<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 MDP09995

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMASSVSSVSSTSDGSQRAVATEGDIVADADSMSCRQSDMPSNNDTLGSKMVSKRPRSELTEVSSHTGKDVCENIQDPNGQVGHSWGWDDEGVVMDINILLSEFGDFSDFFQQEELDFGEPPGTAESHALVIPASDCGDVTFTDSPSTAMDIPEQRLSPVGFTTLDAFDHQIMAPAQDVVAKVQEPHNDTATPAQSHSQVLSSGRFDYLTKAEAKLTFAPEYAAVEILIAEAPTPLFTNPYFPRSKKPGSSSFSARVYSYDVAQSSQIESTGDKPDKTSKLISGNHLHDISSSNLYTLVQGGNKGSDKILKSTDTQPSKGELSPPISGVTSFNFSLVSQKKSGNMFNAGYFLLSMKTALATEIECITFQAAMCRIRHTLLSLRSKASAEFNSATSSFIQTNVSNKSDLTPRSLMDNVGVWRPVVTPKGPKSLESLSANTLTGASPSLSIQRQPVVDLLCAMTLLVQQSTSFVDMSLDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGLLGTCHSKDCAGVDLVDPLSAEVSEPSMISLLQSDIRVALKAAFANMDGPLSVIDWCRGRGNAAESAGTGDAYSFQYSSGDILEPSSSLSIGGDSMSPPQPTSSNRGISELEFQKGYHRVRPTIAVLPSPSMLVGYQDDWLKASVNSLKTWEKAPFEPYALPKPVTYYALCPDIDMLTSAVADFFMQLGTVYEVCKLGTHSPQNNGGQMELSPGKYLPSGLVLVDCPEQLKKVRCGHLGPISSTSDCLQAFSKHWSVKSFVTSISRILKDIKLTSNISTNQKESSSGPCTVIYVVCPFPEPCAILQTLVECSVALGYVISSPERERKLLYSQVAKALNSSASVDEASASNVVMLSGFSIPKLVLQIVTIETVLRMDKPNKELAVLKDIAFTVYNKARRIPRAVSTSDMFQSPTYLGRSQSTMMHVTSPAPTLWKECLVPRMSGPTLSRETDFDASMRSATWDNSWQPARSGGLLDPSKLPDLCAQDDRKYAFEPLFILADPGSADLNALMEPSKSGADASGSRVYGSISGSNSDSGVSPLLDVSESDSAASLHCCYGWTEDWRWLVCIWTDARGELLDSLIFPFGGISSRQDTKVLQSLFIQILQQGCQIMSSSPEASNMRPRDVIITRIGGFLELEIQEWQKAIYSYGGNEVKKWPVQLRRSIPEGIPPSSNGPTLQQQQQQDMALIQDRNMPSSPNPLYSPHPKSSFMKGALGQSGNKKQILVEQSGMDTSRGSLHLVRSISLVAVSQDHSLHLTCQADLLSRPASAGEGSQGSSGPWSYLEGFTPVKSIGSMSASHSYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRRDSAQLTKDEQPSVLSVSIIDHYGGSSGTVQEKMSRGGGGGSKQARNLSQETTGRECEMEMHSVLEAVAAELHSLSWLTVSPVYTERRTALPFHCDMVLRMRRLLHYADKYLSEPKGETTH
Length1488
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-0.249
Instability index56.20
Isoelectric point5.48
Molecular weight160960.93
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

>MDP09995
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     108.38|      34|     385|     557|     596|       1
---------------------------------------------------------------------------
  557-  596 (54.20/44.62)	MDGP.LS.VIDWcrgrgNAAESAGTGDAySFQYS.SGDILEPS
  951-  987 (54.18/28.42)	MSGPtLSrETDF.....DASMRSATWDN.SWQPArSGGLLDPS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     118.46|      33|     385|     914|     947|       2
---------------------------------------------------------------------------
  914-  947 (58.46/35.28)	STSDMFQSPTYLgRSQSTMMHVTSPAPTLWKECL
 1301- 1333 (60.00/31.95)	SIGSMSASHSYL.LVPSPSMRYLSPATLQLPTCL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     120.78|      27|      41|     273|     304|       3
---------------------------------------------------------------------------
  273-  302 (41.95/26.72)	KPDK..TSKLISGnhlHDISSSNLYTLVQGGN
  315-  340 (35.83/14.65)	QPSKgeLSPPISG.....VTSFN.FSLVSQKK
 1204- 1229 (42.99/21.94)	.PSS..PNPLYSP...HPKSSFMKGALGQSGN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      79.42|      23|     886|     113|     144|       5
---------------------------------------------------------------------------
  113-  135 (40.48/30.53)	EELDFGEPPGTAESHALVIPASD
  155-  177 (38.94/12.97)	RLSPVGFTTLDAFDHQIMAPAQD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     226.77|      74|     459|     358|     450|       6
---------------------------------------------------------------------------
  373-  450 (117.22/105.84)	RIRHTLLSLRSKA...SAEFNSATSSfiqtNVSNKSDLT.PRSLMDNVGVWRPVVTPKGPKSLESLSANTLTGASPSLSIQR
  834-  911 (109.55/63.22)	RERKLLYSQVAKAlnsSASVDEASAS....NVVMLSGFSiPKLVLQIVTIETVLRMDKPNKELAVLKDIAFTVYNKARRIPR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.24|      18|     924|     483|     500|       7
---------------------------------------------------------------------------
  483-  500 (35.66/26.66)	SFFWLSLDE..QKRR...GFSCD
 1441- 1463 (25.58/16.52)	SLSWLTVSPvyTERRtalPFHCD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.42|      16|    1083|     192|     208|       8
---------------------------------------------------------------------------
  192-  208 (27.25/17.39)	PAQS..HSQvLSSGRFDYL
 1276- 1293 (28.17/13.59)	PASAgeGSQ.GSSGPWSYL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.59|      13|     489|     525|     537|      11
---------------------------------------------------------------------------
  525-  537 (23.82/14.11)	LVDPLSAEVS...EPS
 1008- 1023 (19.77/10.25)	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 MDP09995 with Med13 domain of Kingdom Viridiplantae
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