<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 MDP05898

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMSKDQQLLMEHLRQKSQHCMSWKDILKSAKMNLMEKRSPLDAEDRVEVAKSYERLLQGLRVASAYELFGRLEDIATKMNLTFVRTPGSANNQSCFITADCFFLEISAEETGSVFLVNVTHEKQTSESVLLRDIINDKRWTELQRHLWGLCSAYIPCKDIDTKNQAFKFMQNLENILHIQSLQRINDNTLPVVEYLRTSDMYFFRRREVGDPPRLYFFCTPLSFWDSETGDFKQLFQNDIDNVMDVSKFKSIIYAELAMENVQGEQFLSISMQSVNALGQFHDIPLSMQIAAVFTLTFPEKLIISMDSVTKIEALTGFKPAFNNQSKILDLILGEILPSGFSVLRSFVLLEDQLHCYTVDLEGCLTEGVVLEKIYWTNLEVLHKILPILRTEALFKHIFTSFIRNITTTQKQFAQKMMFRRDIHVIPSPDLSILECQVKLPREREFFYIVFRLAPINEISVKVGGVVDNADVNLNDVAYEVFSRVWSIPVTIRALVKQLLCLSERNVVVAAAGDGNSGNGDHQNDVVLMQIDCDRSLHLSTDSNCAAHSSVSIPDGNYNMSEYSVCNDDANGVAVADDADDDADAVISVSGIAQSLIIEQQMQKLIVNVDKVLEELLLVCSGRLAGGPNLLDLFKKPKVWRELIPPRRCAGRRGQRSRQQMAPPLAQQCCASAAGQLPAPVAVVAGAAPFGKVGPNLKSRHFSSTSETLTELDELCQLSSSCAEGNGHQSEHVSACGDSAVADGGEQKSSIQDTIDSVLGSVRFPGSMAESLINISSCCINNNNNTNNSNPNSNNSNANTSNNNNTNSNNNNNNSMNALASIRKIELGYGQSSAGVATPMSSSSSPALAAPMSRSSDSTGDVFDYETRSTTTAGMSIDQGGRSLSSSVCSADDLSIAAASASAPTLGVGFWPPAGGVERLDVRGALLNRGMRRRRRCRKAFANTGDRALDMVLKEMRKAERLVRGASSTRRPRRSRLATATASFTADMREVASKVTLKIRSSSAAALPGVQTAQESSSLAVASSSLSSADQGLSSGGKDEQRKSLKLAANANASGGAATLNTWTQPSSSVFRSLSDAAGESCSSRSSSPPPQLVKPASKRKNSLDVVIGKLMDKVGTSPTKLDPSSDVPDSAGDKQRHLYGFCFSPTASQQQKSGTTAASVSASEFTIHKRGECSTTTATATSTGELSDAPEGGIKLVIKKGVIKLKSARHGRGAGAGRFVETGAPSARSRVSSPASAGDRLAASKFELLKQKMQARKIKRQSSTEKSRQRGPRSGALAAVSKTATNRSKLSTVGSSSSGVAELPSVFPGAEGLLFSKSLKGFKIPKIDDNCSKTTTATTAATVTAAPASASDSAITTTTVTFSTTTTATVVPAAASAAATMTTTTTTNIVSATAAAAVVTSASTVATATTTSANATTTASVAVTPLTVVEKRMADGPPMALVVNDGRASPAGVVSGGGGGILRMKPPLLAVQQVPPPCVGSSSKPLIRRSRPVPLPLPPRSLVATGPHFAGPPAVELALPTGPAVPRYVRRTLLPNPPLQTASSPRPPPPQPLLELNKHHQQQMLVHSTTQQRPTKQELLNPMTNQISPKSASPDPTGLVIDDNLNTTAAISSPQKNAEEVDVLSPGLRIAVDEGDETKGPTTHSSSTT
Length1649
PositionMiddle
OrganismTrichinella nelsoni
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella.
Aromaticity0.05
Grand average of hydropathy-0.241
Instability index49.25
Isoelectric point8.80
Molecular weight176338.66
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

>MDP05898
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.79|      16|      17|    1364|    1379|       1
---------------------------------------------------------------------------
 1336- 1354 (20.83/ 7.72)	TATTAATVtaaPASASDSA
 1364- 1379 (25.95/11.37)	TTTTATVV...PAAASAAA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.76|      17|      19|     781|     797|       2
---------------------------------------------------------------------------
  781-  797 (33.82/20.26)	NNNNTNNSNPNSNNSNA
  801-  817 (33.94/20.36)	NNNNTNSNNNNNNSMNA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      70.85|      18|      24|    1493|    1513|       3
---------------------------------------------------------------------------
 1425- 1440 (21.68/ 6.81)	........PLTVVEKRM.ADGPPMA
 1493- 1510 (35.15/13.43)	V.......PLPLPPRSLVATGPHFA
 1539- 1559 (14.02/ 7.71)	LqtassprP.P.PPQPLLELNKH..
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.18|      21|      24|    1380|    1400|       4
---------------------------------------------------------------------------
 1380- 1400 (33.99/16.19)	TMTTTTTTNIVSATAAAAVVT
 1404- 1424 (33.19/15.66)	TVATATTTSANATTTASVAVT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     211.73|      45|      46|    1003|    1047|       5
---------------------------------------------------------------------------
  834-  865 (43.77/16.53)	.....GVAT....PMSSSSSPALAAPM..........SRSSDSTGDVFDYE
  868-  903 (40.17/14.57)	STTTAGMSI....DQGGRS..L.SSSVC.SADDlSIAAASASAP.......
 1003- 1047 (67.51/29.41)	AAALPGVQT....AQESSSLAVASSSLS.SADQ.GLSSGGKDEQRKSLKLA
 1050- 1096 (60.28/25.49)	ANASGGAATlntwTQPSSS..VF.RSLSdAAGE.SCSSRSSSPPPQLVKPA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      97.42|      30|     187|    1109|    1146|       6
---------------------------------------------------------------------------
 1109- 1146 (46.97/44.87)	KLMDKVGTSPTKLdpssdvpdSAGDKQRHLYGFCFSPT
 1148- 1177 (50.45/29.88)	SQQQKSGTTAASV........SASEFTIHKRGECSTTT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.35|      15|      46|    1568|    1582|       8
---------------------------------------------------------------------------
 1568- 1582 (25.11/12.16)	STTQQRPTKQELLNP
 1612- 1626 (23.25/10.73)	SSPQKNAEEVDVLSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      74.40|      24|      46|     238|     261|       9
---------------------------------------------------------------------------
  238-  261 (39.30/26.87)	DIDNVMDVSKFKSIIYAE...LAMENV
  282-  308 (35.10/23.22)	DIPLSMQIAAVFTLTFPEkliISMDSV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      78.15|      17|      17|     722|     738|      11
---------------------------------------------------------------------------
  554-  568 (18.49/ 6.64)	.DGNYNMSEySV..CNDD
  722-  738 (32.79/17.01)	AEGNGHQSE.HVSACGDS
  741-  756 (26.86/12.71)	ADG.GEQKS.SIQDTIDS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      94.39|      29|      41|     917|     953|      12
---------------------------------------------------------------------------
  917-  950 (41.72/48.06)	ERLdVRGAllnRGMRRRRRCRKAFAnTGDRALDM
  959-  987 (52.67/30.27)	ERL.VRGA...SSTRRPRRSRLATA.TASFTADM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.11|      13|      19|     203|     215|      14
---------------------------------------------------------------------------
  203-  215 (25.35/15.10)	FRRREVGDPPRLY
  223-  235 (25.76/15.47)	FWDSETGDFKQLF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      86.96|      20|      20|    1198|    1217|      16
---------------------------------------------------------------------------
 1198- 1217 (32.95/16.89)	IKKGVIKLKSARHGRGAGAG
 1220- 1238 (28.60/13.66)	VETGAPSARS.RVSSPASAG
 1258- 1276 (25.42/11.29)	IKRQSSTEKSRQRGPRSGA.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      35.76|      11|     542|     758|     772|      18
---------------------------------------------------------------------------
  758-  771 (12.81/10.46)	LGSVrFPGsmAESL
 1303- 1313 (22.95/ 6.50)	LPSV.FPG..AEGL
---------------------------------------------------------------------------




































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 MDP05898 with Med1 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) KMQARKIKRQSSTEKSRQRGPRSGALAAVSKT
2) NNNTNNSNPNSNNSNANTSNNNNTNSNNNNNNSMN
3) SAGVATPMSSSSSPALAAPMSRSSDSTGDVFDYETRSTTTAGMSIDQGGR
4) SSLAVASSSLSSADQGLSSGGKDEQRKSLKLAANA
5) VGSSSKPLIRRSRPVPLPLPPRSLVATGPHFAGPPAVELALPTG
6) VPRYVRRTLLPNPPLQTASSPRPPPPQPLLELNKHHQQQMLVHSTTQQRPTKQELLNPMTNQISPKSASPDPTGLVIDDNLNTTAAISSPQKNAEEVDVLSPGLRIAVDEGDETKGPTTHSSSTT
1252
782
832
1016
1479
1525
1283
816
881
1050
1522
1649










Molecular Recognition Features






MoRF SequenceStartStop




1) KSLKLA
2) LAASKFELLKQKMQARKI
3) LVIKKGVIKLKSARH
1042
1241
1196
1047
1258
1210