<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 MDP12555

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQNVQHQLLQSPARLGLPTPSSPSLQNPTAPPKFSSQVSQHLQPHQQANILTTTTTSSTLLPLLPPLSRAQSLLIQMASLSSRLFEVSPNRSHWLSAFRGSFPSFLPSAAPVPQDSYPSSSKETLSVFTSLQTQLFEAVAELQEILDLQDEKQKVTREIRSNDSAILAFANKLKGAERVLDNLVDDYSDYRRPKRVKLENDIEESSVTTVATQLKLSDILSYAHRISYTTFAPPEFGAGQAPLRGALPPAPQDEQMRASQLYNFADLDVGLPKLDEGKEKIIEPLIEPAVETNPLANIQGLITPNIVVPSGWKPGMPVELPTDLPLPPPGWKPGDPIALPPFDSLSLPPKVEEVPARPVPPPGLPRMPEPIQVRHVQLDIEDDSSDYSSDEASSDSED
Length399
PositionMiddle
OrganismNicotiana sylvestris (Wood tobacco) (South American tobacco)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> asterids> lamiids> Solanales> Solanaceae> Nicotianoideae> Nicotianeae> Nicotiana.
Aromaticity0.06
Grand average of hydropathy-0.389
Instability index78.18
Isoelectric point4.82
Molecular weight43676.81
Publications
PubMed=23773524

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

>MDP12555
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     170.18|      51|      76|     234|     295|       1
---------------------------------------------------------------------------
  234-  289 (76.95/43.69)	PPEFGAG...QAPLRGALPPaPQDEQMRASQLYNFADLDVGlPKLDEGKEKIIEPlieP
  310-  363 (93.23/33.34)	PSGWKPGmpvELPTDLPLPP.PGWKPGDPIALPPFDSLSLP.PKVEEVPARPVPP...P
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      72.38|      21|      77|      12|      33|       3
---------------------------------------------------------------------------
   12-   33 (37.07/23.65)	SPAR...LGLPTPSSPSLQnPTAPP
   89-  112 (35.31/17.69)	SPNRshwLSAFRGSFPSFL.PSAAP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      36.04|      12|      15|     178|     189|       4
---------------------------------------------------------------------------
  178-  189 (20.71/17.98)	ERV.LDNLVDDYS
  195-  207 (15.34/11.29)	KRVkLENDIEESS
---------------------------------------------------------------------------




































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 MDP12555 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) LQSPARLGLPTPSSPSLQNPTAPPKFSSQVSQHLQPHQQANIL
2) PVELPTDLPLPPPGWKPGDPIALPPFDSLSLPPKVEEVPARPVPPPGLPRMPEPIQVRHVQLDIEDDSSDYSSDEASSDSED
10
318
52
399










Molecular Recognition Features






MoRF SequenceStartStop




1) GLPRMPEPIQVRHVQLDIEDDSSDY
364
388