<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 MDP00515

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQHQIVQSPARLGLTNPNSPSLQNPTPPKYPSSQPQPQPPPQQQQQPSSTNLSATTTSSALLSLLPPLPRAQSLLLQMASLASKLFEVSPNRTVWVSAFRGSLPSFLSSQIQTTPPPPLESTPTSTKEVLSLFTSLQTQLFEAVAQLQEILDLQDFKQKIAREIRSNDGAILAFANKLKEAERVLDMLVDDYSDYRRPKRLKLEEDGGGGDDDSSTTTVASQLNLSDILSYAHRISYTTFAPPEFGAGQAPLRGALPPAPQEEQMRASQLYAFADLDVGLPKAVEAKEKAVEAIIEPPPAQPVDTNPLANLAALQGLLPPNFTVPSGWKPGMPVELPTNLPVPPPGWKPGDPVPLPPLDSLPIPRMEEPHLRPVPPPGLHKPPEPIQVRHVELDILDPDDDSSDYSSDEGSSDDED
Length417
PositionMiddle
OrganismTheobroma cacao (Cacao) (Cocoa)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Malvales> Malvaceae> Byttnerioideae> Theobroma.
Aromaticity0.05
Grand average of hydropathy-0.467
Instability index70.02
Isoelectric point4.65
Molecular weight45219.44
Publications
PubMed=23731509

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:InterPro
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

>MDP00515
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             6|     179.91|      25|      38|     319|     345|       1
---------------------------------------------------------------------------
    7-   28 (35.96/11.65)	VQSPA..RLGLTN..........PN..SPS.LQNP.TP
   29-   47 (29.93/ 8.38)	PKYPS..SQPQPQ.........PP....PQ.QQQQ...
  102-  122 (26.53/ 6.54)	GSLPSflSSQIQT........TPP....P.....PLES
  319-  334 (19.32/ 7.35)	.....................LPPNftVPS.GWKPGMP
  335-  353 (32.31/ 9.67)	VELPT..NLPVPP.................pGWKPGDP
  354-  386 (35.86/11.59)	VPLPPldSLPIPRmeephlrpVPP....PG.LHKPPEP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     105.12|      20|      38|     258|     277|       2
---------------------------------------------------------------------------
  242-  257 (20.55/ 6.84)	..A.P.PE.FGAGQAPLRGAL
  258-  277 (35.13/16.73)	PPA.PQEEQMRASQLYAFADL
  282-  298 (22.96/ 8.47)	PKA.V.EAKEKAVE..AIIEP
  299-  318 (26.48/10.86)	PPAqPVDTNPLA.NLAALQGL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.67|      16|      20|     191|     206|       4
---------------------------------------------------------------------------
  191-  206 (28.74/16.23)	DDYSDYRRPKRLKLEE
  213-  228 (24.93/13.30)	DDSSTTTVASQLNLSD
---------------------------------------------------------------------------




































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 MDP00515 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) FTVPSGWKPGMPVELPTNLPVPPPGWKPGDPVPLPPLDSLPIPRMEEPHLRPVPPPGLHKPPEPIQVRHVELDILDPDDDSSDYSSDEGSSDDED
2) IVQSPARLGLTNPNSPSLQNPTPPKYPSSQPQPQPPPQQQQQPSSTNLSATTTSSAL
323
6
417
62










Molecular Recognition Features






MoRF SequenceStartStop




1) DEGSSDDED
2) LHKPPEPIQVRHVELDILDP
3) YRRPKRLKLEE
409
380
196
417
399
206