NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446579437|ref|WP_000656783|]
View 

MULTISPECIES: transcriptional repressor GlnR [Bacteria]

Protein Classification

MerR family transcriptional regulator( domain architecture ID 10099899)

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 Bacillus subtilis GlnR, a nitrogen homeostatic transcription regulator which represses many genes including the glnRA operon and tnrA during growth with nitrogen excess

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

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_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 10-88 5.10e-25

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: 90.75  E-value: 5.10e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  10 LFPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGN-RRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMKENQTEAVKV 88
Cdd:cd01105    1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGgQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRVQAEVRRR 80
 
Name Accession Description Interval E-value
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 10-88 5.10e-25

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: 90.75  E-value: 5.10e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  10 LFPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGN-RRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMKENQTEAVKV 88
Cdd:cd01105    1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGgQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRVQAEVRRR 80
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
11-79 2.04e-20

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 78.33  E-value: 2.04e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437    11 FPIGIVMDLTQLSARQIRYYEEHNLVSP-TRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMK 79
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPpIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
13-108 2.15e-16

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 69.16  E-value: 2.15e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVSPT-RTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL-LMKENQTEAVKVKE 90
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPeRTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLdLLDDGEEEVRELLE 80

                         90       100
                 ....*....|....*....|
gi 446579437  91 ETKEISKTELRKI--LRDEL 108
Cdd:COG0789   81 EHLAELEAQIAELqaLRAEL 100
MerR_1 pfam13411
MerR HTH family regulatory protein;
11-76 2.51e-15

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 65.27  E-value: 2.51e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446579437   11 FPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL 76
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
PRK15043 PRK15043
HTH-type transcriptional regulator MlrA;
10-109 8.11e-08

HTH-type transcriptional regulator MlrA;


Pssm-ID: 185003 [Multi-domain]  Cd Length: 243  Bit Score: 49.16  E-value: 8.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  10 LFPIGIVMDLTQLSARQIRYYEE-HNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKqVLLMKENqteaVKV 88
Cdd:PRK15043   3 LYTIGEVALLCDINPVTLRAWQRrYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVK-MLLSNEN----VDV 77

                         90       100
                 ....*....|....*....|.
gi 446579437  89 KEETKEISKTELRKILRDELQ 109
Cdd:PRK15043  78 QNGWRDQQETLLTYLQSGNLH 98
CueR TIGR02044
Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and ...
 13-110 2.37e-07

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


Pssm-ID: 131099 [Multi-domain]  Cd Length: 127  Bit Score: 46.29  E-value: 2.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437   13 IGIVMDLTQLSARQIRYYEEHNLVSPT-RTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL-LMKENQTEAVKVKE 90
Cdd:TIGR02044   3 IGQVAKLTGLSSKMIRYYEEKGLIPPPlRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLnLWNDPNRTSADVKA 82

                          90       100
                  ....*....|....*....|....*.
gi 446579437   91 ET----KEISK--TELRKIlRDELQH 110
Cdd:TIGR02044  83 RTlekvAEIERkiSELQSM-RDQLEA 107
 
Name Accession Description Interval E-value
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 10-88 5.10e-25

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: 90.75  E-value: 5.10e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  10 LFPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGN-RRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMKENQTEAVKV 88
Cdd:cd01105    1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGgQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRVQAEVRRR 80
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
11-79 2.04e-20

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 78.33  E-value: 2.04e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437    11 FPIGIVMDLTQLSARQIRYYEEHNLVSP-TRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMK 79
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPpIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLELL 70
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 11-111 1.68e-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: 74.59  E-value: 1.68e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  11 FPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMKENQTEAVKVKE 90
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLAALLA 80

                         90       100
                 ....*....|....*....|.
gi 446579437  91 ETKEiSKTELRKILRdELQHT 111
Cdd:cd00592   81 LLDE-KLAELEEKIA-RLEAL 99
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
13-108 2.15e-16

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 69.16  E-value: 2.15e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVSPT-RTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL-LMKENQTEAVKVKE 90
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPeRTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLdLLDDGEEEVRELLE 80

                         90       100
                 ....*....|....*....|
gi 446579437  91 ETKEISKTELRKI--LRDEL 108
Cdd:COG0789   81 EHLAELEAQIAELqaLRAEL 100
HTH_HspR-like_MBC cd04767
Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative ...
 10-78 1.33e-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: 67.52  E-value: 1.33e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  10 LFPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGnRRLFSFNDVDKLLEIKDLL-DQGLNMAGIKQVLLM 78
Cdd:cd04767    1 LYPIGVVAELLNIHPETLRIWERHGLIKPARRNG-QRLYSNNDLKRLRFIKKLInEKGLNIAGVKQILSM 69
MerR_1 pfam13411
MerR HTH family regulatory protein;
11-76 2.51e-15

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 65.27  E-value: 2.51e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446579437   11 FPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL 76
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66
HTH_HspR-like cd01279
Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix ...
 10-107 7.78e-14

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: 62.61  E-value: 7.78e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  10 LFPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLL-DQGLNMAGIKQVLLMkENQTEAVKV 88
Cdd:cd01279    1 LYPISVAAELLGIHPQTLRVYDRLGLVSPARTNGGGRRYSNNDLELLRQVQRLSqDEGFNLAGIKRIIEL-YPQVLLLQC 79

                         90
                 ....*....|....*....
gi 446579437  89 KEETKEISKTELRKILRDE 107
Cdd:cd01279   80 RSCEHATELIGCAKPCRKE 98
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 11-59 9.34e-13

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: 58.37  E-value: 9.34e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446579437  11 FPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEI 59
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLRLI 49
HTH_HspR cd04766
Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) ...
 10-80 1.05e-12

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: 59.20  E-value: 1.05e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446579437  10 LFPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLL-DQGLNMAGIKQVLLMKE 80
Cdd:cd04766    1 VYVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTqELGVNLAGVKRILELEE 72
HTH_MlrA-like cd04763
Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix ...
 11-76 6.75e-12

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: 56.77  E-value: 6.75e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446579437  11 FPIGIVMDLTQLSARQIRYYE-EHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL 76
Cdd:cd04763    1 YTIGEVALLTGIKPHVLRAWErEFGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67
HTH_MerR-like_sg3 cd01282
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 13-76 2.72e-11

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133388  Cd Length: 112  Bit Score: 56.08  E-value: 2.72e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL 76
Cdd:cd01282    3 IGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFL 66
HTH_MlrA-like_sg2 cd04765
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 11-108 4.06e-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: 52.64  E-value: 4.06e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  11 FPIGIVMDLTQLSARQIRYYE-EHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLL-DQGLNMAGIKQVLLMKENQTEAVKV 88
Cdd:cd04765    1 FSIGEVAEILGLPPHVLRYWEtEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLyEKGYTIEGAKQALKEDGAAAIREEE 80

                         90       100
                 ....*....|....*....|
gi 446579437  89 KEETKEISKTELRKIlRDEL 108
Cdd:cd04765   81 AEERLPSIRAELLDL-RDQL 99
HTH_CueR cd01108
Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix ...
 13-110 1.10e-08

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: 49.87  E-value: 1.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVSP-TRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMKEN---QTEAVKV 88
Cdd:cd01108    3 IGEAAKLTGLSAKMIRYYEEIGLIPPpSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDpsrASADVKA 82

                         90       100
                 ....*....|....*....|....*....
gi 446579437  89 KEETK--EISktelRKI-----LRDELQH 110
Cdd:cd01108   83 LALEHiaELE----RKIaelqaMRRTLQQ 107
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 11-77 2.87e-08

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


Pssm-ID: 133379  Cd Length: 68  Bit Score: 47.24  E-value: 2.87e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446579437  11 FPIGIVMDLTQLSARQIRYYEE-HNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLL 77
Cdd:cd01104    1 YTIGAVARLTGVSPDTLRAWERrYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALAL 68
PRK15043 PRK15043
HTH-type transcriptional regulator MlrA;
10-109 8.11e-08

HTH-type transcriptional regulator MlrA;


Pssm-ID: 185003 [Multi-domain]  Cd Length: 243  Bit Score: 49.16  E-value: 8.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  10 LFPIGIVMDLTQLSARQIRYYEE-HNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKqVLLMKENqteaVKV 88
Cdd:PRK15043   3 LYTIGEVALLCDINPVTLRAWQRrYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVK-MLLSNEN----VDV 77

                         90       100
                 ....*....|....*....|.
gi 446579437  89 KEETKEISKTELRKILRDELQ 109
Cdd:PRK15043  78 QNGWRDQQETLLTYLQSGNLH 98
MerR pfam00376
MerR family regulatory protein;
13-48 1.61e-07

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 44.33  E-value: 1.61e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 446579437   13 IGIVMDLTQLSARQIRYYEEHNLV-SPTRTKGNRRLF 48
Cdd:pfam00376   2 IGEVAKLLGVSPRTLRYYEKIGLLpPPERTEGGYRRY 38
CueR TIGR02044
Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and ...
 13-110 2.37e-07

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


Pssm-ID: 131099 [Multi-domain]  Cd Length: 127  Bit Score: 46.29  E-value: 2.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437   13 IGIVMDLTQLSARQIRYYEEHNLVSPT-RTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL-LMKENQTEAVKVKE 90
Cdd:TIGR02044   3 IGQVAKLTGLSSKMIRYYEEKGLIPPPlRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLnLWNDPNRTSADVKA 82

                          90       100
                  ....*....|....*....|....*.
gi 446579437   91 ET----KEISK--TELRKIlRDELQH 110
Cdd:TIGR02044  83 RTlekvAEIERkiSELQSM-RDQLEA 107
HTH_MerR2 cd04769
Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix ...
 13-86 1.08e-06

Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133397 [Multi-domain]  Cd Length: 116  Bit Score: 44.28  E-value: 1.08e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMKENQTEAV 86
Cdd:cd04769    3 IGELAQQTGVTIKAIRLYEEKGLLPSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLP 76
HTH_MlrA-like_sg1 cd04764
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 16-76 4.27e-06

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: 41.55  E-value: 4.27e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446579437  16 VMDLTQLSARQIRYYE-EHNLVSPtRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL 76
Cdd:cd04764    6 VSEIIGVKPHTLRYYEkEFNLYIP-RTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 21-76 1.08e-05

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: 42.42  E-value: 1.08e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446579437  21 QLSARQIRYYEEHNLVSPT-RTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL 76
Cdd:cd04790   12 GLSRSTLLYYERIGLLSPSaRSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLL 68
HTH_YfmP cd04774
Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) ...
 22-59 1.31e-05

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: 40.96  E-value: 1.31e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446579437  22 LSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEI 59
Cdd:cd04774   12 LTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERI 49
HTH_HMRTR cd04770
Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; ...
 11-109 1.33e-05

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: 41.39  E-value: 1.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  11 FPIGIVMDLTQLSARQIRYYEEHNLV-SPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMKENQTE----- 84
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLpPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAApcaev 80

                         90       100
                 ....*....|....*....|....*....
gi 446579437  85 ----AVKVKEETKEISktELRKiLRDELQ 109
Cdd:cd04770   81 rallEEKLAEVEAKIA--ELQA-LRAELA 106
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 13-105 2.77e-05

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: 40.16  E-value: 2.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVSPTR-TKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLM-KENQTEAVKVKE 90
Cdd:cd01106    3 VGEVAKLTGVSVRTLHYYDEIGLLKPSRrTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDpSEDLLEALREQK 82

                         90
                 ....*....|....*
gi 446579437  91 ETKEISKTELRKILR 105
Cdd:cd01106   83 ELLEEKKERLDKLIK 97
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 13-103 2.84e-05

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: 40.52  E-value: 2.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVSP-TRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQ--VLLMKENQTEAVKVK 89
Cdd:cd01109    3 IKEVAEKTGLSADTLRYYEKEGLLPPvKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEyaELRREGDSTIPERLE 82

                         90
                 ....*....|....*.
gi 446579437  90 --EETKEISKTELRKI 103
Cdd:cd01109   83 llEEHREELEEQIAEL 98
HTH_MerR-like_sg4 cd04779
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 13-120 5.24e-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 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: 40.18  E-value: 5.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL-----LMKENQTEAVK 87
Cdd:cd04779    3 IGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLeevqrSDKEQREVAQE 82

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446579437  88 VKEETKEISKTELR-KILRDELQHTGRFNRTSLR 120
Cdd:cd04779   83 VQLVCDQIDGLEHRlKQLKPIASQTDRAQRMKMT 116
HTH_CadR-PbrR-like cd04785
Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; ...
 27-111 6.27e-05

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: 39.84  E-value: 6.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  27 IRYYEEHNLVS-PTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMKENQTEAVKvkeETKEISKTELRKI-- 103
Cdd:cd04785   17 IRYYESIGLLPePARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCA---EADAIARAHLADVra 93

                         90
                 ....*....|....*
gi 446579437 104 -------LRDELQHT 111
Cdd:cd04785   94 riadlrrLEAELKRM 108
zntR PRK09514
Zn(2+)-responsive transcriptional regulator;
10-120 1.32e-04

Zn(2+)-responsive transcriptional regulator;


Pssm-ID: 181924 [Multi-domain]  Cd Length: 140  Bit Score: 39.18  E-value: 1.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  10 LFPIGIVMDLTQLSARQIRYYEEHNLVSP-TRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL---LMKENQTEA 85
Cdd:PRK09514   1 MYRIGELAKLAEVTPDTLRFYEKQGLMDPeVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLsirLDPEHHTCQ 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446579437  86 vkvkeETKEISKTELRKILR--DELQHTgrfnRTSLR 120
Cdd:PRK09514  81 -----EVKGIVDEKLAEVEAkiAELQHM----RRSLQ 108
HTH_Cfa-like cd04775
Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative ...
 10-76 6.99e-04

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: 36.36  E-value: 6.99e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446579437  10 LFPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL 76
Cdd:cd04775    1 MYTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCL 67
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 11-95 1.51e-03

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: 35.41  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  11 FPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGN-RRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLMKenqTEAVKVK 89
Cdd:cd04768    1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENgYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTE---MEELTAM 77


                 ....*.
gi 446579437  90 EETKEI 95
Cdd:cd04768   78 LLEKKQ 83
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 11-76 2.64e-03

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: 35.19  E-value: 2.64e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446579437  11 FPIGIVMDLTQLSARQIRYYEEHNLVSPTRT--KGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL 76
Cdd:cd01107    1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVdpDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEIL 68
HTH_MerR-like_sg6 cd04781
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR ...
 13-56 2.78e-03

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 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: 35.34  E-value: 2.78e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKL 56
Cdd:cd04781    3 IAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRL 46
PRK10227 PRK10227
HTH-type transcriptional regulator CueR;
13-94 2.85e-03

HTH-type transcriptional regulator CueR;


Pssm-ID: 182320  Cd Length: 135  Bit Score: 35.40  E-value: 2.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVS-PTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL-LMKENQTEAVKVKE 90
Cdd:PRK10227   3 ISDVAKITGLTSKAIRFYEEKGLVTpPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVnLFNDPQRHSADVKR 82


                 ....
gi 446579437  91 ETKE 94
Cdd:PRK10227  83 RTLE 86
HTH_Cfa cd04789
Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative ...
 22-69 3.95e-03

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: 34.38  E-value: 3.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 446579437  22 LSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNM 69
Cdd:cd04789   13 ISRSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSL 60
HTH_SoxR cd01110
Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) ...
 13-76 4.56e-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: 34.86  E-value: 4.56e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446579437  13 IGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVL 76
Cdd:cd01110    4 VGEVAKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEAL 67
HTH_GnyR cd04776
Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix ...
 23-78 8.56e-03

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: 33.66  E-value: 8.56e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446579437  23 SARQIRYYEEHNLVSPTRtKGNRRLFSFNDVDKLLEIKDLLDQGLNMAGIKQVLLM 78
Cdd:cd04776   13 TPRTLRFYEDKGLLSPER-RGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL 67
 
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