<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. 


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
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