<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 MDP06352

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLLCEMSHVNLNSTNGASLEDCHTNVFVLTELNGLKWCRWCCSNSSIVYSDIADDAVLCGYGRCVTQGFLCVWRRSPPVHSSNRVDLRLAVEKELWIFWYGDEPDWALLCTGLTKIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNRSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLLLANRKLPVLLSPWSLSAELIFNPDKASEPGECQFQQQLWKDWCRFYASLDNGAESTTTTGVGSGSPFKEANNTDRLPKMLDVFVCGVRLKVPTRFVCVVDPDHLATGQQQPGGLLAGFRQWLCEKTVENLICHQLRHSRPTSPSSGESESFGLAGSWNIVDPGQRERCCCSVAQSTNYCGTGAAGSVRFTSKCKSSDSSPKRVGCFHRRVTTGRKLMTSAGLDGSTTATGDDDDQQHQSMVEEATTSALLNSSTTITTTTTTATATAATTTATPIASAVCGSASTSMTSSTMILDHCSADVVGCNAAVEPKLKMRRSVEQSQLLQQQQQLAPDPLVIPPKYTGMESVDVDQQLLTMKRRYNVSTNHDTDSELQLMKLAILKFDPQSYHQQEQRIHHLHVKQRQQQLYQLQLQRQQQQQQQQQQQQNQLSNFISKVSSSVENFSKPMDRFTENFYRALANYSWCQTMETNRKHRSLFQNVLILFSEAMLNCRTIAPVGQRHFALSNARQVEKIYGYKNKNKRKDNNNDRDDHDQNDDVLVGDICKREEKACVKLDTEFQTDDNSAIVHHQMMQEGPSPSSAISDCENEIHAFLSPPPSLGTEEERLNANEKIVAVKMEATNQNNEHGNSSSSSNNNNNNNNNNSSSNNNNNSNSNSNSVAVLSCSQRSSASSAYPSSTQVPVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTSTTAVVVGTQWTNSACSNGANGQGSTMKAASDASSCHDCKEAPEVRVVIPYVLASEVSTAVSAPLRRSTVRFEKILCYKPSRLLPSVYHHPHASAGHLTSLPTYGLGAVSHHSWSNYGPVGSGFGSSSVRLGSQASIGLDSSSSVAGRSIISAPASVRSVAEPSPLSNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEPANSVQHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCVCNMNIRGLEMGHYVNLRQCDDNMSVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLTASHLETVQFSREIVELVRHQSLLQDLTCSLMLFRTSPFSCLNAGASAAIGGGSLSTSLLSVTSSSWSMLGDVEKSVHLGCWPNAAYNAVELRDFTELCQLALEQSMLSLDCNNVALYVEQVPAAKRSATASFINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWRQLHRKCTHRPGSNGREDLSGPEPIPELLVCSDRDWIQVSPFSVRLWDRMCLEPFTQPKDVAFIAVVPDTQHVVRKARGFFRELSRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFESASDGRSIIGSKLKLYAQVCRHYLAPHIFSPVWSAFDRSIFREIGRECPASAATTTCTSSLSNADFVGTALSSQSAEFANTITSATSGASCVSAGATTTTTTTTTTTATTAMTTTTTTATAVTTTVADSASSTAVSYGLNMNNNNNNNSNNNSNNNSANNSLNMMNTTSSSNNSNDSRISDSSTNGNDNGLLSPTSDGPNFPHVVVIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQQNGIVDEDRRLNSVPRTMVNSNSSSNCGGSIGQQRVPLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPIQDRTSCLNGTTGSIGSLGSSSSNSVSSFCGGGSEARDDHGQVLFLAYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRRNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGIPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLPGGANRSTTATVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2365
PositionMiddle
OrganismTrichinella papuae
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.320
Instability index48.39
Isoelectric point6.56
Molecular weight259560.71
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. 


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

>MDP06352
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.81|      15|      20|     602|     621|       1
---------------------------------------------------------------------------
  605-  619 (27.40/25.12)	HHLHVKQRQQQLYQL
  624-  638 (26.41/ 6.94)	QQQQQQQQQQQQNQL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.13|      17|      20|    1003|    1019|       2
---------------------------------------------------------------------------
 1003- 1019 (32.90/19.62)	PSRLLPSVYHHPHASAG
 1025- 1041 (34.23/20.76)	PTYGLGAVSHHSWSNYG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     116.90|      18|      20|     830|     847|       3
---------------------------------------------------------------------------
  830-  847 (33.95/17.23)	NQN.NEHGNSSS.....SSNNNN.N
  849-  866 (36.05/18.82)	NNN.NSSSNNNN.....NSNSNS.N
 1707- 1722 (25.33/10.72)	NSN.N...NSNN.....NSANNSlN
 1723- 1746 (21.57/ 7.87)	MMNtTSSSNNSNdsrisDSSTNG.N
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     242.40|      77|    1202|     400|     499|       4
---------------------------------------------------------------------------
  423-  499 (131.86/94.82)	GRKLMTSAGLDGSTTATGDDD.........DQQHQSMVEEATTSA..LLNSSTTITTTTTTATATAA....TTTATPIASAVCGSASTSMTS
 1604- 1695 (110.54/48.90)	GRECPASAATTTCTSSLSNADfvgtalssqSAEFANTITSATSGAscVSAGATTTTTTTTTTTATTAmtttTTTATAVTTTVADSASSTAVS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.69|      14|      15|    1750|    1763|       5
---------------------------------------------------------------------------
 1750- 1763 (27.55/18.05)	LLSPTSDGPNFPHV
 1768- 1781 (28.15/18.65)	LVNPFNFGPDDQHV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.62|      25|      26|    1270|    1294|       7
---------------------------------------------------------------------------
 1270- 1294 (44.31/28.20)	LTCSLMLFRTSPFSCL.NAGASAAIG
 1298- 1323 (37.31/22.34)	LSTSLLSVTSSSWSMLgDVEKSVHLG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      60.04|      17|      19|    1075|    1093|       8
---------------------------------------------------------------------------
 1075- 1091 (30.93/18.15)	SAPASVRSVAEP.....SPLSN
 1097- 1118 (29.11/ 9.99)	SSPHFVRTPRTPgmelaSPMSN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.26|      18|      19|     550|     567|       9
---------------------------------------------------------------------------
  550-  567 (31.24/23.66)	KYTGMESVDVDQQLLTMK
  569-  586 (30.02/22.37)	RYNVSTNHDTDSELQLMK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     137.52|      41|     209|    1218|    1260|      10
---------------------------------------------------------------------------
 1218- 1260 (66.03/56.70)	HRYLSYKSGvfYEDEDDATG..AVWERLTASHLETVQFSREIVEL
 1432- 1474 (71.49/53.85)	HRKCTHRPG..SNGREDLSGpePIPELLVCSDRDWIQVSPFSVRL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      42.73|      12|     209|    1580|    1599|      11
---------------------------------------------------------------------------
 1555- 1567 (18.13/14.96)	FDRFESASDgRSI
 1588- 1599 (24.60/ 7.12)	FSPVWSAFD.RSI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      45.21|      14|      19|     773|     788|      12
---------------------------------------------------------------------------
  773-  788 (23.89/19.21)	SAIVH.....HQMMqeGPSPS
  789-  807 (21.33/10.07)	SAISDceneiHAFL..SPPPS
---------------------------------------------------------------------------




































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 MDP06352 with Med13 domain of Kingdom Metazoa
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