<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 MDP09985

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMDIPEQRLSPVGFTTLDAFDHQIMAPAQDVVAKVQEPHNDTATPAQSHSQVLSSGRFDYLTKAEAKLTFAPEYAAVEILIAEAPTPLFTNPYFPRSKKPGSSSFSARVYSYDVAQSSQIESTGDKPDKTSKLISGNHLHDISSSNLYTLVQGGNKGSDKILKSTDTQPSKGELSPPISGVTSFNFSLVSQKKSGNMFNAGYFLLSMKTALATEIECITFQAAMCRIRHTLLSLRSKASAEFNSATSSFIQTNVSNKSDLTPRSLMDNVGVWRPVVTPKGPKSLESLSANTLTGASPSLSIQRQPVVDLLCAMTLLVQQSTSFVDMSLDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGLLGTCHSKDCAGVDLVDPLSAEVSEPSMISLLQSDIRVALKAAFANMDGPLSVIDWCRGRGNAAESAGTGDAYSFQYSSGDILEPSSSLSIGGDSMSPPQPTSSNRGISELEFQKGYHRVRPTIAVLPSPSMLVGYQDDWLKASVNSLKTWEKAPFEPYALPKPVTYYALCPDIDMLTSAVADFFMQLGTVYEVCKLGTHSPQNNGGQMELSPGKYLPSGLVLVDCPEQLKKVRCGHLGPISSTSDCLQAFSKHWSVKSFVTSISRILKDIKLTSNISTNQKESSSGPCTVIYVVCPFPEPCAILQTLVECSVALGYVISSPERERKLLYSQVAKALNSSASVDEASASNVVMLSGFSIPKLVLQIVTIETVLRMDKPNKELAVLKDIAFTVYNKARRIPRAVSTSDMFQSPTYLGRSQSTMMHVTSPAPTLWKECLVPRMSGPTLSRETDFDASMRSATWDNSWQPARSGGLLDPSKLPDLCAQDDRKYAFEPLFILADPGSADLNALMEPSKSGADASGSRVYGSISGSNSDSGVSPLLDVSESDSAASLHCCYGWTEDWRWLVCIWTDARGELLDSLIFPFGGISSRQDTKVLQSLFIQILQQGCQIMSSSPEASNMRPRDVIITRIGGFLELEIQEWQKAIYSYGGNEVKKWPVQLRRSIPEGIPPSSNGPTLQQQQQQDMALIQDRNMPSSPNPLYSPHPKSSFMKGALGQSGNKKQILVEQSGMDTSRGSLHLVRSISLVAVSQDHSLHLTCQADLLSRPASAGEGSQGSSGPWSYLEGFTPVKSIGSMSASHSYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRRDSAQLTKDEQPSVLSVSIIDHYGGSSGTVQEKMSRGGGGGSKQARNLSQETTGRECEMEMHSVLEAVAAELHSLSWLTVSPVYTERRTALPFHCDMVLRMRRLLHYADKYLSEPKGETTH
Length1340
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-0.225
Instability index55.68
Isoelectric point6.17
Molecular weight145294.25
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

>MDP09985
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     108.38|      34|     385|     409|     448|       1
---------------------------------------------------------------------------
  409-  448 (54.20/41.68)	MDGP.LS.VIDWcrgrgNAAESAGTGDAySFQYS.SGDILEPS
  803-  839 (54.18/26.50)	MSGPtLSrETDF.....DASMRSATWDN.SWQPArSGGLLDPS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     118.46|      33|     385|     766|     799|       2
---------------------------------------------------------------------------
  766-  799 (58.46/30.65)	STSDMFQSPTYLgRSQSTMMHVTSPAPTLWKECL
 1153- 1185 (60.00/27.74)	SIGSMSASHSYL.LVPSPSMRYLSPATLQLPTCL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     120.78|      27|      41|     125|     156|       3
---------------------------------------------------------------------------
  125-  154 (41.95/30.79)	KPDK..TSKLISGnhlHDISSSNLYTLVQGGN
  167-  192 (35.83/17.12)	QPSKgeLSPPISG.....VTSFN.FSLVSQKK
 1056- 1081 (42.99/25.37)	.PSS..PNPLYSP...HPKSSFMKGALGQSGN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     226.77|      74|     459|     210|     302|       5
---------------------------------------------------------------------------
  225-  302 (117.22/94.02)	RIRHTLLSLRSKA...SAEFNSATSSfiqtNVSNKSDLT.PRSLMDNVGVWRPVVTPKGPKSLESLSANTLTGASPSLSIQR
  686-  763 (109.55/56.17)	RERKLLYSQVAKAlnsSASVDEASAS....NVVMLSGFSiPKLVLQIVTIETVLRMDKPNKELAVLKDIAFTVYNKARRIPR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.24|      18|     924|     335|     352|       6
---------------------------------------------------------------------------
  335-  352 (35.66/19.23)	SFFWLSLDE..QKRR...GFSCD
 1293- 1315 (25.58/11.88)	SLSWLTVSPvyTERRtalPFHCD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.59|      13|     489|     377|     389|      10
---------------------------------------------------------------------------
  377-  389 (23.82/13.24)	LVDPLSAEVS...EPS
  860-  875 (19.77/ 9.63)	LADPGSADLNalmEPS
---------------------------------------------------------------------------




































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 MDP09985 with Med13 domain of Kingdom Viridiplantae
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