptional regulator MerR;
4-72 3.02e-03

mercuric resistance operon transcriptional regulator MerR;


Pssm-ID: 184302  Cd Length: 144  Bit Score: 37.19  E-value: 3.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1027832820   4 DFSIGQLAQLFDIPVATLRYYDEIGLLtPARVNPHSHYRYYGTPQFERLSTIKYLRALGLPLATIADFF 72
Cdd:PRK13752    7 NLTIGVFAKAAGVNVETIRFYQRKGLL-PEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELL 74
MerR-DNA-bind pfam09278
MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in ...
 50-107 3.76e-03

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: 35.17  E-value: 3.76e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1027832820  50 ERLSTIKYLRALGLPLATIADFFVARELSKLTS-----MLTTQQQQVEAQLRLLTAVQQRINT 107
Cdd:pfam09278   2 RRLAFIRRARRLGFSLEEIRELLALYDDPGPPCadvraLLREKLAELEARIAELQALRDELDA 64
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 5-43 3.87e-03

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 34.48  E-value: 3.87e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1027832820   5 FSIGQLAQLFDIPVATLRYYDEIGLLtPARVNPHSHYRY 43
Cdd:cd04762     1 LTTKEAAELLGVSPSTLRRWVKEGKL-KAIRTPGGHRRF 38
 
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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