<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 MDP06056

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLLCEMSHVNLNSTNGASLEDCHTNVFVLTELNGLKWCRWCCSNSSIVYADIPDDAVLCGYGRCVTQGFLCVWRRAPPVHSSNRVDLRLAVEKELWIFWYGDEPDWALLCTGLTKIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNKSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLMLANRKLPVLLSPWSLSGELVFDPDKASEPGESQFQQQLWKDWCRFYASLDSGGAESTTGVGSGSPFKEANSSSTTTTTTTDKLPKMMDVFVCGVRLKVPTRFVCVVDPDNVASSPQQPGSLLAGFRQWLCEKTMENLICHQRRQSGPTSPSAGESDSFGLAGSWNIVDPGQRERCCCSVGQSTSCCGTGAAGSVRFTSKCKSSDVSPKRVGCFHRRVAASRKLVTSAGLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNSTTTATATVTATAASTASAAAAAAPVASAVCSSASMTLSTMFLDHCSANVVGCNVAVEPKSKMRRSVEQSELLQQQQTPDPLVIPPKYTGLESIEVDQRLLSMKRRYNVSTNYDTDGDLQLMKLSFSRYHSHHQEQIHLLHIQQKQQQQQQQQQLQQQQQNQSNSFISRVSSSSVKNFGKPTDQFTEKFYRALTSYSWCQAMETNRKRRFFVQNVLLLFSEAVLNCRSIAPVGQRHLAQSNARQVEKIYGYKNKNKRKDITTNDHDRTDDVLSGDMCKREEEKACVKSDAEFHLTDDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERSNATEKIVTVKMDATNQNNEHANSSSSSNNNNNNNNNSSSTTTTNSNNVAVLSCSQRSSASSAYPSSTQVVAVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTGTTAVAGTQTGASSSGSYGQGSTMKAASYLSGYRDCKDAPEVQVVIPYVLASEFFGAVPASSRRSAARFEKILCYKPSRLLPALYHHHHHHHHHHHHHHHQSASVGHLASLPTYGLGAISHHSWSNCGSFGSWFGSSSVRLGSQASIGLDSSSSATGRSIISAPASVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEPASSVLHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCVCNMNIRGLEMGHYVNLRRCDDNMSVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLAASHLETVPFSREIVELVRHQSLLQDLTCSLMLFRTSPFGCLNAEASGAIGGGGGGGGGGGSLSASLLSVTSSSWSMFEDVEKNIPLGLPNAVYNAVELRDFTELCQLALEQSMLSLDCNNVALYVEQVPAAKRSATSSYINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWRQLHRKCTHRPGSNGREDLSGPEPIPELLVCSDRDWIQVSPFSIRLWDRMCLEPFTQPKDVAFIAVVPDTQYVVRKARGFFRELSRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFESASDGRNIIGAKLKLYAQVCRHYLAPHIFSPVWNAFDRSIFREIGRECPASTPTATCTSSSLSNVDSVGTAVSSQSAELANTTVSASGSGASCVSAGTTGMTTTTTTATAVTTSVADSSSSTAISYGLNNNNNNNTNNSSNNSMNMMNTSSSNNSNDSRMSESSANGNDNNGLLSPTSDGPNFPHVVVIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQHNGIVDEDRRLKSVPRAAVNSNSSSVGGGIGQQRVPLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPIQDRTSCLNGTTGSNGSFGSSSSNSASSFCGGGSESRDDHGQVLFLAYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRHNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGLPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLAGGANRSTSGTVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2356
PositionMiddle
OrganismTrichinella sp. T6
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella> unclassified Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.306
Instability index51.50
Isoelectric point6.65
Molecular weight257320.01
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

>MDP06056
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     980.96|     259|     277|     944|    1218|       1
---------------------------------------------------------------------------
  774-  930 (197.31/108.13)	..........................................................................HHQMMEEG.....PSPSSG......ISDCENEIHAFLS..PPPSLGTE.............EERSNATEKIVtVKMD.ATNQnnehaNSSSSSNNNNNNNNNSSSTTTTNSNNVAVLSCSQRSSASSAYPSSTQVVAV..AGAVVDH.........................................LGI.IYPTPPSQEALQQ.......LSP.ESHAGTGTTAVAGTQTGASS
  944- 1218 (420.15/283.01)	SYLSG..YRDCKDAPEvqvVIPYVLASEFFGAVPASSR.RSAARFEKILCYKPSRLLpaLYhhhhHHHHHHHHHHHQSASVGHlASLPTYGLGAISHHSWSNCGSFGSWFGS..SSVRLGSQASIG........LDSSSSATGRSI.ISAP.ASVR.....SVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEP..ASSVLHPEG.....HSLVMMLllsdTFVHLYRDSNFDscPLCVCNMNIRGLEMGHYVNLRRCDDN.......MSV.LYHSSARNTFTNKCTCGFSA
 1225- 1503 (363.50/210.95)	SYKSGvfYEDEDDATG...AVWERLAASHLETVPFSREiVELVRHQSLLQDLTCSLM..LF....RTSPFGCLNAEASGAIGG.GGGGGGGGGSLSASLLSVTSSSWSMFEDveKNIPLGLPNAVYnavelrdfTELCQLALEQSM.LSLDcNNVA.....LYVEQVPAAKR..SATSSYINGWGYAKTVE...P.SNSLETMAL.LRSLLPllQESLQKPRGlwqakHSVEGPL....TWRQLHRKCTHR..PGSNGREDLSGPE..PIPELLVCSDRdwiqvspFSIrLWDRMCLEPFTQPKDVAFIA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     141.37|      43|      44|    1664|    1706|       2
---------------------------------------------------------------------------
 1664- 1706 (68.20/36.53)	SAGTTGMTTTTTTATAVTTSVADSSSSTAISYGLNNNNNNNTN
 1709- 1751 (73.17/39.76)	SNNSMNMMNTSSSNNSNDSRMSESSANGNDNNGLLSPTSDGPN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.15|      23|      82|     230|     252|       4
---------------------------------------------------------------------------
  230-  252 (45.19/29.75)	VFDPDK.ASEPGESQFQQQLWKDW
  315-  338 (38.96/24.39)	VVDPDNvASSPQQPGSLLAGFRQW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.04|      17|     104|    1838|    1854|       6
---------------------------------------------------------------------------
 1838- 1854 (30.55/14.07)	SVPRAAVNSNSSSVGGG
 1945- 1961 (32.49/15.47)	SFGSSSSNSASSFCGGG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     229.39|      75|     277|    1753|    1890|       8
---------------------------------------------------------------------------
 1784- 1890 (102.51/133.26)	LFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLlddwELQHNGIVDEDR...RLKsvpraavnsnsssvgggigqqRVPLSSSTHLRSLALNVF.....MQIRsvaySClhsC
 2073- 2155 (126.88/66.84)	LLREQCAVCQPMPTIFETPAILSACLISTELDPNM....RIFPDSFVHDDRfgqGAK.....................QCPLSSPEDVSSSHIMVFptsalIQIS....QC...C
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.73|      18|      82|     531|     548|      10
---------------------------------------------------------------------------
  531-  548 (29.65/21.10)	KSKMRRSVEQSELLQQQQ
  614-  631 (32.08/23.49)	QQKQQQQQQQQQLQQQQQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     127.16|      40|      63|    1507|    1550|      13
---------------------------------------------------------------------------
 1507- 1550 (64.25/52.95)	DTQYVVRKARGFFRELSRTYegmrLGRH..CPITRVLKDGIMR.VGK
 1573- 1615 (62.91/41.20)	DGRNIIGAKLKLYAQVCRHY....LAPHifSPVWNAFDRSIFReIGR
---------------------------------------------------------------------------




































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 MDP06056 with Med13 domain of Kingdom Metazoa
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