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Conserved domains on  [gi|501830489|ref|WP_012650591|]
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MULTISPECIES: transcriptional regulator TraR [Rhizobium/Agrobacterium group]

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 7.08e-166

transcriptional regulator TraR; Provisional


:

Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 457.15  E-value: 7.08e-166
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489   1 MQHWLDRLTDLAAIQGDESILTQGLADLTQHFGFTGYAYLHIQHKHTIAVTNYHREWRSTYFDKHFDKLDPVVKRAKSRK 80
Cdd:PRK13870   1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHREWQSVYFDKKFDALDPVVKRARSRK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489  81 QVFAWSGEQDRARQSKEERAFYAHAADFGIRSGVTVPIKTANGSMSMFTLASEKPAIDLDREIDAVAAAAAVGQLHARIS 160
Cdd:PRK13870  81 HIFTWSGEQERPRLSKDERAFYAHAADFGIRSGITIPIKTANGSMSMFTLASEKPVIDLDREIDAVAAAATIGQIHARIS 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501830489 161 FLQTTPTVEDAAWLDPKEATYLRWIAVGMTMEEIADVEGIKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
Cdd:PRK13870 161 FLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
 
Name Accession Description Interval E-value
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
 1-234 7.08e-166

transcriptional regulator TraR; Provisional


Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 457.15  E-value: 7.08e-166
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489   1 MQHWLDRLTDLAAIQGDESILTQGLADLTQHFGFTGYAYLHIQHKHTIAVTNYHREWRSTYFDKHFDKLDPVVKRAKSRK 80
Cdd:PRK13870   1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHREWQSVYFDKKFDALDPVVKRARSRK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489  81 QVFAWSGEQDRARQSKEERAFYAHAADFGIRSGVTVPIKTANGSMSMFTLASEKPAIDLDREIDAVAAAAAVGQLHARIS 160
Cdd:PRK13870  81 HIFTWSGEQERPRLSKDERAFYAHAADFGIRSGITIPIKTANGSMSMFTLASEKPVIDLDREIDAVAAAATIGQIHARIS 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501830489 161 FLQTTPTVEDAAWLDPKEATYLRWIAVGMTMEEIADVEGIKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
Cdd:PRK13870 161 FLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 25-143 2.54e-18

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: 78.56  E-value: 2.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489   25 LADLTQHFGFTGYAYlHIQHKH------TIAVTNYHREWRSTYFDKHFDKLDPVVKRAKSRKQVFAWSGEQDRARQSkEE 98
Cdd:pfam03472   9 LARLAAALGFDHFAY-GARAPLglsapdVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEARG-AE 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 501830489   99 RAFYAHAADFGIRSGVTVPIKTANGSMSMFTLASEKPAIDLDREI 143
Cdd:pfam03472  87 RRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAI 131
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
47-234 5.51e-15

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 70.55  E-value: 5.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489  47 TIAVTNYHREWRSTYFDKHFDKLDPVVKRAKSRKQVFAWSGEQDRARQSKEERAFYAHAADFGIRSGVTVPIKTANGSMS 126
Cdd:COG2771    1 LLLLALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489 127 MFTLASEKPAIDLDREIDAVAAAAAVGQLHARISFLQTTPTVEDAAWLDPKEATYLRWIAVGMTMEEIADVEGIKYNSVR 206
Cdd:COG2771   81 LLALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVR 160

                        170       180
                 ....*....|....*....|....*...
gi 501830489 207 VKLREAMKRFDVRSKAHLTALAIRRKLI 234
Cdd:COG2771  161 THLKRIYRKLGVSSRAELVALALRLGLI 188
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 174-230 2.42e-14

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: 65.25  E-value: 2.42e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 501830489 174 LDPKEATYLRWIAVGMTMEEIADVEGIKYNSVRVKLREAMKRFDVRSKAHLTALAIR 230
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 171-228 1.98e-13

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 62.93  E-value: 1.98e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 501830489   171 AAWLDPKEATYLRWIAVGMTMEEIADVEGIKYNSVRVKLREAMKRFDVRSKAHLTALA 228
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
 
Name Accession Description Interval E-value
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
 1-234 7.08e-166

transcriptional regulator TraR; Provisional


Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 457.15  E-value: 7.08e-166
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489   1 MQHWLDRLTDLAAIQGDESILTQGLADLTQHFGFTGYAYLHIQHKHTIAVTNYHREWRSTYFDKHFDKLDPVVKRAKSRK 80
Cdd:PRK13870   1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHREWQSVYFDKKFDALDPVVKRARSRK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489  81 QVFAWSGEQDRARQSKEERAFYAHAADFGIRSGVTVPIKTANGSMSMFTLASEKPAIDLDREIDAVAAAAAVGQLHARIS 160
Cdd:PRK13870  81 HIFTWSGEQERPRLSKDERAFYAHAADFGIRSGITIPIKTANGSMSMFTLASEKPVIDLDREIDAVAAAATIGQIHARIS 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501830489 161 FLQTTPTVEDAAWLDPKEATYLRWIAVGMTMEEIADVEGIKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
Cdd:PRK13870 161 FLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 25-143 2.54e-18

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: 78.56  E-value: 2.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489   25 LADLTQHFGFTGYAYlHIQHKH------TIAVTNYHREWRSTYFDKHFDKLDPVVKRAKSRKQVFAWSGEQDRARQSkEE 98
Cdd:pfam03472   9 LARLAAALGFDHFAY-GARAPLglsapdVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEARG-AE 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 501830489   99 RAFYAHAADFGIRSGVTVPIKTANGSMSMFTLASEKPAIDLDREI 143
Cdd:pfam03472  87 RRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAI 131
GerE pfam00196
Bacterial regulatory proteins, luxR family;
172-228 4.27e-18

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 75.31  E-value: 4.27e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 501830489  172 AWLDPKEATYLRWIAVGMTMEEIADVEGIKYNSVRVKLREAMKRFDVRSKAHLTALA 228
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
47-234 5.51e-15

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 70.55  E-value: 5.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489  47 TIAVTNYHREWRSTYFDKHFDKLDPVVKRAKSRKQVFAWSGEQDRARQSKEERAFYAHAADFGIRSGVTVPIKTANGSMS 126
Cdd:COG2771    1 LLLLALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489 127 MFTLASEKPAIDLDREIDAVAAAAAVGQLHARISFLQTTPTVEDAAWLDPKEATYLRWIAVGMTMEEIADVEGIKYNSVR 206
Cdd:COG2771   81 LLALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVR 160

                        170       180
                 ....*....|....*....|....*...
gi 501830489 207 VKLREAMKRFDVRSKAHLTALAIRRKLI 234
Cdd:COG2771  161 THLKRIYRKLGVSSRAELVALALRLGLI 188
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 174-230 2.42e-14

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: 65.25  E-value: 2.42e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 501830489 174 LDPKEATYLRWIAVGMTMEEIADVEGIKYNSVRVKLREAMKRFDVRSKAHLTALAIR 230
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 171-228 1.98e-13

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 62.93  E-value: 1.98e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 501830489   171 AAWLDPKEATYLRWIAVGMTMEEIADVEGIKYNSVRVKLREAMKRFDVRSKAHLTALA 228
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 174-234 9.32e-09

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: 52.20  E-value: 9.32e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501830489 174 LDPKEATYLRWIAVGMTMEEIADVEGIKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
PRK10188 PRK10188
transcriptional regulator SdiA;
51-234 1.53e-07

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 50.55  E-value: 1.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489  51 TNYHREWRSTYFDKHFDKLDPVVKRAKSRKQVFAWSGEQDRarqskEERAFYAHAADFGIRSGVTVPIKTANGSMSMFTL 130
Cdd:PRK10188  61 TTYPEAWVSHYQAENYFAIDPVLKPENFSQGHLMWNDDLFS-----EAQALWDAARAHGLRRGVTQCLMLPNRALGFLSF 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501830489 131 --ASEKPAIDLDREIDAVAaaaavgQLHARISfLQTTPTVEDAAWLDP------KEATYLRWIAVGMTMEEIADVEGIKY 202
Cdd:PRK10188 136 srCSAREIPILSDELELRL------QLLVRES-LMALMRLEDEMVMTPemnfskREKEILKWTAEGKTSAEIAMILSISE 208

                        170       180       190
                 ....*....|....*....|....*....|..
gi 501830489 203 NSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
Cdd:PRK10188 209 NTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 174-215 7.91e-03

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 33.62  E-value: 7.91e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 501830489 174 LDPKEAT--YLRWIaVGMTMEEIADVEGIKYNSVRVKLREAMKR 215
Cdd:cd06171   11 LPEREREviLLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK 53
 
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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