<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 MDP00938

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQNVPHQIVQSPARLGLPNPNSPSLQNATPANLFFCKCPHLPNRSHWISAFRGSLPSFLSSQSQPLTSTAPDSYPSSSKEILALFTNLQTQLFEAVAELQEILDLQDGKQKLSHEIRSKDAAILALASKLKEAEQVLDNLVDDYSDYRRSKRSKSEDVAEDSSTTTVASQLKLSDILSYAHRISYTTFAPPEFGAGQAPLRGALPPAPQEEQMRASQLYAFADLDVGLPKTDEHKKKIIEPLIETPVGQPAEPNPLANLAGMQGLLPPNIAVPSGWKPGMPVELPSDLPILPPPGWKPGDPVALPPLDSLPVPPRIEEQQPQHIPPPMLTKAPEPIQVLHVQLDIDDDSSDYSSDVGSSDSED
Length364
PositionMiddle
OrganismCoffea canephora (Robusta coffee)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> asterids> lamiids> Gentianales> Rubiaceae> Ixoroideae> Gardenieae complex> Bertiereae - Coffeeae clade> Coffeeae> Coffea.
Aromaticity0.05
Grand average of hydropathy-0.422
Instability index78.47
Isoelectric point4.81
Molecular weight39570.18
Publications
PubMed=25190796

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
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

>MDP00938
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      91.38|      17|      17|     267|     283|       1
---------------------------------------------------------------------------
  267-  283 (36.07/13.55)	LPP..NIAV..PSGWKPGMPV
  285-  303 (32.64/11.66)	LPS..DLPIlpPPGWKPGDPV
  305-  322 (22.67/ 6.16)	LPPldSLPV..PPRIEEQQP.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      78.92|      28|      39|      77|     114|       2
---------------------------------------------------------------------------
   77-  108 (38.98/45.47)	SSSKEILALFTNLQtqlfEAVAELQEIL.DLQD
  119-  147 (39.94/21.34)	SKDAAILALASKLK....EAEQVLDNLVdDYSD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      95.56|      27|      37|       2|      30|       3
---------------------------------------------------------------------------
    2-   30 (45.21/27.27)	LQNVPHQIvqSPARLGLPNPNSPSLQNAT
   42-   68 (50.36/25.36)	LPNRSHWI..SAFRGSLPSFLSSQSQPLT
---------------------------------------------------------------------------




































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 MDP00938 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) EHKKKIIEPLIETPVGQPAEPNPLANLAGMQG
2) PVELPSDLPILPPPGWKPGDPVALPPLDSLPVPPRIEEQQPQHIPPPMLTKAPEPIQVLHVQLDIDDDSSDYSSDVGSSDSED
234
282
265
364










Molecular Recognition Features






MoRF SequenceStartStop




1) TKAPEPIQVLHVQLDIDD
331
348