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Conserved domains on  [gi|1720424507|ref|XP_030098931|]
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mediator of RNA polymerase II transcription subunit 25 isoform X10 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Med25 pfam11232
Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up ...
 293-442 2.45e-78

Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear.


:

Pssm-ID: 463243  Cd Length: 154  Bit Score: 245.72  E-value: 2.45e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 293 SNKLLAWSGVLEWQEKPKpasvDANTKLTRSLPCQV--YVNHGE-NLKTEQWPQKLIMQLIPQQLLTTLG-PLFRNSRMV 368
Cdd:pfam11232   1 SQRELIWSGVLEWQEKMS----DQNPKITRTLPCQVsnSVKNGEpELKAEKWPQKLIMQLMPKTLLGNIGgALLRNSRVV 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720424507 369 QFHFTNKDLESLKGLYRIMGNGFAGCVHF---PHTAPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVNGIRQVITNHK 442
Cdd:pfam11232  77 VFHFTPTDLEALKSLYRVMSNGFAGCVHFpgiPANPQCDIKVLMLLYSPKKNAFMGLIPNDQAAFVNRLRQVIKKQK 153
Med25_VWA super family cl48110
Mediator complex subunit 25 von Willebrand factor type A; The overall function of the ...
 1-123 8.40e-60

Mediator complex subunit 25 von Willebrand factor type A; The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex.


The actual alignment was detected with superfamily member pfam11265:

Pssm-ID: 463253  Cd Length: 213  Bit Score: 199.06  E-value: 8.40e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507   1 MGGGGESCSLIAEGLSTALQLFDDFKKMREQIG-QTHRVCLLICNSPPYLLPAVESTTYSGCTTESLVQKIGERGIHFSI 79
Cdd:pfam11265  93 SGGGGESCALIAEGLATALQCFDDLQKIRENPGlACQRHCILICNSPPYQLPVMESPTYTGKTAEQLAALMAERNIHLSI 172

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1720424507  80 VSPRKLPALRLLFEKAAPPallEPLQQPADVSQDPRHMVLVRGL 123
Cdd:pfam11265 173 ISPRKIPALFKLFEKAGPD---LPSSPSKNYAKDPRHLVLLRGF 213
Med25_NR-box pfam11244
Mediator complex subunit 25 C-terminal NR box-containing; The overall function of the ...
 554-642 1.24e-34

Mediator complex subunit 25 C-terminal NR box-containing; The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and this C-terminal NR box-containing domain (646-650) from C69-747. The NR box of MED25 is critical for its recruitment to the promoter, probably through an interaction with pre bound RAR.


:

Pssm-ID: 463246 [Multi-domain]  Cd Length: 89  Bit Score: 126.31  E-value: 1.24e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 554 TGVPPPQASLHHLQPPGAPTLLPPHQSMGQPQLGPQLLHPPPAQSWPTQLPQRAPLPGQMLLSGGPRGPVPQPGLQPSVM 633
Cdd:pfam11244   1 TSVPQTQQPLHHMQQAAQGMLPHQHQAPGQQQLGQTLMHQAPAQSWGAQLPPRAPLPGQMLLSGGPRGPVPQPGLAPSVM 80


                  ....*....
gi 1720424507 634 EDDILMDLI 642
Cdd:pfam11244  81 EDDILMDLI 89
Med25_SD1 super family cl25802
Mediator complex subunit 25 synapsin 1; The overall function of the full-length Med25 is ...
 125-280 2.45e-27

Mediator complex subunit 25 synapsin 1; The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, this SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This The function of the SD domains is unclear.


The actual alignment was detected with superfamily member pfam11235:

Pssm-ID: 463244 [Multi-domain]  Cd Length: 157  Bit Score: 108.33  E-value: 2.45e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 125 LPVGGSSTSGSLQTKQAVPLPPAPASAATLSAAPPQALPPVPPQYQVPGNLSAAQVAAQNAVEAAKSQKAGLGPRFSPIN 204
Cdd:pfam11235   1 LPVGGGSAPGPLQSKQPVPLPPAAPSGATLSAAPQQPLPPVPPQYQVPGNLSAAQVAAQNAVEAAKNQKAGLGPRFSPIT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720424507 205 PLQQAAPGVGPPFSQAPAPPLAP-VPPGAPKPPPASQPSLVSTVAPGPVLAAPAQPGAPSLAGTVTPGGVNGPSAAQ 280
Cdd:pfam11235  81 PLQQAAPGVGPPFSQAPAPQLPPgPPGAPKPVPPASQPSLVSTVAPGSGLAPTAQPGAPSMAGTVAPGGVSGPSPAQ 157
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 458-626 1.39e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 48.22  E-value: 1.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 458 QQAPPVL---GPILEEQARPPQNLLQLRAPQPQPqgavgaSAATGQPQPQGATQAPTGAPQGPPGAAPGPPPSGPILRPQ 534
Cdd:pfam03154 168 QTQPPVLqaqSGAASPPSPPPPGTTQAATAGPTP------SAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQR 241

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 535 NPGANPQLRSLLLNPAPPQTGVPP-PQASLH---------------HLQPPGAPTLLPPHQSMGQPQ--LGPQLLHPPPA 596
Cdd:pfam03154 242 LPSPHPPLQPMTQPPPPSQVSPQPlPQPSLHgqmppmphslqtgpsHMQHPVPPQPFPLTPQSSQSQvpPGPSPAAPGQS 321

                         170       180       190
                  ....*....|....*....|....*....|
gi 1720424507 597 QSWPTQLPQRAPLPGQMLLSGGPRGPVPQP 626
Cdd:pfam03154 322 QQRIHTPPSQSQLQSQQPPREQPLPPAPLS 351
 
Name Accession Description Interval E-value
Med25 pfam11232
Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up ...
 293-442 2.45e-78

Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear.


Pssm-ID: 463243  Cd Length: 154  Bit Score: 245.72  E-value: 2.45e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 293 SNKLLAWSGVLEWQEKPKpasvDANTKLTRSLPCQV--YVNHGE-NLKTEQWPQKLIMQLIPQQLLTTLG-PLFRNSRMV 368
Cdd:pfam11232   1 SQRELIWSGVLEWQEKMS----DQNPKITRTLPCQVsnSVKNGEpELKAEKWPQKLIMQLMPKTLLGNIGgALLRNSRVV 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720424507 369 QFHFTNKDLESLKGLYRIMGNGFAGCVHF---PHTAPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVNGIRQVITNHK 442
Cdd:pfam11232  77 VFHFTPTDLEALKSLYRVMSNGFAGCVHFpgiPANPQCDIKVLMLLYSPKKNAFMGLIPNDQAAFVNRLRQVIKKQK 153
Med25_VWA pfam11265
Mediator complex subunit 25 von Willebrand factor type A; The overall function of the ...
 1-123 8.40e-60

Mediator complex subunit 25 von Willebrand factor type A; The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex.


Pssm-ID: 463253  Cd Length: 213  Bit Score: 199.06  E-value: 8.40e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507   1 MGGGGESCSLIAEGLSTALQLFDDFKKMREQIG-QTHRVCLLICNSPPYLLPAVESTTYSGCTTESLVQKIGERGIHFSI 79
Cdd:pfam11265  93 SGGGGESCALIAEGLATALQCFDDLQKIRENPGlACQRHCILICNSPPYQLPVMESPTYTGKTAEQLAALMAERNIHLSI 172

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1720424507  80 VSPRKLPALRLLFEKAAPPallEPLQQPADVSQDPRHMVLVRGL 123
Cdd:pfam11265 173 ISPRKIPALFKLFEKAGPD---LPSSPSKNYAKDPRHLVLLRGF 213
Med25_NR-box pfam11244
Mediator complex subunit 25 C-terminal NR box-containing; The overall function of the ...
 554-642 1.24e-34

Mediator complex subunit 25 C-terminal NR box-containing; The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and this C-terminal NR box-containing domain (646-650) from C69-747. The NR box of MED25 is critical for its recruitment to the promoter, probably through an interaction with pre bound RAR.


Pssm-ID: 463246 [Multi-domain]  Cd Length: 89  Bit Score: 126.31  E-value: 1.24e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 554 TGVPPPQASLHHLQPPGAPTLLPPHQSMGQPQLGPQLLHPPPAQSWPTQLPQRAPLPGQMLLSGGPRGPVPQPGLQPSVM 633
Cdd:pfam11244   1 TSVPQTQQPLHHMQQAAQGMLPHQHQAPGQQQLGQTLMHQAPAQSWGAQLPPRAPLPGQMLLSGGPRGPVPQPGLAPSVM 80


                  ....*....
gi 1720424507 634 EDDILMDLI 642
Cdd:pfam11244  81 EDDILMDLI 89
Med25_SD1 pfam11235
Mediator complex subunit 25 synapsin 1; The overall function of the full-length Med25 is ...
 125-280 2.45e-27

Mediator complex subunit 25 synapsin 1; The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, this SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This The function of the SD domains is unclear.


Pssm-ID: 463244 [Multi-domain]  Cd Length: 157  Bit Score: 108.33  E-value: 2.45e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 125 LPVGGSSTSGSLQTKQAVPLPPAPASAATLSAAPPQALPPVPPQYQVPGNLSAAQVAAQNAVEAAKSQKAGLGPRFSPIN 204
Cdd:pfam11235   1 LPVGGGSAPGPLQSKQPVPLPPAAPSGATLSAAPQQPLPPVPPQYQVPGNLSAAQVAAQNAVEAAKNQKAGLGPRFSPIT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720424507 205 PLQQAAPGVGPPFSQAPAPPLAP-VPPGAPKPPPASQPSLVSTVAPGPVLAAPAQPGAPSLAGTVTPGGVNGPSAAQ 280
Cdd:pfam11235  81 PLQQAAPGVGPPFSQAPAPQLPPgPPGAPKPVPPASQPSLVSTVAPGSGLAPTAQPGAPSMAGTVAPGGVSGPSPAQ 157
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 458-626 1.39e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 48.22  E-value: 1.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 458 QQAPPVL---GPILEEQARPPQNLLQLRAPQPQPqgavgaSAATGQPQPQGATQAPTGAPQGPPGAAPGPPPSGPILRPQ 534
Cdd:pfam03154 168 QTQPPVLqaqSGAASPPSPPPPGTTQAATAGPTP------SAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQR 241

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 535 NPGANPQLRSLLLNPAPPQTGVPP-PQASLH---------------HLQPPGAPTLLPPHQSMGQPQ--LGPQLLHPPPA 596
Cdd:pfam03154 242 LPSPHPPLQPMTQPPPPSQVSPQPlPQPSLHgqmppmphslqtgpsHMQHPVPPQPFPLTPQSSQSQvpPGPSPAAPGQS 321

                         170       180       190
                  ....*....|....*....|....*....|
gi 1720424507 597 QSWPTQLPQRAPLPGQMLLSGGPRGPVPQP 626
Cdd:pfam03154 322 QQRIHTPPSQSQLQSQQPPREQPLPPAPLS 351
PHA03247 PHA03247
large tegument protein UL36; Provisional
 457-630 6.38e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.00  E-value: 6.38e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507  457 AQQAPPVLGPILEEQARPPQNllqlRAPQPQPQGAVGASAATGQPQPQGATQAPTGAPQGPPGAAPGPPPSGPILRPQNP 536
Cdd:PHA03247  2822 ASPAGPLPPPTSAQPTAPPPP----PGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTES 2897

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507  537 GANPQLRSLLLN----PAPPQTGVPPPQASLHHLQPPGAPTLLPPHQSMGQPQLGPQLLHPPPAQSWPTQLPQRAPLPGQ 612
Cdd:PHA03247  2898 FALPPDQPERPPqpqaPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRF 2977

                          170
                   ....*....|....*...
gi 1720424507  613 MLLSGGPRGPVPQPGLQP 630
Cdd:PHA03247  2978 RVPQPAPSREAPASSTPP 2995
PHA03378 PHA03378
EBNA-3B; Provisional
 549-634 6.38e-04

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 43.13  E-value: 6.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 549 PAPPQTGVPPPQASLHHLQPP-GAPTLLPPHQS----MGQPQLGPQLLHPP---PAQSWPTQLPQRAPLPGQMLlSGGPr 620
Cdd:PHA03378  717 PAAATGRARPPAAAPGRARPPaAAPGRARPPAAapgrARPPAAAPGRARPPaaaPGAPTPQPPPQAPPAPQQRP-RGAP- 794

                          90
                  ....*....|....
gi 1720424507 621 GPVPQPGLQPSVME 634
Cdd:PHA03378  795 TPQPPPQAGPTSMQ 808
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 531-631 5.16e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 39.79  E-value: 5.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 531 LRPQNPGANPQLRSL-LLNPAPPQTGVPPPQASLHHLQPPGAPTLLPPHQSMGQPQ-----LGPQLLHPPPAQSWPT--- 601
Cdd:TIGR01628 371 LQDQFMQLQPRMRQLpMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMgpggpLRPNGLAPMNAVRAPSrna 450

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1720424507 602 -QLPQRAPLPGQMLLSGGPRGPVPQPGLQPS 631
Cdd:TIGR01628 451 qNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQ 481
 
Name Accession Description Interval E-value
Med25 pfam11232
Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up ...
 293-442 2.45e-78

Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear.


Pssm-ID: 463243  Cd Length: 154  Bit Score: 245.72  E-value: 2.45e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 293 SNKLLAWSGVLEWQEKPKpasvDANTKLTRSLPCQV--YVNHGE-NLKTEQWPQKLIMQLIPQQLLTTLG-PLFRNSRMV 368
Cdd:pfam11232   1 SQRELIWSGVLEWQEKMS----DQNPKITRTLPCQVsnSVKNGEpELKAEKWPQKLIMQLMPKTLLGNIGgALLRNSRVV 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720424507 369 QFHFTNKDLESLKGLYRIMGNGFAGCVHF---PHTAPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVNGIRQVITNHK 442
Cdd:pfam11232  77 VFHFTPTDLEALKSLYRVMSNGFAGCVHFpgiPANPQCDIKVLMLLYSPKKNAFMGLIPNDQAAFVNRLRQVIKKQK 153
Med25_VWA pfam11265
Mediator complex subunit 25 von Willebrand factor type A; The overall function of the ...
 1-123 8.40e-60

Mediator complex subunit 25 von Willebrand factor type A; The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex.


Pssm-ID: 463253  Cd Length: 213  Bit Score: 199.06  E-value: 8.40e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507   1 MGGGGESCSLIAEGLSTALQLFDDFKKMREQIG-QTHRVCLLICNSPPYLLPAVESTTYSGCTTESLVQKIGERGIHFSI 79
Cdd:pfam11265  93 SGGGGESCALIAEGLATALQCFDDLQKIRENPGlACQRHCILICNSPPYQLPVMESPTYTGKTAEQLAALMAERNIHLSI 172

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1720424507  80 VSPRKLPALRLLFEKAAPPallEPLQQPADVSQDPRHMVLVRGL 123
Cdd:pfam11265 173 ISPRKIPALFKLFEKAGPD---LPSSPSKNYAKDPRHLVLLRGF 213
Med25_NR-box pfam11244
Mediator complex subunit 25 C-terminal NR box-containing; The overall function of the ...
 554-642 1.24e-34

Mediator complex subunit 25 C-terminal NR box-containing; The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and this C-terminal NR box-containing domain (646-650) from C69-747. The NR box of MED25 is critical for its recruitment to the promoter, probably through an interaction with pre bound RAR.


Pssm-ID: 463246 [Multi-domain]  Cd Length: 89  Bit Score: 126.31  E-value: 1.24e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 554 TGVPPPQASLHHLQPPGAPTLLPPHQSMGQPQLGPQLLHPPPAQSWPTQLPQRAPLPGQMLLSGGPRGPVPQPGLQPSVM 633
Cdd:pfam11244   1 TSVPQTQQPLHHMQQAAQGMLPHQHQAPGQQQLGQTLMHQAPAQSWGAQLPPRAPLPGQMLLSGGPRGPVPQPGLAPSVM 80


                  ....*....
gi 1720424507 634 EDDILMDLI 642
Cdd:pfam11244  81 EDDILMDLI 89
Med25_SD1 pfam11235
Mediator complex subunit 25 synapsin 1; The overall function of the full-length Med25 is ...
 125-280 2.45e-27

Mediator complex subunit 25 synapsin 1; The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, this SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This The function of the SD domains is unclear.


Pssm-ID: 463244 [Multi-domain]  Cd Length: 157  Bit Score: 108.33  E-value: 2.45e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 125 LPVGGSSTSGSLQTKQAVPLPPAPASAATLSAAPPQALPPVPPQYQVPGNLSAAQVAAQNAVEAAKSQKAGLGPRFSPIN 204
Cdd:pfam11235   1 LPVGGGSAPGPLQSKQPVPLPPAAPSGATLSAAPQQPLPPVPPQYQVPGNLSAAQVAAQNAVEAAKNQKAGLGPRFSPIT 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720424507 205 PLQQAAPGVGPPFSQAPAPPLAP-VPPGAPKPPPASQPSLVSTVAPGPVLAAPAQPGAPSLAGTVTPGGVNGPSAAQ 280
Cdd:pfam11235  81 PLQQAAPGVGPPFSQAPAPQLPPgPPGAPKPVPPASQPSLVSTVAPGSGLAPTAQPGAPSMAGTVAPGGVSGPSPAQ 157
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 483-629 4.61e-07

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 53.12  E-value: 4.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 483 APQPQPQGAVGASAATGQP-------------QPQGATQAPTGAPQGPPGAAPGPPPSGPILRPQNPGANPQLRSLLLNP 549
Cdd:pfam09770 174 APAPQPAAQPASLPAPSRKmmsleeveaamraQAKKPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQP 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 550 APPQTGVPPPQAslhhLQPPGAPTLlPPHQSMGQPQLGPQLLHPPPAQSWPTQL---PQRAPLPGQMLLSGGPRGPVPQP 626
Cdd:pfam09770 254 QQHPGQGHPVTI----LQRPQSPQP-DPAQPSIQPQAQQFHQQPPPVPVQPTQIlqnPNRLSAARVGYPQNPQPGVQPAP 328


                  ...
gi 1720424507 627 GLQ 629
Cdd:pfam09770 329 AHQ 331
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 458-626 1.39e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 48.22  E-value: 1.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 458 QQAPPVL---GPILEEQARPPQNLLQLRAPQPQPqgavgaSAATGQPQPQGATQAPTGAPQGPPGAAPGPPPSGPILRPQ 534
Cdd:pfam03154 168 QTQPPVLqaqSGAASPPSPPPPGTTQAATAGPTP------SAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQR 241

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 535 NPGANPQLRSLLLNPAPPQTGVPP-PQASLH---------------HLQPPGAPTLLPPHQSMGQPQ--LGPQLLHPPPA 596
Cdd:pfam03154 242 LPSPHPPLQPMTQPPPPSQVSPQPlPQPSLHgqmppmphslqtgpsHMQHPVPPQPFPLTPQSSQSQvpPGPSPAAPGQS 321

                         170       180       190
                  ....*....|....*....|....*....|
gi 1720424507 597 QSWPTQLPQRAPLPGQMLLSGGPRGPVPQP 626
Cdd:pfam03154 322 QQRIHTPPSQSQLQSQQPPREQPLPPAPLS 351
PHA03247 PHA03247
large tegument protein UL36; Provisional
 457-630 6.38e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.00  E-value: 6.38e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507  457 AQQAPPVLGPILEEQARPPQNllqlRAPQPQPQGAVGASAATGQPQPQGATQAPTGAPQGPPGAAPGPPPSGPILRPQNP 536
Cdd:PHA03247  2822 ASPAGPLPPPTSAQPTAPPPP----PGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTES 2897

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507  537 GANPQLRSLLLN----PAPPQTGVPPPQASLHHLQPPGAPTLLPPHQSMGQPQLGPQLLHPPPAQSWPTQLPQRAPLPGQ 612
Cdd:PHA03247  2898 FALPPDQPERPPqpqaPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRF 2977

                          170
                   ....*....|....*...
gi 1720424507  613 MLLSGGPRGPVPQPGLQP 630
Cdd:PHA03247  2978 RVPQPAPSREAPASSTPP 2995
PHA03378 PHA03378
EBNA-3B; Provisional
 549-634 6.38e-04

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 43.13  E-value: 6.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 549 PAPPQTGVPPPQASLHHLQPP-GAPTLLPPHQS----MGQPQLGPQLLHPP---PAQSWPTQLPQRAPLPGQMLlSGGPr 620
Cdd:PHA03378  717 PAAATGRARPPAAAPGRARPPaAAPGRARPPAAapgrARPPAAAPGRARPPaaaPGAPTPQPPPQAPPAPQQRP-RGAP- 794

                          90
                  ....*....|....
gi 1720424507 621 GPVPQPGLQPSVME 634
Cdd:PHA03378  795 TPQPPPQAGPTSMQ 808
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 457-632 1.61e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.51  E-value: 1.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 457 AQQAPPVLGPILEEQARPPQNLLQLRAPQPQpqgAVGASAATGQPQPQGATQAPTGAPQGPPGAAPGPPPSGPILRPQNP 536
Cdd:PRK07764  586 AVVGPAPGAAGGEGPPAPASSGPPEEAARPA---APAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDA 662

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 537 GANPQLRSLLLNPAPPQTGVPPPQASLHHL---QPPGAPTLLPPHQSMGQPQLGPQLLHPPPAQSWPTQLPQRA---PLP 610
Cdd:PRK07764  663 SDGGDGWPAKAGGAAPAAPPPAPAPAAPAApagAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADdpvPLP 742

                         170       180
                  ....*....|....*....|..
gi 1720424507 611 GQMLLSGGPRGPVPQPGLQPSV 632
Cdd:PRK07764  743 PEPDDPPDPAGAPAQPPPPPAP 764
PHA03247 PHA03247
large tegument protein UL36; Provisional
 483-631 1.94e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.46  E-value: 1.94e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507  483 APQPQPQGAVGASAATGQPQPQGATQAPTGAPQGPPgaapGPPPSGPILRPQNPGANPQLRslllnpAPPQTGVPPPQAS 562
Cdd:PHA03247  2809 AAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPG----PPPPSLPLGGSVAPGGDVRRR------PPSRSPAAKPAAP 2878

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720424507  563 LHhlqPP----GAPTLLPPHQSMGQPQLGPQLLHPPPAQSWPTQLPQRAPLPGQMllSGGPRGPVPQPGLQPS 631
Cdd:PHA03247  2879 AR---PPvrrlARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQ--PPPPPPPRPQPPLAPT 2946
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 531-631 5.16e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 39.79  E-value: 5.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 531 LRPQNPGANPQLRSL-LLNPAPPQTGVPPPQASLHHLQPPGAPTLLPPHQSMGQPQ-----LGPQLLHPPPAQSWPT--- 601
Cdd:TIGR01628 371 LQDQFMQLQPRMRQLpMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMgpggpLRPNGLAPMNAVRAPSrna 450

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1720424507 602 -QLPQRAPLPGQMLLSGGPRGPVPQPGLQPS 631
Cdd:TIGR01628 451 qNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQ 481
PHA03378 PHA03378
EBNA-3B; Provisional
 472-627 7.39e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 39.67  E-value: 7.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 472 ARPPQnllqlRAPQPQPQGAvgasAATGQPQPQGATQAPTGAPQGPPGAAPGPPPSGPILRPqnPGANPqlrSLLLNPAP 551
Cdd:PHA03378  694 MQPPP-----RAPTPMRPPA----APPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARP--PAAAP---GRARPPAA 759

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720424507 552 PQTGVPPPQASlhhlqpPGAPTLLPPhqsmgqPQLGPQLLHPPPAQSWPTQLPQRAPLPGQMLlsggPRGPVPQPG 627
Cdd:PHA03378  760 APGRARPPAAA------PGAPTPQPP------PQAPPAPQQRPRGAPTPQPPPQAGPTSMQLM----PRAAPGQQG 819
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
454-612 9.40e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 38.99  E-value: 9.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 454 GMGAQQAppvLGPILEEQARPPQNLLQLRAPQPQPQGAVGASAATGQPQPQGATQAPTgapqgppgaapgpppsgpilRP 533
Cdd:PRK14971  372 GRGPKQH---IKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPT--------------------VS 428

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424507 534 QNPGAnpqlrslllnPAPpqtgVPPPQASLHHLQPPGAPTLLPPhQSMGQPQLGPQLLHP-PPAQSWPTQLPQRAPLPGQ 612
Cdd:PRK14971  429 VDPPA----------AVP----VNPPSTAPQAVRPAQFKEEKKI-PVSKVSSLGPSTLRPiQEKAEQATGNIKEAPTGTQ 493
 
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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