<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 MDP00509

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMWTNVFRIGGLSQISWFQFLPVESDLNSLPDKSIKAEQKDAATLLVLSSHLQLQKEGFLSTWTNSFVGPWDPSQGLHNPDEKIKLWLFIPGRHVSVQESAQSAVSRLRVVASGLWLAPGDSEEVAAALSQALRNHIERALHGFSYMRFGDVFSKYHPPQIEECFRRAQPTVEFIFAATQESIFVHTIISSKHIRALSTSDIEKVLEHSSKNSSYLLPVIISPHGMRGRLSGCSPNDLVKQVYFSGSGKIRTFNGFIGLPYHPSQGSGCQLWGQNCYVKVTLGCSKSGSDKALNSNANIRNLPKHHPTEASAAGRDDQKGSLDLLSVLEKTFIYPSEAVLVPVLQTSFARSSLRRFWLQNWIGPSLAASSLLRHCDGNIDSMERSWVEFSGIHTQHCYNSSSNSNNSSISSISSSSSDSVTTGARDLEADADSSCRQSGLSSNDQMEIDCLKMGSKRPRIGITESYGQAITVTNASSQDAYKSNIGSMEVNHSAITAVGNDQIGSNWDWDDDDRGIVMDIQSLLSEFGDFGDFFENDVLPFGEPPGTAESSAIMFAAPDCGDAGSSPAGVMDVSDQMLLPVCLPSFDSFTPHPPVAIEECLSKSQEVTSSAVTSGPLNHTLASSTGEFDHLMKAEALMTFATEYGAVETPASDSSSIFKKPYLPKSHKAESSNSSPNNYIYGATPPSSPCFDGLDEKTGMPMNLKAYPGGHDLSATYQLKKYYTPVETRKERYDGKLLTHNDSSVTNEVSGTSQFANFNSMNAVKSADRKMTQGICGKEHILLSMKTVLATDVECAMFQASMLRMRHILLSPMSLATISLSRPAGRSVLNHLPGDPSSMTDNVSSRYEVKKKESIPVRIAGDIDGGMLDGHLNAPVGVWRTVGVPKVSKPAASPSIEASPSLTHNSFNEDSILSYGQRQPLQELLDGIVLLVQQATSFVDLVLDADCGDGPYSWLALQEHWRRGFCCGPSMVHAGCGGTLASCHSLDIAGVELVDPLSANIHASSVISLLHSDIKSALKSAFGNLDGPLSVTDWCKGRGQSGDVGASADGSSAESNTNECRDSSTTVTHSVGEAMSPSQTSVGGSSVLKVTGALDGGKVEETSQRRLNQEISGSESEQQQCTRLRPTLFVLPSPAILVGYQDDWLKTSANSLQLWEKAPLEPYALPKPIIYSVICPDIDPLTSAAADFFQQLGTVYETCKLGTHSPQSLGNQMEMDSGKWSSSGFVLLDCPQSMKIESSNASLLGSISDYFLSLSNGWDLACYLKSLSKALKALKLSQFLSTNQKEGISGPCMVIYVVCPFPEPTAVLKTVVESSIAIGSIILPSDRERRSVLYSQVGKALSSSAAADEASISNIPVVSGFSVPKLVLQIVTVDAIFRVTSPPFNELVILKETAFTIYNKARRISRGSTNDVSLSSSLSSRPHSVLTPMTSIPGMWKDCVGSRIPGSSLPREGEIDSSLRGGAWDNSWQTSRAGGLSCDPNRNGDFFYQDEVCYMFEPLFILAESGSVEHGISPTAFGNSTSETSKTVSDESSGAFMQTANSAGSIDPGSGSQLDGSESDGVSSGNNKTPSLHCCYGWTEDWRWLVCIWTDARGELLDCDIFPFGGISSRQDTKGLQCLFVQVLQQGCQILQTCASPDTGVVKPRDFVITRIGNFYELEYLEWQKAIYLVGGSEVKKWPLQLRRSVPDGMPTSTNGTSLQQQEMSLIQDRTLPSSPSPLYSPHTKAGFMKGGLGQPAARKQLMGGHTLVDSCRGLLQWVQSISFVSVSVDHSLQLVFQADSLSPGTQGVSGMGQSGYTEGFTPVKSLGSTSASYMLIPSPSMRFLPPTPLQLPICLTAESPPLAHLLHSKGSAIPLSTGFVVSKAVPSVRKDCRNYTKDEWPSVLSVSLIDYCGGNNVSQDKVIRGIAKPAGRTLISEARDFEIDNHLILKSVAAELHALSWMTVSPGYLERRTALPFHCDMVLRLRRLLHFAEKELSRPPDKTQV
Length1985
PositionKinase
OrganismTheobroma cacao (Cacao) (Cocoa)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Malvales> Malvaceae> Byttnerioideae> Theobroma.
Aromaticity0.07
Grand average of hydropathy-0.206
Instability index50.65
Isoelectric point5.68
Molecular weight214553.46
Publications
PubMed=23731509

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	IBA:GO_Central

GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP00509
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|    1735.06|     562|     645|     357|    1000|       1
---------------------------------------------------------------------------
  401- 1049 (852.58/668.00)	SNSNNSSISSISSSSSDSVTTGARDLEADADSSCR.QSGLSSNDQMEIDClkmgsKRPRIGITESYGQAITVtnASSQDAYKSNIGSMevnhsaitavgndQIgsnwdWDDDD.......RGIVM.....DIQSLLSEFGDF....GDFFENDVLPFGEPPGTAESSAImfaapDCGDAGSSPAGVMDVSDQMLLPVCLPSF.....DSFTPHPPVAIEECLSKSqevTSSAVTSGPLNHTLASSTGE..FDHLMKAEALMTFAtEYGAVETPASDSSSIFKKPYLPKSHKAESsnSSPNNYIY...GATPPSSPCFdGLDEKTGMPMNLKAYPGGHDL.SATYQLKKYYTPVETRKERYDG..KLLTHND..SSVTNE..VSGTSQFANFN........SMNAVKSadrKMTQGICGKEH.ILL...SMKTVLATDVECA...M.FQASMLRMRHILLSPMSLA...TISLSRPAGRSVLNHLPGDpSSMTDNVSSRYEvkkkesiPVRI...AGDIDGGMLDGHL.NAPVGVWRTVGVPKVS...KPAAS.PSIEASPSLTHNSFNEDSILSYGQRQPLQELLDGivlLVQQATSFVDLVLDA.....DCGDGPYSWLALQEHwRRGF.CCGPSMVHAGCgGTLASCHSLDiAGVelVDP...lsanihassvisllhsdiksalksafgNLdgPlSVTDWCKGRGQSGDVGaSADG
 1071- 1643 (766.85/457.77)	GEAMSPSQTSVGGSSVLKVTGALDGGKVEETSQRRlNQEISGSESEQQQC.....TRLRPTLFVLPSPAILV..GYQDDWLKTSANSL.............QL.....WEKAPlepyalpKPIIYsvicpDIDPLTSAAADFfqqlGTVYETCKLGTHSPQSLGNQMEM.....DSGKWSSSGFVLLDCPQSMKIESSNASLlgsisDYFLSLSNGWDLACYLKS...LSKALKALKLSQFLSTNQKEgiSGPCMVIYVVCPFP.EPTAVLKTVVESSIAIGSIILPSDRERRS.......VLYsqvGKALSSSA...AADEAS..ISNIPVVSG........FSVPKLVLQIVT....VDA....IFRVT..SPPFNElvILKETAFTIYNkarrisrgSTNDV.....SLSSSLSSRPHsVLT...PMTSIPGMWKDCVgsrI.PGSSLPREGEIDSSLRGGAwdnSWQTSRAGGLSCDPNRNGD.FFYQDEVCYMFE.......PLFIlaeSGSVEHGISPTAFgNSTSETSKTVSDESSGafmQTANSaGSIDPGSGSQLDGSESDGVSSGNNKTPSLHCCYG...WTEDWRWLVCIWTDArgellDCDIFPFGGISSRQD.TKGLqCLFVQVLQQGC.QILQTCASPD.TGV..VKP.........................................................
 1713- 1901 (115.63/45.94)	........................................................................................................................................................................................................................................................................................................SSPSP.LY.....SPHTKAGF..MKGGLGQPAARKQLMGGHTLvDSCRGLLQWVQSISFVSVSVDHslQLVFQADslSPGTQG..VSGMGQSGYTE........GFTPVKS......LGSTSASY.MLIpspSMRFLPPTPLQLP...IcLTAESPPLAHLLHS..........................................................................................................................................................................................................kgsaiplstgfvvskavpsvrkdcrnytkdEW..P.SVLSVSLIDYCGGNNV.SQDK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.33|      17|      30|     181|     197|       2
---------------------------------------------------------------------------
  181-  197 (29.21/20.67)	SIFVHTIISSKHIRA.LS
  213-  230 (27.11/18.54)	SYLLPVIISPHGMRGrLS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      97.09|      32|     104|     234|     275|       4
---------------------------------------------------------------------------
  234-  275 (42.32/58.98)	PndlVKQVYFSGSgKIRTF..NGFIGlpyhPSQGSGCQLwgQNC
  341-  374 (54.77/34.55)	P...VLQTSFARS.SLRRFwlQNWIG....PSLAASSLL..RHC
---------------------------------------------------------------------------




































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 MDP00509 with Med13 domain of Kingdom Viridiplantae
Unable to open file!