<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Detailed information on MDP30013

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSHSTPSGNGCSLEDCYTNLFSLTEIRGIKWRKLSANPDYTTVDQLEDPVLVSYSKCIKADILSVWRRVARSSDQPRYTTDQLSYNKELWIFWYGDEPENLSRLISPDLRVDSSGGWDNGECGISYECRTLIFKALHNLIEKCLLHRGFVRIGKWFVQPHDVNANGPEKSTHLSFCFNFFLHGESSVCASIEVKQHPPVWRLTNNHLSTAQENPGNLQVILVPYGLCGSLTGNSYRETDQSASKIIEEWSQFYPLDKNDGTDVNKIPPLVEVIVAGVRMKYPSCYVLLCEIEDAPTRAPNLTAQRPGVAPGGGLLTPPTSPAAAVLLPGADAGGKVQCAPYTGAHTDANTELMAKSSRAFSARITEKVTQDNLVTAGIAKRSMETISDEAAVGVWNFNDPSVKTTCNCARHRGAKNKLGQQNKSVVPLVGKKGDKPDKLERQQSRLSRGSLPFHRRHIVVEDATQNDMPLVLSGSTAPFNSAPGNSLLPQLNNSTETNGGTVASVEAASPADMSPMTGPQSPPDPAMPKLSPHPPVDAGTDNKTAKLITEAPPQTNPASEFIKPTTASTPKVADNILSPLSWPGQQSEAKTASINNWIKTSQPHPEVPGIKRPVLPAKDTDEDELVTKFLYDYQSIHSWSEYPVKRARVERSSSVVEIGPESPSLSLNHQSQKHKTKQPDPYDFIDDEQSINPATVSKRMFRSSRDEYINNKKMDDEKMDFGDPFTEIPDSASSPPETPSGTKHLIHTSDLKPSYDDLAHIFDSDDSDKDDPEHFGNLGQTMDKYEDGTTKFPLNNAMTVTDGAISVSELSKMYPTPPSNNTSNDRSPGPHDVMDNHISLEKQVIKTEFIHAIKEDFFRDLPAVFEPAGQAEFMGSDKYSPIVLQSSKLSPLPRPPDYKGHWQFSSFEKPVPPSYTNIPSIENIPSMSSRMPSSAVENSPATFLSNSVGQQRTPLSNYNELQSPASNASSYLNKTLNSIDNQGTNHQIPEVHSLVVNVFLMDSRLNLFRDVNFDSCNICVCNMNIKGADTEIYLSDSSAESATRCVCGFSAIVNRRFGHNSGLFYEDEVDITGIKNDRYEGRKPSLLALEYQKDKVSEYADWPHEILNLLVSQFSIPYPSASTIQHLLRLGMMNTTSGFTEDSSSLLDILQLQDGNDITYMALDLGRQAMEHCSPNKLDDPNHKSTCLHKWQFLQGASRIPQNSQDCVQVLKSLQPILQDAIQNKRSIPLWEHKYKLSGPLTWKEFHQLAGRGSDENSTPQPIPSFLAGLDGDWVSLSPYSLRYWDKQFLEPYGKPRDIAYIVLAPDNDYIINAIILFFKELSNVYELSRMGRHSPVSLKLRDGIMRVGKKIAEKFSTEDHPDDWFKFIGNSNVASKLRLYSQVCRSFLAPLLAQQNLDQSVFEPMSNNRPGYKPAETKPDVNQSEHNAFTMPAPQPHTAEDKENVETPGNARDSLYLDAEQTTSQECPALMVYLIDSFTYGSDWDPSVERLTKVGLLKCYNQLVKSLPETLQQNISLQIIPLSTILETMEKGFNMQTLQSICFSVFSMCRWNLAHSILGRHLTGFGPAAAAEIFLRKKEADKAGSIKLHGPPFVLAPTKDTQTILAESCGDKLERSFVLFCAYCMSEDQRYLLAACTDEQGEMMETCSINIEIPNRSRRKKASARKIGLQKLWDFLLGVVSMSSVPCRLIIGRFGRIGHGEMKGWSGLLSKKNLELAGKKMKQMCGQCSLTIGNCDTPGILSACLVSLESLTSFNIMADAVKMEEKMSSNCPLQTPRDASTTHILVFPTSAIAQANSHAPVMEISGTITMEDTMPMDDLVDSGEQGNNLYSILDQECLLEVFDEITTNYPDQGNALGNISNPGSPTGDSAPHNTHSMNGQFQKNATSNDPQDEMPNLLNQPLALGYFISTASPGPLPRWFWSASPEKEFQCPSCFKAALHIHSSSKHDEFSYTHHKNSHPLDSNLTPDVLRYVLETYNALSWLTFDPVQNDRQSCLPIHFMVLMQMYHALNAFV
Length2015
PositionMiddle
OrganismCrassostrea gigas (Pacific oyster) (Crassostrea angulata)
KingdomMetazoa
LineageEukaryota> Metazoa> Spiralia> Lophotrochozoa> Mollusca> Bivalvia> Autobranchia> Pteriomorphia> Ostreida> Ostreoidea> Ostreidae> Crassostrea.
Aromaticity0.08
Grand average of hydropathy-0.462
Instability index53.57
Isoelectric point5.59
Molecular weight223633.51
Publications
PubMed=22992520

Function

Annotated function Component of the Mediator complex, a coactivator involved in regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene- specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. 
GO - Cellular Component
mediator complex	GO:0016592	IEA:InterPro

GO - Biological Function
transcription coregulator activity	GO:0003712	IEA:InterPro

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IEA:InterPro









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP30013
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      66.28|      18|      19|     295|     312|       1
---------------------------------------------------------------------------
  295-  312 (33.84/16.60)	PTRAPNLTAQRPGVAPGG
  317-  334 (32.45/15.64)	PPTSPAAAVLLPGADAGG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     499.11|     159|     676|    1118|    1292|       2
---------------------------------------------------------------------------
 1113- 1286 (251.32/227.02)	QFSIPYPSASTIQHLLrLG.....MMNTTSGFTEDSSSLLDILQLQDGNDITyMALDLGRQAMEHCSPNKLDDPNHKStclhKW.QFLqGASRIPQNSQDCVQVLKS.LQPILqdAIQN.KRSI..PLWEHKYKLSGPLTWKEFHQlagrgSDENSTPQPIPSFLAGLDGDWVSlSPYSLR...YWD
 1288- 1459 (247.79/172.11)	QFLEPYGKPRDIAYIV.LApdndyIINAIILFFKELSNVYELSRMGRHSPVS.LKLRDGIMRVGKKIAEKFSTEDHPD....DWfKFI.GNSNVASKLRLYSQVCRSfLAPLL..AQQNlDQSVfePMSNNRPGYKPAETKPDVNQ.....SEHNAFTMPAPQPHTAEDKENVE.TPGNARdslYLD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      66.09|      19|     340|     196|     214|       3
---------------------------------------------------------------------------
  196-  214 (39.27/22.17)	HPPVWRLTNNH....LSTA..QENP
  533-  557 (26.81/12.83)	HPPVDAGTDNKtaklITEAppQTNP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     110.82|      32|     670|     249|     283|       4
---------------------------------------------------------------------------
  249-  283 (49.73/32.76)	WsQFYPLDKNDGTDVNKIPPLVEVIVAGVRMkyPS
  902-  933 (61.09/30.51)	W.QFSSFEKPVPPSYTNIPSIENIPSMSSRM..PS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     291.48|      78|     167|     638|     730|       5
---------------------------------------------------------------------------
  588-  632 (55.33/23.37)	.........................EAKTASINNWI...KTSQPHP.EVPGIKRPVLPAK......DTDEDELVTKFLYD..........
  638-  724 (120.95/92.61)	SWSEYPVKRAR..VERSSSVVEIGPESPSLSLNHQSqkhKTKQPDPYDFIDDEQSINPATvsKRMFRSSRDEYINNKKMDdekmDFGD.P
  788-  862 (115.20/58.38)	GTTKFPLNNAMtvTDGAISVSELSKMYPTPPSNNTS...NDRSPGPHDVMDNHISLE.....KQVIKT...EFIHAIKED....FFRDlP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.60|      12|      23|    1010|    1021|       6
---------------------------------------------------------------------------
 1010- 1021 (25.19/13.67)	DVNFDSCNICVC
 1036- 1047 (22.42/11.42)	DSSAESATRCVC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      79.30|      20|    1362|     166|     191|       8
---------------------------------------------------------------------------
  167-  186 (39.38/28.32)	PEKSTHLSFCFNFFLHGESS
 1926- 1945 (39.92/13.38)	PEKEFQCPSCFKAALHIHSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      95.42|      29|     676|     865|     893|      10
---------------------------------------------------------------------------
  865-  893 (52.98/30.10)	FEPAGQAE.FM...GSDKYSPIVLQSSKLSPLP
 1566- 1598 (42.44/22.63)	FGPAAAAEiFLrkkEADKAGSIKLHGPPFVLAP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      34.91|      11|      23|     411|     421|      13
---------------------------------------------------------------------------
  411-  421 (20.18/14.86)	HRGAK.NKLGQQ
  431-  442 (14.74/ 8.45)	KKGDKpDKLERQ
---------------------------------------------------------------------------




































Explaination for Stockholm format
  The  "Stockholm" format is a system for marking up features in a multiple alignment. These mark-up annotations are preceded by a 'magic' label, of which there are four types. The Stockholm format is used by HMMER, Pfam, and Belvu. Mark-up lines include any characters except whitespace. Underscore ("_") is used instead of space. 

 #=GR (seqname) PP (Generic per-Sequence AND per-Column markup, exactly 1 char per column) where PP is Posterior Probability  [0-9*], (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00) 
 
 #=GC PP_cons line is Stockholm-format consensus posterior probability annotation for the entire column.  It’s calculated simply as the arithmetic mean of the per-residue posterior probabilities in that column.  This should prove useful in phylogenetic inference applications, for example, where it’s common to mask away non confidently aligned columns of a multiple alignment. The PP_cons line provides an objective measure of the confidence assigned to each column.
 
 #=GC RF line is Stockholm-format reference coordinate annotation, with an x marking each column that the profile considered to be consensus.





Alignment of MDP30013 with Med13 domain of Kingdom Metazoa
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