<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 MDP05986

Description Mediator of RNA polymerase II transcription subunit 1 (Fragment)
SequenceLRVVSNRCSGLSLVFEERAYKLKHTRKQKNIVWLFQTIHQPLLIKTCKSLILSLGRSVILNVKCIYNKENISCTGYYVERPTVADGTPAPEKPTLYVMERYIEKCKNEFNVKFLGTEKRSPLDAEDRVEVAKSYERLLQGLRVASAYELFGRLEDIATKMNLTFVRTPGTANNQSCFITADCFFLEISAEETGSVFLVNVTHEKQTSESVLLRDIINDKRWTELQRHLWGLCSAYIPCKDIDTKNQAFKFMQNLENILHIQSLQRINDNTLPVVEYLRTSDMYFFRRREVGDPPRLYFFCTPLSFWDSETGDFKQLFQNDIDNVMDVSKFKSTIYAELAMENVQGEQFLSISMQSVNALGQFHDIPMSMQIAAVFTLTFPEKLIISMDSVTKIEALTGFKPAFSNQSKILDLILGEILSSGFSVLRSFVLLEDQLHCYTVDLEGCLTEGVVLEKIYWTNLDVLHKILPILRTEALFKHIFTSFIRNITTTQKQFAQKIFRRDIHVIPSPDLSILECQVKLPREREFFYIVFRLAPINEISVKVGGVVDNADVNLNDVAYEVFSRVWSIPVTIRALVKQLLCLSERNVVVAAAGDGNSGNGDHQNDVVLMQIDCDRSLHLSTDSNCAAHSSVSIPDGNYNMSEYSVCNDDANGVAVADDADDDADAVISVSGIAQSLIIEQQMQKLIVNVDKVLEELLLVCSGRLAGGPNLLDLFKKPKVWRELIPPRRCAGRRGQRSRQQMAPPLAQQCCASAAGQLPAPVAAVAAAAPFGKVGPNLKSRHFSSTSETLTELDELCQLSSSCAEGNGHQSEHASACGDSAVADGGEQKSSIQDTIDSVLGSVRFPGSMAESLINISSCCINNNNNTNNSNPNSNNSNANTSNNNNTNSNNNNNNSNNSMNALASIRKIELGYGQSSAGVAAPMSSSSSPALAAPMSRSSDSTGDVFDYETRSTTTAGMSIDQGGRSLSSSVCCADDLSIAAASASAPTLDVGFWPPAGGVERLDVRGALLNRGMRRRRRCRKAFANTGDRALDMVLKEMRKAERLVRGASSTRRPRRSRLATATASFTADMREVASKVTLKIRSSSAAALPGVQTAQESSSLAVASSSLSSADQGSSSGGKDEQKKSLKLAANANASGGAGAATLNTWTQPSSSVFRSLSDATGESCSSRSSSPPPQLVKPASKRKNSLDVVIGKLMDKVGTSPTKLDPSSDVPDSAGDKQRHLYGFCFSPTASQQQKSGTTAASVSASEFTIHKRGECSTTTTAMATSTGELSDAPEGGIKLVIKKGVIKLKSARHGRGAGAGRFVETGAPSARPRVSSPASAGDRLAASKFELLKQKMQARKIKRQSSTEKSRQRGPRSGALAAASKTAANRSKLSTVGSSSSGVAELPSVFPGAEGLLFSKSLKGFKIPKIDDNSSKTTTATTAATVTAAPASTSDSANTTTTVTVSTTTTATVVPAAASAAATMTTTTTTTNIVSATAAAAVVTSASTVATGTTTSANATTTASVAVTPLTVVEKRMADGPPMALVVNDGRASPAGVVSGGGGGILRMKPPLLAVQQVPPPCVGGSSKPLIRRSRPVPLPLPPRSLVATGPHFAGPPAVELALPTGPAVPRYVRRTLLPNPPLQTASSPRPPPPQPLLELNKHHQQQMLVHSTTQQRPTKQELLNPMTNQMSPKSASPDPTGLVIDDNLNTTAAISSPQKNAEEVDVLSPGLRIAVDEGDETKGPTTHSSSTT
Length1737
PositionMiddle
OrganismTrichinella sp. T9
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella> unclassified Trichinella.
Aromaticity0.05
Grand average of hydropathy-0.246
Instability index48.35
Isoelectric point8.91
Molecular weight186011.56
Publications









Function






Annotated function

Component of the Mediator complex, a coactivator involved in
the 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. 


ECO:0000256	RuleBase:RU364059

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

>MDP05986
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     103.10|      24|      24|    1451|    1474|       1
---------------------------------------------------------------------------
 1425- 1449 (29.43/14.81)	.TTAATVTaaPASTSDSANTTTTVTV
 1451- 1474 (42.81/25.38)	TTTTATVV..PAAASAAATMTTTTTT
 1480- 1499 (30.86/15.94)	ATAAAAVV......TSASTVATGTTT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      88.96|      25|      26|    1538|    1563|       2
---------------------------------------------------------------------------
 1538- 1556 (27.68/11.73)	......PA.G.VVSGGGGGILR.MKP.PL
 1558- 1583 (25.89/11.83)	AVQQVP..pP.CVGGSSKPLIRrSRPvPL
 1602- 1627 (35.39/14.44)	AVELALPT.GpAVPRYVRRTLL.PNP.PL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.92|      15|      26|     861|     885|       3
---------------------------------------------------------------------------
  861-  878 (21.51/28.80)	NNNNntNNSNpNSNNSNA
  889-  903 (30.40/ 9.82)	NNNN..NNSN.NSMNALA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      63.92|      13|      20|    1108|    1120|       4
---------------------------------------------------------------------------
 1108- 1120 (23.35/12.47)	SLSSADQGSSSGG
 1127- 1139 (18.62/ 8.15)	SLKLAANANASGG
 1144- 1156 (21.95/11.19)	TLNTWTQPSSSVF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      93.36|      24|      24|    1050|    1073|       6
---------------------------------------------------------------------------
 1015- 1038 (22.64/ 8.70)	....RRRRRCRKAFAnTGDRALDMvlKE
 1050- 1073 (42.97/22.94)	SS.TRRPRRSRLATA.TASFTADM..RE
 1076- 1098 (27.75/12.29)	SKvTLKIRSSSAAAL.PGVQTA....QE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     291.49|      72|     280|     928|    1001|       7
---------------------------------------------------------------------------
  928- 1001 (115.09/68.36)	SPALAAPMSRSSDSTGD....VF...DY........ETRSTTTAG......MSIDQGGRSLSSSVCCADDLSIAAASASAPTLD....VGfwPPAGGVE
 1203- 1282 (84.15/43.11)	SPTKLDPSSDVPDSAGDkqrhLY...GFcfsptasqQQKSGTTAAsvsaseFTIHKRGE.......CS.TTTTAMATSTGELSD........APEGGIK
 1311- 1387 (92.24/47.99)	APS.ARPRVSSPASAGD....RLaasKF........ELLKQKMQA......RKIKRQSSTEKSRQRGPRSGALAAASKTAANRSklstVG..SSSSGV.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.67|      15|      15|     741|     755|       8
---------------------------------------------------------------------------
  741-  755 (28.68/14.63)	MAPPLAQQCCASAAG
  757-  771 (23.99/11.02)	LPAPVAAVAAAAPFG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.59|      20|     278|     196|     215|       9
---------------------------------------------------------------------------
  196-  215 (33.57/25.82)	FLVNVTH.EKQTSESVLLRDI
  483-  503 (31.02/23.24)	FIRNITTtQKQFAQKIFRRDI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.81|      12|      17|     796|     809|      11
---------------------------------------------------------------------------
  796-  809 (16.42/15.80)	CQlSSSCAEGnGHQ
  816-  827 (23.39/11.57)	CG.DSAVADG.GEQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.11|      13|      19|     285|     297|      12
---------------------------------------------------------------------------
  285-  297 (25.35/15.81)	FRRREVGDPPRLY
  305-  317 (25.76/16.19)	FWDSETGDFKQLF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.29|      14|     837|     697|     710|      15
---------------------------------------------------------------------------
  697-  710 (25.87/14.18)	LLVCSGRLAGGPNL
 1514- 1527 (26.42/14.64)	LTVVEKRMADGPPM
---------------------------------------------------------------------------




































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 MDP05986 with Med1 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) KMQARKIKRQSSTEKSRQRGPRSGALAAASKTAANRSKLSTVGS
2) KSGTTAASVSASEFTIHKRGECSTTTTAMATSTGELSDAPE
3) KTTTATTAATVTAAPASTSDSANTTTTVTVSTTT
4) NNNTNNSNPNSNNSNANTSNNNNTNSNNNNNNSNNSMN
5) QQVPPPCVGGSSKPLIRRSRPVPLPLPPRSLVATGPHFAGPPAVELALPTG
6) RHGRGAGAGRFVETGAPSARPRVSSPASAG
7) SAGVAAPMSSSSSPALAAPMSRSSDSTGDVFDYETRSTTTAGMSID
8) SSSLAVASSSLSSADQGSSSGGKDEQKKSLKLAANANA
9) VPRYVRRTLLPNPPLQTASSPRPPPPQPLLELNKHHQQQMLVHSTTQQRPTKQELLNPMTNQMSPKSASPDPTGLVIDDNLNTTAAISSPQKNAEEVDVLSPGLRIAVDEGDETKGPTTHSSSTT
1339
1238
1420
863
1560
1296
916
1099
1613
1382
1278
1453
900
1610
1325
961
1136
1737










Molecular Recognition Features






MoRF SequenceStartStop




1) KKSLKLAA
2) LRIAVD
3) RLAASKFELLKQKMQARKI
4) VIKKGVIKLKSARHG
1125
1716
1327
1284
1132
1721
1345
1298