<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. 


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
Unable to open file!