<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 MDP31136

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQPQIVQSPARLGLTNPTSPSLQNPTPPKLPSQQPSLSPTLLSLLAPLPRAQSLLIQMASLASKLFEVSPNRSLWLNAFRGNFPTFLSSQSQSLPSTAPDSSPSSTKEILSQFTALQTQLFEAVAELQEILDLQDAKLKIAREVRSKDAALLSFSKKLKDVEQVLDNLVDDYSDFSRPKRTKQEDGAEDDSSCTTTTVASQLNLSDILSYAHRISYTTFAPPEFGAGQAPLRGALPPAPQDEQMRASQLYNFANLDVGLPKTVEREEETIHTILEAPRPEPTEANQLPKLGALQGLLPPNITVPSGWIPGMPVELPSDVPVPPPGWKPGDPVPLPPLGSAPAPRVEEQQLRPNAHQPLPKAPATIQVQHVQLDIPDQDDDSSDYTSDDASSEDED
Length396
PositionMiddle
OrganismPrunus persica (Peach) (Amygdalus persica)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> fabids> Rosales> Rosaceae> Amygdaloideae> Amygdaleae> Prunus.
Aromaticity0.05
Grand average of hydropathy-0.460
Instability index75.87
Isoelectric point4.59
Molecular weight42977.74
Publications
PubMed=23525075

Function

Annotated function Component of the Mediator complex, a coactivator involved in the 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. 
ECO:0000256	RuleBase:RU364141
GO - Cellular Component
core mediator complex	GO:0070847	IBA:GO_Central
mediator complex	GO:0016592	IEA:EnsemblPlants
GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central
GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central

Interaction

Binary Interactions











Repeat regions





Repeats

>MDP31136
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      75.38|      18|      18|     304|     321|       1
---------------------------------------------------------------------------
  300-  317 (39.28/20.60)	PNITV.PSGWIPGMPVELP
  318-  336 (36.10/18.35)	SDVPVpPPGWKPGDPVPLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.96|      15|      19|     337|     351|       3
---------------------------------------------------------------------------
  337-  351 (27.30/11.73)	PLGSAPAP.RVEEQQL
  358-  373 (23.66/ 9.20)	PLPKAPATiQVQHVQL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      76.56|      18|      18|     155|     172|       4
---------------------------------------------------------------------------
  155-  172 (29.70/18.62)	FSKKLKDVEQVLDNLVDD
  176-  191 (26.92/16.27)	FSRP.KRTKQ.EDGAEDD
  192-  207 (19.94/10.36)	SSCTTTTVASQL.NLSD.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      72.16|      16|      42|      40|      55|       5
---------------------------------------------------------------------------
   40-   55 (27.40/14.82)	PTLLSLLAPLPRAQSL
   60-   75 (24.64/12.56)	ASLASKLFEVSPNRSL
   85-   95 (20.12/ 8.87)	PTFLS.....SQSQSL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      70.38|      24|      63|     208|     237|       6
---------------------------------------------------------------------------
  208-  237 (30.29/28.10)	ILSyAHRISYTTFA.pPEFGAgqapLRGALP
  274-  299 (40.09/17.43)	ILE.APRPEPTEANqlPKLGA....LQGLLP
---------------------------------------------------------------------------




































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 MDP31136 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) PKTVEREEETIHTILEAPRPEPTEANQLPKLGALQG
2) VPSGWIPGMPVELPSDVPVPPPGWKPGDPVPLPPLGSAPAPRVEEQQLRPNAHQPLPKAPATIQVQHVQLDIPDQDDDSSDYTSDDASSEDED
3) VQSPARLGLTNPTSPSLQNPTPPKLPSQQPS
261
304
7
296
396
37










Molecular Recognition Features






MoRF SequenceStartStop




1) DYTSDDASSEDED
2) QQLRPNAHQPLPKAPATIQVQHVQLDIPD
384
349
396
377