<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 MDP06030

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLLCEMSHVNLNSTNGASLEDCHTNVFVLTELNGLKWCRWCCSNSSIVYADIPDDAVLCGYGRCVTQGFLCVWRRAPPVHSSNRVDLRLAVEKELWIFWYGDEPDWALLCTGLTKIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNKSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLMLANRKLPVLLSPWSLSGELVFDPDKASESGESQFQQQLWKDWCRFYASLDSGGAESTTGVGSGSPFKEANSSSSTTTTTTTDKLPKMMDVFVCGVRLKVPTRFVCVVDPENVASSPQQSGSLLAGFRQWLCEKTMENLICHQRRQSGPTSPSAGESDSFGLAGSWNIVDPGQRERCCCSVGQSTSCCGTGAAGSVRFTSKCKSSDVSPKRVGCFHRRVAASRKLMTSAGLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNSTTTATATVTTTAASTASAAAAAAAAAPVASAVCSSASMTSSTMFLDHCSANMVGCNVAVEPKSKMRRSVEQSELLQQQQTPDPLVIPPKYTGLESIEVDQRLLSMKRRYNVSTNYDTDGDLQLMKLSFSRYHSHHQEQIHLLHIQQQQQQQQQQQLLQQQQQNQSNSFISRVSSSSVKNFGKPTDQFTEKFYRALTSYSWCQAMETNRKRRFFVQNVLLLFSEAVLNCRSIAPVGQRHLAQSNARQVEKIYGYKNKNKRKDITTNDHDRTDDVLSGDMCKREEEKACVKSDAEFHLTDDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERLNATEKIVAVKMDATNQNNEHANSSSSSNNNNNNNNNSSSTTTTNSNNVAVLSCSQRSSASSAYPSSTQVVAVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTGTTAVAGTQTSACSSGSYGQGSTMKAASYLSGYRDCKDAPEVQVVIPYVLASEFFGAVPASSRRSAVRFEKILCYKPSRLLPALYHHHHHHHHHHHHHHHHHQSASVGHLASLPTYGLGAISHHSWSNCGSFGSWFGSSSVRLGSQASIGLDSSSSATGRSIISAPASVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEPASSVLHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCDDNMSVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLTASHLETVPFSREIVELVRHQSLLQDLTWAIGGGGGGGGGGGGGGGGGSLSTSLLSVTSSSWSMFDDVEKNIPLGLPNAVYNAVELRDFTELCQLALEQSMLSLDCNNVALYVEQVPAAKRSATSSYINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWRQLHRKCTHRPGSNGREDLSGPEPIPELLVCSDRDWIQVSPFSIRLWDRMCLEPFTQPKDVAFIAVVPDTQYVVRKARGFFRELSRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFESASDGRNIIGAKLKLYAQVCRHYLAPHIFSPVWNAFDRSIFREIGRECPASTPTTTCTSSSLSNVDSVGTAVSSQSAELANTTVSASGSGASCVSAGTTGMTTTTTTATAVTTSVADSSSSTAISYGLNNNNNNNTNNSSNNSMNMMNTSSSNNSNDSRMSESSANGNDNNGLLSPTSDGPNFPHVVVIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQHNGIVDEDRRLKSMPRAAVNSNSSSVGGGIGQQRVPLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPIQDRTSCLNGTTGSNGSFGSSSSNSASSFCGGGSESRDDHGQVLFLAYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRHNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGLPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLAGGANRSTSGTVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2329
PositionMiddle
OrganismTrichinella sp. T9
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella> unclassified Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.315
Instability index51.70
Isoelectric point6.56
Molecular weight254201.22
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

>MDP06030
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     127.16|      40|      63|    1480|    1523|       1
---------------------------------------------------------------------------
 1480- 1523 (64.25/64.40)	DTQYVVRKARGFFRELSRTYegmrLGRH..CPITRVLKDGIMR.VGK
 1546- 1588 (62.91/50.10)	DGRNIIGAKLKLYAQVCRHY....LAPHifSPVWNAFDRSIFReIGR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     132.92|      32|     213|    1593|    1625|       2
---------------------------------------------------------------------------
  837-  865 (26.99/ 8.80)	......ANSSSSSNNNNNNNNNSSsttttNSNNVA..
 1593- 1624 (51.28/24.76)	STPTTTCTSSSLSNVDSVGTAVSS.....QSAELANT
 1659- 1691 (54.65/23.12)	DSSSSTAISYGLNNNNNNNTNNSS....nNSMNMMNT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     496.52|     119|     213|     870|     996|       3
---------------------------------------------------------------------------
  870-  988 (195.09/98.85)	SQRSSASSAYPSSTQVVAVAGAVVDHLGI..IYPTPPSQEALQQLSPESHAGTGTTAVAGTQTSACSSGSYGQGSTMKAASYLSG.....YRD.....CKDA.PEVQVVIPYVLASEFFGAVPASSRRSAVR
 1088- 1206 (167.89/83.36)	SVRSVAEPS.PVNNNPPSVSS...PHF.V..RTPRTPGME...LASPMSNASSAYAKNLSSIEPA.SSVLHPEGHSLVMMLLLSDtfvhlYRDsnfdsCPLC.DDNMSVLYHSSARNTF.TNKCTCGFSASR
 1214- 1316 (133.54/73.25)	......SGVFYEDED..DATGAVWERLTAshLETVPFSREIVELVRHQSLLQDLTWAIGGGGGGGGGGGGGGGGGSL.STSLLSV.....TSS.....SWSMfDDVEKNIPLGLPNAVYNAV..........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     153.16|      38|     215|    1900|    1937|       4
---------------------------------------------------------------------------
 1900- 1937 (68.96/37.90)	APIQDRTSCL..NGTTG...S.......NGSFGSSSSNSASSFCGGGSES
 2120- 2161 (49.20/24.63)	ALIQISQCCImtGGLPGadeT.......DGDFESIWKDLMISPEGDGLE.
 2162- 2199 (35.00/15.10)	.......SGL..NDIFG...SmseanlmNDSTVGFDANSSHTRGLAISES
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|      89.65|      13|      18|     779|     791|      12
---------------------------------------------------------------------------
  351-  364 (22.13/ 8.79)	HQRRQSGPtSPSAG
  779-  791 (26.87/12.35)	HQMMEEGP.SPSSG
  800-  810 (21.79/ 8.54)	HAFL..SP.PPSLG
 1029- 1039 (18.87/ 6.35)	H..LASLP.TYGLG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      86.12|      20|      50|      50|      74|      19
---------------------------------------------------------------------------
   50-   69 (40.09/18.55)	DIPDDAVLC.GYGRCVTQG.FL
  101-  118 (22.66/ 7.79)	DEPDWALLCtGLTK.IEEG...
 1741- 1759 (23.37/ 8.71)	..PDDQHVR.DLNRLVTTGlFR
---------------------------------------------------------------------------




































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 MDP06030 with Med13 domain of Kingdom Metazoa
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