<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 MDP09997

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMDIPEQRLSPVGFTTLDAFDHQIMAPAQDVVAKVQEPHNDTATPAQSHSQVLSSGRFDYLTKAEAKLTFAPEYAAVEILIAEAPTPLFTNPYFPRSKKPGSSSFSARVYSYDVAQSSQIESTGDKPDKTSKLISGNHLHDISSSNLYTLVQGGNKGSDKILKSTDTQPSKGELSPPISGVTSFNFSLVSQKKSGNMFNAGYFLLSMKTALATEIECITFQAAMCRIRHTLLSLRSKASAEFNSATSSFIQTNVSNKSDLTPRSLMDNVGVWRPVVTPKGPKSLESLSANTLTGASPSLSIQRQPVVDLLCAMTLLVQQSTSFVDMSLDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGLLGTCHSKDCAGVDLVDPLSAEVSEPSMISLLQSDIRVALKAAFANMDGPLSVIDWCRGRGNAAESAGTGDAYSFQYSSGDILEPSSSLSIGGDSMSPPQPTSSNRGDLRVTAGISELEFQKGYHRVRPTIAVLPSPSMLVGYQDDWLKASVNSLKTWEKAPFEPYALPKPVTYYALCPDIDMLTSAVADFFMQLGTVYEVCKLGTHSPQNNGGQMELSPGKYLPSGLVLVDCPEQLKKVRCGHLGPISSTSDCLQAFSKHWSVKSFVTSISRILKDIKLTSNISTNQKESSSGPCTVIYVVCPFPEPCAILQTLVECSVALGYVISSPERERKLLYSQVAKALNSSASVDEASASNVVMLSGFSIPKLVLQIVTIETVLRMDKPNKELAVLKDIAFTVYNKARRIPRAVSTSDMFQSPTYLGRSQSTMMHVTSPAPTLWKECLVPRMSGPTLSRETDFDASMRSATWDNSWQPARSGGLLDPSKLPDLCAQDDRKYAFEPLFILADPGSADLNALMEPSKSGADASGSRVYGSISGSNSDSGVSPLLDVSESDSAASLHCCYGWTEDWRWLVCIWTDARGELLDSLIFPFGGISSRQDTKVLQSLFIQILQQGCQIMSSSPEASNMRPRDVIITRIGGFLELEIQEWQKAIYSYGGNEVKKWPVQLRRSIPEGIPPSSNGPTLQQQQQQDMALIQDRNMPSSPNPLYSPHPKSSFMKGALGQSGNKKQILVEQSGMDTSRGSLHLVRSISLVAVSQDHSLHLTCQADLLSRPASAGEGSQGSSGPWSYLEGFTPVKSIGSMSASHSYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRRDSAQLTKDEQPSVLSVSIIDHYGGSSGTVQEKMSRGGGGGSKQARNLSQETTGRECEMEMHSVLEAVAAELHSLSWLTVSPVYTERRTALPFHCDMVLRMRRLLHYADKYLSEPKGETTH
Length1347
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 index55.52
Isoelectric point6.17
Molecular weight146007.04
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

>MDP09997
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     549.92|     171|     489|     225|     473|       1
---------------------------------------------------------------------------
  237-  416 (275.11/230.03)	ASAEFNsatSSFIQTNVSNKSDLTPRSLMDNVGVWRPvVTPKGPKSLESLSANTLTGASPSLSIQRQPVVDLLCA..MTLLVQQSTSF..VDMSLDMDDGDGSFFWLSLDEQKRRGF...SCDPSMVHAGCGGLLGTCHSKDCagvdlVDPLSAEVSEPSM...ISLLQSDIRVALKAAFANMD...GPLSVI
  478-  661 (274.80/184.72)	SELEFQ...KGYHRVRPTIAVLPSPSMLVGYQDDWLK.ASVNSLKTWEKAPFEPYALPKPVTYYALCPDIDMLTSavADFFMQLGTVYevCKLGTHSPQNNGGQMELSPGKYLPSGLvlvDCPEQLKKVRCGHLGPISSTSDC.....LQAFSKHWSVKSFvtsISRILKDIKLTSNISTNQKEsssGPCTVI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.42|      16|    1090|      44|      60|       2
---------------------------------------------------------------------------
   44-   60 (27.25/17.85)	PAQS..HSQvLSSGRFDYL
 1135- 1152 (28.17/13.98)	PASAgeGSQ.GSSGPWSYL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     137.17|      39|     384|     773|     813|       3
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  773-  813 (65.80/39.08)	STSDMFQSPTYLgRSQSTMMHVTSPAPTLWKECLVPRmSGP
 1160- 1198 (71.37/34.58)	SIGSMSASHSYL.LVPSPSMRYLSPATLQLPTCLTSE.SPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.64|      20|      41|     125|     150|       4
---------------------------------------------------------------------------
  125-  150 (25.09/25.66)	KPDK..TSKLISGnhlhdISSSNlYTLV
  167-  188 (32.55/15.43)	QPSKgeLSPPISG.....VTSFN.FSLV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      80.38|      23|    1027|       3|      29|       5
---------------------------------------------------------------------------
    3-   29 (37.29/38.46)	IPEQRLSPvgftTLDAFDHQIMAPAQD
 1037- 1059 (43.09/31.35)	IPPSSNGP....TLQQQQQQDMALIQD
---------------------------------------------------------------------------




































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 MDP09997 with Med13 domain of Kingdom Viridiplantae
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