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Conserved domains on  [gi|497340815|ref|WP_009655028|]
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PRD domain-containing protein [Selenomonas sp. FOBRC6]

Protein Classification

Bg1G family transcriptional antiterminator( domain architecture ID 1004078)

Bg1G family transcriptional antiterminator similar to Dickeya chrysanthemi beta-glucoside operon antiterminator that mediates the positive regulation of the beta-glucoside (arb) operon by functioning as a transcriptional antiterminator

CATH:  1.10.1790.10
Gene Ontology:  GO:0045893|GO:0003723

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09772 super family cl31605
transcriptional antiterminator BglG; Provisional
 1-270 9.77e-49

transcriptional antiterminator BglG; Provisional


The actual alignment was detected with superfamily member PRK09772:

Pssm-ID: 170086 [Multi-domain]  Cd Length: 278  Bit Score: 162.95  E-value: 9.77e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815   1 MKILRVYSNNVVLASDEGGAEVVAIGKGLGFGAHVGDTIAETAVEKLFVLKDKQVQNRLGEIIGDLPSVYLEIAGDILKA 80
Cdd:PRK09772   3 MQITKILNNNVVVVIDDQQREKVVMGRGIGFQKRAGERINSSGIEKEYALSSHELNGRLSELLSHIPLEVMATCDRIISL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815  81 IQDEAGRpLDEAIYLTLTDHISVSLAREKAGVRCVNPLLPEIRLLYPEEFRLAQLAVPIIRRFLDVTISEDEIGFITLHI 160
Cdd:PRK09772  83 AQERLGK-LQDSIYISLTDHCQFAIKRFQQNVLLPNPLLWDIQRLYPKEFQLGEEALTIIDKRLGVQLPKDEVGFIAMHL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815 161 VNAYMNHRMVDTMKVTRMIRDILAMIEAAFPEAYRKKGLPYDRLLRHLQLFLWTLVTAETVVQEESYFYTWGKSEHKDAY 240
Cdd:PRK09772 162 VSAQMSGNMEDVAGVTQLMREMLQLIKFQFSLNYQEESLSYQRLVTHLKFLSWRILEHASINDSDESLQQAVKQNYPQAW 241

                        250       260       270
                 ....*....|....*....|....*....|
gi 497340815 241 ACVQQIAAYLEEETGKKITNGEQGYLLLHL 270
Cdd:PRK09772 242 QCAERIAIFIGLQYQRKISPAEIMFLAINI 271
 
Name Accession Description Interval E-value
PRK09772 PRK09772
transcriptional antiterminator BglG; Provisional
 1-270 9.77e-49

transcriptional antiterminator BglG; Provisional


Pssm-ID: 170086 [Multi-domain]  Cd Length: 278  Bit Score: 162.95  E-value: 9.77e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815   1 MKILRVYSNNVVLASDEGGAEVVAIGKGLGFGAHVGDTIAETAVEKLFVLKDKQVQNRLGEIIGDLPSVYLEIAGDILKA 80
Cdd:PRK09772   3 MQITKILNNNVVVVIDDQQREKVVMGRGIGFQKRAGERINSSGIEKEYALSSHELNGRLSELLSHIPLEVMATCDRIISL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815  81 IQDEAGRpLDEAIYLTLTDHISVSLAREKAGVRCVNPLLPEIRLLYPEEFRLAQLAVPIIRRFLDVTISEDEIGFITLHI 160
Cdd:PRK09772  83 AQERLGK-LQDSIYISLTDHCQFAIKRFQQNVLLPNPLLWDIQRLYPKEFQLGEEALTIIDKRLGVQLPKDEVGFIAMHL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815 161 VNAYMNHRMVDTMKVTRMIRDILAMIEAAFPEAYRKKGLPYDRLLRHLQLFLWTLVTAETVVQEESYFYTWGKSEHKDAY 240
Cdd:PRK09772 162 VSAQMSGNMEDVAGVTQLMREMLQLIKFQFSLNYQEESLSYQRLVTHLKFLSWRILEHASINDSDESLQQAVKQNYPQAW 241

                        250       260       270
                 ....*....|....*....|....*....|
gi 497340815 241 ACVQQIAAYLEEETGKKITNGEQGYLLLHL 270
Cdd:PRK09772 242 QCAERIAIFIGLQYQRKISPAEIMFLAINI 271
BglG COG3711
Transcriptional antiterminator [Transcription];
62-274 8.46e-30

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 117.65  E-value: 8.46e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815  62 IIGDLPSVYLEIAGDILKAIQDEAGRPLDEAIYLTLTDHISVSLAREKAG--VRCVNPLLPEIRllYPEEFRLAQLAVPI 139
Cdd:COG3711  170 LLKLIPEEDLELIEEIIEEAEKKLGIKLSDSIYINLTDHIAIAIKRIKKGkyIKLDNPLLWEIK--KPKEYEIAKEILKL 247

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815 140 IRRFLDVTISEDEIGFITLHIVNAYMNHRM----VDTMKVTRMIRDILAMIEAAFPEAYRKKGLPYDRLLRHLQLFLWTL 215
Cdd:COG3711  248 IEERLGISLPEDEIGYIALHLLGARLNNDNelseIITLEITKLIKEIINIIEEELGIDLDEDSLLYERLITHLKPAINRL 327

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 497340815 216 ---VTAETVVQEESyfytwgKSEHKDAYACVQQIAAYLEEETGKKITNGEQGYLLLHLVNLI 274
Cdd:COG3711  328 kygIPIRNPLLEEI------KEKYPEAFELAKKIAKYLEKELGIEIPEDEIGYLTLHFGAAL 383
CAT_RBD smart01061
CAT RNA binding domain; This RNA binding domain is found at the amino terminus of ...
 1-54 5.72e-22

CAT RNA binding domain; This RNA binding domain is found at the amino terminus of transcriptional antitermination proteins such as BglG, SacY and LicT. These proteins control the expression of sugar metabolising operons in Gram+ and Gram- bacteria. This domain has been called the CAT (Co-AntiTerminator) domain. It binds as a dimer.to short Ribonucleotidic Anti-Terminator (RAT) hairpin, each monomer interacting symmetrically with both strands of the RAT hairpin. In the full-length protein, CAT is followed by two phosphorylatable PTS regulation domains that modulate the RNA binding activity of CAT. Upon activation, the dimeric proteins bind to RAT targets in the nascent mRNA, thereby preventing abortive dissociation of the RNA polymerase from the DNA template.


Pssm-ID: 215004  Cd Length: 55  Bit Score: 85.99  E-value: 5.72e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 497340815     1 MKILRVYSNNVVLASDEGGAEVVAIGKGLGFGAHVGDTIAETAVEKLFVLKDKQ 54
Cdd:smart01061   1 MRIKKVLNNNVVLAEDENGQEVIVMGKGIGFGKKKGDLIDESKIEKIFVLKDEE 54
CAT_RBD pfam03123
CAT RNA binding domain; This RNA binding domain is found at the amino terminus of ...
 2-57 2.09e-20

CAT RNA binding domain; This RNA binding domain is found at the amino terminus of transcriptional antitermination proteins such as BglG, SacY and LicT. These proteins control the expression of sugar metabolising operons in Gram+ and Gram- bacteria. This domain has been called the CAT (Co-AntiTerminator) domain. It binds as a dimer to short Ribonucleotidic Anti-Terminator (RAT) hairpin, each monomer interacting symmetrically with both strands of the RAT hairpin. In the full-length protein, CAT is followed by two phosphorylatable PTS regulation domains (pfam00874) that modulate the RNA binding activity of CAT. Upon activation, the dimeric proteins bind to RAT targets in the nascent mRNA, thereby preventing abortive dissociation of the RNA polymerase from the DNA template.


Pssm-ID: 460815  Cd Length: 56  Bit Score: 82.09  E-value: 2.09e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 497340815    2 KILRVYSNNVVLASDEGGAEVVAIGKGLGFGAHVGDTIAETAVEKLFVLKDKQVQN 57
Cdd:pfam03123   1 KIKKVLNNNVVLAKDDNGEEVILMGKGIGFGKKKGDLIDESKIEKIFVLKDEEESE 56
 
Name Accession Description Interval E-value
PRK09772 PRK09772
transcriptional antiterminator BglG; Provisional
 1-270 9.77e-49

transcriptional antiterminator BglG; Provisional


Pssm-ID: 170086 [Multi-domain]  Cd Length: 278  Bit Score: 162.95  E-value: 9.77e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815   1 MKILRVYSNNVVLASDEGGAEVVAIGKGLGFGAHVGDTIAETAVEKLFVLKDKQVQNRLGEIIGDLPSVYLEIAGDILKA 80
Cdd:PRK09772   3 MQITKILNNNVVVVIDDQQREKVVMGRGIGFQKRAGERINSSGIEKEYALSSHELNGRLSELLSHIPLEVMATCDRIISL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815  81 IQDEAGRpLDEAIYLTLTDHISVSLAREKAGVRCVNPLLPEIRLLYPEEFRLAQLAVPIIRRFLDVTISEDEIGFITLHI 160
Cdd:PRK09772  83 AQERLGK-LQDSIYISLTDHCQFAIKRFQQNVLLPNPLLWDIQRLYPKEFQLGEEALTIIDKRLGVQLPKDEVGFIAMHL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815 161 VNAYMNHRMVDTMKVTRMIRDILAMIEAAFPEAYRKKGLPYDRLLRHLQLFLWTLVTAETVVQEESYFYTWGKSEHKDAY 240
Cdd:PRK09772 162 VSAQMSGNMEDVAGVTQLMREMLQLIKFQFSLNYQEESLSYQRLVTHLKFLSWRILEHASINDSDESLQQAVKQNYPQAW 241

                        250       260       270
                 ....*....|....*....|....*....|
gi 497340815 241 ACVQQIAAYLEEETGKKITNGEQGYLLLHL 270
Cdd:PRK09772 242 QCAERIAIFIGLQYQRKISPAEIMFLAINI 271
BglG COG3711
Transcriptional antiterminator [Transcription];
62-274 8.46e-30

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 117.65  E-value: 8.46e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815  62 IIGDLPSVYLEIAGDILKAIQDEAGRPLDEAIYLTLTDHISVSLAREKAG--VRCVNPLLPEIRllYPEEFRLAQLAVPI 139
Cdd:COG3711  170 LLKLIPEEDLELIEEIIEEAEKKLGIKLSDSIYINLTDHIAIAIKRIKKGkyIKLDNPLLWEIK--KPKEYEIAKEILKL 247

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815 140 IRRFLDVTISEDEIGFITLHIVNAYMNHRM----VDTMKVTRMIRDILAMIEAAFPEAYRKKGLPYDRLLRHLQLFLWTL 215
Cdd:COG3711  248 IEERLGISLPEDEIGYIALHLLGARLNNDNelseIITLEITKLIKEIINIIEEELGIDLDEDSLLYERLITHLKPAINRL 327

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 497340815 216 ---VTAETVVQEESyfytwgKSEHKDAYACVQQIAAYLEEETGKKITNGEQGYLLLHLVNLI 274
Cdd:COG3711  328 kygIPIRNPLLEEI------KEKYPEAFELAKKIAKYLEKELGIEIPEDEIGYLTLHFGAAL 383
CAT_RBD smart01061
CAT RNA binding domain; This RNA binding domain is found at the amino terminus of ...
 1-54 5.72e-22

CAT RNA binding domain; This RNA binding domain is found at the amino terminus of transcriptional antitermination proteins such as BglG, SacY and LicT. These proteins control the expression of sugar metabolising operons in Gram+ and Gram- bacteria. This domain has been called the CAT (Co-AntiTerminator) domain. It binds as a dimer.to short Ribonucleotidic Anti-Terminator (RAT) hairpin, each monomer interacting symmetrically with both strands of the RAT hairpin. In the full-length protein, CAT is followed by two phosphorylatable PTS regulation domains that modulate the RNA binding activity of CAT. Upon activation, the dimeric proteins bind to RAT targets in the nascent mRNA, thereby preventing abortive dissociation of the RNA polymerase from the DNA template.


Pssm-ID: 215004  Cd Length: 55  Bit Score: 85.99  E-value: 5.72e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 497340815     1 MKILRVYSNNVVLASDEGGAEVVAIGKGLGFGAHVGDTIAETAVEKLFVLKDKQ 54
Cdd:smart01061   1 MRIKKVLNNNVVLAEDENGQEVIVMGKGIGFGKKKGDLIDESKIEKIFVLKDEE 54
CAT_RBD pfam03123
CAT RNA binding domain; This RNA binding domain is found at the amino terminus of ...
 2-57 2.09e-20

CAT RNA binding domain; This RNA binding domain is found at the amino terminus of transcriptional antitermination proteins such as BglG, SacY and LicT. These proteins control the expression of sugar metabolising operons in Gram+ and Gram- bacteria. This domain has been called the CAT (Co-AntiTerminator) domain. It binds as a dimer to short Ribonucleotidic Anti-Terminator (RAT) hairpin, each monomer interacting symmetrically with both strands of the RAT hairpin. In the full-length protein, CAT is followed by two phosphorylatable PTS regulation domains (pfam00874) that modulate the RNA binding activity of CAT. Upon activation, the dimeric proteins bind to RAT targets in the nascent mRNA, thereby preventing abortive dissociation of the RNA polymerase from the DNA template.


Pssm-ID: 460815  Cd Length: 56  Bit Score: 82.09  E-value: 2.09e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 497340815    2 KILRVYSNNVVLASDEGGAEVVAIGKGLGFGAHVGDTIAETAVEKLFVLKDKQVQN 57
Cdd:pfam03123   1 KIKKVLNNNVVLAKDDNGEEVILMGKGIGFGKKKGDLIDESKIEKIFVLKDEEESE 56
PRD pfam00874
PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory ...
 76-163 1.44e-16

PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterized by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators pfam03123) or DNA (for activators), and a duplicated PRD module which is phosphorylated by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations modify the conformation and stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain. The structure of the LicT PRD domains has been solved in both the active (pdb:1h99) and inactive state (pdb:1tlv), revealing massive structural rearrangements upon activation.


Pssm-ID: 459973 [Multi-domain]  Cd Length: 90  Bit Score: 73.06  E-value: 1.44e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815   76 DILKAIQDEAGRPL-DEAIYLTLTDHISVSLAREKAGVRCVNPLLPEIRLLYPEEFRLAQLAVPIIRRFLDVTISEDEIG 154
Cdd:pfam00874   2 EIIELIEKKLGITFdDDILYIRLILHLAFAIERIKEGITIENPLLEEIKEKYPKEFEIAKKILEILEEELGIELPEDEIG 81


                  ....*....
gi 497340815  155 FITLHIVNA 163
Cdd:pfam00874  82 YIALHFLSA 90
LevR COG3933
Transcriptional regulatory protein LevR, contains PRD, AAA+ and EIIA domains [Transcription];
56-166 1.06e-14

Transcriptional regulatory protein LevR, contains PRD, AAA+ and EIIA domains [Transcription];


Pssm-ID: 443134 [Multi-domain]  Cd Length: 916  Bit Score: 74.00  E-value: 1.06e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815  56 QNRLGEIIGDLpsvYLEIAGDILKAIQDEAGRPLDEAIYLTLTDHISVSLAREKAGVRCVNPLLPEIRLLYPEEFRLAQL 135
Cdd:COG3933  446 KEELAKIVDED---IINVVEEILELAEKKLGRKFSENFIYALSLHLSSFIERIKEGKEIINPNLNEIKKKYPKEFKVAKE 522

                         90       100       110
                 ....*....|....*....|....*....|.
gi 497340815 136 AVPIIRRFLDVTISEDEIGFITLHIVNAYMN 166
Cdd:COG3933  523 IKELIEQELDIEIPEDEVGFLTLFLVSLNEN 553
BglG COG3711
Transcriptional antiterminator [Transcription];
70-175 2.25e-14

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 72.58  E-value: 2.25e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815  70 YLEIAGDILKAIQDEAGRPL--DEAIYLTLTDHISVSLAREKAGVRCVNPLLPEIRLLYPEEFRLAQLAVPIIRRFLDVT 147
Cdd:COG3711  287 ITKLIKEIINIIEEELGIDLdeDSLLYERLITHLKPAINRLKYGIPIRNPLLEEIKEKYPEAFELAKKIAKYLEKELGIE 366

                         90       100
                 ....*....|....*....|....*...
gi 497340815 148 ISEDEIGFITLHIVNAYMNHRMVDTMKV 175
Cdd:COG3711  367 IPEDEIGYLTLHFGAALERQKESKKKRV 394
PRD pfam00874
PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory ...
 201-273 1.33e-04

PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterized by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators pfam03123) or DNA (for activators), and a duplicated PRD module which is phosphorylated by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations modify the conformation and stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain. The structure of the LicT PRD domains has been solved in both the active (pdb:1h99) and inactive state (pdb:1tlv), revealing massive structural rearrangements upon activation.


Pssm-ID: 459973 [Multi-domain]  Cd Length: 90  Bit Score: 39.93  E-value: 1.33e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 497340815  201 YDRLLRHLQLFLWTLVTAETVVQEESYFYtwgKSEHKDAYACVQQIAAYLEEETGKKITNGEQGYLLLHLVNL 273
Cdd:pfam00874  21 YIRLILHLAFAIERIKEGITIENPLLEEI---KEKYPKEFEIAKKILEILEEELGIELPEDEIGYIALHFLSA 90
PspF COG1221
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ...
 39-175 3.77e-03

Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription, Signal transduction mechanisms];


Pssm-ID: 440834 [Multi-domain]  Cd Length: 835  Bit Score: 38.55  E-value: 3.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497340815  39 IAETAVEKLF------VLKDKQVQNRLGEIIGDLPSVYLEIAgdilKAIQDEAGRPLDEAIYLTLTDHISVSLAREKAGV 112
Cdd:COG1221  437 IISKDIESYFkklifkLDKSNISEELLLIVVDEVIVNVVEIF----EEAEKKLLRYNSSNLFIALSLHLLSTLLRIKKGK 512

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 497340815 113 RCVNPLLPEIRLLYPEEFRLAQLAVPIIRRFLDVTISEDEIGFITLHIVNAYMNHRMVDTMKV 175
Cdd:COG1221  513 KIINPQLNEIKKKYYEEFILAAEAIKIIEEELKILIPDEEEGFILLLLIELKEEKSLSENVIV 575
 
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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