<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 MDP06285

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLLCEMSHVNLNSTNGASLEDCHTNVFVLTELNGLKWCRWCCSNSSIVYSDIADDAVLCGYGRCVTQGFLCVWRRSPPVHSSNRVDLRLAVEKELWIFWYGDEPDWALLCTGLTKIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNRSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLLLANRKLPVLLSPWSLSAELIFDPDKASEPGECQFQQQLWKDWCRFYASLDNGAESTTTGVGSGSPFKEANNTDRLPKMLDVFVCGVRLKVPTRFVCVVDPDHLATGQQQPGGLLAGFRQWLCEKTVENLICHQLRHSRPTSPSSGESESFGLAGSWNIVDPGQRERCCCSVAQSTNYCGTGAAGSVRFTSKCKSSDSSPKRVGCFHRRVTTGRKLMTSAGLDGSTTATGDDDDQQHQSMVEEATTSAMLNSSTTTTTTTATATATAATTTATPIASAVCGSASTSMTSSTMILDHCSADVVGCNAAVEPKLKMRRSVEQSQLLQQQQQLTPDPLVIPPKYTGMESVDVDQQLLTMKRRYNISTNHDTDSELQLMKLAILKFDPQSYHHDCHPHQQEQRIHHLHVKQRQQQLYQLQLQRQQQQQQQQQQQQQQQQQQQQQQQQNQLGNFISKVSSSVENFSKPMDRFTENFYRALANYSWCQTMETNRKHRSLFQNVLILFSEAMLNCRTIAPVGQRHFALSNARQVEKIYGYKNKNKRKDNNNDRDDHDQNDDVLVGDICKREEKACVKLDTEFQTDDNSAIVHHQMMQEGPSPSSAISDCENEIHAFLSPPPSLGTEEERLNANEKIVAVKMEATNQNNEHGNSSSNNNNNNNNNNSSSNNSNNNSNSNSNSVAVLSCSQRSSASSAYPSSTQVPVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTSTTAVVVGTQWTNSACSNGANGQGSTMKAASDASSCHDCKEAPEVRVVIPYVLASEFSTAVSAPLRRSTVRFEKILCYKPSRLLPSVYHHPHASAGHLTSLPTYGLGAISHHSWSNYGPVGSGFGSSSVRLGSQASIGLDSSSSAAGRSIISAPASVRSVAEPSPLSNNPPSVSSPHFARTPRTPGMELASPMSNASSAYAKNLSSIEPANSVQHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCVCNMNIRGLEMGHYVNLRQCDDNMGVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLTASHLETVQFSREIVELVRHQSLLQDLTCSLMLFRTSPFSCLNAGASAAIGGGSLSTSLLSVTSSSWSMLGDVEKSVHLGCWPNAVYNAVELRDFTELCQLALEQSMLSLDCNNVALYVEQVPAAKRSATASFINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWRQLHRKCTHRPGSNGREDLSGPEPIPELLVCSDRDWIQVSPFSVRLWDRMCLEPFTQPKDVAFIAVVPDTQHVVRKARGFFRELSRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFESASDGRSIIGSKLKLYAQVCRHYLAPHIFSPVWSAFDRSIFREIGRECPASAATTTCTSSLSNADSVGTALSSQSAEFANTITSATSGSGASCVSAGATTTTTATTTTTATTAMTTTTNTATAVTTTVADSASSTAVSYGLNMNNNNNNSSNNNSNNNSANNSLNMMNTTSSSNNSNDSRISDSSTNGNDNGLLSPTSDGPNFPHVVVIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQQNGIVDEDRRLNSVPRTMVNSNSSSNCGGSIGQQRVPLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPVQDRTSCLNGTTGSIGSLGSSSSNSVSSFCGGGSEARDDHGQVLFLAYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRRNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGIPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLPGGANRSTTATVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2383
PositionMiddle
OrganismTrichinella zimbabwensis
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.344
Instability index49.12
Isoelectric point6.51
Molecular weight261657.75
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

>MDP06285
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|      98.23|      15|      17|    1674|    1688|       1
---------------------------------------------------------------------------
  463-  477 (25.34/10.29)	TTTTTTTATATATAA
  478-  492 (24.52/ 9.74)	TTTATPIASAVCGSA
 1674- 1688 (25.31/10.27)	TTTTTATTTTTATTA
 1693- 1707 (23.07/ 8.77)	TNTATAVTTTVADSA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      68.92|      17|      17|     618|     634|       2
---------------------------------------------------------------------------
  618-  634 (33.87/19.90)	QQQLYQLQLQRQQQQQQ
  636-  652 (35.05/20.83)	QQQQQQQQQQQQQQQQQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     103.59|      19|      20|     847|     865|       3
---------------------------------------------------------------------------
  847-  865 (36.57/19.06)	NQNNEHGNSSSNNNNNNNN
  866-  882 (29.83/14.04)	..NNSSSNNSNNNSNSNSN
 1717- 1735 (37.19/19.52)	NMNNNNNNSSNNNSNNNSA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.69|      14|      15|    1768|    1781|       4
---------------------------------------------------------------------------
 1768- 1781 (27.55/14.76)	LLSPTSDGPNFPHV
 1786- 1799 (28.15/15.26)	LVNPFNFGPDDQHV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.27|      15|      20|    1028|    1046|       5
---------------------------------------------------------------------------
 1028- 1046 (24.02/24.04)	HHPHASAGHLTSlptyGLG
 1050- 1064 (32.24/19.04)	HHSWSNYGPVGS....GFG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.09|      19|      20|    1083|    1102|       6
---------------------------------------------------------------------------
 1083- 1102 (26.67/20.58)	SAAGRSiISAPASVRSVAEP
 1106- 1124 (36.42/23.97)	SNNPPS.VSSPHFARTPRTP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.23|      16|      26|    1627|    1642|       7
---------------------------------------------------------------------------
 1627- 1642 (27.33/15.30)	AATTTCTSSLSNADSV
 1654- 1669 (27.90/15.79)	ANTITSATSGSGASCV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.39|      18|      18|     549|     566|       8
---------------------------------------------------------------------------
  549-  566 (31.25/20.33)	KYTGMESVDVDQQLLTMK
  568-  585 (30.14/19.32)	RYNISTNHDTDSELQLMK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.64|      26|      28|    1321|    1346|       9
---------------------------------------------------------------------------
 1321- 1346 (48.90/29.27)	VTSSSWSMLGD..VEKS.VHLGCWPNAVY
 1349- 1377 (35.75/19.29)	VELRDFTELCQlaLEQSmLSLDCNNVALY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.57|      14|      19|     790|     805|      10
---------------------------------------------------------------------------
  790-  805 (25.06/16.97)	SAIVH.....HQMMqeGPSPS
  806-  824 (22.51/ 9.10)	SAISDceneiHAFL..SPPPS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     267.35|      87|     105|    1872|    1974|      11
---------------------------------------------------------------------------
 1872- 1974 (133.89/128.47)	SNS.SSNCGGsiGQQrvplSSSTHLRSLALNVFMQIRSVAYSC.........LHSCLPKVMTGfgpaaSRHELLRRKQN.SAGFRLYSAPV.VLApvqdrTSC..LNGTTGSIGSLG
 1978- 2078 (133.45/88.48)	SNSvSSFCGG..GSE....ARDDHGQVLFLAYCLSAKQQWLLCtvtdqqgavLDSCVINMMLN.....NRRNVVKRELIwSALRRLWDYVVgILA.....SSCrpWRIVIGRLGRLG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.05|      19|      22|    1419|    1440|      12
---------------------------------------------------------------------------
 1395- 1427 (25.61/16.23)	G.WGYAKTVEPsnsletmallrsllPLLQESLQK
 1430- 1449 (33.44/19.79)	GlWQAKHSVEG..............PLTWRQLHR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      74.11|      23|      29|     680|     702|      13
---------------------------------------------------------------------------
  680-  702 (43.77/24.58)	FYRALANYS....WCQTM.ETNRKHRSL
  703-  730 (30.34/14.74)	FQNVLILFSeamlNCRTIaPVGQRHFAL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.20|      11|      21|    1178|    1191|      14
---------------------------------------------------------------------------
 1178- 1191 (18.57/19.72)	NFDSCPlcvCNMNI
 1201- 1211 (21.63/11.75)	NLRQCD...DNMGV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.94|      17|      22|     747|     763|      15
---------------------------------------------------------------------------
  747-  763 (31.34/22.40)	KRKDNNNDRDDHD.QNDD
  771-  788 (24.60/15.76)	KREEKACVKLDTEfQTDD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.25|      25|    1160|     300|     332|      16
---------------------------------------------------------------------------
  300-  332 (36.41/48.20)	VPTRFVCvVDPDHLatgQQQPGGLlagfRQW..LC
 1469- 1495 (45.84/30.54)	IPELLVC.SDRDWI...QVSPFSV....RLWdrMC
---------------------------------------------------------------------------




































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 MDP06285 with Med13 domain of Kingdom Metazoa
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