<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 MDP09990

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMWTNIFKIGELQTVSWFQFLPIEPDASAASEKSSKVEQKDALNSIVLSAYLHLQSEGFLSTWTNSFVGPWDPSQGEHNPDEKIKLWLFLPGCHSSVSEIAQPAVNKLRVASNGLWVAPGNSEEVAAALSQALRNSLERRAQPTVEFVFAATEEAIFVHVVISARYVRNLCSDDIEKVLAHSPPSIGEGLPVVVAPSGMLGRLVGCCPSDLVRQVYSSKSLTPNLPGFSQPTVCQLRGQSYYVEVALGFPAASAKKVSEFEHIHIKKELDPVKDAMVGSDGQRKVESPDGLPILERTFIYPPEAVLVPMVHQAFVRFSSKRMCLQGSLGSSSWEAWPFWNFAPSSYFQNSSFLGSSCGLGVNSNYLRLRRKKNKCNSMASSVSSVSSTSDGSQRAVATEGDIVADADSMSCRQSDMPSNNDTLGSKMVSKRPRSELTEVSSHTGKDVCENIQDPNGQVGHSWGWDDEGVVMDINILLSEFGDFSDFFQQEELDFGEPPGTAESHALVIPASDCGDVTFTDSPSTAMDIPEQRLSPVGFTTLDAFDHQIMAPAQDVVAKVQEPHNDTATPAQSHSQVLSSGRFDYLTKAEAKLTFAPEYAAVEILIAEAPTPLFTNPYFPRSKKPGSSSFSARVYSYDVAQSSQIESTGDKPDKTSKLISGNHLHDISSSNLYTLVQGGNKGSDKILKSTDTQPSKGELSPPISGVTSFNFSLVSQKKSGNMFNAGYFLLSMKTALATEIECITFQAAMCRIRHTLLSLRSKASAEFNSATSSFIQTNVSNKSDLTPRSLMDNVGVWRPVVTPKGPKSLESLSANTLTGASPSLSIQRQPVVDLLCAMTLLVQQSTSFVDMSLDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGLLGTCHSKDCAGVDLVDPLSAEVSEPSMISLLQSDIRVALKAAFANMDGPLSVIDWCRGRGNAAESAGTGDAYSFQYSSGDILEPSSSLSIGGDSMSPPQPTSSNRGISELEFQKGYHRVRPTIAVLPSPSMLVGYQDDWLKASVNSLKTWEKAPFEPYALPKPVTYYALCPDIDMLTSAVADFFMQLGTVYEVCKLGTHSPQNNGGQMELSPGKYLPSGLVLVDCPEQLKKVRCGHLGPISSTSDCLQAFSKHWSVKSFVTSISRILKDIKLTSNISTNQKESSSGPCTVIYVVCPFPEPCAILQTLVECSVALGYVISSPERERKLLYSQVAKALNSSASVDEASASNVVMLSGFSIPKLVLQIVTIETVLRMDKPNKELAVLKDIAFTVYNKARRIPRAVSTSDMFQSPTYLGRSQSTMMHVTSPAPTLWKECLVPRMSGPTLSRETDFDASMRSATWDNSWQPARSGGLLDPSKLPDLCAQDDRKYAFEPLFILADPGSADLNALMEPSKSGADASGSRVYGSISGSNSDSGVSPLLDVSESDSAASLHCCYGWTEDWRWLVCIWTDARGELLDSLIFPFGGISSRQDTKVLQSLFIQILQQGCQIMSSSPEASNMRPRDVIITRIGGFLELEIQEWQKAIYSYGGNEVKKWPVQLRRSIPEGIPPSSNGPTLQQQQQQDMALIQDRNMPSSPNPLYSPHPKSSFMKGALGQSGNKKQILVEQSGMDTSRGSLHLVRSISLVAVSQDHSLHLTCQADLLSRPASAGEGSQGSSGPWSYLEGFTPVKSIGSMSASHSYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRRDSAQLTKDEQPSVLSVSIIDHYGGSSGTVQEKMSRGGGGGSKQARNLSQETTGRECEMEMHSVLEAVAAELHSLSWLTVSPVYTERRTALPFHCDMVLRMRRLLHYADKYLSEPKGETTH
Length1864
PositionKinase
OrganismZea mays (Maize)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> PACMAD clade> Panicoideae> Andropogonodae> Andropogoneae> Tripsacinae> Zea.
Aromaticity0.07
Grand average of hydropathy-0.223
Instability index55.98
Isoelectric point5.70
Molecular weight202307.58
Publications
PubMed=19965430

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

>MDP09990
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     364.16|     115|     129|    1571|    1693|       1
---------------------------------------------------------------------------
 1571- 1693 (182.23/149.60)	MALiqDRNMPSSPNPL.YSPHPKSSFMKGALGQSGNKKQILVEQSGMDTSRGSLHLVRSISLVavsqDH..SLHLTCQaDLLSRPASAGEG.....SQGSSGPWSYLEGFTPVKSIGSMSASHSYLLVpSP
 1703- 1825 (181.93/124.75)	LQL..PTCLTSESPPLaHLLHSKGTAIPLAMGYVVSKAVPPVRRDSAQLTKDEQPSVLSVSII....DHygGSSGTVQ.EKMSRGGGGGSKqarnlSQETTGRECEMEMHSVLEAVAAELHSLSWLTV.SP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     289.35|      94|     128|     233|     335|       2
---------------------------------------------------------------------------
  233-  335 (146.86/104.10)	CQLRGQSYYVEV........ALGFPAASAKKVSEFEHIHIKKELDPVKDAmvGSDGQRKVESPDGLPILERTFIYP.PEAVLVPMVHQafvrfSSKRMC..LQ...GSLGsSSWeAW
  356-  463 (142.49/79.29)	CGLGVNSNYLRLrrkknkcnSMASSVSSVSSTSDGSQRAVATEGDIVADA..DSMSCRQSDMPSNNDTLGSKMVSKrPRSELTEVSSH.....TGKDVCenIQdpnGQVG.HSW.GW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     130.97|      41|     126|    1205|    1329|       3
---------------------------------------------------------------------------
 1152- 1200 (61.14/128.27)	RILKDIKlTSNISTNQKESSSGPCTVIYVVCPFPepcailqTL.VECSVA
 1284- 1325 (69.82/26.96)	RIPRAVS.TSDMFQSPTYLGRSQSTMMHVTSPAP.......TLwKECLVP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     347.33|     103|     127|     865|     978|       4
---------------------------------------------------------------------------
  874-  938 (87.44/53.46)	.............................................SCDPSMVHAGCGGLLGTCHSKDCaGVDLVDPLSAEVSEPSM...ISLLQSD........IRVALKAAFA..NMDGPLS
  939- 1052 (152.33/80.63)	VIDWCRGRGNAAESAGTGdAYSFQYSSGDI.LEPSSSLSIG..gdSMSPPQPTSSNRGISELEFQK...GYHRVRPTIAVLPSPSM...LVGYQDDwlkasvnsLKTWEKAPFEpyALPKPVT
 1067- 1151 (107.56/52.19)	VADFFMQLGTVYEVCKLG.THSPQNNGGQMeLSPGKYLPSGlvlvDCPEQLKKVRCGHLGPISSTSDC.....LQAFSKHWSVKSFvtsIS................................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     125.88|      39|      41|     500|     540|       5
---------------------------------------------------------------------------
  500-  540 (64.57/44.91)	AESHALVIPASDCgdVTFTDSPSTAMDIPEQRLSPV...G.FTTL
  542-  584 (61.30/36.11)	AFDHQIMAPAQDV..VAKVQEPHNDTATPAQSHSQVlssGrFDYL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     101.98|      31|     102|    1351|    1383|      10
---------------------------------------------------------------------------
 1351- 1383 (51.10/38.54)	WQPARsGGLLDPSKLP..DLCAQDDRKyAFEPLFI
 1455- 1487 (50.88/28.97)	WTDAR.GELLDSLIFPfgGISSRQDTK.VLQSLFI
---------------------------------------------------------------------------




































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 MDP09990 with Med13 domain of Kingdom Viridiplantae
Unable to open file!