<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 MDP06284

Description Mediator of RNA polymerase II transcription subunit 1 (Fragment)
SequenceLFVNQGVLLYSTLDVFITKKIFLALDIMSKDLQLLMEHLRQKSQHCMSWKDILKSAKVNLMEKRSPLDAQDRVEVAKSYERLLQGLRVASSYELFGRLEDIATKMNLTFVRTPGSANSQSCFITADCFFLEICAEETGSVFLVNVTHEKQTSESVLLRDIINDKRWTELQRHLWGLYSAYIQCKDIDTKNQAFKFMQNLENILHIQSLQRINDNTLPVVEYLRTSDMYFFRRREVGDPPRLYFFCTPLSFWDSETGDFKQLFQNEVDNVMDVSKFKSVIYAELAMENVQGEQFLSISMQSVNTLGQFNDVPLSMQIAAVFTLTFPEKLIISMDSVTKIEALTGFKPAFNNQSKILDLILDEILPSGFSVLRSFVLLEDQLHYYTVDLEGCLTEGVVLEKIFWTNLEVLHKILPILRTEALFKHMFTSFIRNIATTQQQFAQKMFRRDIHVIPSPDLSILECQVKLPQEREFFYIVFRLAPINEISVKVAGVDNADENLNDVAYKVFSRVWSIPVTIRALLKQLLRLSERNVVVAAAGDGNSGNGDQNAVVPMQIDCDRSLHLSSDSNCAAHSSVSIPDGNYNMSEYSICNDDANDFAVAVAVADDDDDDADADAVISVSGIAQSLNIEQQMQKLIVNVDKVLEELLLVCSGRLAGGPNLLDLFKKPKVWRELIPPRRCAGRRGQRSRQQMAPSLAQQCCASAAGQLPAPVAAAAAAAPFGKVGPNLKSRHFSSTSETLTELDELCQLSSSCAEGNGHQGQSEPVAACGDAAVADGEQKSSIQDTIDSVLGSVRFPGSMAESLINISSCCINNNNNTNNSNPNNNNSNTNTSNNNNNNNNNNNNNNMNALASIRKIELGYGQSSATVAAPMASSSPALAPLSRSSDSTGDVFDYETRSTTTAGAIDQGGRSLSSTVCCADDMSIRAASYADAGAAAAAASASAPTLDVGFWPPAGGVERLDVRGALLNRGMRRRRRCRKAFANTGDRALDMVLKEMRKAERLVRGAGGTRRPRRSRLATATASFTADMREVASKVTLKIRSSSAALPGQGAQESSLASSSLSPADQGSSSGAPGGKDEQRKSFKLAANAGGAVGAAAAVPSQLQPAAAAALSTWTQPPSSVFRSLSHAADEPCSSQSSAAPPQLVKPASKRKNSLDVVIGKLMDKVGTSPTKPDPPSDVPDSAGDKQRHFYGFCFSPTASQQQKSGTVAAAGSASEFTIQRRGECSATTAVPPSASDLSDAPEGGIKLVIKKSVIKLKSARHGRGAGAGHFAETGAPSGRPRVSSPSSAGERLAASKFELLKQKMQARKIKRQSSTEKSRQRGPRSGALAAVSKTASNKSKLSTVGPSPGVAELPSVFPGAEGLLFSKSLKGFKIPKIEDNSSKTTTTTTATTATVVTAAASASASAITTTAVAASTTTTATVATAAASAAATMTTTTTTTIASATASAAVVTNASTVATATTTSANATTTASVAVTPSTVVEKRLADGPPMALVVNDGRASPAGVVSGGGGGILRMKPPLLAVQQVPPPCGGGSSKPLIRRSRPVPLPLPPRSLVATGAHFSAPPAVELTLPTGPAVPRYVRRTLLPNPPLQTASSARPPSQPLLELNKHHQQQMLVQQPQQRPTKQELLNPMTNQTSPKSASPEPTGLVIDDNLNTTAAITSPQKSAEEVDVLSPGLRIAVDEGDETKGATTHSSSTT
Length1699
PositionMiddle
OrganismTrichinella zimbabwensis
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella.
Aromaticity0.05
Grand average of hydropathy-0.231
Instability index49.13
Isoelectric point8.67
Molecular weight181222.88
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

>MDP06284
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     102.68|      15|      18|    1416|    1430|       1
---------------------------------------------------------------------------
 1389- 1403 (24.21/11.36)	TATTATVVTAAASAS
 1416- 1430 (27.77/14.11)	TTTTATVATAAASAA
 1435- 1449 (26.59/13.20)	TTTTTTIASATASAA
 1460- 1474 (24.11/11.28)	ATTTSANATTTASVA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.81|      16|      19|     812|     827|       2
---------------------------------------------------------------------------
  812-  827 (33.55/21.38)	NNNNTNNSNPNNNNSN
  832-  847 (34.26/21.98)	NNNNNNNNNNNNNNMN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     114.74|      20|      20|    1510|    1529|       3
---------------------------------------------------------------------------
 1510- 1529 (38.51/21.11)	GGG.....ILRM.......KP.PLLAVQQVPPP
 1531- 1552 (21.51/ 8.18)	GGGsskplIRRS.......RPvPL....PLPPR
 1556- 1573 (27.78/12.95)	ATG.....AHFS.......AP.P..AVELTLPT
 1574- 1600 (26.95/12.32)	GPA.....VPRYvrrtllpNP.PLQTASSARPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             5|     279.84|      56|      56|    1166|    1221|       4
---------------------------------------------------------------------------
  932-  958 (28.21/ 8.56)	........GAAAAAA...SASAPTLD.V..........................................G.FWP....PA.....GGVER....................................
 1096- 1141 (60.03/26.73)	AAVPSQLQPAAAAAL...S........................................................TWTQPP.....SSVFRSlshAADE............PCSSQS.....SAAPP
 1146- 1196 (87.92/42.64)	PASKRKNSLDV.VIG...K....LMDKV..........................................G.TSPTKPDPP.....SDVPDS...AGDK............QRHFYG.....FCFSP
 1197- 1274 (64.90/29.50)	TASQQQKSGTVAAAG...SASEFTIQRR..........................................GeCSATTAVPPsasdlSDAPE....GGIKlvikksviklksARHGRGagaghFAETG
 1275- 1366 (38.77/14.59)	APSGRPRVSSPSSAGerlAASKFELLKQkmqarkikrqssteksrqrgprsgalaavsktasnksklstvG.PSPGVAELP.....SVFPGA...EG.........................LLFS.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     112.07|      35|      46|      30|      66|       5
---------------------------------------------------------------------------
   30-   66 (58.36/53.13)	KDLQLLMEHLRQKSQHCM..SWKDIlkSAKVNLMEKRSP
   77-  113 (53.71/41.48)	KSYERLLQGLRVASSYELfgRLEDI..ATKMNLTFVRTP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.59|      28|      46|     256|     288|       6
---------------------------------------------------------------------------
  256-  288 (41.22/43.82)	GDFkqlfqNEVDNVMDVSKFKSVIYAE...LAMENV
  305-  335 (43.37/31.77)	GQF.....NDVPLSMQIAAVFTLTFPEkliISMDSV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      62.42|      21|      47|     476|     497|       7
---------------------------------------------------------------------------
  476-  497 (31.86/28.79)	FRLAPINeISVKVAG...VDNADEN
  524-  547 (30.57/21.44)	LRLSERN.VVVAAAGdgnSGNGDQN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      92.79|      22|      22|    1624|    1645|       9
---------------------------------------------------------------------------
 1602- 1626 (31.95/15.04)	QPLLElnkHHQQQMLVQQPQQRPTK
 1627- 1648 (38.14/19.34)	QELLN...PMTNQTSPKSASPEPTG
 1652- 1670 (22.70/ 8.62)	DDNLN...TTAAITSPQKSAEE...
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      60.44|      18|      66|    1004|    1021|      10
---------------------------------------------------------------------------
  963-  984 (26.64/16.68)	GAllnRGMRRRRRCRKAFAnTG
 1004- 1021 (33.80/23.52)	GA...GGTRRPRRSRLATA.TA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      72.70|      24|     216|     688|     713|      12
---------------------------------------------------------------------------
  688-  712 (40.61/29.87)	QQMAPSLAQQC.....CASAAG...QlPAPVAA
  735-  766 (32.09/13.79)	SETLTELDELCqlsssCAEGNGhqgQ.SEPVAA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.25|      19|     158|     716|     734|      13
---------------------------------------------------------------------------
  716-  734 (35.85/20.88)	AAPFGKVGPNLK..SRHFSST
  867-  887 (28.40/14.83)	AAPMASSSPALAplSRSSDST
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      64.52|      17|      47|     361|     377|      14
---------------------------------------------------------------------------
  359-  375 (26.37/18.59)	LD.......EILPSGFSV.....LRSFVL
  376-  396 (19.28/11.39)	LE.......DQLHY.YTVdlegcLTEGVV
  397-  420 (18.87/10.98)	LEkifwtnlEVLHKILPI.....LRTEAL
---------------------------------------------------------------------------




































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 MDP06284 with Med1 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) KMQARKIKRQSSTEKSRQRGPRSGALAAVSKTASNKSKLSTVGPSPGVAEL
2) MASSSPALAPLSRSSDSTGDVFDYETRSTT
3) MKPPLLAVQQVPPPCGGGSSKPLIRRSRPVPLPLPPRSLVATGAHFSAPPAVELTLPTGPAVPRYVRRTLLPNPPLQTASSARPPSQPLLELNKHHQQQMLVQQPQQRPTKQELLNPMTNQTSPKSASPEPTGLVIDDNLNTTAAITSPQKSAEEVDVLSPGLRIAVDEGDETKGATTHSSSTT
4) NNNTNNSNPNNNNSNTNTSNNNNNNNNNNNNNNMN
5) SARHGRGAGAGHFAETGAPSGRPRVSSPSSAGER
6) SSAALPGQGAQESSLASSSLSPADQGSSSGAPGGKDEQRKSFKLAA
7) SSVFRSLSHAADEPCSSQSSAAPPQLVKPASKR
1303
870
1516
813
1258
1041
1118
1353
899
1699
847
1291
1086
1150










Molecular Recognition Features






MoRF SequenceStartStop




1) LAASKFELLKQKMQARK
2) LVIKKSVIKLKSARHGR
3) SFKLA
1292
1247
1081
1308
1263
1085