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Conserved domains on  [gi|1473287884|ref|WP_117757475|]
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MULTISPECIES: MerR family transcriptional regulator [Collinsella]

Protein Classification

MerR family transcriptional regulator( domain architecture ID 323)

MerR family transcriptional regulator activates transcription through protein-dependent DNA distortion and the majority of regulators in the family respond to environmental stimuli, such as oxidative stress, heavy metals or antibiotics

CATH:  1.10.10.10
Gene Ontology:  GO:0006355|GO:0003677|GO:0003700
PubMed:  17302809|12829265|15808743|35130613
SCOP:  3000158

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_MerR-SF super family cl02600
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 6-110 6.62e-29

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.


The actual alignment was detected with superfamily member cd01107:

Pssm-ID: 470628 [Multi-domain]  Cd Length: 108  Bit Score: 106.45  E-value: 6.62e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEK-GYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIGEMTDHL 84
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDtGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLL 80

                          90       100
                  ....*....|....*....|....*.
gi 1473287884  85 RSRVQALDEQIAGLKAERASVQERLS 110
Cdd:cd01107    81 REKLAELEAEIEELQRILRLLEDRLK 106
 
Name Accession Description Interval E-value
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 6-110 6.62e-29

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: 106.45  E-value: 6.62e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEK-GYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIGEMTDHL 84
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDtGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLL 80

                          90       100
                  ....*....|....*....|....*.
gi 1473287884  85 RSRVQALDEQIAGLKAERASVQERLS 110
Cdd:cd01107    81 REKLAELEAEIEELQRILRLLEDRLK 106
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
8-105 1.68e-22

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 89.19  E-value: 1.68e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIG--EMTDHLR 85
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGeeEVRELLE 80

                          90       100
                  ....*....|....*....|
gi 1473287884  86 SRVQALDEQIAGLKAERASV 105
Cdd:COG0789    81 EHLAELEAQIAELQALRAEL 100
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
6-71 2.08e-15

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 69.47  E-value: 2.08e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1473287884    6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRL 71
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKEL 66
MerR_1 pfam13411
MerR HTH family regulatory protein;
6-71 4.42e-13

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 62.96  E-value: 4.42e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVvNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRL 71
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPR-TERGRRYYTDEDVERLRLIKALLERGLSLKEIKEL 65
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
5-110 2.84e-12

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 63.06  E-value: 2.84e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   5 MYAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTST---------F 75
Cdd:PRK09514    1 MYRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIrldpehhtcQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1473287884  76 DIGEMTDhlrSRVQALDEQIAGLKAERASVQeRLS 110
Cdd:PRK09514   81 EVKGIVD---EKLAEVEAKIAELQHMRRSLQ-RLN 111
 
Name Accession Description Interval E-value
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 6-110 6.62e-29

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: 106.45  E-value: 6.62e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEK-GYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIGEMTDHL 84
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDtGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKLL 80

                          90       100
                  ....*....|....*....|....*.
gi 1473287884  85 RSRVQALDEQIAGLKAERASVQERLS 110
Cdd:cd01107    81 REKLAELEAEIEELQRILRLLEDRLK 106
HTH_BltR cd04782
Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) ...
 6-99 5.88e-25

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: 95.76  E-value: 5.88e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIGEMTDHLR 85
Cdd:cd04782     1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRNPDELIELLK 80

                          90
                  ....*....|....
gi 1473287884  86 SRVQALDEQIAGLK 99
Cdd:cd04782    81 KQEKEIKEEIEELQ 94
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 6-100 2.24e-23

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: 91.64  E-value: 2.24e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTfDIGEMTDHLR 85
Cdd:cd04768     1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDT-EMEELTAMLL 79

                          90
                  ....*....|....*
gi 1473287884  86 SRVQALDEQIAGLKA 100
Cdd:cd04768    80 EKKQAIQQKIDRLQQ 94
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
8-105 1.68e-22

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 89.19  E-value: 1.68e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIG--EMTDHLR 85
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGeeEVRELLE 80

                          90       100
                  ....*....|....*....|
gi 1473287884  86 SRVQALDEQIAGLKAERASV 105
Cdd:COG0789    81 EHLAELEAQIAELQALRAEL 100
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 6-107 5.56e-21

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: 85.23  E-value: 5.56e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLT--STFDIgemTDH 83
Cdd:cd01106     1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLkdPSEDL---LEA 77

                          90       100
                  ....*....|....*....|....
gi 1473287884  84 LRSRVQALDEQIAGLKAERASVQE 107
Cdd:cd01106    78 LREQKELLEEKKERLDKLIKTIDR 101
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 5-105 3.53e-19

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: 82.48  E-value: 3.53e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   5 MYAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDiGEMTDHL 84
Cdd:cd04790     1 MLTISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPG-DDATDVL 79

                          90       100
                  ....*....|....*....|.
gi 1473287884  85 RSRVQALDEQIAGLKAERASV 105
Cdd:cd04790    80 RRRLAELNREIQRLRQQQRAI 100
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 6-109 4.01e-18

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: 77.67  E-value: 4.01e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVvNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIGemtDHLR 85
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPER-SENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEE---LSLA 76

                          90       100
                  ....*....|....*....|....
gi 1473287884  86 SRVQALDEQIAGLKAERASVQERL 109
Cdd:cd00592    77 ALLALLDEKLAELEEKIARLEALL 100
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 6-114 2.68e-17

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: 75.96  E-value: 2.68e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIGEMTdhLR 85
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDST--IP 78

                          90       100
                  ....*....|....*....|....*....
gi 1473287884  86 SRVQALDEQIAGLKAERASVQERLSFYDE 114
Cdd:cd01109    79 ERLELLEEHREELEEQIAELQETLAYLDY 107
HTH_Cfa-like cd04775
Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative ...
 5-106 4.47e-16

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: 72.19  E-value: 4.47e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   5 MYAISEMASLFNVSRQTLIYYDKIGLFkPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDR-LTSTFDIGEMTDh 83
Cdd:cd04775     1 MYTIGQMSRKFGVSRSTLLYYESIGLI-PSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGcLAQPHVQAILEE- 78

                          90       100
                  ....*....|....*....|...
gi 1473287884  84 lrsRVQALDEQIAGLKAERASVQ 106
Cdd:cd04775    79 ---RLQSLNREIQRLRQQQQVLA 98
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
6-71 2.08e-15

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 69.47  E-value: 2.08e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1473287884    6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRL 71
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKEL 66
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 8-110 2.09e-15

Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133398 [Multi-domain]  Cd Length: 123  Bit Score: 71.05  E-value: 2.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIG-----EMTD 82
Cdd:cd04770     3 IGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGaapcaEVRA 82

                          90       100
                  ....*....|....*....|....*...
gi 1473287884  83 HLRSRVQALDEQIAGLKAERASVQERLS 110
Cdd:cd04770    83 LLEEKLAEVEAKIAELQALRAELAGLLS 110
MerR_1 pfam13411
MerR HTH family regulatory protein;
6-71 4.42e-13

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 62.96  E-value: 4.42e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVvNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRL 71
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPR-TERGRRYYTDEDVERLRLIKALLERGLSLKEIKEL 65
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
5-110 2.84e-12

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 63.06  E-value: 2.84e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   5 MYAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTST---------F 75
Cdd:PRK09514    1 MYRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIrldpehhtcQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1473287884  76 DIGEMTDhlrSRVQALDEQIAGLKAERASVQeRLS 110
Cdd:PRK09514   81 EVKGIVD---EKLAEVEAKIAELQHMRRSLQ-RLN 111
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 8-107 1.15e-11

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: 60.65  E-value: 1.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDigemtDHLRS- 86
Cdd:cd01108     3 IGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWR-----DPSRAs 77

                          90       100       110
                  ....*....|....*....|....*....|
gi 1473287884  87 ---------RVQALDEQIAGLKAERASVQE 107
Cdd:cd01108    78 advkalaleHIAELERKIAELQAMRRTLQQ 107
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 8-102 3.43e-11

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: 58.54  E-value: 3.43e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTS--TFDIGEMtdhLR 85
Cdd:cd04788     3 IGELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDgpDFDPLEL---LR 79

                          90
                  ....*....|....*..
gi 1473287884  86 SRVQALDEQIAGLKAER 102
Cdd:cd04788    80 RQLARLEEQLELATRLR 96
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 6-101 4.45e-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 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: 59.44  E-value: 4.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAvVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEI-DRLTSTFDIGEMTDHL 84
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPE-RSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIkDQLEEVQRSDKEQREV 79

                          90
                  ....*....|....*..
gi 1473287884  85 RSRVQALDEQIAGLKAE 101
Cdd:cd04779    80 AQEVQLVCDQIDGLEHR 96
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 6-55 1.48e-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: 1.48e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAvVNEKGYRFYSPTQIPLMRLI 55
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLLSPA-RTEGGYRLYSDADLERLRLI 49
HTH_Cfa cd04789
Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative ...
 5-102 1.84e-10

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: 56.73  E-value: 1.84e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   5 MYAISEMASLFNVSRQTLIYYDKIGLFKpAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDR-LTSTFDIGEMTDh 83
Cdd:cd04789     1 MYTISELAEKAGISRSTLLYYEKLGLIT-GTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLAcLQGKLTRSLLLE- 78

                          90
                  ....*....|....*....
gi 1473287884  84 lrsRVQALDEQIAGLKAER 102
Cdd:cd04789    79 ---RLSSLAEQIARKQQAR 94
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
 5-115 5.07e-10

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: 55.84  E-value: 5.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   5 MYaISEMASLFNVSRQTLIYYDKIGLFkPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIGEMT--D 82
Cdd:cd04769     1 MY-IGELAQQTGVTIKAIRLYEEKGLL-PSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLpwP 78

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1473287884  83 HLRSRV----QALDEQIAGLKAERASVQERLSFYDEA 115
Cdd:cd04769    79 HLQQALedkkQEIRAQITELQQLLARLDAFEASLKDA 115
MerR pfam00376
MerR family regulatory protein;
8-44 8.28e-10

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 53.19  E-value: 8.28e-10
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFY 44
Cdd:pfam00376   2 IGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38
HTH_CadR-PbrR cd04784
Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; ...
 8-106 2.05e-09

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: 54.50  E-value: 2.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRL--------TSTFDIGE 79
Cdd:cd04784     3 IGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLlqlqddpeASCAEVNA 82

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1473287884  80 MTD----HLRSRVQALDEQIAGLKAERASVQ 106
Cdd:cd04784    83 LIDehlaHVRARIAELQALEKQLQALRERCD 113
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 8-110 9.80e-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: 52.69  E-value: 9.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIGE-----MTD 82
Cdd:cd04787     3 VKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGEspcpmVRR 82

                          90       100
                  ....*....|....*....|....*...
gi 1473287884  83 HLRSRVQALDEQIAGLKAERASVQERLS 110
Cdd:cd04787    83 LIEQRLAETERRIKELLKLRDRMQQAVS 110
HTH_MerR1 cd04783
Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix ...
 8-107 5.84e-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: 50.30  E-value: 5.84e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEID---RLTSTFDIGEMTDHL 84
Cdd:cd04783     3 IGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAellELDDGTDCSEARELA 82

                          90       100
                  ....*....|....*....|...
gi 1473287884  85 RSRVQALDEQIAGLKAERASVQE 107
Cdd:cd04783    83 EQKLAEVDEKIADLQRMRASLQE 105
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 6-109 2.94e-07

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: 48.30  E-value: 2.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKgyRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIG------- 78
Cdd:cd04776     1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQT--RVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPggnrkql 78

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1473287884  79 ----EMTDHLRSRVQA----LDEQIAGLKAERASVQERL 109
Cdd:cd04776    79 ekmlEKIEKRRAELEQqrrdIDAALAELDAAEERCRERL 117
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 6-91 3.31e-07

Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.


Pssm-ID: 133400  Cd Length: 108  Bit Score: 47.74  E-value: 3.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEI----DRLTSTFDIGEMT 81
Cdd:cd04773     1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIatvvEQLRHAGGTEALA 80

                          90
                  ....*....|
gi 1473287884  82 DHLRSRVQAL 91
Cdd:cd04773    81 AALEQRRVAL 90
HTH_MlrA-like_sg1 cd04764
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 6-68 9.15e-07

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: 45.40  E-value: 9.15e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDK-IGLFKPAvvNEKGYRFYSPTQIPLMRLICMLRDLGLELDEI 68
Cdd:cd04764     1 YTIKEVSEIIGVKPHTLRYYEKeFNLYIPR--TENGRRYYTDEDIELLKKIKTLLEKGLSIKEI 62
HTH_HspR cd04766
Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) ...
 6-101 3.51e-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: 44.56  E-value: 3.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAvVNEKGYRFYSPTQIPLMRLIC-MLRDLGLELDEIDRLTstfdigemtdHL 84
Cdd:cd04766     2 YVISVAAELSGMHPQTLRLYERLGLLSPS-RTDGGTRRYSERDIERLRRIQrLTQELGVNLAGVKRIL----------EL 70

                          90
                  ....*....|....*..
gi 1473287884  85 RSRVQALDEQIAGLKAE 101
Cdd:cd04766    71 EEELAELRAELDELRAR 87
HTH_MerR-like_sg6 cd04781
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 8-106 5.87e-06

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133408  Cd Length: 120  Bit Score: 44.58  E-value: 5.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFkPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIGEMT-DHLRS 86
Cdd:cd04781     3 IAEVARQSGLPASTLRYYEEKGLI-ASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDrQLLKA 81

                          90       100
                  ....*....|....*....|
gi 1473287884  87 RVQALDEQIAGLKAERASVQ 106
Cdd:cd04781    82 KAAELDQQIQRLQAMRELLR 101
PRK10227 PRK10227
HTH-type transcriptional regulator CueR;
8-102 2.81e-05

HTH-type transcriptional regulator CueR;


Pssm-ID: 182320  Cd Length: 135  Bit Score: 43.10  E-value: 2.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTF-DIGEMTDHLRS 86
Cdd:PRK10227    3 ISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFnDPQRHSADVKR 82

                          90       100
                  ....*....|....*....|
gi 1473287884  87 R----VQALDEQIAGLKAER 102
Cdd:PRK10227   83 RtlekVAEIERHIEELQSMR 102
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 6-68 4.98e-05

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: 41.06  E-value: 4.98e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEI 68
Cdd:cd01105     2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAA 64
HTH_MerR-like_sg7 cd04786
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 8-101 7.98e-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 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: 41.73  E-value: 7.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   8 ISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRL----TSTFDIGEMTDH 83
Cdd:cd04786     3 IGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLlpadASNWQHDELLAA 82

                          90       100
                  ....*....|....*....|.
gi 1473287884  84 LRSRV---QALDEQIAGLKAE 101
Cdd:cd04786    83 LERKVadiEALEARLAQNKAQ 103
HTH_HspR-like cd01279
Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix ...
 5-103 8.36e-05

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: 40.66  E-value: 8.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   5 MYAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGyRFYSPTQIPLMRLICML-RDLGLELDEIDRLTStfdigemtdh 83
Cdd:cd01279     1 LYPISVAAELLGIHPQTLRVYDRLGLVSPARTNGGG-RRYSNNDLELLRQVQRLsQDEGFNLAGIKRIIE---------- 69

                          90       100
                  ....*....|....*....|
gi 1473287884  84 LRSRVQALDEQIAGLKAERA 103
Cdd:cd01279    70 LYPQVLLLQCRSCEHATELI 89
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
 6-107 1.74e-04

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: 40.61  E-value: 1.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTS-----TFDIGEM 80
Cdd:cd04785     1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLAlsdrpDRSCAEA 80

                          90       100
                  ....*....|....*....|....*..
gi 1473287884  81 TDHLRSRVQALDEQIAGLKAERASVQE 107
Cdd:cd04785    81 DAIARAHLADVRARIADLRRLEAELKR 107
HTH_MerD cd01111
Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) ...
 6-98 3.01e-04

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: 39.29  E-value: 3.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKPAVVNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTSTFDIGEMTD--- 82
Cdd:cd01111     1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDAGDGKQpea 80

                          90       100
                  ....*....|....*....|....*.
gi 1473287884  83 ---HLRSRVQ-------ALDEQIAGL 98
Cdd:cd01111    81 claQLRQKIEvrraalnALTTQLAEM 106
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 6-49 3.49e-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: 37.56  E-value: 3.49e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1473287884   6 YAISEMASLFNVSRQTLIYYDKIGLFKpAVVNEKGYRFYSPTQI 49
Cdd:cd04762     1 LTTKEAAELLGVSPSTLRRWVKEGKLK-AIRTPGGHRRFPEEDL 43
HTH_HspR-like_MBC cd04767
Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative ...
 5-73 7.10e-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: 38.63  E-value: 7.10e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1473287884   5 MYAISEMASLFNVSRQTLIYYDKIGLFKPAvvNEKGYRFYSptQIPLMRLIC---MLRDLGLELDEIDRLTS 73
Cdd:cd04767     1 LYPIGVVAELLNIHPETLRIWERHGLIKPA--RRNGQRLYS--NNDLKRLRFikkLINEKGLNIAGVKQILS 68
MerR-DNA-bind pfam09278
MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in ...
 52-107 1.78e-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: 35.94  E-value: 1.78e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1473287884  52 MRLICMLRDLGLELDEIDRL-----TSTFDIGEMTDHLRSRVQALDEQIAGLKAERASVQE 107
Cdd:pfam09278   4 LAFIRRARRLGFSLEEIRELlalydDPGPPCADVRALLREKLAELEARIAELQALRDELDA 64
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 6-73 5.64e-03

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


Pssm-ID: 133379  Cd Length: 68  Bit Score: 34.91  E-value: 5.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1473287884   6 YAISEMASLFNVSRQTL-IYYDKIGLFKPAVvNEKGYRFYSPTQIPLMRLICMLRDLGLELDEIDRLTS 73
Cdd:cd01104     1 YTIGAVARLTGVSPDTLrAWERRYGLPAPQR-TDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68
 
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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