<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 MDP09996

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMDINILLSEFGDFSDFFQQEELDFGEPPGTAESHALVIPASDCGDVTFTDSPSTAMDIPEQRLSPVGFTTLDAFDHQIMAPAQDVVAKVQEPHNDTATPAQSHSQVLSSGRFDYLTKAEAKLTFAPEYAAVEILIAEAPTPLFTNPYFPRSKKPGSSSFSARVYSYDVAQSSQIESTGDKPDKTSKLISGNHLHDISSSNLYTLVQGGNKGSDKILKSTDTQPSKGELSPPISGVTSFNFSLVSQKKSGNMFNAGYFLLSMKTALATEIECITFQAAMCRIRHTLLSLRSKASAEFNSATSSFIQTNVSNKSDLTPRSLMDNVGVWRPVVTPKGPKSLESLSANTLTGASPSLSIQRQPVVDLLCAMTLLVQQSTSFVDMSLDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGLLGTCHSKDCAGVDLVDPLSAEVSEPSMISLLQSDIRVALKAAFANMDGPLSVIDWCRGRGNAAESAGTGDAYSFQYSSGDILEPSSSLSIGGDSMSPPQPTSSNRGISELEFQKGYHRVRPTIAVLPSPSMLVGYQDDWLKASVNSLKTWEKAPFEPYALPKPVTYYALCPDIDMLTSAVADFFMQLGTVYEVCKLGTHSPQNNGGQMELSPGKYLPSGLVLVDCPEQLKKVRCGHLGPISSTSDCLQAFSKHWSVKSFVTSISRILKDIKLTSNISTNQKESSSGPCTVIYVVCPFPEPCAILQTLVECSVALGYVISSPERERKLLYSQVAKALNSSASVDEASASNVVMLSGFSIPKLVLQIVTIETVLRMDKPNKELAVLKDIAFTVYNKARRIPRAVSTSDMFQSPTYLGRSQSTMMHVTSPAPTLWKECLVPRMSGPTLSRETDFDASMRSATWDNSWQPARSGGLLDPSKLPDLCAQDDRKYAFEPLFILADPGSADLNALMEPSKSGADASGSRVYGSISGSNSDSGVSPLLDVSESDSAASLHCCYGWTEDWRWLVCIWTDARGELLDSLIFPFGGISSRQDTKVLQSLFIQILQQGCQIMSSSPEASNMRPRDVIITRIGGFLELEIQEWQKAIYSYGGNEVKKWPVQLRRSIPEGIPPSSNGPTLQQQQQQDMALIQDRNMPSSPNPLYSPHPKSSFMKGALGQSGNKKQILVEQSGMDTSRGSLHLVRSISLVAVSQDHSLHLTCQADLLSRPASAGEGSQGSSGPWSYLEGFTPVKSIGSMSASHSYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRRDSAQLTKDEQPSVLSVSIIDHYGGSSGTVQEKMSRGGGGGSKQARNLSQETTGRECEMEMHSVLEAVAAELHSLSWLTVSPVYTERRTALPFHCDMVLRMRRLLHYADKYLSEPKGETTH
Length1395
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-0.220
Instability index55.85
Isoelectric point5.68
Molecular weight151188.54
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

>MDP09996
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     108.38|      34|     385|     464|     503|       1
---------------------------------------------------------------------------
  464-  503 (54.20/38.13)	MDGP.LS.VIDWcrgrgNAAESAGTGDAySFQYS.SGDILEPS
  858-  894 (54.18/24.27)	MSGPtLSrETDF.....DASMRSATWDN.SWQPArSGGLLDPS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     118.46|      33|     385|     821|     854|       2
---------------------------------------------------------------------------
  821-  854 (58.46/44.99)	STSDMFQSPTYLgRSQSTMMHVTSPAPTLWKECL
 1208- 1240 (60.00/40.72)	SIGSMSASHSYL.LVPSPSMRYLSPATLQLPTCL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     137.92|      33|      41|     174|     211|       3
---------------------------------------------------------------------------
  174-  209 (52.27/33.13)	IESTGDKPDK..TSKLISGnhlHDISSSNLYTLVQGGN
  216-  247 (45.05/22.26)	LKSTDTQPSKgeLSPPISG.....VTSFN.FSLVSQKK
 1111- 1136 (40.59/19.56)	.......PSS..PNPLYSP...HPKSSFMKGALGQSGN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      98.87|      28|     895|      15|      51|       5
---------------------------------------------------------------------------
   15-   42 (50.44/39.62)	DFFQQEELDFGEPPGTAESHALVIPASD
   57-   84 (48.43/20.48)	DIPEQRLSPVGFTTLDAFDHQIMAPAQD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     238.46|      72|     895|     350|     424|       6
---------------------------------------------------------------------------
  350-  424 (117.05/95.23)	SPSLSIQRQPVVdLLCAMTLLVQQSTSFVDMSLDMDDGDGSFFWLSLDeQKRRGFSCDPSMvHAGCGGLLGTCHS
 1277- 1348 (121.41/84.49)	SAQLTKDEQPSV.LSVSIIDHYGGSSGTVQEKMSRGGGGGSKQARNLS.QETTGRECEMEM.HSVLEAVAAELHS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     175.76|      58|     459|     265|     341|       7
---------------------------------------------------------------------------
  280-  341 (92.48/100.88)	RIRHTLLSLRSKA...SAEFNSATSSfiqtNVSNKSDLT.PRSLMDNVGVWRPVVTPKGPKSLESL
  741-  802 (83.27/51.05)	RERKLLYSQVAKAlnsSASVDEASAS....NVVMLSGFSiPKLVLQIVTIETVLRMDKPNKELAVL
---------------------------------------------------------------------------




































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 MDP09996 with Med13 domain of Kingdom Viridiplantae
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