<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 MDP03340

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMPQFLFVKFDYPLGELQNVSWFQFLPIEPDPSTVSERSSKAEQKDALNNIVLSAHIHLQSEGFLSTWTNSFVGPWDPSQGEHNPVVSNGLWVAPGNSEEVAAALCQALRNSLERRAQPTIEFVFAATEEAVFVHVVISARYMRNLCSDDIEKVLTHSPRSIGEGLPVIVAPSGMLGRLVGCCPSDLVKQVYSSKLSAATLPGFTQPTICQLRGQSYYVEVALGFPAAPTDKVPESENNQIKKELDSVKDPQLSVDEHQKLECADSVPVLERTFIYPPEAVMVPMVHQAFVRFSSKRMSLQGCMGNSLWEGWPFWNFSPSSYFRNSTYLGSSRGLGVNSNFLRLRRQKNSNYSSMASSISSVSSTSNGSEHAVAAEGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEITEVSSRAGKESVDNNQGANGQGRTWGWDEEGVVMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLAIPGSDCGDATFSDSPSTAMDIPEQKLSPVGLSSLEVFNHQTMAPIHDVVSKVQEPQKDIASPTGSQSVVLSSGRSSYLNRAEALLTYAPEYAAVDISFGETPTSLFTNPYQPRSIKPGSSSSNSRVYSYDTAQSFQMESGEDKPEKSVRLASGNLSRDIGSSSLYTVVQVGKKECDKGLSNTDILSGKEESSKPISGEALFDSSLVTQRKSDGMFNAGYFVLSMKTALATEIECIRFQAAMCRIRHTVLSLRSKASAELKSALPSLMHTDVSNKLDLIPKYDIKRKENIPARLSIDVDNEVYDRSQLENVGVWRPVGTPKGTTPLDSFSAKTYTGPSQGLPAKRQPIVDLLNAMALIVQQSTSFVDIALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGTCHSKDCAGVDLVDPLSAEVSDSCVISLLQSDIKAALKTAFVSMDGPLLVTDWCRGRSNAAESASTGDAYSFQHPTGDIRESSIGGDSLSPPQSSHAISNDRGISELEHHRGYHRVRPTIAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIDMLTSAATDFFLQLGTIYEVCKLGTHSAQNCGGQMELSPGKYLSSGLVLIECPVQVKIGNGHSSSTSATYECLQTLSKNWTVKSFIASLTRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFPEPSAVLETLVECSVALGSVMLSPEREKKSFLYSQVAKALNCNASVDESSASNVVMLSGFSVPKLVLQIVTIETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAIGTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMPGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKILDVCVQDDRKYAFEPLFILAEPGSVDYNVGMESSKSGVDASGSGMYSSITGGGSDSGASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDNLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRMGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGISSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGVGQSGNKKQILVEQAGMDSSKGEGNQSSSGPLSYLEGFTPVKSVGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRKDSARLAKEDSPSVLSVSIIDHYGGSIAAVQEKMSRGSGKQTRSFNQEATGRDHEMEMHHVLEAVAAELHSLSWMTVSPVYTERRSALPFHCDMVLRLRRLLHYADGHLSQSTEKDVT
Length1817
PositionKinase
OrganismLeersia perrieri
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Leersia.
Aromaticity0.07
Grand average of hydropathy-0.256
Instability index57.69
Isoelectric point5.46
Molecular weight197462.58
Publications









Function






Annotated function

Component of the Mediator complex, a coactivator involved in
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

>MDP03340
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      74.27|      23|      32|     435|     458|       1
---------------------------------------------------------------------------
  435-  458 (39.24/31.45)	WGwDEEGVVMDINLLI..SEFGD..FSD
  467-  493 (35.03/21.00)	FG.EPPGTAESHSLAIpgSDCGDatFSD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     133.88|      50|      97|     537|     618|       2
---------------------------------------------------------------------------
  495-  556 (59.30/70.70)	PSTAMDIPEQ..KLSPvGLSSlevFNHQTMApiHDVVSKVQ.EpqKDiaSPtgSQSVVLSSGRSS
  582-  636 (74.58/41.47)	PTSLFTNPYQprSIKP.GSSS...SNSRVYS..YDTAQSFQmEsgED..KP..EKSVRLASGNLS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.76|      15|      24|     740|     754|       3
---------------------------------------------------------------------------
  740-  754 (25.66/18.59)	KSALPSLMHTDVSNK
  766-  780 (25.10/17.99)	KENIPARLSIDVDNE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     210.23|      99|     483|     308|     423|       4
---------------------------------------------------------------------------
  308-  377 (77.56/56.30)	...................................................................................................................................................................................................................................................................................................................................................................................................................................WE..GWPfWNFSPSSYFRNSTYLGSSRGLGVnsnflrlRRQKNSN.YSSMASSISSVSSTSNGSEHAVAAEGD
  378-  423 (20.85/23.29)	LSADAD...SMAChqsDlPSNI.AGSKMVSKRPRSEitevsSRAGKESVD..........................................................................................................................................................................................................................................................................................................................................................................................................................................................
  793-  857 (79.81/41.02)	..................................................nnqgangqgrtwgwdeegvvmdinllisefgdfsdffqeeeldfgeppgtaeshslaipgsdcgdatfsdspstamdipeqklspvglsslevfnhqtmapihdvvskvqepqkdiasptgsqsvvlssgrssylnraealltyapeyaavdisfgetptslftnpyqprsikpgssssnsrvysydtaqsfqmesgedkpeksvrlasgnlsrdigssslytvvqvgkkecdkglsntdilsgkeesskpisgealfdsslvtqrksdgmfnagyfvlsmktalateiecirfqaamcrirhtvlslrskasaelksalpslmhtdvsnkldlipkydikrkeniparlsidvdnevydrsqlenvgvWRpvGTP.KGTTPLDSFSAKTYTGPSQGLPA.......KRQPIVDlLNAMALIVQQSTSFVDIALDMDDGDGS
  861-  901 (32.01/10.36)	LSLDEQkrrGFSC...D.PSMVhAGCGGILGTCHSK.....DCAGVDLVD..........................................................................................................................................................................................................................................................................................................................................................................................................................................................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      80.84|      22|      97|    1324|    1349|       5
---------------------------------------------------------------------------
 1324- 1349 (36.57/29.43)	MPGStlsrETEFDASMRSSVTWDNSW
 1424- 1445 (44.27/25.93)	LEGS....DNDNAASLHCCYGWTEDW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.09|      12|      97|    1074|    1085|       6
---------------------------------------------------------------------------
 1074- 1085 (23.12/12.56)	IYEVCKLGTHSA
 1174- 1185 (24.97/14.17)	IYVVCPFPEPSA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      95.68|      30|     482|     180|     217|      10
---------------------------------------------------------------------------
  146-  178 (42.39/22.66)	CSDDIEKVLTHSPRSIGEgLPVIVAPSgmLGRL
  182-  211 (53.30/35.11)	CPSDLVKQVYSSKLSAAT.LPGFTQPT..ICQL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.52|      22|     200|    1384|    1423|      11
---------------------------------------------------------------------------
 1392- 1413 (40.33/36.33)	GMESSKSGVDASGSGMYSSITG
 1608- 1629 (41.19/ 7.84)	GMDSSKGEGNQSSSGPLSYLEG
---------------------------------------------------------------------------




































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 MDP03340 with Med13 domain of Kingdom Viridiplantae
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