<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 MDP06052

Description Mediator of RNA polymerase II transcription subunit 1 (Fragment)
SequenceLDIMSKDQQLLMEHLRQKSQHCMSWKDILKSAKMNLMEKRSPLDAEDRVEVAKSYERLLQGLRVASAYELFGRLEDIATKMNLTFVRTPGTANNQSCFITADCFFLEISAEETGSVFLVNVTHEKQTSESVLLRDIINDKRWTELQRHLWGLCSAYIPCKDIDTKNQAFKFMQNLENILHIQSLQRINDNTLPVVEYLRTSDMYFFRRREVGDPPRLYFFCTPLSFWDSETGDFKQLFQNDIDNVMDVSKFKSIIYAELAMENVQGEQFLSISMQSVNALGQFHDIPLSMQIAAVFTLTFPEKLIISMDSVTKIEALTGFKPAFSNQSKILDLILGEILSSGFSVLRSFVLLEDQLHCYTVDLEGCLTEGVVLEKIYWTNLEVLHKILPILRTEALFKHIFTSFIRNITTTQKQFAQKIFRRDIHVIPSPDLSILECQVKLPREREFFYIVFRLAPINEISVKVGGVVDNADVNLNDVAYEVFSRVWSIPVTIRALVKQLLCLSERNVVVAAAGDGSGGNGDHQNDVVLMQIDCDRSLHLSTDSNCAAHSSVSIPDGNYNMSEYSVCNDDANGVAVADDDDADAVISVSGIAQSLIIEQQMQKLIVNVDKVLEELLLVCSGRLAGGPNLLDLFKKPKVWRELIPPRRCVSRRGQRSRQQMAPPLAQQCCASAVGQLPAPVAAVAAAAPFGKVGPNLKSRHFSSTSETLTELDELCQLSSSCAEGNGHQSEHASACGDSAVADGGEQKSSIQDTIDSVLGSVRFPGSMAESLINISSCCINNNNNTNNSNPNSNNSNANTSNNNNTNSNNNNNNNSMNALASIRKIELGYGQSSAGVAAPMSSSSSPALAAPMSRSSDSTGDVFDYETRSTTTAGMSIDQGGRSLSSSVCCADDLSIAAASASAPTLDVGFWPPEGGVERLDVRGALLNRGMRRRRRCRKAFANTGDRALDMVLKEMRKAERLVRGASSTRRPRRSRLATATASFTADMREVASKVTLKIRSSSAAALPGVQTAQESSSLAVASSSLSSADQGSSSGGKDEQKKSLKLAANASASGGAATLNTWTQPSSSVFRSLSDAIGESCSSRSSSPPPQLVKPASKRKNSLDVVIGKLMDKVGTSPTKLDPSSDVPDSAGDKQRHLYGFCFSPTASQQQKSGTTAASVSASEFTIHKRGECSTTTTTAMATSTGELSDAPEGGIKLVIKKGVIKLKSTRHGRGAGAGRFVETGAPSARPRVSSPASAGDRLAASKFELLKQKMQARKIKRQSSTEKSRQRGPRSGALAAVSKTATNRSKLSTVGSSSSGVAELPSVFPGAEGLLFSKSLKGFKIPKIDDNSSKTTTATTAATVTAAPASASDSANTTTTVTVSTTTTATVVPAAASAAATMTTTTTTTNIVSATAAAAVVTSASTVAAGTTTSANATTTASVAVTPLTVVEKRMADGPPMALVVNDGRASPAGVVSGGGGGILRMKPPLLAVQQVPPPCVGGSSKPLIRRSRPVPLPLPPRSLVASGPHFAGPPAVELALPTGPAVPRYVRRTLLPNPPLQTASSPRPPPPQPLLELNKHHQQQMLVHSTTQQRPTKQELLNPMTNQMSPKSASPDPTGLVIDDNLNTTAAISSPQKNAEEVDVLSPGLRIAVDEGDETKGPTTHSSSTT
Length1653
PositionMiddle
OrganismTrichinella sp. T6
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Enoplea> Dorylaimia> Trichinellida> Trichinellidae> Trichinella> unclassified Trichinella.
Aromaticity0.05
Grand average of hydropathy-0.243
Instability index49.22
Isoelectric point8.73
Molecular weight176726.04
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

>MDP06052
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      75.58|      19|      20|    1367|    1385|       1
---------------------------------------------------------------------------
 1358- 1382 (27.46/13.80)	NTT..ttvtvsTTTTATVVPAAASAAA
 1383- 1401 (26.54/13.07)	TMT.......tTTTTTNIVSATA.AAA
 1402- 1427 (21.58/ 9.11)	VVTsastvaagTTTSANAT.TTASVAV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      77.80|      20|      20|     781|     800|       2
---------------------------------------------------------------------------
  773-  792 (38.86/23.46)	NISSCCINNNNNTNNSNPNS
  793-  812 (38.94/23.52)	NNSNANTSNNNNTNSNNNNN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     115.57|      19|      20|    1463|    1481|       3
---------------------------------------------------------------------------
 1463- 1481 (37.62/22.14)	GG........ILRMKPPL.LAVQQVP...PP
 1484- 1503 (25.64/12.30)	GG..........SSKPLI.RRSRPVPlplPP
 1509- 1525 (28.02/14.26)	SG........PHFAGPP...AVELAL...PT
 1526- 1553 (24.29/11.19)	GPavpryvrrTLLPNPPLqTASSPRP...PP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|      82.26|      13|      17|    1025|    1037|       4
---------------------------------------------------------------------------
 1025- 1037 (22.62/10.18)	SLSSADQGSSSGG
 1044- 1056 (18.71/ 7.01)	SLKLAANASASGG
 1059- 1071 (20.77/ 8.68)	TLNTWTQPSSSVF
 1073- 1085 (20.16/ 8.18)	SLSDAIGESCSSR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      45.74|      13|      20|     644|     662|       5
---------------------------------------------------------------------------
  646-  662 (19.58/26.79)	RRCVSRRGQRSrqqmAP
  667-  679 (26.16/11.04)	QCCASAVGQLP....AP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      45.72|      15|      20|    1152|    1166|       8
---------------------------------------------------------------------------
 1152- 1166 (25.20/13.94)	QKSG......TTAASVSASEF
 1169- 1189 (20.52/ 9.95)	HKRGecstttTTAMATSTGEL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.96|      19|      20|     540|     558|       9
---------------------------------------------------------------------------
  540-  558 (33.22/19.72)	LSTDSNCAAHSS.VSIPDGN
  561-  580 (28.74/16.04)	MSEYSVCNDDANgVAVADDD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      94.39|      29|      44|     918|     954|      10
---------------------------------------------------------------------------
  918-  951 (41.72/47.43)	ERLdVRGAllnRGMRRRRRCRKAFAnTGDRALDM
  960-  988 (52.67/29.89)	ERL.VRGA...SSTRRPRRSRLATA.TASFTADM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.06|      19|      20|    1560|    1579|      11
---------------------------------------------------------------------------
 1560- 1579 (30.37/24.95)	LNKHHQQQMLVHSTTQQrPT
 1583- 1601 (34.69/23.16)	LLNPMTNQMSPKSASPD.PT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.87|      16|      20|     277|     294|      12
---------------------------------------------------------------------------
  270-  285 (27.87/17.88)	LSISMQ..SVNALGQFHD
  286-  303 (23.00/20.61)	IPLSMQiaAVFTLTFPEK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.13|      16|      44|      33|      48|      13
---------------------------------------------------------------------------
   33-   48 (28.77/19.54)	KMNLMEKRSPLDAEDR
   80-   95 (29.36/20.11)	KMNLTFVRTPGTANNQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.62|      16|      20|     197|     213|      14
---------------------------------------------------------------------------
  197-  213 (25.66/20.35)	YLRTSDMYFFrRREVGD
  218-  233 (32.95/21.24)	YFFCTPLSFW.DSETGD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.52|      18|      20|    1264|    1281|      15
---------------------------------------------------------------------------
 1264- 1281 (30.05/15.66)	QSSTEKSRQR..GPRSGALA
 1285- 1304 (23.48/10.56)	KTATNRSKLStvGSSSSGVA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     112.18|      37|      49|     825|     862|      19
---------------------------------------------------------------------------
  825-  862 (58.91/33.85)	IELgYGQSSAGVAAPM...SSSSSPALAAPMS....RSSDSTGDV
  865-  908 (53.27/26.08)	YET.RSTTTAGMSIDQggrSLSSSVCCADDLSiaaaSASAPTLDV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.11|      21|      44|     337|     380|      20
---------------------------------------------------------------------------
  337-  360 (31.25/61.45)	EILSSGFSVLRSFVLLEdqlHCYT
  382-  402 (35.87/12.77)	EVLHKILPILRTEALFK...HIFT
---------------------------------------------------------------------------




































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 MDP06052 with Med1 domain of Kingdom Metazoa
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