<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 MDP09989

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMWTNIFKIGELQTVSWFQFLPIEPDASAASEKSSKVEQKDALNSIVLSAYLHLQSEGFLSTWTNSFVGPWDPSQGEHNPDEKIKLWLFLPGCHSSVSEIAQPAVNKLRVASNGLWVAPGNSEEVAAALSQALRNSLERSLKGLSYARFGDVFTKYNPPTRNQNSFRRAQPTVEFVFAATEEAIFVHVVISARYVRNLCSDDIEKVLAHSPPSIGEGLPVVVAPSGMLGRLVGCCPSDLVRQVYSSKSLTPNLPGFSQPTVCQLRGQSYYVEVALGFPAASAKKVSEFEHIHIKKELDPVKDAMVGSDGQRKVESPDGLPILERTFIYPPEAVLVPMVHQAFVRFSSKRMCLQGSLGSSSWEAWPFWNFAPSSYFQNSSFLGSSCGLGVNSNYLRLRRKKNKCNSMASSVSSVSSTSDGSQRAVATEGDIVADADSMSCRQSDMPSNNDTLGSKMVSKRPRSELTEVSSHTGKDVCENIQDPNGQVGHSWGWDDEGVVMDINILLSEFGDFSDFFQQEELDFGEPPGTAESHALVIPASDCGDVTFTDSPSTAMDIPEQRLSPVGFTTLDAFDHQIMAPAQDVVAKVQEPHNDTATPAQSHSQVLSSGRFDYLTKAEAKLTFAPEYAAVEILIAEAPTPLFTNPYFPRSKKPGSSSFSARVYSYDVAQSSQIESTGDKPDKTSKLISGNHLHDISSSNFSGVTSFNFSLVSQKKSGNMFNAGYFLLSMKTALATEIECITFQAAMCRIRHTLLSLRSKASAEFNSATSSFIQTNVSNKSDLTPRSLMDNVGVWRPVVTPKGPKSLESLSANTLTGASPSLSIQRQPVVDLLCAMTLLVQQSTSFVDMSLDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGLLGTCHSKDCAGVDLVDPLSAEVSEPSMISLLQSDIRVALKAAFANMDGPLSVIDWCRGRGNAAESAGTGDAYSFQYSSGDILEPSSSLSIGGDSMSPPQPTSSNRGISELEFQKGYHRVRPTIAVLPSPSMLVGYQDDWLKASVNSLKTWEKAPFEPYALPKPVTYYALCPDIDMLTSAVADFFMQLGTVYEVCKLGTHSPQNNGGQMELSPGKYLPSGLVLVDCPEQLKKVRCGHLGPISSTSDCLQAFSKHWSVKSFVTSISRILKDIKLTSNISTNQKESSSGPCTVIYVVCPFPEPCAILQTLVECSVALGYVISSPERERKLLYSQVAKALNSSASVDEASASNVVMLSGFSIPKLVLQIVTIETVLRMDKPNKELAVLKDIAFTVYNKARRIPRAVSTSDMFQSPTYLGRSQSTMMHVTSPAPTLWKECLVPRMSGPTLSRETDFDASMRSATWDNSWQPARSGGLLDPSKLPDLCAQDDRKYAFEPLFILADPGSADLNALMEPSKSGADASGSRVYGSISGSNSDSGVSPLLDVSESDSAASLHCCYGWTEDWRWLVCIWTDARGELLDSLIFPFGGISSRQDTKVLQSLFIQILQQGCQIMSSSPEASNMRPRDVIITRIGGFLELEIQEWQKAIYSYGGNEVKKWPVQLRRSIPEGIPPSSNGPTLQQQQQQDMALIQDRNMPSSPNPLYSPHPKSSFMKGALGQSGNKKQILVEQSGMDTSRGSLHLVRSISLVAVSQDHSLHLTCQADLLSRPASAGEGSQGSSGPWSYLEGFTPVKSIGSMSASHSYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRRDSAQLTKDEQPSVLSVSIIDHYGGSSGTVQEKMSRGGGGGSKQARNLSQETTGRECEMEMHSVLEAVAAELHSLSWLTVSPVYTERRTALPFHCDMVLRMRRLLHYADKYLSEPKGETTH
Length1861
PositionKinase
OrganismZea mays (Maize)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> PACMAD clade> Panicoideae> Andropogonodae> Andropogoneae> Tripsacinae> Zea.
Aromaticity0.08
Grand average of hydropathy-0.226
Instability index56.00
Isoelectric point5.78
Molecular weight202346.58
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

>MDP09989
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     202.41|      66|     310|     984|    1111|       1
---------------------------------------------------------------------------
  314-  383 (107.89/52.25)	SPDGLPILE..RTF..IYPPEAVLvPmVHQAFVRFSSKRmcLQGSLGS.SSWEAWPFWNFA...PSSYF...QNSSFLGSS
  987- 1063 (94.52/82.08)	SNRGISELEfqKGYhrVRPTIAVL.P.SPSMLVGYQDDW..LKASVNSlKTWEKAPFEPYAlpkPVTYYalcPDIDMLTSA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     112.59|      33|      34|     185|     218|       2
---------------------------------------------------------------------------
  172-  191 (22.07/ 8.44)	..........VEFVFAATE....EAIFVHVVISA
  192-  225 (54.21/38.55)	RYVrNLCSDDIEKVLAHSPPSIGEGLPVVVAPSG
  229-  253 (36.32/19.80)	RLV.GCCPSDLVRQV.YSSKSLTPNLP.......
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.35|      28|     310|      94|     121|       3
---------------------------------------------------------------------------
   89-  116 (49.00/33.43)	LPGCHSSV.SEIAQPAVNKLRVASNGLWV
  117-  145 (40.35/26.01)	APGNSEEVaAALSQALRNSLERSLKGLSY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     141.94|      33|     107|    1348|    1380|       4
---------------------------------------------------------------------------
 1348- 1380 (63.60/35.95)	WQPARSG.....GLLDPSKLP..DLCAQDDRKYAFEPLFI
 1382- 1411 (30.60/13.29)	...ADPGsadlnALMEPSK.S..GADASGSRVYG....SI
 1452- 1484 (47.75/25.07)	WTDAR.G.....ELLDSLIFPfgGISSRQDTK.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 MDP09989 with Med13 domain of Kingdom Viridiplantae
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