<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 MDP06342

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLLCEMSHVNLNSTNGASLEDCHTNVFVLTELNGLKWCRWCCSNSSIVYADIPDDAVLCGYGRCVTQGFLCVWRRAPPVHSSNRVDLQIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNKSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLMLANRKLPVLLSPWSLSGELVFDPDKASEPGESQFQQQLWKDWCRFYASLDSGGAESTTGVGSGSPFKEANSSSTTTTTTTDKLPKMMDVFVCGVRLKVPTRFVCVVDPDNVASSPQQPGSLLAGFRQWLCEKTMENLICHQRRQSGPTSPSAGESDSFGLAGSWNIVDPGQRERCCCSVGQSTSCCGTGAAGSVRFTSKCKSSDVSPKRVGCFHRRVAASRKLMTSAGLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNSTTTATATQQQTPDPLVIPPKYTGLESIEVDQRLLSMKRRYNVKAVLNCRSIAPVGQRHLAQSNARQVEKIYGYKNKNKRKDITTNDHDRTDDVLSGDMCKREEEKACVKSDAEFHLTDDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERSNATEKIVTVKMDATNQNNEHANSSSSSNNNNNNNNNSSTTTTTNSNNVAVLSCSQRSSASSAYPSSTQVVAVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTGTTAVAGTQTGASSSGSYGQGSTMKAASYLSGYRDCKDAPEVQVVIPYVLASEFFGAVPASSRRSAARFEKILCYKPSRLLPALYHHHHHHHHHHHHHHHHHHQSASVGHLASLPTYGLGAISHHSWSNCGSFGSWFGSSSVRLGSQASIGLDSSSSATGRSIISAPASVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEPASSVLHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCVCNMNIRGLEMGHYVNLRRCDDNMSVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLTASHLETVPFSREIVELVRHQSLLQDLTCSLMLFRTSPFGCLNAEASGAIGGGGGGGGGGSLSASLLSVTSSSWSMFDDVEKNIPLGLPNAVYNAVELRDFTELCQLALEQSMLSLDCNNVALYVEQVPAAKRSATSSYINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWRQLHRKCTHRPGSNGREDLSGPEPIPELLVCSDRDWIQVSPFSIRLWDRMCLEPFTQPKDVAFIAVVPDTQYVVRKARGFFRELSRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFESASDGRNIIGAKLKLYAQVCRHYLAPHIFSPVWNAFDRSIFREIGRECPASTPTATCTSSSLSNVDSVGTAVSSQSAELANTTVSASGSGASCVSAGTTGMTTTTTTATAVTTSVADSSSSTAISYGLNNNNNNNNTNNSSNNSMNMMNTSSSNNSNDSRMSESSANGNDNNGLLSPTSDGPNFPHVVVIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQHNGIVDEDRRLKSMPRAAVNSNSSSVGGGIGQQRVPLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPIQDRTSCLNGTTGSNGSFGSSSSNSASSFCGGGSESRDDHGQVLFLSYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRHNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGLPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLAGGANRSTSGTVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2155
PositionMiddle
OrganismTrichinella nativa
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.305
Instability index50.79
Isoelectric point6.60
Molecular weight234820.96
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

>MDP06342
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     175.99|      49|     309|    1416|    1500|       1
---------------------------------------------------------------------------
  598-  646 (82.96/30.13)	PPSLGTEEERSNATEKIVTVKMDATNQNNEHANSSSSSNNNNNNNNNSS
 1416- 1464 (73.91/24.79)	PASTPTATCTSSSLSNVDSVGTAVSSQSAELANTTVSASGSGASCVSAG
 1501- 1519 (19.12/50.07)	...........................NN...NTNNSSNNSMNMMNTSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     317.09|      92|     308|       2|     104|       2
---------------------------------------------------------------------------
    3-  104 (154.36/105.91)	CEMSHVNL.....NSTNGASLEDCHTNVFvltELNGlKWC.......RWCCSNssivYADIPD....................................DAVLCGYGRCVTQGFL..CVwrRAPP..VHSSNRVDLQIEEG..SWEKGVEYETRTM
  225-  311 (34.60/11.29)	......................................WC.......RF........YASLDSggaesttgvgsgspfkeanssstttttttdklpkmmDVFVCGVRLKVPTRFV..CV...VDPdnVASSPQQPGSLLAGfrQW...........
  313-  407 (128.13/64.65)	CEKTMENLichqrRQSGPTSPSAGESDSF...GLAG.SWNivdpgqrERCCCS.......VGQ....................................STSCCGTGAAGSVRFTskC...KSSD..V.SPKRV......G..CFHRRVAASRKLM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.61|      19|     309|     869|     889|       3
---------------------------------------------------------------------------
  869-  888 (26.87/20.63)	SATGRSiISAPASVRSVAEP
  892-  910 (36.73/18.75)	NNNPPS.VSSPHFVRTPRTP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.47|      26|     541|     742|     767|       9
---------------------------------------------------------------------------
  742-  767 (47.58/36.00)	LSGYRDCKDAPEVQVV..IPYVL..ASEFF
 1288- 1317 (36.89/26.00)	LEPFTQPKDVAFIAVVpdTQYVVrkARGFF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      77.30|      24|     541|    1360|    1415|      10
---------------------------------------------------------------------------
  176-  204 (36.08/ 7.02)	Y.RLCRQlMLAnrklPVLLSP.WSLSGELVF
 1383- 1408 (41.22/12.82)	YaQVCRH.YLA....PHIFSPvWNAFDRSIF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     129.00|      38|     219|    1726|    1763|      12
---------------------------------------------------------------------------
 1726- 1763 (70.08/37.27)	APIQDRTSCL..NGTTG...SNGSFGSSSSNSASSFCGGGSES
 1946- 1988 (58.92/30.06)	ALIQISQCCImtGGLPGadeTDGDFESIWKDLMISPEGDGLES
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     135.03|      43|     219|    1020|    1074|      13
---------------------------------------------------------------------------
 1020- 1074 (61.53/59.37)	HRYLSYKSGvfYEDEDDATG..AVWERLTASH...LETVPFSreivelVRhqslLQDLTC
 1240- 1287 (73.50/41.91)	HRKCTHRPG..SNGREDLSGpePIPELLVCSDrdwIQVSPFS......IR....LWDRMC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      76.19|      22|     375|    1194|    1215|      15
---------------------------------------------------------------------------
 1194- 1215 (37.14/20.86)	VEPSNSLETMALLRSLLPLLQE
 1572- 1593 (39.05/22.29)	VRDLNRLVTTGLFRCYLEILQE
---------------------------------------------------------------------------




































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 MDP06342 with Med13 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) GQRHLAQSNARQVEKIYGYKNKNKRKDITTNDHDRTDDVLSGDMCKRE
2) LTDDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERSNATEKIVTVKMDATNQNNEHANSSSSSNNNNNNNNNSSTTTTTNSNNVAVL
3) MTSAGLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNSTTTATATQQQTPDPLVIPPKYT
4) PPSQEALQQLSPESHAGTGTTAVAGTQTGASSSGSY
5) SVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASP
6) TAISYGLNNNNNNNNTNNSSNNSMNMMNTSSSNNSNDSRMSESSANGNDNNGLLSPTS
500
561
407
695
881
1489
547
659
467
730
917
1546










Molecular Recognition Features






MoRF SequenceStartStop




NANANA