NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|489496909|ref|WP_003401823|]
View 

MULTISPECIES: heat shock transcriptional regulator HspR [Mycobacterium]

Protein Classification

MerR family transcriptional regulator( domain architecture ID 10101106)

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; similar to Streptomyces albus HspR

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
HTH_HspR-like cd01279
Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix ...
12-109 6.13e-49

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: 151.60  E-value: 6.13e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  12 TFLISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLSQDEGVNLAGIKRIIELTSQVEALQSR 91
Cdd:cd01279    1 LYPISVAAELLGIHPQTLRVYDRLGLVSPARTNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIELYPQVLLLQCR 80
                         90
                 ....*....|....*...
gi 489496909  92 LQEMAEELAVLRANQRRE 109
Cdd:cd01279   81 SCEHATELIGCAKPCRKE 98
 
Name Accession Description Interval E-value
HTH_HspR-like cd01279
Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix ...
12-109 6.13e-49

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: 151.60  E-value: 6.13e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  12 TFLISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLSQDEGVNLAGIKRIIELTSQVEALQSR 91
Cdd:cd01279    1 LYPISVAAELLGIHPQTLRVYDRLGLVSPARTNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIELYPQVLLLQCR 80
                         90
                 ....*....|....*...
gi 489496909  92 LQEMAEELAVLRANQRRE 109
Cdd:cd01279   81 SCEHATELIGCAKPCRKE 98
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
13-82 7.24e-21

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 79.49  E-value: 7.24e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489496909    13 FLISVAAELAGMHAQTLRTYDRLGLVSP-RRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIELT 82
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPpIRTEGGYRLYSDEDLERLRFIKRL-KELGFSLEEIKELLELL 70
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
15-108 4.28e-20

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 78.41  E-value: 4.28e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSP-RRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIELTSQ-----VEAL 88
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPpERTEGGYRLYSEEDVERLRFIRRL-RELGFSLAEIRELLDLLDDgeeevRELL 79
                         90       100
                 ....*....|....*....|
gi 489496909  89 QSRLQEMAEELAVLRANQRR 108
Cdd:COG0789   80 EEHLAELEAQIAELQALRAE 99
MerR_1 pfam13411
MerR HTH family regulatory protein;
15-79 3.24e-15

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 64.88  E-value: 3.24e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489496909   15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRII 79
Cdd:pfam13411   3 ISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKAL-LERGLSLKEIKELL 66
PRK15043 PRK15043
HTH-type transcriptional regulator MlrA;
13-99 7.34e-04

HTH-type transcriptional regulator MlrA;


Pssm-ID: 185003 [Multi-domain]  Cd Length: 243  Bit Score: 37.60  E-value: 7.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  13 FLISVAAELAGMHAQTLRTYDR-LGLVSPRRTSGGGRRYSLHDVELLRQVQHLSqDEGVNLAGIKRIieLTSQVEALQSR 91
Cdd:PRK15043   4 YTIGEVALLCDINPVTLRAWQRrYGLLKPQRTDGGHRLFNDADIDRIREIKRWI-DNGVQVSKVKML--LSNENVDVQNG 80

                 ....*...
gi 489496909  92 LQEMAEEL 99
Cdd:PRK15043  81 WRDQQETL 88
 
Name Accession Description Interval E-value
HTH_HspR-like cd01279
Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix ...
12-109 6.13e-49

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: 151.60  E-value: 6.13e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  12 TFLISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLSQDEGVNLAGIKRIIELTSQVEALQSR 91
Cdd:cd01279    1 LYPISVAAELLGIHPQTLRVYDRLGLVSPARTNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIELYPQVLLLQCR 80
                         90
                 ....*....|....*...
gi 489496909  92 LQEMAEELAVLRANQRRE 109
Cdd:cd01279   81 SCEHATELIGCAKPCRKE 98
HTH_HspR cd04766
Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) ...
13-109 4.55e-42

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: 133.93  E-value: 4.55e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  13 FLISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLSQDEGVNLAGIKRIIEltsqveaLQSRL 92
Cdd:cd04766    2 YVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILE-------LEEEL 74
                         90
                 ....*....|....*..
gi 489496909  93 QEMAEELAVLRANQRRE 109
Cdd:cd04766   75 AELRAELDELRARLRRE 91
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
13-82 7.24e-21

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 79.49  E-value: 7.24e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489496909    13 FLISVAAELAGMHAQTLRTYDRLGLVSP-RRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIELT 82
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPpIRTEGGYRLYSDEDLERLRFIKRL-KELGFSLEEIKELLELL 70
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
15-108 4.28e-20

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 78.41  E-value: 4.28e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSP-RRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIELTSQ-----VEAL 88
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPpERTEGGYRLYSEEDVERLRFIRRL-RELGFSLAEIRELLDLLDDgeeevRELL 79
                         90       100
                 ....*....|....*....|
gi 489496909  89 QSRLQEMAEELAVLRANQRR 108
Cdd:COG0789   80 EEHLAELEAQIAELQALRAE 99
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
15-106 4.33e-19

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: 75.74  E-value: 4.33e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIELTSQ-------VEA 87
Cdd:cd00592    3 IGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRL-RELGLSLKEIRELLDARDEelslaalLAL 81
                         90
                 ....*....|....*....
gi 489496909  88 LQSRLQEMAEELAVLRANQ 106
Cdd:cd00592   82 LDEKLAELEEKIARLEALL 100
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
13-61 1.34e-15

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: 65.31  E-value: 1.34e-15
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 489496909  13 FLISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQV 61
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLRLI 49
MerR_1 pfam13411
MerR HTH family regulatory protein;
15-79 3.24e-15

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 64.88  E-value: 3.24e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489496909   15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRII 79
Cdd:pfam13411   3 ISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKAL-LERGLSLKEIKELL 66
HTH_HspR-like_MBC cd04767
Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative ...
13-79 7.54e-15

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: 65.59  E-value: 7.54e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489496909  13 FLISVAAELAGMHAQTLRTYDRLGLVSPRRtSGGGRRYSLHDVELLRQVQHLSQDEGVNLAGIKRII 79
Cdd:cd04767    2 YPIGVVAELLNIHPETLRIWERHGLIKPAR-RNGQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQIL 67
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
12-84 7.57e-12

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: 56.85  E-value: 7.57e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489496909  12 TFLISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGG-RRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIELTSQ 84
Cdd:cd01105    1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGqRKYSLADVDRLLVIKEL-LDEGFTLAAAVEKLRRRRV 73
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
15-107 2.72e-11

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: 55.93  E-value: 2.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSP-RRTSGGGRRYSLHDVELLRQVQHLSQdEGVNLAGIKRIIELTSQVEA-LQSRL 92
Cdd:cd01109    3 IKEVAEKTGLSADTLRYYEKEGLLPPvKRDENGIRDFTEEDLEWLEFIKCLRN-TGMSIKDIKEYAELRREGDStIPERL 81
                         90
                 ....*....|....*
gi 489496909  93 QEMAEELAVLRANQR 107
Cdd:cd01109   82 ELLEEHREELEEQIA 96
HTH_MlrA-like_sg2 cd04765
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
13-104 1.44e-10

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: 53.79  E-value: 1.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  13 FLISVAAELAGMHAQTLRTY-DRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLSQDEGVNLAGIKRII----ELTSQVEA 87
Cdd:cd04765    1 FSIGEVAEILGLPPHVLRYWeTEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALkedgAAAIREEE 80
                         90
                 ....*....|....*..
gi 489496909  88 LQSRLQEMAEELAVLRA 104
Cdd:cd04765   81 AEERLPSIRAELLDLRD 97
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
15-106 1.72e-10

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: 53.64  E-value: 1.72e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRR-YSLHDVELLRQVQHLsQDEGVNLAGIKRIIE---------LTSQ 84
Cdd:cd01106    3 VGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRlYTEEDLERLQQILFL-KELGFSLKEIKELLKdpsedlleaLREQ 81
                         90       100
                 ....*....|....*....|..
gi 489496909  85 VEALQSRLQEMAEELAVLRANQ 106
Cdd:cd01106   82 KELLEEKKERLDKLIKTIDRTL 103
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
15-108 5.77e-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 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: 52.61  E-value: 5.77e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIELTSQVEA------- 87
Cdd:cd01282    3 IGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRL-LAAGLTLEEIREFLPCLRGGEPtfrpcpd 81
                         90       100
                 ....*....|....*....|....*
gi 489496909  88 ----LQSRLQEMAEELAVLRANQRR 108
Cdd:cd01282   82 llavLRRELARIDRQIADLTRSRDR 106
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
15-83 1.60e-09

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: 50.32  E-value: 1.60e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYD-RLGLVSPRRTSGGGRRYSLHDVELLRQVQHLsQDEGVNlagIKRIIELTS 83
Cdd:cd01104    3 IGAVARLTGVSPDTLRAWErRYGLPAPQRTDGGHRLYSEADVARLRLIRRL-TSEGVR---ISQAAALAL 68
MerR pfam00376
MerR family regulatory protein;
15-50 2.67e-08

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 46.64  E-value: 2.67e-08
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 489496909   15 ISVAAELAGMHAQTLRTYDRLGLV-SPRRTSGGGRRY 50
Cdd:pfam00376   2 IGEVAKLLGVSPRTLRYYEKIGLLpPPERTEGGYRRY 38
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
13-97 3.14e-08

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: 47.73  E-value: 3.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  13 FLISVAAELAGMHAQTLRTYDRLGLVSPRR-TSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIE---------LT 82
Cdd:cd04768    1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKiAENGYRYYSYAQLYQLQFILFL-RELGFSLAEIKELLDtemeeltamLL 79
                         90
                 ....*....|....*
gi 489496909  83 SQVEALQSRLQEMAE 97
Cdd:cd04768   80 EKKQAIQQKIDRLQQ 94
HTH_MerR1 cd04783
Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix ...
15-104 3.51e-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: 48.38  E-value: 3.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVS-PRRTSGGGRRYSLHDVELLRQVQhLSQDEGVNLAGIKRIIELTSQVEAlqSRLQ 93
Cdd:cd04783    3 IGELAKAAGVNVETIRYYQRRGLLPePPRPEGGYRRYPEETVTRLRFIK-RAQELGFTLDEIAELLELDDGTDC--SEAR 79
                         90
                 ....*....|..
gi 489496909  94 EMAEE-LAVLRA 104
Cdd:cd04783   80 ELAEQkLAEVDE 91
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
19-108 4.31e-08

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: 47.51  E-value: 4.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  19 AELAGMHAQTLRTYDRLGLVSPRRTSG--GGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIELTSQVEA---LQSRLQ 93
Cdd:cd01107    7 AKLSNLSIKALRYYDKIGLLKPAYVDPdtGYRYYSAEQLERLNRIKYL-RDLGFPLEEIKEILDADNDDELrklLREKLA 85
                         90
                 ....*....|....*
gi 489496909  94 EMAEELAVLRANQRR 108
Cdd:cd01107   86 ELEAEIEELQRILRL 100
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
19-100 4.62e-08

Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133415 [Multi-domain]  Cd Length: 96  Bit Score: 47.37  E-value: 4.62e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  19 AELAGMHAQTLRTYDRLGLVSP-RRTSGGGRRYSLHDVELLRQVQHLSQdEGVNLAGIKRIIE--LTSQVEALQSRLQEM 95
Cdd:cd04788    7 ARRTGLSVRTLHHYDHIGLLSPsQRTEGGHRLYDRADIRRLHQIIALRR-LGFSLREIGRALDgpDFDPLELLRRQLARL 85

                 ....*
gi 489496909  96 AEELA 100
Cdd:cd04788   86 EEQLE 90
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
15-107 1.22e-07

Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133417 [Multi-domain]  Cd Length: 172  Bit Score: 47.81  E-value: 1.22e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSP-RRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIElTSQVEA---LQS 90
Cdd:cd04790    4 ISQLARQFGLSRSTLLYYERIGLLSPsARSESNYRLYGERDLERLEQICAY-RSAGVSLEDIRSLLQ-QPGDDAtdvLRR 81
                         90
                 ....*....|....*..
gi 489496909  91 RLQEMAEELAVLRANQR 107
Cdd:cd04790   82 RLAELNREIQRLRQQQR 98
HTH_BltR cd04782
Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) ...
13-103 2.12e-07

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: 45.68  E-value: 2.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  13 FLISVAAELAGMHAQTLRTYDRLGLVSPR-RTSGGGRRYSLHDVELLRQVQHLSQdEGVNLAGIKRIIELTSQ---VEAL 88
Cdd:cd04782    1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEiVKENGYRYYTLEQFEQLDIILLLKE-LGISLKEIKDYLDNRNPdelIELL 79
                         90
                 ....*....|....*
gi 489496909  89 QSRLQEMAEELAVLR 103
Cdd:cd04782   80 KKQEKEIKEEIEELQ 94
HTH_MlrA-like cd04763
Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix ...
13-79 3.14e-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: 44.45  E-value: 3.14e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489496909  13 FLISVAAELAGMHAQTLRTYDR-LGLVSPRRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRII 79
Cdd:cd04763    1 YTIGEVALLTGIKPHVLRAWEReFGLLKPQRSDGGHRLFNDADIDRILEIKRW-IDNGVQVSKVKKLL 67
HTH_Cfa-like cd04775
Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative ...
13-106 1.97e-06

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: 43.30  E-value: 1.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  13 FLISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIELTSQVEALQSRL 92
Cdd:cd04775    2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFL-QAGGLPLEEIAGCLAQPHVQAILEERL 80
                         90
                 ....*....|....
gi 489496909  93 QEMAEELAVLRANQ 106
Cdd:cd04775   81 QSLNREIQRLRQQQ 94
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
15-100 2.36e-06

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: 43.30  E-value: 2.36e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVS-PRRTSGGGRRYSLHDVELLRQVQHlSQDEGVNLAGIKRIIELT----------- 82
Cdd:cd04785    3 IGELARRTGVNVETIRYYESIGLLPePARTAGGYRLYGAAHVERLRFIRR-ARDLGFSLEEIRALLALSdrpdrscaead 81
                         90       100
                 ....*....|....*....|....*
gi 489496909  83 -------SQVEALQSRLQEMAEELA 100
Cdd:cd04785   82 aiarahlADVRARIADLRRLEAELK 106
HTH_YfmP cd04774
Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) ...
15-99 2.61e-06

Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133401 [Multi-domain]  Cd Length: 96  Bit Score: 42.88  E-value: 2.61e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLSQDEGVNLAGIKRIIELTSQVEALQSRL-Q 93
Cdd:cd04774    3 VDEVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLERPLEPVDGGHRYsA 82

                 ....*.
gi 489496909  94 EMAEEL 99
Cdd:cd04774   83 ESLREI 88
HTH_Cfa cd04789
Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative ...
13-100 4.27e-06

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: 42.47  E-value: 4.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  13 FLISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIELTSQVEALQSRL 92
Cdd:cd04789    2 YTISELAEKAGISRSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQQL-QAGGLSLKECLACLQGKLTRSLLLERL 80

                 ....*...
gi 489496909  93 QEMAEELA 100
Cdd:cd04789   81 SSLAEQIA 88
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
19-108 4.84e-06

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: 42.68  E-value: 4.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  19 AELAGMHAQTLRTYDRLGLVSPRRTSGGG-RRYSLHDVELLRQVQHLSQdEGVNLAGIKRIIELTSQVEA--------LQ 89
Cdd:cd04787    7 ANAAGVTPDTVRFYTRIGLLRPTRDPVNGyRLYSEKDLSRLRFILSARQ-LGFSLKDIKEILSHADQGESpcpmvrrlIE 85
                         90
                 ....*....|....*....
gi 489496909  90 SRLQEMAEELAVLRANQRR 108
Cdd:cd04787   86 QRLAETERRIKELLKLRDR 104
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
15-56 1.01e-04

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 39.59  E-value: 1.01e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVE 56
Cdd:COG2452    3 PGEAAELLGVSPKTLRRWEKEGKLPAIRTPGGHRRYPESEVE 44
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
15-58 1.22e-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: 1.22e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELL 58
Cdd:cd04762    3 TKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERL 46
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
15-120 1.42e-04

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 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: 39.03  E-value: 1.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQV-----QHLSQDE------------GVNLAGIKR 77
Cdd:cd04779    3 IGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIehlkgQRLSLAEikdqleevqrsdKEQREVAQE 82
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 489496909  78 IIELTSQVEALQSRLQEMAEELAVLRANQRRE--VAVVPKSTALV 120
Cdd:cd04779   83 VQLVCDQIDGLEHRLKQLKPIASQTDRAQRMKmtKELSQQVLTLI 127
MerR_2 pfam13591
MerR HTH family regulatory protein;
35-95 3.72e-04

MerR HTH family regulatory protein;


Pssm-ID: 433334  Cd Length: 84  Bit Score: 36.73  E-value: 3.72e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489496909   35 LGLVSPRrTSGGGRRYSLHDVELLRQVQHLSQDEGVNLAGIKRIIELTSQVEALQSRLQEM 95
Cdd:pfam13591  23 HGLIEPE-TVGEEWYFSLSQLYRLEKAVRLYRDLDINLEGIAVILDLLDRIEHLQREIRSL 82
HTH_TioE_rpt1 cd04772
First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
19-74 5.36e-04

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: 36.60  E-value: 5.36e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489496909  19 AELAGMHAQTLRTYDRLGLVSP-RRTSGGGRRYSLHDVELLRQVQHLSQDEGVNLAG 74
Cdd:cd04772    7 ARAIGLSPQTVRNYESLGLIPPaERTANGYRIYTDKHIAALRAYRALLPGYGYRVAQ 63
PRK15043 PRK15043
HTH-type transcriptional regulator MlrA;
13-99 7.34e-04

HTH-type transcriptional regulator MlrA;


Pssm-ID: 185003 [Multi-domain]  Cd Length: 243  Bit Score: 37.60  E-value: 7.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  13 FLISVAAELAGMHAQTLRTYDR-LGLVSPRRTSGGGRRYSLHDVELLRQVQHLSqDEGVNLAGIKRIieLTSQVEALQSR 91
Cdd:PRK15043   4 YTIGEVALLCDINPVTLRAWQRrYGLLKPQRTDGGHRLFNDADIDRIREIKRWI-DNGVQVSKVKML--LSNENVDVQNG 80

                 ....*...
gi 489496909  92 LQEMAEEL 99
Cdd:PRK15043  81 WRDQQETL 88
PRK13752 PRK13752
mercuric resistance operon transcriptional regulator MerR;
15-102 1.76e-03

mercuric resistance operon transcriptional regulator MerR;


Pssm-ID: 184302  Cd Length: 144  Bit Score: 36.04  E-value: 1.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVS-PRRTSGGGRRYSLHDVELLRQVQHlSQDEGVNLAGIKRIIEL---TSQVEA--- 87
Cdd:PRK13752  10 IGVFAKAAGVNVETIRFYQRKGLLPePDKPYGSIRRYGEADVTRVRFVKS-AQRLGFSLDEIAELLRLedgTHCEEAssl 88
                         90
                 ....*....|....*
gi 489496909  88 LQSRLQEMAEELAVL 102
Cdd:PRK13752  89 AEHKLKDVREKMADL 103
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
15-111 4.24e-03

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: 34.65  E-value: 4.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  15 ISVAAELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHDVELLRQVQHLsQDEGVNLAGIKRIIeltsqvEALQSRLQE 94
Cdd:cd04769    3 IGELAQQTGVTIKAIRLYEEKGLLPSPKRSGNYRVYDAQHVECLRFIKEA-RQLGFTLAELKAIF------AGHEGRAVL 75
                         90
                 ....*....|....*..
gi 489496909  95 MAEELAVLRANQRREVA 111
Cdd:cd04769   76 PWPHLQQALEDKKQEIR 92
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
14-112 5.03e-03

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: 34.26  E-value: 5.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489496909  14 LISVAAELAGMHAQTLRTYDRLGLVSP-RRTSGGGRRYSLHDVELLRqVQHLSQDEGVNLAGIKRIIEltsQVEALQSrl 92
Cdd:cd04773    2 TIGELAHLLGVPPSTLRHWEKEGLLSPdREPETGYRVYDPSDVRDAR-LIHLLRRGGYLLEQIATVVE---QLRHAGG-- 75
                         90       100
                 ....*....|....*....|
gi 489496909  93 qemAEELAVLRANQRREVAV 112
Cdd:cd04773   76 ---TEALAAALEQRRVALTQ 92
HTH_SoxR cd01110
Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) ...
19-76 7.32e-03

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: 34.09  E-value: 7.32e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489496909  19 AELAGMHAQTLRTYDRLGLVSPRRTSGGGRRYSLHD---VELLRQVQHLsqdeGVNLAGIK 76
Cdd:cd01110    8 AKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVlrrIAFIKVAQRL----GLSLAEIA 64
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH