<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 MDP06394

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMKFKANEMSSGMPLKSKPGVDHSRNNTMYTCSTQRTTVILRSSSVYSLTVALPSSTSSSGQIHLLDQSASATTIHQPLLIKTCESLILSLGRSVILNVKCIYNKENISCTGYYVERPTVADGTPAPEKPTLYVMERYIEKCKNEFNVKFLGTEKRSPLDAEDRVEVAKSYERLLQGLRVASAYELFGRLEDIATKMNLTFVRTPGTANNQSCFITADCFFLEISAEETGSVFLVNVTHEKQTSESVLLRDIINDKRWTELQRHLWGLCSAYIPCKDIDTKNQAFKFMQNLENILHIQSLQRINENTLPVVEYLRTSDMYFFRRREVGDPPRLYFFCTPLSFWDSETGDFKQLFQNDIDNVMDVSKFKSIIYAELAMENVQGEQFLSISMQSVSALGQFHDIPLSMQIAAVFTLTFPEKLIISMDSVTKIEALTGFKPAFSNQSKILDLILGEILSSGFSVLRSFVLLEDQLHCYTVDLEGCLTEGVVLEKIYWTNLEVLHKILPILRTEALFKHIFTSFIRNITTTQKQFAQKIFRRDIHVIPSPDLSILECQVKLPREREFFYIVFRLAPINEISVKVGGVVDNADVNLNDVAYEVFSRVWSIPVTIRALVKQLLCLSERNVVVAAAGDGNSGNGDHQNDVVLMQIDCDRSLHLSTDSNCAAHSSVSIPDGNYNMSEYSVCNDDANGVAVADDADDDADAVISVSGIAQSLIIEQQMQKLIVNVDKVLEELLLVCSGRLAGGPNLLDLFKKPKVWRELIPPRRCAGRRGQRSRQQMAPPLAQQCCASAAGQLPAPVAAVAAAAPFGKVGPNLKSRHFSSTSETLTELDELCQLSSSCAEGNGHQSEHASACGDSAVADGGEQKSSIQDTIDSVLGSVRFPGSMAESLINISSCCINNNNNTNNSNPNSNNSNANTSNNNNTNSNNNNNNNNSMNALASIRKIELGYGQSSAGVAAPMSSSSSPALAAPMSRSSDSTGDVFDYETRSTTTAGMSIDQGGRSLSSSVCCADDLSIAAASASTPTLDVGFWPPAGGVERLDVRGALLNRGMRRRRRCRKAFANTGDRALDMVLKEMRKAERLVRGASSTRRPRRSRLATATASFTADMREVASKVTLKIRSSSAAALPGVQTAQESSSLAVASSSLSSADQGSSSGGKDEQKKSLKLAANANASGGAGAATLNTWTQPSSSVFRSLSDATGESCSSRSSSPPPQLVKPASKRKNSLDVVIGKLMDKVGTSPTKLDPSSDVPDSAGDKQRHLYGFCFSPTASQQQKSGTTAASVSASEFTIHKRGECSTTTAMATSTGELSDAPEGGIKLVIKKGVIKLKSARHGRGAGAGRFVETGAPSARPRVSSPASAGDRLAASKFELLKQKMQARKIKRQSSTEKSRQRGPRSGALAAASKTAANRSKLSTVGSSSSGVAELPSVFPGAEGLLFSKSLKGFKIPKIDDNSSKTTTTTTAATVTAAPASTSDSANTTTTVTVSTTTTATVVPAAASAAATMTTTTTTTNIVSASAAAAVVTSASTVATGTTTSANATTTASVAVTPLTVVEKRMADGPPMALVVNDGRASPAGVVSGGGGGILRMKPPLLAVQQVPPPCVGSSSKPLIRRSRPVPLPLPPRSLVATGPHFAGPPAVELALPTGPAVPRYVRRTLLPNPPLQTASSPRPPPPQPLLELNKHHQQQMLVHSTTQQRPTKQELLNPMTNQMSPKSASPDPTGLVIDDNLNTTAAISSPQKNAEEVDVLSPGLRIAVDEGDETKGPTTHSSSTT
Length1771
PositionMiddle
OrganismTrichinella sp. T8
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella> unclassified Trichinella.
Aromaticity0.05
Grand average of hydropathy-0.244
Instability index48.91
Isoelectric point8.79
Molecular weight189258.96
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

>MDP06394
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     133.14|      26|      26|    1455|    1480|       1
---------------------------------------------------------------------------
 1274- 1297 (30.94/11.81)	..SGTTAASVSASEFTIHKRGECSTT
 1455- 1480 (44.66/20.07)	TTTTTTAATVTAAPASTSDSANTTTT
 1482- 1501 (33.06/13.09)	TVSTTTTATVV..PAAASAAA....T
 1522- 1540 (24.48/ 7.92)	....TSASTV.ATGTTTS..ANATTT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.59|      11|      17|     898|     911|       2
---------------------------------------------------------------------------
  898-  908 (23.89/ 7.76)	NNNNTNNSNPN
  918-  928 (22.71/10.16)	NNNNTNSNNNN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      80.26|      24|      35|    1045|    1076|       3
---------------------------------------------------------------------------
 1045- 1069 (41.93/44.17)	LNRG...MRRRRRCRKAFAnTGDRALDM
 1080- 1106 (38.33/18.96)	LVRGassTRRPRRSRLATA.TASFTADM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.95|      13|      17|     776|     792|       4
---------------------------------------------------------------------------
  758-  770 (23.38/ 6.54)	ELIPP...RRCAGRRG
  776-  791 (20.57/15.95)	QMAPPlaqQCCASAAG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     100.81|      30|      64|     273|     302|       5
---------------------------------------------------------------------------
  273-  302 (52.40/37.37)	PCKDIDTKNQAFK..FMQNLENILHIQSLQRI
  338-  369 (48.41/33.92)	PLSFWDSETGDFKqlFQNDIDNVMDVSKFKSI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      63.92|      13|      17|    1143|    1155|       6
---------------------------------------------------------------------------
 1143- 1155 (23.35/12.80)	SLSSADQGSSSGG
 1162- 1174 (18.62/ 8.35)	SLKLAANANASGG
 1179- 1191 (21.95/11.47)	TLNTWTQPSSSVF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.40|      11|      20|    1589|    1599|       7
---------------------------------------------------------------------------
 1589- 1599 (22.24/10.98)	PL.LAVQQVPPP
 1660- 1671 (18.16/ 7.34)	PLqTASSPRPPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.03|      17|      64|    1559|    1575|       8
---------------------------------------------------------------------------
 1559- 1575 (29.96/19.64)	PPMALVVNDGR.ASPAGV
 1620- 1637 (26.07/15.75)	PPRSLVATGPHfAGPPAV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     142.82|      50|      64|    1327|    1381|       9
---------------------------------------------------------------------------
 1327- 1381 (75.92/60.68)	KS....ARHGRGAGAGRfveTGAPsaRPRVSSPASAGDRLA..ASKFE.....LLKQKMQARKIKR
 1387- 1447 (66.90/40.28)	KSrqrgPRSGALAAASK...TAAN..RSKLSTVGSSSSGVAelPSVFPgaeglLFSKSLKGFKIPK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      61.71|      17|     279|     963|     979|      10
---------------------------------------------------------------------------
  972-  994 (21.02/ 6.96)	RS.SDSTGDvfdyetRSTTTAGMS
 1000- 1017 (19.64/ 6.03)	RSlSSSVCC......ADDLSIAAA
 1018- 1036 (21.05/ 6.97)	SA.STPTLD...vgfWPP.AGGVE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.59|      20|     279|     232|     251|      11
---------------------------------------------------------------------------
  232-  251 (33.57/25.35)	FLVNV.THEKQTSESVLLRDI
  519-  539 (31.02/22.80)	FIRNItTTQKQFAQKIFRRDI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.11|      21|      43|     452|     475|      14
---------------------------------------------------------------------------
  452-  475 (31.25/29.16)	EILSSGFSVLRSFVLLEdqlHCYT
  497-  517 (35.87/23.93)	EVLHKILPILRTEALFK...HIFT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.92|      15|      43|    1690|    1704|      15
---------------------------------------------------------------------------
 1690- 1704 (25.72/11.44)	STTQQRPTKQELLNP
 1734- 1748 (23.21/ 9.69)	SSPQKNAEEVDVLSP
---------------------------------------------------------------------------




































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 MDP06394 with Med1 domain of Kingdom Metazoa
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