<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 MDP06238

Description Mediator of RNA polymerase II transcription subunit 13 (Fragment)
SequenceLLCEMSHVNLNSTNGASLEDCHTNVFVLTELNGLKWCRWCCSNSSIVYADIPDDAVLCGYGRCVTQGFLCVWRRAPPVHSSNRVDLRLAVEKELWIFWYGDEPDWALLCTGLTKIEEGSWEKGVEYETRTMLFKALHNQIDRVLLNANFLRFGNWYVNPLNYPKTKNKSNRPKYVIAFSLSFFVHGENNVCVTVSVQRHVPVYRLCRQLMLANRKLPVLLSPWSLSGELVFDPDKTSESGESQFQQQLWKDWCRFYASLDSGGAESTTGVGSGSPFKEANSSSTTTTTTTDKLPKMMDVFVCGVRLKVPTRFVCVVDPDNVASSPQQSGSLLAGFRQWLCEKTMENLICHQRRQSGPTSPSAGESDSFGLAGSWNIVDPGQRERCCCSVGQSTSCCGTGAAGSVRFTSKCKSSDVSPKRVGCFHRRVAASRKLMTSAGLDGSSTAAGDDDDQQHQTMVEEAGTSTTSALLNSTTTATATVTTTAASTASAAAAAAAPVASAVCSSASMTSSTMFLDHCSANVVGCNVAVEPKSKMRRSVEQSELLQQQQTPDPLVIPPKYTGLESIEVDQRLLSMKRRYNVSTNYDTDGDLQLMKLSFSRYHSHHQEQIHLLHIQQQQQQQQQQQQQQNQSNSFISRVSSSSVKNFGKPTDQFTEKFYRALTSYSWCQAMETNRKRRFFVQNVLLLFSEAVLNCRSIAPVGQRHLAQSNARQVEKIYGYKNKNKRKDITTNDHDRTDDVLSGDMCKREEEKACVKSDAEFHLTDDSSAIVHHQMMEEGPSPSSGISDCENEIHAFLSPPPSLGTEEERLNATEKIVAVKMDATNQNNEHANSSSSSNNNNNNNNNSSTTTTTNSNNVAVLSCSQRSSASSAYPSSTQVVAVAGAVVDHLGIIYPTPPSQEALQQLSPESHAGTGTTAVAGTQTGACSSGSYGQGSTMKAASYLSGYRDCKDAPEVQVVIPYVLASEFFGAVPASSRRSAVRFEKILCYKPSRLLPALYHHHHHHHHHHHHHHHHQSASVGHLASLPTYGLGAISHHSWSNCGSFGSWFGSSSVRLGSQASIGLDSSSSATGRSIISAPASVRSVAEPSPVNNNPPSVSSPHFVRTPRTPGMELASPMSNASSAYAKNLSSIEPASSVLHPEGHSLVMMLLLSDTFVHLYRDSNFDSCPLCVCNMNIRGLEMGHYVNLRRCDDNMSVLYHSSARNTFTNKCTCGFSASRHRYLSYKSGVFYEDEDDATGAVWERLTASHLETVPFSREIVELVRHQSLLQDLTCSLMLFRTSPFGCLNAEASGAIGGGGGGGGGGGGGGGGGGSLSTSLLSVTSSSWSMFDDVEKNIPLGLPNAVYNAVELRDFTELCQLALEQSMLSLDCNNVALYVEQVPAAKRSATSSYINGWGYAKTVEPSNSLETMALLRSLLPLLQESLQKPRGLWQAKHSVEGPLTWRQLHRKCTHRPGSNGREDLSGPEPIPELLVCSDRDWIQVSPFSIRLWDRMCLEPFTQPKDVAFIAVVPDTQYVVRKARGFFRELSRTYEGMRLGRHCPITRVLKDGIMRVGKTHAKQLDQKPVDPWFDRFESASDGRNIIGAKLKLYAQVCRHYLAPHIFSPVWNAFDRSIFREIGRECPVSTPTTTCTSSSLSNVDSVGTAVSSQSAELANTTVSASGSGASCVSAGTTGMTTTTTTATAVTTSVADSSSSTAISYGLNNNNNNNNNNTNNSSNNSMNMMNTSSSNNSNDSRMSESSTNGNDNNGLLSPTSDGPNFPHVVVIYLVNPFNFGPDDQHVRDLNRLVTTGLFRCYLEILQEVPATFRSSMQLQIIPLQTVLDTSLLDDWELQHNGIVDEDRRLKSMPRAAVNSNSSSVGGGIGQQRVPLSSSTHLRSLALNVFMQIRSVAYSCLHSCLPKVMTGFGPAASRHELLRRKQNSAGFRLYSAPVVLAPIQDRTSCLNGTTGSNGSFGSSSSNSASSFCGGGSESRDDHGQVLFLAYCLSAKQQWLLCTVTDQQGAVLDSCVINMMLNNRHNVVKRELIWSALRRLWDYVVGILASSCRPWRIVIGRLGRLGHEELKAWAHLLSKSQLRSTSRLLREQCAVCQPMPTIFETPAILSACLISTELDPNMRIFPDSFVHDDRFGQGAKQCPLSSPEDVSSSHIMVFPTSALIQISQCCIMTGGLPGADETDGDFESIWKDLMISPEGDGLESGLNDIFGSMSEANLMNDSTVGFDANSSHTRGLAISESSDESIQLQPLALGFLVSTAPTGPVPEWFWTVRPSARDLLPVHLRSALHIHTSGVQQSDDHLLAGGANRSTSGTVHPLDSSLTTDVLRYVLETYNALSWLCLDFRTGDRVSCFPLHIQALSRLYRAMDALL
Length2364
PositionMiddle
OrganismTrichinella britovi (Parasitic roundworm)
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella.
Aromaticity0.07
Grand average of hydropathy-0.311
Instability index51.58
Isoelectric point6.62
Molecular weight258038.66
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

>MDP06238
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      70.32|      21|     214|    1637|    1657|       1
---------------------------------------------------------------------------
 1637- 1657 (33.98/17.84)	SNVDSVGTAVSSQSAELANTT
 1854- 1874 (36.34/19.63)	SNSSSVGGGIGQQRVPLSSST
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     183.59|      40|     214|    1726|    1768|       2
---------------------------------------------------------------------------
  824-  859 (56.86/25.66)	....NQNNEHANSSSSS......N.....NN..NNNNNNSSTTTTTNSNNVAV
  860-  895 (27.19/ 8.65)	LSCSQRSSASSAYPSST......QvvavaGAvvDHLGIIYPT...........
 1690- 1722 (28.65/ 9.61)	..........ADSSSSTaisyglN.....NN..NNNNNNNTNNSSNNSMN...
 1726- 1765 (70.88/42.22)	TSSSNNSNDSRMSESST......N.....GN..DNNGLLSPTSDGPNFPHVVV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.57|      13|      44|    1619|    1632|       3
---------------------------------------------------------------------------
 1619- 1632 (22.41/22.43)	GRECpVSTPTTTCT
 1664- 1676 (25.16/17.62)	GASC.VSAGTTGMT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.82|      10|     214|      36|      45|       4
---------------------------------------------------------------------------
   36-   45 (25.82/13.79)	WCRWCCSNSS
  252-  261 (22.01/10.62)	WCRFYASLDS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      93.37|      28|     211|     906|     948|       6
---------------------------------------------------------------------------
  486-  513 (46.45/14.04)	STASAAAAAAAPVASAVCSSASM.TSSTM
  909-  937 (46.92/32.17)	SHAGTGTTAVAGTQTGACSSGSYgQGSTM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      78.40|      23|      50|      48|      74|       8
---------------------------------------------------------------------------
   48-   74 (36.41/33.00)	YADIPDDAVLC.GYGRcVTQGflcVWRR
   99-  122 (41.99/22.72)	YGDEPDWALLCtGLTK.IEEG...SWEK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.83|      13|     211|     767|     781|      11
---------------------------------------------------------------------------
  767-  781 (21.40/19.00)	SAIVH.....HQMMeeGPSP
  783-  800 (19.43/ 9.66)	SGISDceneiHAFL..SPPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.61|      21|      44|    1314|    1337|      15
---------------------------------------------------------------------------
 1314- 1337 (26.82/29.05)	LSTSLLSVTSSSWSMFddVEKnIP
 1361- 1381 (36.79/24.35)	LEQSMLSLDCNNVALY..VEQ.VP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     129.12|      39|     544|    1781|    1819|      21
---------------------------------------------------------------------------
 1781- 1819 (66.53/45.98)	VRDLNRLVTTGLFRCYLEILQEVP...ATFRSSMQLQIIPLQ
 2308- 2349 (62.58/42.75)	VHPLDSSLTTDVLRYVLETYNALSwlcLDFRTGDRVSCFPLH
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     170.89|      51|      52|    1037|    1087|      24
---------------------------------------------------------------------------
 1016- 1042 (27.00/10.43)	..........................SASVGHLAS.LPTyGLGAISHHSWSNCG
 1043- 1093 (84.74/53.25)	SFGS.WFGSSSVRLGSQASIGLDSSSSATGRSIIS.APA.SVRSVAEPSPVNNN
 1096- 1140 (59.15/34.27)	SVSSpHFVRTPRTPGMELASPMSNASSAYAKNLSSiEPA.S..SVLHP......
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.35|      26|     542|    1535|    1586|      25
---------------------------------------------------------------------------
  635-  660 (45.33/15.54)	ISRVSSSSVKNFG.KPTDQFTEKFYRA
 1550- 1576 (44.02/36.12)	IMRVGKTHAKQLDqKPVDPWFDRFESA
---------------------------------------------------------------------------




































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 MDP06238 with Med13 domain of Kingdom Metazoa
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