<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 MDP09984

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMWTNIFKIGELQTVSWFQFLPIEPDASAASEKSSKVEQKDALNSIVLSAYLHLQSEGFLSTWTNSFVGPWDPSQGEHNPDEKIKLWLFLPGCHSSVSEIAQPAVNKLRVASNGLWVAPGNSEEVAAALSQALRNSLERSLKGLSYARFGDVFTKYNPPTRNQNSFRRAQPTVEFVFAATEEAIFVHVVISARYVRNLCSDDIEKVLAHSPPSIGEGLPVVVAPSGMLGRLVGCCPSDLVRQVYSSKSLTPNLPGFSQPTVCQLRGQSYYVEVALGFPAASAKKVSEFEHIHIKKELDPVKDAMVGSDGQRKVESPDGLPILERTFIYPPEAVLVPMVHQAFVRFSSKRMCLQGSLGSSSWEAWPFWNFAPSSYFQNSSFLGSSCGLGVNSNYLRLRRKKNKCNSMASSVSSVSSTSDGSQRAVATEGDIVADADSMSCRQSDMPSNNDTLGSKMVSKRPRSELTEVSSHTGKDVCENIQDPNGQVGHSWGWDDEGVVMDINILLSEFGDFSDFFQQEELDFGEPPGTAESHALVIPASDCGDVTFTDSPSTAMDIPEQRLSPVGFTTLDAFDHQIMAPAQDVVAKVQEPHNDTATPAQSHSQVLSSGRFDYLTKAEAKLTFAPEYAAVEILIAEAPTPLFTNPYFPRSKKPGSSSFSARVYSYDVAQSSQIESTGDKPDKTSKLISGNHLHDISSSNLYTLVQGGNKGSDKILKSTDTQPSKGELSPPISGVTSFNFSLVSQKKSGNMFNAGYFLLSMKTALATEIECITFQAAMCRIRHTLLSLRSKASAEFNSATSSFIQTNVSNKSDLTPRSLMDNVGVWRPVVTPKGPKSLESLSANTLTGASPSLSIQRQPVVDLLCAMTLLVQQSTSFVDMSLDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGLLGTCHSKDCAGVDLVDPLSAEVSEPSMISLLQSDIRVALKAAFANMDGPLSVIDWCRGRGNAAESAGTGDAYSFQYSSGDILEPSSSLSIGGDSMSPPQPTSSNRDLRVTAGISELEFQKGYHRVRPTIAVLPSPSMLVGYQDDWLKASVNSLKTWEKAPFEPYALPKPVTYYALCPDIDMLTSAVADFFMQLGTVYEVCKLGTHSPQNNGGQMELSPGKYLPSGLVLVDCPEQLKKVRCGHLGPISSTSDCLQAFSKHWSVKSFVTSISRILKDIKLTSNISTNQKESSSGPCTVIYVVCPFPEPCAILQTLVECSVALGYVISSPERERKLLYSQVAKALNSSASVDEASASNVVMLSGFSIPKLVLQIVTIETVLRMDKPNKELAVLKDIAFTVYNKARRIPRAVSTSDMFQSPTYLGRSQSTMMHVTSPAPTLWKECLVPRMSGPTLSRETDFDASMRSATWDNSWQPARSGGLLDPSKLPDLCAQDDRKYAFEPLFILADPGSADLNALMEPSKSGADASGSRVYGSISGSNSDSGVSPLLDVSESDSAASLHCCYGWTEDWRWLVCIWTDARGELLDSLIFPFGGISSRQDTKVLQSLFIQILQQGCQIMSSSPEASNMRPRDVIITRIGGFLELEIQEWQKAIYSYGGNEVKKWPVQLRRSIPEGIPPSSNGPTLQQQQQQDMALIQDRNMPSSPNPLYSPHPKSSFMKGALGQSGNKKQILVEQSGMDTSRGSLHLVRSISLVAVSQDHSLHLTCQADLLSRPASAGEGSQGSSGPWSYLEGFTPVKSIGSMSASHSYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRRDSAQLTKDEQPSVLSVSIIDHYGGSSGTVQEKMSRGGGGGSKQARNLSQETTGRECEMEMHSVLEAVAAELHSLSWLTVSPVYTERRTALPFHCDMVLRMRRLLHYADKYLSEPKGETTH
Length1898
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-0.233
Instability index55.64
Isoelectric point5.82
Molecular weight206209.91
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

>MDP09984
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     141.94|      33|     107|    1385|    1417|       1
---------------------------------------------------------------------------
 1385- 1417 (63.60/32.52)	WQPARSG.....GLLDPSKLP..DLCAQDDRKYAFEPLFI
 1419- 1448 (30.60/11.92)	...ADPGsadlnALMEPSK.S..GADASGSRVYG....SI
 1489- 1521 (47.75/22.63)	WTDAR.G.....ELLDSLIFPfgGISSRQDTK.VLQSLFI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      87.05|      24|     107|     926|     949|       2
---------------------------------------------------------------------------
  926-  949 (41.10/25.51)	GVDLVDPLSAEVSEPSMISLLQSD
 1036- 1059 (45.95/29.58)	GYHRVRPTIAVLPSPSMLVGYQDD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      91.72|      31|     319|     666|     705|       4
---------------------------------------------------------------------------
  666-  702 (42.23/45.04)	AQSSQIESTGDKPDK..TSKLISGnhlhdISSSNlYTLV
  708-  740 (49.49/25.01)	GSDKILKSTDTQPSKgeLSPPISG.....VTSFN.FSLV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      68.89|      22|      26|      85|     107|       7
---------------------------------------------------------------------------
   85-  107 (35.91/25.06)	LWLfLPGCHSSV.SEIAQPAVNKL
  114-  136 (32.98/17.60)	LWV.APGNSEEVaAALSQALRNSL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     173.00|      59|     592|     499|     571|       9
---------------------------------------------------------------------------
  499-  571 (89.33/73.06)	DINILLSEFGDFsdFFQQE......ELdfgeppGTaesHAlviPASDCGDVTFTDS...PS..TAMDIPEQ.......RLSPVGFTT..LDAF
 1093- 1171 (83.67/41.59)	DIDMLTSAVADF..FMQLGtvyevcKL......GT...HS...PQNNGGQMELSPGkylPSglVLVDCPEQlkkvrcgHLGPISSTSdcLQAF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      77.59|      25|     592|     235|     260|      10
---------------------------------------------------------------------------
  199-  227 (33.88/13.29)	SDDIEKVlaHSPPSIGEGLPVVVAPSgmL
  236-  260 (43.71/20.11)	SDLVRQV..YSSKSLTPNLPGFSQPT..V
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      86.81|      24|     708|     351|     374|      13
---------------------------------------------------------------------------
  351-  374 (50.06/31.96)	LQGSLGS.SSWEAWPFWNFA...PSSYF
 1061- 1088 (36.75/21.25)	LKASVNSlKTWEKAPFEPYAlpkPVTYY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      62.76|      18|     958|     887|     904|      18
---------------------------------------------------------------------------
  887-  904 (36.08/23.68)	SFFWLSLDE..QKRR...GFSCD
 1851- 1873 (26.68/15.25)	SLSWLTVSPvyTERRtalPFHCD
---------------------------------------------------------------------------




































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 MDP09984 with Med13 domain of Kingdom Viridiplantae
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