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Conserved domains on  [gi|489997020|ref|WP_003900026|]
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MULTISPECIES: hypoxia response transcriptional regulator [Mycobacterium]

Protein Classification

heavy metal-responsive transcriptional regulator( domain architecture ID 10140950)

heavy metal-responsive transcriptional regulator mediates responses to heavy metal stress

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 1-129 1.61e-57

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: 175.06  E-value: 1.61e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLLDHasygppTEHDHSTVCWIL 129
Cdd:cd04770   81 RALLEEKLAEVEAKIAELQALRAELAGLLSA------CDGDESVICPIL 123
 
Name Accession Description Interval E-value
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 1-129 1.61e-57

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: 175.06  E-value: 1.61e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLLDHasygppTEHDHSTVCWIL 129
Cdd:cd04770   81 RALLEEKLAEVEAKIAELQALRAELAGLLSA------CDGDESVICPIL 123
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
3-105 4.85e-33

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 111.92  E-value: 4.85e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEapcAHVRQ 82
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGE---EEVRE 77

                         90       100
                 ....*....|....*....|...
gi 489997020  83 LLSTRIDEVRAQIAELIALEGHL 105
Cdd:COG0789   78 LLEEHLAELEAQIAELQALRAEL 100
CadR-PbrR TIGR02047
Cd(II)/Pb(II)-responsive transcriptional regulator; This model represents the cadmium(II) and ...
 1-108 7.23e-30

Cd(II)/Pb(II)-responsive transcriptional regulator; This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Regulatory functions, DNA interactions]


Pssm-ID: 131102  Cd Length: 127  Bit Score: 104.88  E-value: 7.23e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020    1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:TIGR02047   1 MKIGELAQKTGVSVETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKSCSDV 80

                          90       100
                  ....*....|....*....|....*...
gi 489997020   81 RQLLSTRIDEVRAQIAELIALEGHLQTL 108
Cdd:TIGR02047  81 NALLDEHISHVRARIIKLQALIEQLVDL 108
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
1-70 1.49e-26

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 94.51  E-value: 1.49e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020     1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIH 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
2-130 3.16e-26

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 95.81  E-value: 3.16e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   2 KISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIH-DRGEAPCAHV 80
Cdd:PRK09514   3 RIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRlDPEHHTCQEV 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLLDhASYGppTEHDhSTVCWILE 130
Cdd:PRK09514  83 KGIVDEKLAEVEAKIAELQHMRRSLQRLND-ACCG--TAHS-AVYCSILE 128
MerR-DNA-bind pfam09278
MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in ...
 44-108 9.65e-19

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: 74.46  E-value: 9.65e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489997020   44 VDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHVRQLLSTRIDEVRAQIAELIALEGHLQTL 108
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELLALYDDPGPPCADVRALLREKLAELEARIAELQALRDELDAL 65
 
Name Accession Description Interval E-value
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 1-129 1.61e-57

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: 175.06  E-value: 1.61e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLLDHasygppTEHDHSTVCWIL 129
Cdd:cd04770   81 RALLEEKLAEVEAKIAELQALRAELAGLLSA------CDGDESVICPIL 123
HTH_CadR-PbrR cd04784
Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; ...
 1-131 2.04e-36

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: 121.52  E-value: 2.04e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:cd04784    1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLLDHASYGPPTEHdhstvCWILES 131
Cdd:cd04784   81 NALIDEHLAHVRARIAELQALEKQLQALRERCDGARTIEE-----CGILQG 126
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 1-131 1.09e-34

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: 117.28  E-value: 1.09e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:cd01108    1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRASADV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLLDHASyGpptehDHSTVCWILES 131
Cdd:cd01108   81 KALALEHIAELERKIAELQAMRRTLQQLADSCH-G-----DDRPDCPILEG 125
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
3-105 4.85e-33

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 111.92  E-value: 4.85e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEapcAHVRQ 82
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGE---EEVRE 77

                         90       100
                 ....*....|....*....|...
gi 489997020  83 LLSTRIDEVRAQIAELIALEGHL 105
Cdd:COG0789   78 LLEEHLAELEAQIAELQALRAEL 100
HTH_MerR1 cd04783
Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix ...
 1-110 2.03e-31

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: 108.85  E-value: 2.03e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGeaPCAHV 80
Cdd:cd04783    1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDGT--DCSEA 78

                         90       100       110
                 ....*....|....*....|....*....|
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLLD 110
Cdd:cd04783   79 RELAEQKLAEVDEKIADLQRMRASLQELVS 108
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
 1-131 7.56e-31

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: 107.25  E-value: 7.56e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:cd04785    1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCAEA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLLDHASYGPPTEhdhstvCWILES 131
Cdd:cd04785   81 DAIARAHLADVRARIADLRRLEAELKRMVAACSGGRVAD------CRIIEA 125
CadR-PbrR TIGR02047
Cd(II)/Pb(II)-responsive transcriptional regulator; This model represents the cadmium(II) and ...
 1-108 7.23e-30

Cd(II)/Pb(II)-responsive transcriptional regulator; This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Regulatory functions, DNA interactions]


Pssm-ID: 131102  Cd Length: 127  Bit Score: 104.88  E-value: 7.23e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020    1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:TIGR02047   1 MKIGELAQKTGVSVETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKSCSDV 80

                          90       100
                  ....*....|....*....|....*...
gi 489997020   81 RQLLSTRIDEVRAQIAELIALEGHLQTL 108
Cdd:TIGR02047  81 NALLDEHISHVRARIIKLQALIEQLVDL 108
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 1-131 2.44e-29

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: 103.54  E-value: 2.44e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:cd04787    1 MKVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLLD---HASYGPPTEHdhsTVCWILES 131
Cdd:cd04787   81 RRLIEQRLAETERRIKELLKLRDRMQQAVSqwqQMPDGAPDGH---SICHLIES 131
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 1-102 2.73e-29

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: 102.71  E-value: 2.73e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPaRTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEApCAHV 80
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPE-RSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELS-LAAL 78

                         90       100
                 ....*....|....*....|..
gi 489997020  81 RQLLSTRIDEVRAQIAELIALE 102
Cdd:cd00592   79 LALLDEKLAELEEKIARLEALL 100
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 1-108 3.32e-27

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: 97.53  E-value: 3.32e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100
                 ....*....|....*....|....*...
gi 489997020  81 RQLLSTRIDEVRAQIAEliaLEGHLQTL 108
Cdd:cd01109   81 LELLEEHREELEEQIAE---LQETLAYL 105
MerR TIGR02051
Hg(II)-responsive transcriptional regulator; This model represents the mercury (II) responsive ...
 2-131 4.15e-27

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


Pssm-ID: 131106  Cd Length: 124  Bit Score: 97.84  E-value: 4.15e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020    2 KISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRgeAPCAHVR 81
Cdd:TIGR02051   1 TIGELAKAAGVNVETIRYYERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLVDG--THCREMY 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 489997020   82 QLLSTRIDEVRAQIAELIALEGHLQTLLDHAsygpPTEHDHSTvCWILES 131
Cdd:TIGR02051  79 ELASRKLKSVQAKMADLLRIERLLEELLEQC----PANKGNTS-CPIIES 123
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 1-110 1.17e-26

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: 96.14  E-value: 1.17e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPpARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEA---PC 77
Cdd:cd01282    1 MRIGELAARTGVSVRSLRYYEEQGLLVP-ERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLRGGEPtfrPC 79

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489997020  78 AHVRQLLSTRIDEVRAQIAELIALEGHLQTLLD 110
Cdd:cd01282   80 PDLLAVLRRELARIDRQIADLTRSRDRLDAYLA 112
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
1-70 1.49e-26

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 94.51  E-value: 1.49e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020     1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIH 70
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
2-130 3.16e-26

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 95.81  E-value: 3.16e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   2 KISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIH-DRGEAPCAHV 80
Cdd:PRK09514   3 RIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRlDPEHHTCQEV 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLLDhASYGppTEHDhSTVCWILE 130
Cdd:PRK09514  83 KGIVDEKLAEVEAKIAELQHMRRSLQRLND-ACCG--TAHS-AVYCSILE 128
CueR TIGR02044
Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and ...
 1-130 3.20e-25

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


Pssm-ID: 131099 [Multi-domain]  Cd Length: 127  Bit Score: 92.90  E-value: 3.20e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020    1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAI-HDRGEAPcAH 79
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLwNDPNRTS-AD 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 489997020   80 VRQLLSTRIDEVRAQIAELIALEGHLQTLLDhASYGpptehDHSTVCWILE 130
Cdd:TIGR02044  80 VKARTLEKVAEIERKISELQSMRDQLEALAQ-ACPG-----DDSPDCPIIE 124
ZntR TIGR02043
Zn(II)-responsive transcriptional regulator; This model represents the zinc and cadmium (II) ...
 1-131 7.03e-24

Zn(II)-responsive transcriptional regulator; This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Regulatory functions, DNA interactions]


Pssm-ID: 131098 [Multi-domain]  Cd Length: 131  Bit Score: 89.92  E-value: 7.03e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020    1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIH-DRGEAPCAH 79
Cdd:TIGR02043   2 FQIGELAKLCGVTSDTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSIKlDATEHSCAE 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 489997020   80 VRQLLSTRIDEVRAQIAELIALEGHLQTLLDhASYGPPTEHDHstvCWILES 131
Cdd:TIGR02043  82 VKAIVDAKLELVDEKINELTKIRRSLKKLSD-ACCGHTNDASH---CSILEA 129
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
 1-110 3.03e-23

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: 87.81  E-value: 3.03e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASgYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHD-RGEAPCAH 79
Cdd:cd04769    1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSGN-YRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEgRAVLPWPH 79

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489997020  80 VRQLLSTRIDEVRAQIAELIALEGHLQTLLD 110
Cdd:cd04769   80 LQQALEDKKQEIRAQITELQQLLARLDAFEA 110
HTH_MerR-like_sg6 cd04781
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 1-121 8.31e-23

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: 86.57  E-value: 8.31e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTaSGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAihdrGEAPCAHV 80
Cdd:cd04781    1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRR-GLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLS----HDGKPPID 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 489997020  81 RQLLSTRIDEVRAQIAELialeGHLQTLLDHASYGPPTEHD 121
Cdd:cd04781   76 RQLLKAKAAELDQQIQRL----QAMRELLRHVAQCPAPSHL 112
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 2-111 1.59e-20

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: 80.25  E-value: 1.59e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   2 KISEVAALTNTSTKTLRFYENSGLLpPPART--ASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRgeapcAH 79
Cdd:cd01107    2 TIGEFAKLSNLSIKALRYYDKIGLL-KPAYVdpDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADND-----DE 75

                         90       100       110
                 ....*....|....*....|....*....|..
gi 489997020  80 VRQLLSTRIDEVRAQIAELIALEGHLQTLLDH 111
Cdd:cd01107   76 LRKLLREKLAELEAEIEELQRILRLLEDRLKQ 107
MerR-DNA-bind pfam09278
MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in ...
 44-108 9.65e-19

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: 74.46  E-value: 9.65e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489997020   44 VDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHVRQLLSTRIDEVRAQIAELIALEGHLQTL 108
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELLALYDDPGPPCADVRALLREKLAELEARIAELQALRDELDAL 65
MerR_1 pfam13411
MerR HTH family regulatory protein;
1-67 1.17e-18

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 74.51  E-value: 1.17e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489997020    1 MKISEVAALTNTSTKTLRFYENSGLLPPPaRTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQIL 67
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPP-RTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
HTH_MerR-like_sg7 cd04786
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 1-105 2.50e-16

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: 70.24  E-value: 2.50e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAI------HDrge 74
Cdd:cd04786    1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPAdasnwqHD--- 77

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489997020  75 apcahvrQLLSTrideVRAQIAELIALEGHL 105
Cdd:cd04786   78 -------ELLAA----LERKVADIEALEARL 97
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 1-50 2.68e-16

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: 68.00  E-value: 2.68e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLpPPARTASGYRNYGPEIVDRLRFI 50
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLL-SPARTEGGYRLYSDADLERLRLI 49
PRK10227 PRK10227
HTH-type transcriptional regulator CueR;
1-108 2.94e-16

HTH-type transcriptional regulator CueR;


Pssm-ID: 182320  Cd Length: 135  Bit Score: 70.45  E-value: 2.94e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:PRK10227   1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFNDPQRHSADV 80

                         90       100
                 ....*....|....*....|....*...
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTL 108
Cdd:PRK10227  81 KRRTLEKVAEIERHIEELQSMRDQLLAL 108
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 1-111 1.38e-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: 64.81  E-value: 1.38e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILaihdrgEAPCAHV 80
Cdd:cd01106    1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELL------KDPSEDL 74

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489997020  81 RQLLstridevRAQIAELIALEGHLQTLLDH 111
Cdd:cd01106   75 LEAL-------REQKELLEEKKERLDKLIKT 98
MerR pfam00376
MerR family regulatory protein;
2-39 3.09e-14

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 62.44  E-value: 3.09e-14
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 489997020    2 KISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNY 39
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 3-114 8.41e-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: 64.76  E-value: 8.41e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHVR- 81
Cdd:cd04790    4 ISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDATDVLRRRl 83

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489997020  82 QLLSTRIDEVRAQ---IAELIALEGHL--QTLLDHASY 114
Cdd:cd04790   84 AELNREIQRLRQQqraIATLLKQPTLLkeQRLVTKEKW 121
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 1-101 3.09e-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: 61.24  E-value: 3.09e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILaihdrgEAPCAHV 80
Cdd:cd04788    1 WKIGELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRAL------DGPDFDP 74

                         90       100
                 ....*....|....*....|.
gi 489997020  81 RQLLSTRIDEVRAQIAELIAL 101
Cdd:cd04788   75 LELLRRQLARLEEQLELATRL 95
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 3-102 6.74e-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: 60.44  E-value: 6.74e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPcahvrQ 82
Cdd:cd04768    3 IGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEELTA-----M 77

                         90       100
                 ....*....|....*....|
gi 489997020  83 LLSTRIDeVRAQIAELIALE 102
Cdd:cd04768   78 LLEKKQA-IQQKIDRLQQLE 96
HTH_SoxR cd01110
Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) ...
 1-105 9.58e-13

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: 61.05  E-value: 9.58e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPpARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHV 80
Cdd:cd01110    2 LSVGEVAKRSGVAVSALHFYEQKGLIAS-WRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALATLPEDRTPTKAD 80

                         90       100
                 ....*....|....*....|....*.
gi 489997020  81 RQLLSTRI-DEVRAQIAELIALEGHL 105
Cdd:cd01110   81 WERLSRAWrDRLDERIAELQQLRDQL 106
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 1-110 1.02e-12

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: 60.62  E-value: 1.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLpPPARTAsGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHD--RGEAP-- 76
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLL-SPERRG-QTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDppGGNRKql 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489997020  77 ------CAHVRQLLSTRIDEVRAQIAELIALEGHLQTLLD 110
Cdd:cd04776   79 ekmlekIEKRRAELEQQRRDIDAALAELDAAEERCRERLA 118
PRK13752 PRK13752
mercuric resistance operon transcriptional regulator MerR;
1-109 3.83e-12

mercuric resistance operon transcriptional regulator MerR;


Pssm-ID: 184302  Cd Length: 144  Bit Score: 59.92  E-value: 3.83e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEapCAHV 80
Cdd:PRK13752   8 LTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLEDGTH--CEEA 85

                         90       100
                 ....*....|....*....|....*....
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLL 109
Cdd:PRK13752  86 SSLAEHKLKDVREKMADLARMEAVLSELV 114
HTH_Cfa-like cd04775
Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative ...
 2-109 1.91e-11

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: 56.78  E-value: 1.91e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   2 KISEVAALTNTSTKTLRFYENSGLLPPpARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAihdrgeapCAHVR 81
Cdd:cd04775    3 TIGQMSRKFGVSRSTLLYYESIGLIPS-ARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLA--------QPHVQ 73

                         90       100
                 ....*....|....*....|....*...
gi 489997020  82 QLLSTRIDEVRAQIAELIALEGHLQTLL 109
Cdd:cd04775   74 AILEERLQSLNREIQRLRQQQQVLAAIL 101
HTH_Cfa cd04789
Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative ...
 1-109 4.84e-11

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: 55.96  E-value: 4.84e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPpARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAihdrGEAPcahv 80
Cdd:cd04789    2 YTISELAEKAGISRSTLLYYEKLGLITG-TRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ----GKLT---- 72

                         90       100
                 ....*....|....*....|....*....
gi 489997020  81 RQLLSTRIDEVRAQIAELIALEGHLQTLL 109
Cdd:cd04789   73 RSLLLERLSSLAEQIARKQQARDLLAALL 101
HTH_MerR-like_sg5 cd04780
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 1-71 4.91e-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 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: 55.80  E-value: 4.91e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFI-HRGQAAGLALQEVRQILAIHD 71
Cdd:cd04780    1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIrALQQEGGLPISQIKEVLDAIA 72
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 2-110 3.42e-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: 54.43  E-value: 3.42e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   2 KISEVAALTNTSTKTLRFYENSGLLPPpARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHVR 81
Cdd:cd04779    2 RIGQLAHLAGVSKRTIDYYTNLGLLTP-ERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQRSDKEQREVA 80

                         90       100
                 ....*....|....*....|....*....
gi 489997020  82 QllstRIDEVRAQIAELIALEGHLQTLLD 110
Cdd:cd04779   81 Q----EVQLVCDQIDGLEHRLKQLKPIAS 105
HTH_MerD cd01111
Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) ...
 2-98 4.18e-10

Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133386  Cd Length: 107  Bit Score: 53.54  E-value: 4.18e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   2 KISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAH-V 80
Cdd:cd01111    2 SISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDAGDGKQPEaC 81

                         90
                 ....*....|....*...
gi 489997020  81 RQLLSTRIDEVRAQIAEL 98
Cdd:cd01111   82 LAQLRQKIEVRRAALNAL 99
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 1-75 1.13e-09

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: 52.36  E-value: 1.13e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQIL-AIHDRGEA 75
Cdd:cd04773    1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVeQLRHAGGT 76
HTH_HspR cd04766
Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) ...
 3-100 1.46e-09

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: 51.50  E-value: 1.46e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLpPPARTASGYRNYGPEIVDRLRFIHR-GQAAGLALQEVRQILAihdrgeapcahvr 81
Cdd:cd04766    4 ISVAAELSGMHPQTLRLYERLGLL-SPSRTDGGTRRYSERDIERLRRIQRlTQELGVNLAGVKRILE------------- 69

                         90
                 ....*....|....*....
gi 489997020  82 qlLSTRIDEVRAQIAELIA 100
Cdd:cd04766   70 --LEEELAELRAELDELRA 86
HTH_BltR cd04782
Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) ...
 2-102 2.44e-09

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: 51.08  E-value: 2.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   2 KISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAihDRGEAPCAHvr 81
Cdd:cd04782    2 TTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLD--NRNPDELIE-- 77

                         90       100
                 ....*....|....*....|.
gi 489997020  82 qLLSTRIDEVRAQIAELIALE 102
Cdd:cd04782   78 -LLKKQEKEIKEEIEELQKIK 97
HTH_TioE_rpt1 cd04772
First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 4-68 2.50e-09

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: 51.24  E-value: 2.50e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489997020   4 SEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFiHRGQAAGLALQEVRQILA 68
Cdd:cd04772    4 VDLARAIGLSPQTVRNYESLGLIPPAERTANGYRIYTDKHIAALRA-YRALLPGYGYRVAQRIMR 67
HTH_MlrA-like_sg1 cd04764
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 2-67 4.82e-09

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


Pssm-ID: 133392  Cd Length: 67  Bit Score: 49.64  E-value: 4.82e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489997020   2 KISEVAALTNTSTKTLRFYENS-GLLPPpaRTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQIL 67
Cdd:cd04764    2 TIKEVSEIIGVKPHTLRYYEKEfNLYIP--RTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66
HTH_YfmP cd04774
Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) ...
 1-67 1.29e-08

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: 49.43  E-value: 1.29e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLpPPARTASGYRNYGPEIVDRLRFIHRGQAA-GLALQEVRQIL 67
Cdd:cd04774    1 YKVDEVAKRLGLTKRTLKYYEEIGLV-SPERSEGRYRLYSEEDLKRLERILRLREVlGFSLQEVTHFL 67
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 3-68 3.59e-08

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: 47.24  E-value: 3.59e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILA 68
Cdd:cd01104    3 IGAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68
HTH_MlrA-like cd04763
Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix ...
 2-68 1.51e-07

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: 45.99  E-value: 1.51e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489997020   2 KISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILA 68
Cdd:cd04763    2 TIGEVALLTGIKPHVLRAWEREFGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLLS 68
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 3-72 3.95e-07

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: 3.95e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDR 72
Cdd:cd01105    4 IGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRV 73
HTH_HspR-like_MBC cd04767
Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative ...
 3-81 1.08e-06

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: 44.79  E-value: 1.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLPPPARtaSGYRNYGPEIVDRLRFIHR-GQAAGLALQEVRQILAIhdrgeAPCAHVR 81
Cdd:cd04767    4 IGVVAELLNIHPETLRIWERHGLIKPARR--NGQRLYSNNDLKRLRFIKKlINEKGLNIAGVKQILSM-----YPCWSIR 76
HTH_HspR-like cd01279
Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix ...
 3-75 7.46e-06

Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator HspR and related proteins, 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 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: 133387  Cd Length: 98  Bit Score: 42.20  E-value: 7.46e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLPPpARTASGYRNYGPEIVDRLRFIHR-GQAAGLALQEVRQILAIHDRGEA 75
Cdd:cd01279    4 ISVAAELLGIHPQTLRVYDRLGLVSP-ARTNGGGRRYSNNDLELLRQVQRlSQDEGFNLAGIKRIIELYPQVLL 76
HTH_MlrA-like_sg2 cd04765
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 2-98 1.73e-04

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.


Pssm-ID: 133393  Cd Length: 99  Bit Score: 38.39  E-value: 1.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   2 KISEVAALTNTSTKTLRFYEN--SGLLPPpaRTASGYRNYGPEIVDRLRFIHR---GQaaGLALQEVRQILAihDRGEAP 76
Cdd:cd04765    2 SIGEVAEILGLPPHVLRYWETefPQLKPV--KRAGGRRYYRPKDVELLLLIKHllyEK--GYTIEGAKQALK--EDGAAA 75

                         90       100
                 ....*....|....*....|..
gi 489997020  77 CAHVRqlLSTRIDEVRAQIAEL 98
Cdd:cd04765   76 IREEE--AEERLPSIRAELLDL 95
PRK15043 PRK15043
HTH-type transcriptional regulator MlrA;
3-71 1.93e-04

HTH-type transcriptional regulator MlrA;


Pssm-ID: 185003 [Multi-domain]  Cd Length: 243  Bit Score: 39.92  E-value: 1.93e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHD 71
Cdd:PRK15043   6 IGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNEN 74
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 1-39 1.98e-04

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: 37.18  E-value: 1.98e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLpPPARTASGYRNY 39
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKL-KAIRTPGGHRRF 38
PRK15002 PRK15002
redox-sensitive transcriptional activator SoxR;
5-105 1.62e-03

redox-sensitive transcriptional activator SoxR;


Pssm-ID: 184964  Cd Length: 154  Bit Score: 36.49  E-value: 1.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   5 EVAALTNTSTKTLRFYENSGLLpPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQILAIHDRGEAPCAHVRQLL 84
Cdd:PRK15002  16 EVAKRSGVAVSALHFYESKGLI-TSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKEWKQL 94

                         90       100
                 ....*....|....*....|..
gi 489997020  85 STRI-DEVRAQIAELIALEGHL 105
Cdd:PRK15002  95 SSQWrEELDRRIHTLVALRDEL 116
PRK13749 PRK13749
HTH-type transcriptional regulator MerD;
3-126 4.33e-03

HTH-type transcriptional regulator MerD;


Pssm-ID: 184299  Cd Length: 121  Bit Score: 34.89  E-value: 4.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489997020   3 ISEVAALTNTSTKTLRFYENSGLLPPPARTASGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQIL-----AIHDRGEAPC 77
Cdd:PRK13749   6 VSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCraldaADGDEAAAQL 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 489997020  78 AHVRQLLSTRidevRAQIAEliaLEGHLQTLldhasygpPTEHDHSTVC 126
Cdd:PRK13749  86 AVLRQLVERR----REALAD---LEVQLATM--------PTEPAQHAES 119
HTH_MerR-like_sg1 cd04777
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 1-67 4.74e-03

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


Pssm-ID: 133404 [Multi-domain]  Cd Length: 107  Bit Score: 34.69  E-value: 4.74e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489997020   1 MKISEVAALTNTSTKTLRFYENSGLLPPPARtaSGYRNYGPEIVDRLRFIHRGQAAGLALQEVRQIL 67
Cdd:cd04777    1 MKIGKFAKKNNITIDTVRHYIDLGLLIPEKK--GGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIF 65
HTH_MerR-like_sg2 cd04778
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 2-31 9.01e-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 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133405 [Multi-domain]  Cd Length: 219  Bit Score: 35.06  E-value: 9.01e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 489997020   2 KISEVAALTNTSTKTLRFYENSGLLPPPAR 31
Cdd:cd04778    3 RIDDLARAAGTTVRNVRAYQDRGLLPPPRR 32
 
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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