<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 MDP05986

Description Mediator of RNA polymerase II transcription subunit 1 (Fragment)
SequenceLRVVSNRCSGLSLVFEERAYKLKHTRKQKNIVWLFQTIHQPLLIKTCKSLILSLGRSVILNVKCIYNKENISCTGYYVERPTVADGTPAPEKPTLYVMERYIEKCKNEFNVKFLGTEKRSPLDAEDRVEVAKSYERLLQGLRVASAYELFGRLEDIATKMNLTFVRTPGTANNQSCFITADCFFLEISAEETGSVFLVNVTHEKQTSESVLLRDIINDKRWTELQRHLWGLCSAYIPCKDIDTKNQAFKFMQNLENILHIQSLQRINDNTLPVVEYLRTSDMYFFRRREVGDPPRLYFFCTPLSFWDSETGDFKQLFQNDIDNVMDVSKFKSTIYAELAMENVQGEQFLSISMQSVNALGQFHDIPMSMQIAAVFTLTFPEKLIISMDSVTKIEALTGFKPAFSNQSKILDLILGEILSSGFSVLRSFVLLEDQLHCYTVDLEGCLTEGVVLEKIYWTNLDVLHKILPILRTEALFKHIFTSFIRNITTTQKQFAQKIFRRDIHVIPSPDLSILECQVKLPREREFFYIVFRLAPINEISVKVGGVVDNADVNLNDVAYEVFSRVWSIPVTIRALVKQLLCLSERNVVVAAAGDGNSGNGDHQNDVVLMQIDCDRSLHLSTDSNCAAHSSVSIPDGNYNMSEYSVCNDDANGVAVADDADDDADAVISVSGIAQSLIIEQQMQKLIVNVDKVLEELLLVCSGRLAGGPNLLDLFKKPKVWRELIPPRRCAGRRGQRSRQQMAPPLAQQCCASAAGQLPAPVAAVAAAAPFGKVGPNLKSRHFSSTSETLTELDELCQLSSSCAEGNGHQSEHASACGDSAVADGGEQKSSIQDTIDSVLGSVRFPGSMAESLINISSCCINNNNNTNNSNPNSNNSNANTSNNNNTNSNNNNNNSNNSMNALASIRKIELGYGQSSAGVAAPMSSSSSPALAAPMSRSSDSTGDVFDYETRSTTTAGMSIDQGGRSLSSSVCCADDLSIAAASASAPTLDVGFWPPAGGVERLDVRGALLNRGMRRRRRCRKAFANTGDRALDMVLKEMRKAERLVRGASSTRRPRRSRLATATASFTADMREVASKVTLKIRSSSAAALPGVQTAQESSSLAVASSSLSSADQGSSSGGKDEQKKSLKLAANANASGGAGAATLNTWTQPSSSVFRSLSDATGESCSSRSSSPPPQLVKPASKRKNSLDVVIGKLMDKVGTSPTKLDPSSDVPDSAGDKQRHLYGFCFSPTASQQQKSGTTAASVSASEFTIHKRGECSTTTTAMATSTGELSDAPEGGIKLVIKKGVIKLKSARHGRGAGAGRFVETGAPSARPRVSSPASAGDRLAASKFELLKQKMQARKIKRQSSTEKSRQRGPRSGALAAASKTAANRSKLSTVGSSSSGVAELPSVFPGAEGLLFSKSLKGFKIPKIDDNSSKTTTATTAATVTAAPASTSDSANTTTTVTVSTTTTATVVPAAASAAATMTTTTTTTNIVSATAAAAVVTSASTVATGTTTSANATTTASVAVTPLTVVEKRMADGPPMALVVNDGRASPAGVVSGGGGGILRMKPPLLAVQQVPPPCVGGSSKPLIRRSRPVPLPLPPRSLVATGPHFAGPPAVELALPTGPAVPRYVRRTLLPNPPLQTASSPRPPPPQPLLELNKHHQQQMLVHSTTQQRPTKQELLNPMTNQMSPKSASPDPTGLVIDDNLNTTAAISSPQKNAEEVDVLSPGLRIAVDEGDETKGPTTHSSSTT
Length1737
PositionMiddle
OrganismTrichinella sp. T9
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella> unclassified Trichinella.
Aromaticity0.05
Grand average of hydropathy-0.246
Instability index48.35
Isoelectric point8.91
Molecular weight186011.56
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

>MDP05986
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     103.10|      24|      24|    1451|    1474|       1
---------------------------------------------------------------------------
 1425- 1449 (29.43/14.81)	.TTAATVTaaPASTSDSANTTTTVTV
 1451- 1474 (42.81/25.38)	TTTTATVV..PAAASAAATMTTTTTT
 1480- 1499 (30.86/15.94)	ATAAAAVV......TSASTVATGTTT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      88.96|      25|      26|    1538|    1563|       2
---------------------------------------------------------------------------
 1538- 1556 (27.68/11.73)	......PA.G.VVSGGGGGILR.MKP.PL
 1558- 1583 (25.89/11.83)	AVQQVP..pP.CVGGSSKPLIRrSRPvPL
 1602- 1627 (35.39/14.44)	AVELALPT.GpAVPRYVRRTLL.PNP.PL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.92|      15|      26|     861|     885|       3
---------------------------------------------------------------------------
  861-  878 (21.51/28.80)	NNNNntNNSNpNSNNSNA
  889-  903 (30.40/ 9.82)	NNNN..NNSN.NSMNALA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      63.92|      13|      20|    1108|    1120|       4
---------------------------------------------------------------------------
 1108- 1120 (23.35/12.47)	SLSSADQGSSSGG
 1127- 1139 (18.62/ 8.15)	SLKLAANANASGG
 1144- 1156 (21.95/11.19)	TLNTWTQPSSSVF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      93.36|      24|      24|    1050|    1073|       6
---------------------------------------------------------------------------
 1015- 1038 (22.64/ 8.70)	....RRRRRCRKAFAnTGDRALDMvlKE
 1050- 1073 (42.97/22.94)	SS.TRRPRRSRLATA.TASFTADM..RE
 1076- 1098 (27.75/12.29)	SKvTLKIRSSSAAAL.PGVQTA....QE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     291.49|      72|     280|     928|    1001|       7
---------------------------------------------------------------------------
  928- 1001 (115.09/68.36)	SPALAAPMSRSSDSTGD....VF...DY........ETRSTTTAG......MSIDQGGRSLSSSVCCADDLSIAAASASAPTLD....VGfwPPAGGVE
 1203- 1282 (84.15/43.11)	SPTKLDPSSDVPDSAGDkqrhLY...GFcfsptasqQQKSGTTAAsvsaseFTIHKRGE.......CS.TTTTAMATSTGELSD........APEGGIK
 1311- 1387 (92.24/47.99)	APS.ARPRVSSPASAGD....RLaasKF........ELLKQKMQA......RKIKRQSSTEKSRQRGPRSGALAAASKTAANRSklstVG..SSSSGV.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.67|      15|      15|     741|     755|       8
---------------------------------------------------------------------------
  741-  755 (28.68/14.63)	MAPPLAQQCCASAAG
  757-  771 (23.99/11.02)	LPAPVAAVAAAAPFG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.59|      20|     278|     196|     215|       9
---------------------------------------------------------------------------
  196-  215 (33.57/25.82)	FLVNVTH.EKQTSESVLLRDI
  483-  503 (31.02/23.24)	FIRNITTtQKQFAQKIFRRDI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.81|      12|      17|     796|     809|      11
---------------------------------------------------------------------------
  796-  809 (16.42/15.80)	CQlSSSCAEGnGHQ
  816-  827 (23.39/11.57)	CG.DSAVADG.GEQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.11|      13|      19|     285|     297|      12
---------------------------------------------------------------------------
  285-  297 (25.35/15.81)	FRRREVGDPPRLY
  305-  317 (25.76/16.19)	FWDSETGDFKQLF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.29|      14|     837|     697|     710|      15
---------------------------------------------------------------------------
  697-  710 (25.87/14.18)	LLVCSGRLAGGPNL
 1514- 1527 (26.42/14.64)	LTVVEKRMADGPPM
---------------------------------------------------------------------------




































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 MDP05986 with Med1 domain of Kingdom Metazoa
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