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Conserved domains on  [gi|154813|gb|AAA64793|]
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regulatory protein (plasmid) [Plasmid Ti]

Protein Classification

similar to transcriptional activator protein TraR( domain architecture ID 11486913)

protein similar to transcriptional activator protein TraR

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
 1-234 1.50e-175

transcriptional regulator TraR; Provisional


:

Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 481.42  E-value: 1.50e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813      1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRK 80
Cdd:PRK13870   1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHREWQSVYFDKKFDALDPVVKRARSRK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813     81 HIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARIS 160
Cdd:PRK13870  81 HIFTWSGEQERPRLSKDERAFYAHAADFGIRSGITIPIKTANGSMSMFTLASEKPVIDLDREIDAVAAAATIGQIHARIS 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 154813    161 FLRTTPTAEDAACVDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRERMKRFDVRSKAHLTALAIRRKLI 234
Cdd:PRK13870 161 FLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
 
Name Accession Description Interval E-value
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
 1-234 1.50e-175

transcriptional regulator TraR; Provisional


Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 481.42  E-value: 1.50e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813      1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRK 80
Cdd:PRK13870   1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHREWQSVYFDKKFDALDPVVKRARSRK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813     81 HIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARIS 160
Cdd:PRK13870  81 HIFTWSGEQERPRLSKDERAFYAHAADFGIRSGITIPIKTANGSMSMFTLASEKPVIDLDREIDAVAAAATIGQIHARIS 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 154813    161 FLRTTPTAEDAACVDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRERMKRFDVRSKAHLTALAIRRKLI 234
Cdd:PRK13870 161 FLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 21-159 3.75e-20

Autoinducer binding domain; This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 427319  Cd Length: 148  Bit Score: 83.18  E-value: 3.75e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813      21 LKTGLADIADHFGFTGYAYLHIQHRHITA-----VTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSgEHERPTLS 95
Cdd:pfam03472   5 LFDALARLAAALGFDHFAYGARAPLGLSApdvlvLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWS-DVLFAEAR 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 154813      96 KDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQ-IHARI 159
Cdd:pfam03472  84 GAERRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAIEAAARLQLLAIyAHLRL 148
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
53-234 3.25e-13

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 65.93  E-value: 3.25e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813    53 YHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMAS 132
Cdd:COG2771   7 ALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLL 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813   133 DKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAACVDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRER 212
Cdd:COG2771  87 LLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRI 166

                       170       180
                ....*....|....*....|..
gi 154813   213 MKRFDVRSKAHLTALAIRRKLI 234
Cdd:COG2771 167 YRKLGVSSRAELVALALRLGLI 188
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 176-230 6.89e-12

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 58.70  E-value: 6.89e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 154813   176 PKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRERMKRFDVRSKAHLTALAIR 230
Cdd:cd06170   3 PREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 176-228 3.00e-10

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 54.46  E-value: 3.00e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 154813      176 PKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRERMKRFDVRSKAHLTALA 228
Cdd:smart00421   6 PREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
 
Name Accession Description Interval E-value
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
 1-234 1.50e-175

transcriptional regulator TraR; Provisional


Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 481.42  E-value: 1.50e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813      1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRK 80
Cdd:PRK13870   1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHREWQSVYFDKKFDALDPVVKRARSRK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813     81 HIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARIS 160
Cdd:PRK13870  81 HIFTWSGEQERPRLSKDERAFYAHAADFGIRSGITIPIKTANGSMSMFTLASEKPVIDLDREIDAVAAAATIGQIHARIS 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 154813    161 FLRTTPTAEDAACVDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRERMKRFDVRSKAHLTALAIRRKLI 234
Cdd:PRK13870 161 FLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 21-159 3.75e-20

Autoinducer binding domain; This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 427319  Cd Length: 148  Bit Score: 83.18  E-value: 3.75e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813      21 LKTGLADIADHFGFTGYAYLHIQHRHITA-----VTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSgEHERPTLS 95
Cdd:pfam03472   5 LFDALARLAAALGFDHFAYGARAPLGLSApdvlvLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWS-DVLFAEAR 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 154813      96 KDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQ-IHARI 159
Cdd:pfam03472  84 GAERRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAIEAAARLQLLAIyAHLRL 148
GerE pfam00196
Bacterial regulatory proteins, luxR family;
175-228 1.82e-15

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 68.38  E-value: 1.82e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 154813     175 DPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRERMKRFDVRSKAHLTALA 228
Cdd:pfam00196   4 SPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
53-234 3.25e-13

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 65.93  E-value: 3.25e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813    53 YHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMAS 132
Cdd:COG2771   7 ALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLL 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813   133 DKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAACVDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRER 212
Cdd:COG2771  87 LLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRI 166

                       170       180
                ....*....|....*....|..
gi 154813   213 MKRFDVRSKAHLTALAIRRKLI 234
Cdd:COG2771 167 YRKLGVSSRAELVALALRLGLI 188
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 176-230 6.89e-12

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 58.70  E-value: 6.89e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 154813   176 PKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRERMKRFDVRSKAHLTALAIR 230
Cdd:cd06170   3 PREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
PRK10188 PRK10188
transcriptional regulator SdiA;
47-234 5.31e-11

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 60.57  E-value: 5.31e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813     47 ITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEherptLSKDERAFYDHASDFGIRSGITIPIKTAN---G 123
Cdd:PRK10188  57 VAFYTTYPEAWVSHYQAENYFAIDPVLKPENFSQGHLMWNDD-----LFSEAQALWDAARAHGLRRGVTQCLMLPNralG 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154813    124 FMSmFTMASDKPVIDLDREIDAVAaaatigQIHARISfLRTTPTAEDAACVDP------KEATYLRWIAVGKTMEEIADV 197
Cdd:PRK10188 132 FLS-FSRCSAREIPILSDELELRL------QLLVRES-LMALMRLEDEMVMTPemnfskREKEILKWTAEGKTSAEIAMI 203

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 154813    198 EGVKYNSVRVKLRERMKRFDVRSKAHLTALAIRRKLI 234
Cdd:PRK10188 204 LSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 176-228 3.00e-10

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 54.46  E-value: 3.00e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 154813      176 PKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRERMKRFDVRSKAHLTALA 228
Cdd:smart00421   6 PREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 176-234 7.24e-07

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 46.81  E-value: 7.24e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 154813   176 PKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLRERMKRFDVRSKAHLTALAIRRKLI 234
Cdd:COG2197  72 PREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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