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Conserved domains on  [gi|528474094|ref|XP_005163997|]
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mediator of RNA polymerase II transcription subunit 25 isoform X2 [Danio rerio]

Protein Classification

Med25_VWA and Med25 domain-containing protein( domain architecture ID 11188880)

protein containing domains Med25_VWA, Med25, and Med25_NR-box

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Med25_VWA pfam11265
Mediator complex subunit 25 von Willebrand factor type A; The overall function of the ...
 10-222 1.67e-119

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: 355.84  E-value: 1.67e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094   10 NQVSDVVFVIEGTANLGPYFESLRNNYILPTIEYFNGGPPAETDFGGDYGGTQYGLVVFNTVDCAPESYVQCHAPTSSAF 89
Cdd:pfam11265   2 SVVADVVFVVEGTANLGAYFNELKTNYILPTLEYFNGGPIEERDYGSENGSTLYGLVVYHAADCLPEPSVQCYGPTSSPH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094   90 EFVSWIDSIQFMGGGAESCSLIAEGLSVALQLFDDFKKMREQIG-QTHKVCVLLCNSPPYLLPAVESVSYTGCTADSLVQ 168
Cdd:pfam11265  82 KFLQWLDKIDFSGGGGESCALIAEGLATALQCFDDLQKIRENPGlACQRHCILICNSPPYQLPVMESPTYTGKTAEQLAA 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 528474094  169 IIRDRGIHFSVIAPRKLPALRSLFERASsvAGPPESSHPDYSQDPFHMVLVRGI 222
Cdd:pfam11265 162 LMAERNIHLSIISPRKIPALFKLFEKAG--PDLPSSPSKNYAKDPRHLVLLRGF 213
Med25 pfam11232
Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up ...
 392-541 2.96e-73

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: 233.78  E-value: 2.96e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094  392 NKVVAWSGVLEWQEKPKassmDSNTKLTRSLPCQVQ--VSQGE-NLNTDQWPQKLIMQLIPQQLLTTLG-PLFRNSRMVQ 467
Cdd:pfam11232   2 QRELIWSGVLEWQEKMS----DQNPKITRTLPCQVSnsVKNGEpELKAEKWPQKLIMQLMPKTLLGNIGgALLRNSRVVV 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528474094  468 FLFTNKDMESLKGLFRIMTSGFAGCVHF---PHSAPCEVRVLMLLYSSRKRIFMGLIPNDQSGFVNGIRQVITNHKQ 541
Cdd:pfam11232  78 FHFTPTDLEALKSLYRVMSNGFAGCVHFpgiPANPQCDIKVLMLLYSPKKNAFMGLIPNDQAAFVNRLRQVIKKQKQ 154
Med25_NR-box super family cl24239
Mediator complex subunit 25 C-terminal NR box-containing; The overall function of the ...
 644-701 3.06e-06

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.


The actual alignment was detected with superfamily member pfam11244:

Pssm-ID: 463246 [Multi-domain]  Cd Length: 89  Bit Score: 45.80  E-value: 3.06e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094  644 QQMVHAAPGG--GAQMQPqwRQPHQGPLMVPTGPRGPVTQnPGMPsvSSVMEDEILMDLI 701
Cdd:pfam11244  35 QTLMHQAPAQswGAQLPP--RAPLPGQMLLSGGPRGPVPQ-PGLA--PSVMEDDILMDLI 89
 
Name Accession Description Interval E-value
Med25_VWA pfam11265
Mediator complex subunit 25 von Willebrand factor type A; The overall function of the ...
 10-222 1.67e-119

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: 355.84  E-value: 1.67e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094   10 NQVSDVVFVIEGTANLGPYFESLRNNYILPTIEYFNGGPPAETDFGGDYGGTQYGLVVFNTVDCAPESYVQCHAPTSSAF 89
Cdd:pfam11265   2 SVVADVVFVVEGTANLGAYFNELKTNYILPTLEYFNGGPIEERDYGSENGSTLYGLVVYHAADCLPEPSVQCYGPTSSPH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094   90 EFVSWIDSIQFMGGGAESCSLIAEGLSVALQLFDDFKKMREQIG-QTHKVCVLLCNSPPYLLPAVESVSYTGCTADSLVQ 168
Cdd:pfam11265  82 KFLQWLDKIDFSGGGGESCALIAEGLATALQCFDDLQKIRENPGlACQRHCILICNSPPYQLPVMESPTYTGKTAEQLAA 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 528474094  169 IIRDRGIHFSVIAPRKLPALRSLFERASsvAGPPESSHPDYSQDPFHMVLVRGI 222
Cdd:pfam11265 162 LMAERNIHLSIISPRKIPALFKLFEKAG--PDLPSSPSKNYAKDPRHLVLLRGF 213
Med25 pfam11232
Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up ...
 392-541 2.96e-73

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: 233.78  E-value: 2.96e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094  392 NKVVAWSGVLEWQEKPKassmDSNTKLTRSLPCQVQ--VSQGE-NLNTDQWPQKLIMQLIPQQLLTTLG-PLFRNSRMVQ 467
Cdd:pfam11232   2 QRELIWSGVLEWQEKMS----DQNPKITRTLPCQVSnsVKNGEpELKAEKWPQKLIMQLMPKTLLGNIGgALLRNSRVVV 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528474094  468 FLFTNKDMESLKGLFRIMTSGFAGCVHF---PHSAPCEVRVLMLLYSSRKRIFMGLIPNDQSGFVNGIRQVITNHKQ 541
Cdd:pfam11232  78 FHFTPTDLEALKSLYRVMSNGFAGCVHFpgiPANPQCDIKVLMLLYSPKKNAFMGLIPNDQAAFVNRLRQVIKKQKQ 154
Med25_NR-box pfam11244
Mediator complex subunit 25 C-terminal NR box-containing; The overall function of the ...
 644-701 3.06e-06

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: 45.80  E-value: 3.06e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094  644 QQMVHAAPGG--GAQMQPqwRQPHQGPLMVPTGPRGPVTQnPGMPsvSSVMEDEILMDLI 701
Cdd:pfam11244  35 QTLMHQAPAQswGAQLPP--RAPLPGQMLLSGGPRGPVPQ-PGLA--PSVMEDDILMDLI 89
ChlD COG1240
vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and ...
 60-181 9.86e-05

vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and metabolism];


Pssm-ID: 440853 [Multi-domain]  Cd Length: 262  Bit Score: 44.54  E-value: 9.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094  60 GTQYGLVVFNTvdcapESYVQChAPTSSAFEFVSWIDSIQFMGGGAescslIAEGLSVALQLFDDFKKMReqigqtHKVC 139
Cdd:COG1240  128 RDRVGLVAFGG-----EAEVLL-PLTRDREALKRALDELPPGGGTP-----LGDALALALELLKRADPAR------RKVI 190

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 528474094 140 VLL----CNSPPYllpavesvsytgcTADSLVQIIRDRGIHFSVIA 181
Cdd:COG1240  191 VLLtdgrDNAGRI-------------DPLEAAELAAAAGIRIYTIG 223
 
Name Accession Description Interval E-value
Med25_VWA pfam11265
Mediator complex subunit 25 von Willebrand factor type A; The overall function of the ...
 10-222 1.67e-119

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: 355.84  E-value: 1.67e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094   10 NQVSDVVFVIEGTANLGPYFESLRNNYILPTIEYFNGGPPAETDFGGDYGGTQYGLVVFNTVDCAPESYVQCHAPTSSAF 89
Cdd:pfam11265   2 SVVADVVFVVEGTANLGAYFNELKTNYILPTLEYFNGGPIEERDYGSENGSTLYGLVVYHAADCLPEPSVQCYGPTSSPH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094   90 EFVSWIDSIQFMGGGAESCSLIAEGLSVALQLFDDFKKMREQIG-QTHKVCVLLCNSPPYLLPAVESVSYTGCTADSLVQ 168
Cdd:pfam11265  82 KFLQWLDKIDFSGGGGESCALIAEGLATALQCFDDLQKIRENPGlACQRHCILICNSPPYQLPVMESPTYTGKTAEQLAA 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 528474094  169 IIRDRGIHFSVIAPRKLPALRSLFERASsvAGPPESSHPDYSQDPFHMVLVRGI 222
Cdd:pfam11265 162 LMAERNIHLSIISPRKIPALFKLFEKAG--PDLPSSPSKNYAKDPRHLVLLRGF 213
Med25 pfam11232
Mediator complex subunit 25 PTOV activation and synapsin 2; Mediator is a large complex of up ...
 392-541 2.96e-73

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: 233.78  E-value: 2.96e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094  392 NKVVAWSGVLEWQEKPKassmDSNTKLTRSLPCQVQ--VSQGE-NLNTDQWPQKLIMQLIPQQLLTTLG-PLFRNSRMVQ 467
Cdd:pfam11232   2 QRELIWSGVLEWQEKMS----DQNPKITRTLPCQVSnsVKNGEpELKAEKWPQKLIMQLMPKTLLGNIGgALLRNSRVVV 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528474094  468 FLFTNKDMESLKGLFRIMTSGFAGCVHF---PHSAPCEVRVLMLLYSSRKRIFMGLIPNDQSGFVNGIRQVITNHKQ 541
Cdd:pfam11232  78 FHFTPTDLEALKSLYRVMSNGFAGCVHFpgiPANPQCDIKVLMLLYSPKKNAFMGLIPNDQAAFVNRLRQVIKKQKQ 154
Med25_NR-box pfam11244
Mediator complex subunit 25 C-terminal NR box-containing; The overall function of the ...
 644-701 3.06e-06

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: 45.80  E-value: 3.06e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094  644 QQMVHAAPGG--GAQMQPqwRQPHQGPLMVPTGPRGPVTQnPGMPsvSSVMEDEILMDLI 701
Cdd:pfam11244  35 QTLMHQAPAQswGAQLPP--RAPLPGQMLLSGGPRGPVPQ-PGLA--PSVMEDDILMDLI 89
VWA pfam00092
von Willebrand factor type A domain;
14-142 9.57e-06

von Willebrand factor type A domain;


Pssm-ID: 459670 [Multi-domain]  Cd Length: 174  Bit Score: 46.50  E-value: 9.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094   14 DVVFVIEGTANLGPY-FESLRnNYILPTIEYFNGGPPaetdfggdygGTQYGLVVFNtvdcapeSYVQCHAPTSSAF--- 89
Cdd:pfam00092   1 DIVFLLDGSGSIGGDnFEKVK-EFLKKLVESLDIGPD----------GTRVGLVQYS-------SDVRTEFPLNDYSske 62

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 528474094   90 EFVSWIDSIQFMGGGAescSLIAEGLSVALQLFddFKKMREQIGQTHKVCVLL 142
Cdd:pfam00092  63 ELLSAVDNLRYLGGGT---TNTGKALKYALENL--FSSAAGARPGAPKVVVLL 110
ChlD COG1240
vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and ...
 60-181 9.86e-05

vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and metabolism];


Pssm-ID: 440853 [Multi-domain]  Cd Length: 262  Bit Score: 44.54  E-value: 9.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528474094  60 GTQYGLVVFNTvdcapESYVQChAPTSSAFEFVSWIDSIQFMGGGAescslIAEGLSVALQLFDDFKKMReqigqtHKVC 139
Cdd:COG1240  128 RDRVGLVAFGG-----EAEVLL-PLTRDREALKRALDELPPGGGTP-----LGDALALALELLKRADPAR------RKVI 190

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 528474094 140 VLL----CNSPPYllpavesvsytgcTADSLVQIIRDRGIHFSVIA 181
Cdd:COG1240  191 VLLtdgrDNAGRI-------------DPLEAAELAAAAGIRIYTIG 223
 
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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