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Conserved domains on  [gi|2024358918|ref|XP_015150354|]
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mediator of RNA polymerase II transcription subunit 13-like [Gallus gallus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Med13_C pfam06333
Mediator complex subunit 13 C-terminal domain; Mediator is a large complex of up to 33 ...
1803-2205 2.45e-114

Mediator complex subunit 13 C-terminal domain; Mediator is a large complex of up to 33 proteins that is conserved from plants through 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-activity 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. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood. This domain is also identified as an RNaseH domain of the medPIWI PIWI/Argonaute module. medPIWI is the core domain found in the Med13 protein. The medPIWI module in Med13 is predicted to bind double-stranded nucleic acids, triggering the experimentally-observed conformational switch in the CDK8 subcomplex which regulates the Mediator complex.


:

Pssm-ID: 461879  Cd Length: 322  Bit Score: 366.22  E-value: 2.45e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1803 YSPPFILAPI--KDKQTELG-ETFGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLETCIVNIdlpNRSRRSKLSAR 1879
Cdd:pfam06333    1 YAPPFVLAPPlpRTIQFKLApEPSSPLLQEGSVLHVAYCLSEDQRWLTAAWTDNRGELQETASYCL---RRRRRKKARPR 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1880 KIGLQKLWEWCIGIVQMTSLPWRVVIGRLGRLGHGELKDWSILLGECSLQtiskqlkevcrmcgissadSPSILSACLVA 1959
Cdd:pfam06333   78 SEVLQEIWEFTLDIMSKTQVPWRLVIAKLGRMDHGELKAWSSLLSRENLQ-------------------RPSILSATLVS 138
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1960 MEPQGSFVVMPDAVTMGSVFGRSTAlnlqSSQLNTPQDASCTHILVFPTSATIQVAPANYPNEdgfsPTNDDMFDLPFPD 2039
Cdd:pfam06333  139 VEPDPSLRLMPPAPTPPSVFGQQSS----STPVSTPQDSSCTHILVFSPSATGQSTPPSGPNE----PANAPTTPTDSSP 210
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 2040 DMDNDIRIL-ITGNLHsspnsspvpspgspsGIGVGSHYQHSRSQGErllsreapeelKQQPLALGYFVsTAKaenlpqw 2118
Cdd:pfam06333  211 EPDPDALLIdITDETW---------------GVILSHRLNNSPSLTE-----------LQPPLASGYLV-KRP------- 256
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 2119 fwsscPQAQNQCPLFLKASLHHhisiaqtdellparnSQRVPHPlDSKTTSDVLRFVLEQYNALSWLTCNPATQDRSSCL 2198
Cdd:pfam06333  257 -----GTADNDCPVFLKVNLLH---------------TQQVPSS-YTVLTEDVLREVLEQYRALSWLARARGTRDRRSCL 315

                   ....*..
gi 2024358918 2199 PVHFVVL 2205
Cdd:pfam06333  316 PWHLAAA 322
MID_MedPIWI pfam18296
MID domain of medPIWI; MID domain of the medPIWI PIWI/Argonaute module. medPIWI is the core ...
1416-1767 2.12e-65

MID domain of medPIWI; MID domain of the medPIWI PIWI/Argonaute module. medPIWI is the core globular domain of the Med13 protein. Med13 is one member of the CDK8 subcomplex of the Mediator transcriptional coactivator complex. The medPIWI module in Med13 is predicted to bind double-stranded nucleic acids, triggering the experimentally-observed conformational switch in the CDK8 subcomplex which regulates the Mediator complex.


:

Pssm-ID: 465699  Cd Length: 192  Bit Score: 220.21  E-value: 2.12e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1416 RDVAYIVVCPENEALLDGAKTFFRDLSAVYEMCRLGQHKPICKVLRDGIMRVGKTVAQkLTDELVSEWFNQPWgteECDN 1495
Cdd:pfam18296    1 KDVAYYVVCPDNDALLSAARTFFRDLGAVYESCKLGTHSPISKVRRDGILRVGGFVPQ-LSDDGLSDWFLSSG---DSDY 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1496 HSRLKLYAQVCRHHLAPYLATLQldsslllppkyqtpapasqtqtipgntgpvpsnstclstsgapptgssfnstpnggt 1575
Cdd:pfam18296   77 ASKLKSYAQVCKHQLGPYLSSNP--------------------------------------------------------- 99
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1576 tslpagsssssgssvpqlsassatpgvnqmsatptpgfsgnigsgqntstggnaadrsqgstgpggdteagqnlsqqqqe 1655
Cdd:pfam18296      --------------------------------------------------------------------------------
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1656 gqegvtererigiptepesADSNAYPPAVVIYMVDPFTYTADEESASTNFWLLSLMRCYTEMLD-NLPENMRNSFILQIV 1734
Cdd:pfam18296  100 -------------------KDEDTNPPAIVVYIVNPFSDAAALSDLCSAFWKLGLLRCYVEMLDsNLPELSRPELVLQIV 160
                          330       340       350
                   ....*....|....*....|....*....|....*
gi 2024358918 1735 PCQYMLQtmkDEQVFYIQ--HLKSLAFSVYCQCRR 1767
Cdd:pfam18296  161 PIEYILS---PDSLVVLDqaHLKSLAFSVYSRCRR 192
Med13_N super family cl20416
Mediator complex subunit 13 N-terminal; Mediator is a large complex of up to 33 proteins that ...
13-222 9.42e-07

Mediator complex subunit 13 N-terminal; Mediator is a large complex of up to 33 proteins that is conserved from plants through 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-activity 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. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood.


The actual alignment was detected with superfamily member pfam11597:

Pssm-ID: 463303  Cd Length: 314  Bit Score: 53.24  E-value: 9.42e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918   13 SLEDCHSNLFSLAELTGIKWRRYNFEGHGDCGPIISAPAQDDPILLSFIRCLQAnllcvwrrdVKPDCKELWIF------ 86
Cdd:pfam11597    3 FLSNCLTNVYALGGFSEIAYRVYTPKEDDDQALLELRRLRALELQLRELSPLVL---------VDYDRLSLWVFsffdsv 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918   87 --WWGDEPNLVDVIHRELH-----------MVEEGLWENGLSYEC--RTLLFKAIHNLLERCLM-DKNFVRIGKWFIRPY 150
Cdd:pfam11597   74 dpTDPKDGLNLLLKGSGLSrsesgtftpsdLARLPDYSKPNQPPTqiYALFLKAVRKSILLNLSrNRGAIPFGNRTLLSS 153
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2024358918  151 DKDEKP-VNKSEHLSCAFTF-FLHGESNVCTSVEIaqHQPIYLINEEHIHMAQSSPSPFQ-VLVSPYGLNGTLTG 222
Cdd:pfam11597  154 SDSDSEeGEGWWSLLRLDPHlTSNGDLTLSLSTIL--QPGLLRLSSYLPLPDELPLLPGTaVYLAPSGIRARLLS 226
Herpes_BLLF1 super family cl37540
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
1516-1624 6.93e-04

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


The actual alignment was detected with superfamily member pfam05109:

Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 44.91  E-value: 6.93e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1516 TLQLDSSLLLPPKYQTPAPASQTQTIPGNTGPVPSNSTclstSGAPPTGSSFNSTPNGGTTSLPAGSSSSSGSSVPQLSA 1595
Cdd:pfam05109  445 TTGLPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTT----SGASPVTPSPSPRDNGTESKAPDMTSPTSAVTTPTPNA 520
                           90       100       110
                   ....*....|....*....|....*....|
gi 2024358918 1596 SSATPGVnqmsATPTP-GFSGNIGSGQNTS 1624
Cdd:pfam05109  521 TSPTPAV----TTPTPnATSPTLGKTSPTS 546
 
Name Accession Description Interval E-value
Med13_C pfam06333
Mediator complex subunit 13 C-terminal domain; Mediator is a large complex of up to 33 ...
1803-2205 2.45e-114

Mediator complex subunit 13 C-terminal domain; Mediator is a large complex of up to 33 proteins that is conserved from plants through 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-activity 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. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood. This domain is also identified as an RNaseH domain of the medPIWI PIWI/Argonaute module. medPIWI is the core domain found in the Med13 protein. The medPIWI module in Med13 is predicted to bind double-stranded nucleic acids, triggering the experimentally-observed conformational switch in the CDK8 subcomplex which regulates the Mediator complex.


Pssm-ID: 461879  Cd Length: 322  Bit Score: 366.22  E-value: 2.45e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1803 YSPPFILAPI--KDKQTELG-ETFGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLETCIVNIdlpNRSRRSKLSAR 1879
Cdd:pfam06333    1 YAPPFVLAPPlpRTIQFKLApEPSSPLLQEGSVLHVAYCLSEDQRWLTAAWTDNRGELQETASYCL---RRRRRKKARPR 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1880 KIGLQKLWEWCIGIVQMTSLPWRVVIGRLGRLGHGELKDWSILLGECSLQtiskqlkevcrmcgissadSPSILSACLVA 1959
Cdd:pfam06333   78 SEVLQEIWEFTLDIMSKTQVPWRLVIAKLGRMDHGELKAWSSLLSRENLQ-------------------RPSILSATLVS 138
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1960 MEPQGSFVVMPDAVTMGSVFGRSTAlnlqSSQLNTPQDASCTHILVFPTSATIQVAPANYPNEdgfsPTNDDMFDLPFPD 2039
Cdd:pfam06333  139 VEPDPSLRLMPPAPTPPSVFGQQSS----STPVSTPQDSSCTHILVFSPSATGQSTPPSGPNE----PANAPTTPTDSSP 210
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 2040 DMDNDIRIL-ITGNLHsspnsspvpspgspsGIGVGSHYQHSRSQGErllsreapeelKQQPLALGYFVsTAKaenlpqw 2118
Cdd:pfam06333  211 EPDPDALLIdITDETW---------------GVILSHRLNNSPSLTE-----------LQPPLASGYLV-KRP------- 256
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 2119 fwsscPQAQNQCPLFLKASLHHhisiaqtdellparnSQRVPHPlDSKTTSDVLRFVLEQYNALSWLTCNPATQDRSSCL 2198
Cdd:pfam06333  257 -----GTADNDCPVFLKVNLLH---------------TQQVPSS-YTVLTEDVLREVLEQYRALSWLARARGTRDRRSCL 315

                   ....*..
gi 2024358918 2199 PVHFVVL 2205
Cdd:pfam06333  316 PWHLAAA 322
MID_MedPIWI pfam18296
MID domain of medPIWI; MID domain of the medPIWI PIWI/Argonaute module. medPIWI is the core ...
1416-1767 2.12e-65

MID domain of medPIWI; MID domain of the medPIWI PIWI/Argonaute module. medPIWI is the core globular domain of the Med13 protein. Med13 is one member of the CDK8 subcomplex of the Mediator transcriptional coactivator complex. The medPIWI module in Med13 is predicted to bind double-stranded nucleic acids, triggering the experimentally-observed conformational switch in the CDK8 subcomplex which regulates the Mediator complex.


Pssm-ID: 465699  Cd Length: 192  Bit Score: 220.21  E-value: 2.12e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1416 RDVAYIVVCPENEALLDGAKTFFRDLSAVYEMCRLGQHKPICKVLRDGIMRVGKTVAQkLTDELVSEWFNQPWgteECDN 1495
Cdd:pfam18296    1 KDVAYYVVCPDNDALLSAARTFFRDLGAVYESCKLGTHSPISKVRRDGILRVGGFVPQ-LSDDGLSDWFLSSG---DSDY 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1496 HSRLKLYAQVCRHHLAPYLATLQldsslllppkyqtpapasqtqtipgntgpvpsnstclstsgapptgssfnstpnggt 1575
Cdd:pfam18296   77 ASKLKSYAQVCKHQLGPYLSSNP--------------------------------------------------------- 99
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1576 tslpagsssssgssvpqlsassatpgvnqmsatptpgfsgnigsgqntstggnaadrsqgstgpggdteagqnlsqqqqe 1655
Cdd:pfam18296      --------------------------------------------------------------------------------
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1656 gqegvtererigiptepesADSNAYPPAVVIYMVDPFTYTADEESASTNFWLLSLMRCYTEMLD-NLPENMRNSFILQIV 1734
Cdd:pfam18296  100 -------------------KDEDTNPPAIVVYIVNPFSDAAALSDLCSAFWKLGLLRCYVEMLDsNLPELSRPELVLQIV 160
                          330       340       350
                   ....*....|....*....|....*....|....*
gi 2024358918 1735 PCQYMLQtmkDEQVFYIQ--HLKSLAFSVYCQCRR 1767
Cdd:pfam18296  161 PIEYILS---PDSLVVLDqaHLKSLAFSVYSRCRR 192
Med13_N pfam11597
Mediator complex subunit 13 N-terminal; Mediator is a large complex of up to 33 proteins that ...
13-222 9.42e-07

Mediator complex subunit 13 N-terminal; Mediator is a large complex of up to 33 proteins that is conserved from plants through 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-activity 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. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood.


Pssm-ID: 463303  Cd Length: 314  Bit Score: 53.24  E-value: 9.42e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918   13 SLEDCHSNLFSLAELTGIKWRRYNFEGHGDCGPIISAPAQDDPILLSFIRCLQAnllcvwrrdVKPDCKELWIF------ 86
Cdd:pfam11597    3 FLSNCLTNVYALGGFSEIAYRVYTPKEDDDQALLELRRLRALELQLRELSPLVL---------VDYDRLSLWVFsffdsv 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918   87 --WWGDEPNLVDVIHRELH-----------MVEEGLWENGLSYEC--RTLLFKAIHNLLERCLM-DKNFVRIGKWFIRPY 150
Cdd:pfam11597   74 dpTDPKDGLNLLLKGSGLSrsesgtftpsdLARLPDYSKPNQPPTqiYALFLKAVRKSILLNLSrNRGAIPFGNRTLLSS 153
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2024358918  151 DKDEKP-VNKSEHLSCAFTF-FLHGESNVCTSVEIaqHQPIYLINEEHIHMAQSSPSPFQ-VLVSPYGLNGTLTG 222
Cdd:pfam11597  154 SDSDSEeGEGWWSLLRLDPHlTSNGDLTLSLSTIL--QPGLLRLSSYLPLPDELPLLPGTaVYLAPSGIRARLLS 226
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
1516-1624 6.93e-04

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 44.91  E-value: 6.93e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1516 TLQLDSSLLLPPKYQTPAPASQTQTIPGNTGPVPSNSTclstSGAPPTGSSFNSTPNGGTTSLPAGSSSSSGSSVPQLSA 1595
Cdd:pfam05109  445 TTGLPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTT----SGASPVTPSPSPRDNGTESKAPDMTSPTSAVTTPTPNA 520
                           90       100       110
                   ....*....|....*....|....*....|
gi 2024358918 1596 SSATPGVnqmsATPTP-GFSGNIGSGQNTS 1624
Cdd:pfam05109  521 TSPTPAV----TTPTPnATSPTLGKTSPTS 546
dermokine cd21118
dermokine; Dermokine, also known as epidermis-specific secreted protein SK30/SK89, is a ...
1526-1638 2.94e-03

dermokine; Dermokine, also known as epidermis-specific secreted protein SK30/SK89, is a skin-specific glycoprotein that may play a regulatory role in the crosstalk between barrier dysfunction and inflammation, and therefore play a role in inflammatory diseases such as psoriasis. Dermokine is one of the most highly expressed proteins in differentiating keratinocytes, found mainly in the spinous and granular layers of the epidermis, but also in the epithelia of the small intestine, macrophages of the lung, and endothelial cells of the lung. Mouse dermokine has been reported to be encoded by 22 exons, and its expression leads to alpha, beta, and gamma transcripts.


Pssm-ID: 411053 [Multi-domain]  Cd Length: 495  Bit Score: 42.68  E-value: 2.94e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1526 PPKYQTPAPASQTQtiPGNtGPVPSNSTCLSTSGAPPTGSSFNSTPNGGTTSLPAGSSSSSGSSVPQLSASSATPGVNQM 1605
Cdd:cd21118    174 PLNYGTNSQGAVAQ--PGY-GTVRGNNQNSGCTNPPPSGSHESFSNSGGSSSSGSSGSQGSHGSNGQGSSGSSGGQGNGG 250
                           90       100       110
                   ....*....|....*....|....*....|...
gi 2024358918 1606 SATPTPGFSGNIGSGQNTSTGGNAADRSQGSTG 1638
Cdd:cd21118    251 NNGSSSSNSGNSGGSNGGSSGNSGSGSGGSSSG 283
 
Name Accession Description Interval E-value
Med13_C pfam06333
Mediator complex subunit 13 C-terminal domain; Mediator is a large complex of up to 33 ...
1803-2205 2.45e-114

Mediator complex subunit 13 C-terminal domain; Mediator is a large complex of up to 33 proteins that is conserved from plants through 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-activity 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. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood. This domain is also identified as an RNaseH domain of the medPIWI PIWI/Argonaute module. medPIWI is the core domain found in the Med13 protein. The medPIWI module in Med13 is predicted to bind double-stranded nucleic acids, triggering the experimentally-observed conformational switch in the CDK8 subcomplex which regulates the Mediator complex.


Pssm-ID: 461879  Cd Length: 322  Bit Score: 366.22  E-value: 2.45e-114
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1803 YSPPFILAPI--KDKQTELG-ETFGEASQKYNVLFVGYCLSHDQRWLLASCTDLHGELLETCIVNIdlpNRSRRSKLSAR 1879
Cdd:pfam06333    1 YAPPFVLAPPlpRTIQFKLApEPSSPLLQEGSVLHVAYCLSEDQRWLTAAWTDNRGELQETASYCL---RRRRRKKARPR 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1880 KIGLQKLWEWCIGIVQMTSLPWRVVIGRLGRLGHGELKDWSILLGECSLQtiskqlkevcrmcgissadSPSILSACLVA 1959
Cdd:pfam06333   78 SEVLQEIWEFTLDIMSKTQVPWRLVIAKLGRMDHGELKAWSSLLSRENLQ-------------------RPSILSATLVS 138
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1960 MEPQGSFVVMPDAVTMGSVFGRSTAlnlqSSQLNTPQDASCTHILVFPTSATIQVAPANYPNEdgfsPTNDDMFDLPFPD 2039
Cdd:pfam06333  139 VEPDPSLRLMPPAPTPPSVFGQQSS----STPVSTPQDSSCTHILVFSPSATGQSTPPSGPNE----PANAPTTPTDSSP 210
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 2040 DMDNDIRIL-ITGNLHsspnsspvpspgspsGIGVGSHYQHSRSQGErllsreapeelKQQPLALGYFVsTAKaenlpqw 2118
Cdd:pfam06333  211 EPDPDALLIdITDETW---------------GVILSHRLNNSPSLTE-----------LQPPLASGYLV-KRP------- 256
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 2119 fwsscPQAQNQCPLFLKASLHHhisiaqtdellparnSQRVPHPlDSKTTSDVLRFVLEQYNALSWLTCNPATQDRSSCL 2198
Cdd:pfam06333  257 -----GTADNDCPVFLKVNLLH---------------TQQVPSS-YTVLTEDVLREVLEQYRALSWLARARGTRDRRSCL 315

                   ....*..
gi 2024358918 2199 PVHFVVL 2205
Cdd:pfam06333  316 PWHLAAA 322
MID_MedPIWI pfam18296
MID domain of medPIWI; MID domain of the medPIWI PIWI/Argonaute module. medPIWI is the core ...
1416-1767 2.12e-65

MID domain of medPIWI; MID domain of the medPIWI PIWI/Argonaute module. medPIWI is the core globular domain of the Med13 protein. Med13 is one member of the CDK8 subcomplex of the Mediator transcriptional coactivator complex. The medPIWI module in Med13 is predicted to bind double-stranded nucleic acids, triggering the experimentally-observed conformational switch in the CDK8 subcomplex which regulates the Mediator complex.


Pssm-ID: 465699  Cd Length: 192  Bit Score: 220.21  E-value: 2.12e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1416 RDVAYIVVCPENEALLDGAKTFFRDLSAVYEMCRLGQHKPICKVLRDGIMRVGKTVAQkLTDELVSEWFNQPWgteECDN 1495
Cdd:pfam18296    1 KDVAYYVVCPDNDALLSAARTFFRDLGAVYESCKLGTHSPISKVRRDGILRVGGFVPQ-LSDDGLSDWFLSSG---DSDY 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1496 HSRLKLYAQVCRHHLAPYLATLQldsslllppkyqtpapasqtqtipgntgpvpsnstclstsgapptgssfnstpnggt 1575
Cdd:pfam18296   77 ASKLKSYAQVCKHQLGPYLSSNP--------------------------------------------------------- 99
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1576 tslpagsssssgssvpqlsassatpgvnqmsatptpgfsgnigsgqntstggnaadrsqgstgpggdteagqnlsqqqqe 1655
Cdd:pfam18296      --------------------------------------------------------------------------------
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1656 gqegvtererigiptepesADSNAYPPAVVIYMVDPFTYTADEESASTNFWLLSLMRCYTEMLD-NLPENMRNSFILQIV 1734
Cdd:pfam18296  100 -------------------KDEDTNPPAIVVYIVNPFSDAAALSDLCSAFWKLGLLRCYVEMLDsNLPELSRPELVLQIV 160
                          330       340       350
                   ....*....|....*....|....*....|....*
gi 2024358918 1735 PCQYMLQtmkDEQVFYIQ--HLKSLAFSVYCQCRR 1767
Cdd:pfam18296  161 PIEYILS---PDSLVVLDqaHLKSLAFSVYSRCRR 192
Med13_N pfam11597
Mediator complex subunit 13 N-terminal; Mediator is a large complex of up to 33 proteins that ...
13-222 9.42e-07

Mediator complex subunit 13 N-terminal; Mediator is a large complex of up to 33 proteins that is conserved from plants through 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-activity 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. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood.


Pssm-ID: 463303  Cd Length: 314  Bit Score: 53.24  E-value: 9.42e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918   13 SLEDCHSNLFSLAELTGIKWRRYNFEGHGDCGPIISAPAQDDPILLSFIRCLQAnllcvwrrdVKPDCKELWIF------ 86
Cdd:pfam11597    3 FLSNCLTNVYALGGFSEIAYRVYTPKEDDDQALLELRRLRALELQLRELSPLVL---------VDYDRLSLWVFsffdsv 73
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918   87 --WWGDEPNLVDVIHRELH-----------MVEEGLWENGLSYEC--RTLLFKAIHNLLERCLM-DKNFVRIGKWFIRPY 150
Cdd:pfam11597   74 dpTDPKDGLNLLLKGSGLSrsesgtftpsdLARLPDYSKPNQPPTqiYALFLKAVRKSILLNLSrNRGAIPFGNRTLLSS 153
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2024358918  151 DKDEKP-VNKSEHLSCAFTF-FLHGESNVCTSVEIaqHQPIYLINEEHIHMAQSSPSPFQ-VLVSPYGLNGTLTG 222
Cdd:pfam11597  154 SDSDSEeGEGWWSLLRLDPHlTSNGDLTLSLSTIL--QPGLLRLSSYLPLPDELPLLPGTaVYLAPSGIRARLLS 226
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
1516-1624 6.93e-04

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 44.91  E-value: 6.93e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1516 TLQLDSSLLLPPKYQTPAPASQTQTIPGNTGPVPSNSTclstSGAPPTGSSFNSTPNGGTTSLPAGSSSSSGSSVPQLSA 1595
Cdd:pfam05109  445 TTGLPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTT----SGASPVTPSPSPRDNGTESKAPDMTSPTSAVTTPTPNA 520
                           90       100       110
                   ....*....|....*....|....*....|
gi 2024358918 1596 SSATPGVnqmsATPTP-GFSGNIGSGQNTS 1624
Cdd:pfam05109  521 TSPTPAV----TTPTPnATSPTLGKTSPTS 546
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
1531-1637 1.45e-03

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 43.75  E-value: 1.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1531 TPAPASQTQTiPGNTGPVPsNSTCLSTSGAPPTGSSFNSTPNGgTTSLPAGSSSSSGSSVPQLSASSATPGVnqmsATPT 1610
Cdd:pfam05109  515 TPTPNATSPT-PAVTTPTP-NATSPTLGKTSPTSAVTTPTPNA-TSPTPAVTTPTPNATIPTLGKTSPTSAV----TTPT 587
                           90       100
                   ....*....|....*....|....*...
gi 2024358918 1611 P-GFSGNIGSgqnTSTGGNAADRSQGST 1637
Cdd:pfam05109  588 PnATSPTVGE---TSPQANTTNHTLGGT 612
dermokine cd21118
dermokine; Dermokine, also known as epidermis-specific secreted protein SK30/SK89, is a ...
1526-1638 2.94e-03

dermokine; Dermokine, also known as epidermis-specific secreted protein SK30/SK89, is a skin-specific glycoprotein that may play a regulatory role in the crosstalk between barrier dysfunction and inflammation, and therefore play a role in inflammatory diseases such as psoriasis. Dermokine is one of the most highly expressed proteins in differentiating keratinocytes, found mainly in the spinous and granular layers of the epidermis, but also in the epithelia of the small intestine, macrophages of the lung, and endothelial cells of the lung. Mouse dermokine has been reported to be encoded by 22 exons, and its expression leads to alpha, beta, and gamma transcripts.


Pssm-ID: 411053 [Multi-domain]  Cd Length: 495  Bit Score: 42.68  E-value: 2.94e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024358918 1526 PPKYQTPAPASQTQtiPGNtGPVPSNSTCLSTSGAPPTGSSFNSTPNGGTTSLPAGSSSSSGSSVPQLSASSATPGVNQM 1605
Cdd:cd21118    174 PLNYGTNSQGAVAQ--PGY-GTVRGNNQNSGCTNPPPSGSHESFSNSGGSSSSGSSGSQGSHGSNGQGSSGSSGGQGNGG 250
                           90       100       110
                   ....*....|....*....|....*....|...
gi 2024358918 1606 SATPTPGFSGNIGSGQNTSTGGNAADRSQGSTG 1638
Cdd:cd21118    251 NNGSSSSNSGNSGGSNGGSSGNSGSGSGGSSSG 283
 
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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