<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 MDP29506

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMPEFPSPSSPAGGGRRRTLNNADNKPDLHGTMNDPYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVDPRAVVLHGREPHGEQGGGGATGERGHSRSRAERTDPTTTAPFFSGSNRRQVADLFRRPPSSFSDVFGMLIRDPRCYVYSCIGYLKVDIFDRSHFCLFLIEKANNVTAKCNNSLKKSLIVHAIGLACVKKGELQNVSWFQFLPVEPDPSTASERSSKAEQKDALNNIVLSAHLHLQSEGFLSTWTNSFVGPWDPSQGEHNPVVSNGLWVAPGNLEEVAAALCQALRNSLERRAQPTIEFVFAATEEAIFVHVIISARYMRNLCSDDIEKVLTHSPRSVGEGLPVIVAPSGMLGRLVGCCPSDLVRQVYSSKLSAATLPGFTQPTMCQLRGQSYYVEVALGFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLESADSVPVLERTFIYPPEAVMVPMVHQAFVRFSSKRMCSQACVGNSSWEGWPFWNFSPSSYFRNSSCLGSSRGLGVNSNFLRLRRQKNSNYSSMASSISSVSSTSNGSEHAVAAEGGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCSWGWDEEGVAMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLVIPGPDCGDATFTDSPSTAMDIPEQRFSPVGLSSLEVFNHQTVAPIHDVVSKVQEPQKDIASPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGETPTSLFTNPYQPRSIKPGSSSFNSRVYSYDAAQSSQMESGEDKPEKSVRLASGNLSRDIGSSNLYTVVQVGKKESDKGLKNTDIQSGKEEASRPISGETSLDSSVVSQRKSDSMFNAGYFLLSMKTALATEMECIKFQAAMCRIRHTLLSLSSKASAELKSALSSLVHTDVSNKLDLVPKYDIKRKENIPARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGMCHSKDCAGVDLVDPLSAEVSDSSVISLLQSDIKAALKTAFANMDGPLLVTDWCRGRSNAAEYASMGDAYSFQHPTGDIRESSSSISIGGDSMSPPQSSHVISNDRGTSELEHHRGYHRVRPTVAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTSAATDFFLQLGTIYEVCKLGTHSPQNSGGQMELSPGKYLSSGLVLTECPDQVKIGNGHSSSISSTSEYLQALSRNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFPEPSAVLETLVECSVALGSVMLSPERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTVETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSSGMESSKSGVDASGSGIYSSISGGGSDSGASASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGEGNQTSSGPSSYLEGFTPVKSIGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRKDSARLANEDRPSVLSVSIIDHYGGSIAAVQEKMSRGSGKQTRNFTQEAAGRDHETEMHNVLEAVAAELHSLSWMTVSPVYMERRSALPSHCDMVLRLRRLLHYADRHLSQSTEKGDVA
Length2055
PositionKinase
OrganismOryza glaberrima (African rice)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza.
Aromaticity0.07
Grand average of hydropathy-0.296
Instability index56.10
Isoelectric point5.98
Molecular weight223124.85
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

>MDP29506
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|    1238.76|     404|     485|     641|    1088|       1
---------------------------------------------------------------------------
  641- 1088 (620.64/411.40)	MDINLLISEF....GDFSDFFQE.EELDFGEPPGTA.ESHSLVIPGpdcGDAtfTDSPSTAMDIPEQRfspvGLSSLEvfNHQTVAPIHDVVSKVQEPQ.....KDIASPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGeTPTSLFTNPYQPRSI.KPGSSSFNSRVYSYDAAQSSQMESG...EDKPEKsVRLASGNlSRDIGSSNLY..................TVVQVGKKESDKGLKNTDIQSGKEEASRPISGETslDSSVVsqrksdsmfnagyfllsmktaLATEMEC.IKFQAAMC...RIRHTLL......SLSSKASAELKSALSSLVHTDVSnkldlVPK..YDIKRKENIpARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDG.DGSFFWLSLDEQKRRGFsCDPSMVHAGC..................GGI...LGMCHSK
 1127- 1597 (618.12/328.45)	MDGPLLVTDWcrgrSNAAEYASMgDAYSFQHPTGDIrESSSSISIG...GDS..MSPPQSSHVISNDR....GTSELE..HHRGYHRVRPTVAVLPLPSllvgyQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTS.AATDFFLQLGTIYEVcKLGTHSPQNSGGQMELSPGKYLSSGlvlTECPDQ.VKIGNGH.SSSISSTSEYlqalsrnwtvksfvtsltRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFP..EPSAV.....................LETLVECsVALGSVMLspeRERKSFLysqvakALNCNASVDESSASNVVMLSGFS.....IPKlvLQIVTVETL.LRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASmRSSVTWDNSWPGRAGGF.MDPNKIPDVCvqddrkyafeplfilaepGSVdysSGMESSK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.98|      27|     509|    1089|    1115|       2
---------------------------------------------------------------------------
 1089- 1115 (46.21/24.20)	DCAGVDLVDPLSAEVSDS..SVISLLQ.SD
 1601- 1630 (36.77/17.66)	DASGSGIYSSISGGGSDSgaSASALLEgSD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     205.85|      66|    1493|     330|     406|       3
---------------------------------------------------------------------------
  330-  406 (97.68/87.38)	VIISARYMRNL.CSDDIekvLTHsPrSVGEGLPVIVAPSGMlgrLVGCCPsdlVRQVYSSKLSAATLPG....FTQPTMCQL
 1828- 1898 (108.17/64.95)	VAISQDHSLHLtCQADL...LTR.P.TPGEGNQTSSGPSSY...LEGFTP...VKSIGSMSASYLLVPSpsmrYLSPATLQL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     101.10|      26|      29|     573|     599|       4
---------------------------------------------------------------------------
  548-  567 (24.05/ 8.19)	.......SMASSIS.SVSSTSNGSEHAV
  573-  599 (38.89/22.40)	DLsADADSMACHQS.DLPSNIAGSKMVS
  605-  631 (38.16/17.88)	EI.PEVSSRAGKESvDNNQGVNGQGRCS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     256.43|      77|    1606|      23|     109|       5
---------------------------------------------------------------------------
   23-  109 (114.47/93.96)	DNKPDLHGTMNdpYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVdprAVVLHgrepHGEQGGGGATgERGHSRSR
 1632- 1708 (141.96/84.66)	DNAASLHCCYG..WTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLF...IQILQ....HGCQIMSSAP.ESSNTRPR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.86|      22|      22|     484|     505|       7
---------------------------------------------------------------------------
  484-  505 (43.32/23.65)	FVRFS.SKRMCSQACVGNSSWEG
  508-  530 (38.54/20.22)	FWNFSpSSYFRNSSCLGSSRGLG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      71.93|      22|    1793|     199|     222|       8
---------------------------------------------------------------------------
  199-  222 (32.66/29.93)	HAIgLACVkKGELQNVSWFQFLPV
 1995- 2016 (39.26/24.91)	HNV.LEAV.AAELHSLSWMTVSPV
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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 MDP29506 with Med13 domain of Kingdom Viridiplantae
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