<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 MDP06029

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLLCEMSHVNLNSTNGASLEDCHTNVFVLTELNGLKWCRWCCSNSSIVYADIPDDAVLCGYGRCVTQGFLCVWRRAPPVHSSNRVDLRLAVEKELWIFWYGDEPDWALLCTGLTKIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNKSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLMLANRKLPVLLSPWSLSGELVFDPDKASESGESQFQQQLWKDWCRFYASLDSGGAESTTGVGSGSPFKEANSSSSTTTTTTTDKLPKMMDVFVCGVRLKVPTRFVCVVDPENVASSPQQSGSLLAGFRQWLCEKTMENLICHQRRQSGPTSPSAGESDSFGLAGSWNIVDPGQRERCCCSVGQSTSCCGTGAAGSVRFTSKCKSSDVSPKRVGCFHRRVAASRKLMTSAGLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNSTTTATATVTTTAASTASAAAAAAAAAPVASAVCSSASMTSSTMFLDHCSANMVGCNVAVEPKSKMRRSVEQSELLQQQQTPDPLVIPPKYTGLESIEVDQRLLSMKRRYNVSTNYDTDGDLQLMKLSFSRYHSHHQEQIHLLHIQQQQQQQQQQQLLQQQQQNQSNSFISRVSSSSVKNFGKPTDQFTEKFYRALTSYSWCQAMETNRKRRFFVQNVLLLFSEAVLNCRSIAPVGQRHLAQSNARQVEKIYGYKNKNKRKDITTNDHDRTDDVLSGDMCKREEEKACVKSDAEFHLTDDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERLNATEKIVAVKMDATNQNNEHANSSSSSNNNNNNNNNSSSTTTTNSNNVAVLSCSQRSSASSAYPSSTQVVAVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTGTTAVAGTQTSACSSGSYGQGSTMKAASYLSGYRDCKDAPEVQVVIPYVLASEFFGAVPASSRRSAVRFEKILCYKPSRLLPALYHHHHHHHHHHHHHHHHHQSASVGHLASLPTYGLGAISHHSWSNCGSFGSWFGSSSVRLGSQASIGLDSSSSATGRSIISAPASVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEPASSVLHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCDDNMSVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLTASHLETVPFSREIVELVRHQSLLQDLTWAIGGGGGGGGGGGGGGGGGSLSTSLLSVTSSSWSMFDDVEKNIPLGLPNAVYNAVELRDFTELCQLALEQSMLSLDCNNVALSATSSYINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWHLSGPEPIPELLVCSDRDWIQVSPFSIRLWDRMCLEPFTQPKDVAFIAVVPDTHRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFEIWNAFDRSIFREIGRECPASTPTTTCTSSSLSNVDSVGTAVSSQSAELANTTVSASGSGASCVSAGTTGMTTTTTTATAVTTSVADSSSSTAISMNMMNTSSSNNSNDSLIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQHNGIVDEDRRLKSMPRAAVNSNSSSVGGGIGQQRVPLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPIQDRTSCLNGTTGSNGSFGSSSSNSASSFCGGGSESRDDHGQVLFLAYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRHNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGLPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLAGGANRSTSGTVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2210
PositionMiddle
OrganismTrichinella sp. T9
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella> unclassified Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.281
Instability index51.60
Isoelectric point6.33
Molecular weight241037.88
Publications









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. 


ECO:0000256	RuleBase:RU364134

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

>MDP06029
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     388.16|      99|     213|    1510|    1614|       1
---------------------------------------------------------------------------
  441-  518 (96.13/49.04)	...........................DGSSTAAGDDDDQQHQTMVEEAG..tSTTSALLNSTTTATATVTTTAASTASAAAAAAAAAPVASAVCS..SASMTS..STMFL
 1510- 1614 (151.74/98.49)	IFREIgRECPAStptttCTSSSLSNV.DSVGTAVSSQSAELANTTVSASG...SGASCVSAGTTGMTTTTTTATAVTTSVADSSSSTAISMNMMNT..SSSNNSNDSLIYL
 1729- 1828 (140.28/77.80)	VFMQI.RSVAYS.....CLHSCLPKVmTGFGPAASRH..ELLRRKQNSAGfrlYSAPVVLAPIQDRTSCLNGTTGSNGSFGSSSSNSA...SSFCGggSESRDDHGQVLFL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     104.32|      25|      52|    1071|    1095|       2
---------------------------------------------------------------------------
 1071- 1095 (41.24/19.92)	LDSSSSATGRSIIS.APASVRSVAEP
 1099- 1117 (28.19/11.18)	.....NNNPPS.VS.SPHFVRTPRTP
 1125- 1148 (34.89/15.66)	MSNASSAYAKNLSSiEPAS..SVLHP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     248.74|      74|     335|     853|     978|       3
---------------------------------------------------------------------------
  903-  977 (123.87/133.39)	PPSQEALQQLSPESHAGTGTTAVAGTQTSACSSGSYGQGSTMkAASYLSGYRDCKDA.PEVQVVIPYVLASEFFGA
 1241- 1315 (124.86/57.68)	PFSREIVELVRHQSLLQDLTWAIGGGGGGGGGGGGGGGGGSL.STSLLSVTSSSWSMfDDVEKNIPLGLPNAVYNA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.89|      13|      20|    1158|    1170|       5
---------------------------------------------------------------------------
 1158- 1170 (23.11/13.33)	LLSDTFVHLYRDS
 1177- 1189 (24.78/14.84)	LCDDNMSVLYHSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     162.49|      37|     335|      58|      94|       6
---------------------------------------------------------------------------
   58-   94 (67.19/38.39)	CGYGRCVTQGFL..CVWRRAPPVHSSNRVDL...RLAVEKEL
  303-  334 (47.81/25.08)	CGVRLKVPTRFV..CVVDPENVASSPQQSGS...LLA.....
  397-  434 (47.48/24.85)	CGTGAAGSVRFTskC...KSSDV.SPKRVGCfhrRVAASRKL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.48|      14|      16|     786|     801|       8
---------------------------------------------------------------------------
  786-  801 (21.72/18.09)	PSPSSGISdcENEIHA
  805-  818 (24.76/12.52)	PPPSLGTE..EERLNA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.19|      15|     568|     264|     288|      17
---------------------------------------------------------------------------
  274-  288 (27.67/26.23)	SPFKEANSSSSTTTT
  845-  859 (27.52/ 6.58)	NNNNNNNNSSSTTTT
---------------------------------------------------------------------------




































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 MDP06029 with Med13 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) DDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERLNATEKIVAVKMDATNQNNEHANSSSSSNNNNNNNNNSSSTTTTNSNNVAVL
2) GLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNST
3) SVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASP
4) VEPKSKMRRSVEQSELLQQQQTPDPLVIPPKY
771
439
1088
532
867
474
1124
563










Molecular Recognition Features






MoRF SequenceStartStop




NANANA