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Conserved domains on  [gi|1409477048|gb|RAQ33661|]
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PRD domain-containing protein [Enterococcus faecium]

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
 1-274 1.43e-35

transcriptional antiterminator BglG; Provisional


The actual alignment was detected with superfamily member PRK09772:

Pssm-ID: 170086 [Multi-domain]  Cd Length: 278  Bit Score: 129.06  E-value: 1.43e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048   1 MKIKKIFNQNAVLV-DDGGQEKVAIGKGIGFDRKRNDLIFDRDVERIFVMEP-EGQIKLQNLLNQIDERFLFAAETIIDH 78
Cdd:PRK09772    3 MQITKILNNNVVVViDDQQREKVVMGRGIGFQKRAGERINSSGIEKEYALSShELNGRLSELLSHIPLEVMATCDRIISL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048  79 AETVLmEKLNEHVLIALTDHIAFSAENINNGIVIRNKLLREIEVLYSDEFSIAQWAVEYLTKELGIPYTYDEAGYIAIHI 158
Cdd:PRK09772   83 AQERL-GKLQDSIYISLTDHCQFAIKRFQQNVLLPNPLLWDIQRLYPKEFQLGEEALTIIDKRLGVQLPKDEVGFIAMHL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048 159 HSGRsgRNNNHRSIREVT-IVSDIIHLVESELETDIHSEpfSLNYSRLVNHLRLLLQRThAQQYAVLDTE--IVEMVKRK 235
Cdd:PRK09772  162 VSAQ--MSGNMEDVAGVTqLMREMLQLIKFQFSLNYQEE--SLSYQRLVTHLKFLSWRI-LEHASINDSDesLQQAVKQN 236

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1409477048 236 YPESYKISKKIRVLLTKEYQLAITKEELGYLAIHIERLR 274
Cdd:PRK09772  237 YPQAWQCAERIAIFIGLQYQRKISPAEIMFLAINIERVR 275
 
Name Accession Description Interval E-value
PRK09772 PRK09772
transcriptional antiterminator BglG; Provisional
 1-274 1.43e-35

transcriptional antiterminator BglG; Provisional


Pssm-ID: 170086 [Multi-domain]  Cd Length: 278  Bit Score: 129.06  E-value: 1.43e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048   1 MKIKKIFNQNAVLV-DDGGQEKVAIGKGIGFDRKRNDLIFDRDVERIFVMEP-EGQIKLQNLLNQIDERFLFAAETIIDH 78
Cdd:PRK09772    3 MQITKILNNNVVVViDDQQREKVVMGRGIGFQKRAGERINSSGIEKEYALSShELNGRLSELLSHIPLEVMATCDRIISL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048  79 AETVLmEKLNEHVLIALTDHIAFSAENINNGIVIRNKLLREIEVLYSDEFSIAQWAVEYLTKELGIPYTYDEAGYIAIHI 158
Cdd:PRK09772   83 AQERL-GKLQDSIYISLTDHCQFAIKRFQQNVLLPNPLLWDIQRLYPKEFQLGEEALTIIDKRLGVQLPKDEVGFIAMHL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048 159 HSGRsgRNNNHRSIREVT-IVSDIIHLVESELETDIHSEpfSLNYSRLVNHLRLLLQRThAQQYAVLDTE--IVEMVKRK 235
Cdd:PRK09772  162 VSAQ--MSGNMEDVAGVTqLMREMLQLIKFQFSLNYQEE--SLSYQRLVTHLKFLSWRI-LEHASINDSDesLQQAVKQN 236

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1409477048 236 YPESYKISKKIRVLLTKEYQLAITKEELGYLAIHIERLR 274
Cdd:PRK09772  237 YPQAWQCAERIAIFIGLQYQRKISPAEIMFLAINIERVR 275
BglG COG3711
Transcriptional antiterminator [Transcription];
60-273 5.05e-35

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 133.06  E-value: 5.05e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048  60 LLNQIDERFLFAAETIIDHAETVLMEKLNEHVLIALTDHIAFSAENINNGIVIRNKLLREIEVLYSDEFSIAQWAVEYLT 139
Cdd:COG3711   170 LLKLIPEEDLELIEEIIEEAEKKLGIKLSDSIYINLTDHIAIAIKRIKKGKYIKLDNPLLWEIKKPKEYEIAKEILKLIE 249

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048 140 KELGIPYTYDEAGYIAIHIHSGRSGRNN---NHRSIREVTIVSDIIHLVESELETDIHSEpfSLNYSRLVNHLRLLLQRT 216
Cdd:COG3711   250 ERLGISLPEDEIGYIALHLLGARLNNDNelsEIITLEITKLIKEIINIIEEELGIDLDED--SLLYERLITHLKPAINRL 327

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1409477048 217 HAQQYavLDTEIVEMVKRKYPESYKISKKIRVLLTKEYQLAITKEELGYLAIHIERL 273
Cdd:COG3711   328 KYGIP--IRNPLLEEIKEKYPEAFELAKKIAKYLEKELGIEIPEDEIGYLTLHFGAA 382
CAT_RBD smart01061
CAT RNA binding domain; This RNA binding domain is found at the amino terminus of ...
 1-54 1.01e-16

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: 72.51  E-value: 1.01e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1409477048    1 MKIKKIFNQNAVLV-DDGGQEKVAIGKGIGFDRKRNDLIFDRDVERIFVMEPEGQ 54
Cdd:smart01061   1 MRIKKVLNNNVVLAeDENGQEVIVMGKGIGFGKKKGDLIDESKIEKIFVLKDEED 55
CAT_RBD pfam03123
CAT RNA binding domain; This RNA binding domain is found at the amino terminus of ...
 2-56 5.18e-15

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: 67.84  E-value: 5.18e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1409477048   2 KIKKIFNQNAVLV-DDGGQEKVAIGKGIGFDRKRNDLIFDRDVERIFVMEPEGQIK 56
Cdd:pfam03123   1 KIKKVLNNNVVLAkDDNGEEVILMGKGIGFGKKKGDLIDESKIEKIFVLKDEEESE 56
 
Name Accession Description Interval E-value
PRK09772 PRK09772
transcriptional antiterminator BglG; Provisional
 1-274 1.43e-35

transcriptional antiterminator BglG; Provisional


Pssm-ID: 170086 [Multi-domain]  Cd Length: 278  Bit Score: 129.06  E-value: 1.43e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048   1 MKIKKIFNQNAVLV-DDGGQEKVAIGKGIGFDRKRNDLIFDRDVERIFVMEP-EGQIKLQNLLNQIDERFLFAAETIIDH 78
Cdd:PRK09772    3 MQITKILNNNVVVViDDQQREKVVMGRGIGFQKRAGERINSSGIEKEYALSShELNGRLSELLSHIPLEVMATCDRIISL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048  79 AETVLmEKLNEHVLIALTDHIAFSAENINNGIVIRNKLLREIEVLYSDEFSIAQWAVEYLTKELGIPYTYDEAGYIAIHI 158
Cdd:PRK09772   83 AQERL-GKLQDSIYISLTDHCQFAIKRFQQNVLLPNPLLWDIQRLYPKEFQLGEEALTIIDKRLGVQLPKDEVGFIAMHL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048 159 HSGRsgRNNNHRSIREVT-IVSDIIHLVESELETDIHSEpfSLNYSRLVNHLRLLLQRThAQQYAVLDTE--IVEMVKRK 235
Cdd:PRK09772  162 VSAQ--MSGNMEDVAGVTqLMREMLQLIKFQFSLNYQEE--SLSYQRLVTHLKFLSWRI-LEHASINDSDesLQQAVKQN 236

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1409477048 236 YPESYKISKKIRVLLTKEYQLAITKEELGYLAIHIERLR 274
Cdd:PRK09772  237 YPQAWQCAERIAIFIGLQYQRKISPAEIMFLAINIERVR 275
BglG COG3711
Transcriptional antiterminator [Transcription];
60-273 5.05e-35

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 133.06  E-value: 5.05e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048  60 LLNQIDERFLFAAETIIDHAETVLMEKLNEHVLIALTDHIAFSAENINNGIVIRNKLLREIEVLYSDEFSIAQWAVEYLT 139
Cdd:COG3711   170 LLKLIPEEDLELIEEIIEEAEKKLGIKLSDSIYINLTDHIAIAIKRIKKGKYIKLDNPLLWEIKKPKEYEIAKEILKLIE 249

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048 140 KELGIPYTYDEAGYIAIHIHSGRSGRNN---NHRSIREVTIVSDIIHLVESELETDIHSEpfSLNYSRLVNHLRLLLQRT 216
Cdd:COG3711   250 ERLGISLPEDEIGYIALHLLGARLNNDNelsEIITLEITKLIKEIINIIEEELGIDLDED--SLLYERLITHLKPAINRL 327

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1409477048 217 HAQQYavLDTEIVEMVKRKYPESYKISKKIRVLLTKEYQLAITKEELGYLAIHIERL 273
Cdd:COG3711   328 KYGIP--IRNPLLEEIKEKYPEAFELAKKIAKYLEKELGIEIPEDEIGYLTLHFGAA 382
CAT_RBD smart01061
CAT RNA binding domain; This RNA binding domain is found at the amino terminus of ...
 1-54 1.01e-16

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: 72.51  E-value: 1.01e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1409477048    1 MKIKKIFNQNAVLV-DDGGQEKVAIGKGIGFDRKRNDLIFDRDVERIFVMEPEGQ 54
Cdd:smart01061   1 MRIKKVLNNNVVLAeDENGQEVIVMGKGIGFGKKKGDLIDESKIEKIFVLKDEED 55
CAT_RBD pfam03123
CAT RNA binding domain; This RNA binding domain is found at the amino terminus of ...
 2-56 5.18e-15

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: 67.84  E-value: 5.18e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1409477048   2 KIKKIFNQNAVLV-DDGGQEKVAIGKGIGFDRKRNDLIFDRDVERIFVMEPEGQIK 56
Cdd:pfam03123   1 KIKKVLNNNVVLAkDDNGEEVILMGKGIGFGKKKGDLIDESKIEKIFVLKDEEESE 56
PRD pfam00874
PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory ...
 73-160 1.18e-14

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: 68.05  E-value: 1.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048  73 ETIIDHAETVLMEKL-NEHVLIALTDHIAFSAENINNGIVIRNKLLREIEVLYSDEFSIAQWAVEYLTKELGIPYTYDEA 151
Cdd:pfam00874   1 EEIIELIEKKLGITFdDDILYIRLILHLAFAIERIKEGITIENPLLEEIKEKYPKEFEIAKKILEILEEELGIELPEDEI 80


                  ....*....
gi 1409477048 152 GYIAIHIHS 160
Cdd:pfam00874  81 GYIALHFLS 89
PRD pfam00874
PRD domain; The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory ...
 180-273 3.97e-11

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: 58.42  E-value: 3.97e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048 180 DIIHLVESELETDIHSEpfsLNYSRLVNHLRLLLQRTHAQQYavLDTEIVEMVKRKYPESYKISKKIRVLLTKEYQLAIT 259
Cdd:pfam00874   2 EIIELIEKKLGITFDDD---ILYIRLILHLAFAIERIKEGIT--IENPLLEEIKEKYPKEFEIAKKILEILEEELGIELP 76

                          90
                  ....*....|....
gi 1409477048 260 KEELGYLAIHIERL 273
Cdd:pfam00874  77 EDEIGYIALHFLSA 90
LevR COG3933
Transcriptional regulatory protein LevR, contains PRD, AAA+ and EIIA domains [Transcription];
19-169 1.24e-10

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


Pssm-ID: 443134 [Multi-domain]  Cd Length: 916  Bit Score: 62.06  E-value: 1.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048  19 QEKVAIGKGIGFDRKRNDLIFDRDVERIFVMEPEGQIK-LQNLLNQIDERFLFAAETIIDHAETVLMEKLNEHVLIALTD 97
Cdd:COG3933   407 KKKLLLELGIDEEEINIIIEIDIDVHLLKFIYDDNKNFnKEELAKIVDEDIINVVEEILELAEKKLGRKFSENFIYALSL 486

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1409477048  98 HIAFSAENINNGIVIRNKLLREIEVLYSDEFSIAQWAVEYLTKELGIPYTYDEAGYIAIHIHSGRSGRNNNH 169
Cdd:COG3933   487 HLSSFIERIKEGKEIINPNLNEIKKKYPKEFKVAKEIKELIEQELDIEIPEDEVGFLTLFLVSLNENNESGK 558
LevR COG3933
Transcriptional regulatory protein LevR, contains PRD, AAA+ and EIIA domains [Transcription];
166-268 7.17e-03

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


Pssm-ID: 443134 [Multi-domain]  Cd Length: 916  Bit Score: 37.79  E-value: 7.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1409477048 166 NNNHRSIREVtIVSDIIHLVESELEtdIHSEPFSLNYS-RLVNHLRLLLQRT--HAQQYAVLDTEIVEMVKRKYPESYKI 242
Cdd:COG3933   443 NFNKEELAKI-VDEDIINVVEEILE--LAEKKLGRKFSeNFIYALSLHLSSFieRIKEGKEIINPNLNEIKKKYPKEFKV 519

                          90       100
                  ....*....|....*....|....*.
gi 1409477048 243 SKKIRVLLTKEYQLAITKEELGYLAI 268
Cdd:COG3933   520 AKEIKELIEQELDIEIPEDEVGFLTL 545
 
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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