<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 MDP27606

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMDTYIDSRFERLEKALATLIDSVTKYHPSPIQAEELKNADNELCKGLEQVEIHQRNHLKIQQLRQMSNSLDAQIRETLTSLATTRKDLVTTQVTTYPSEPNYPILYEELLGFARRISKTSMPPAAILNAMAAAAAATNQDSQTPVPDSQTQMAMTPSAQTPNPMQSPAPTNGVAEQQTQASAHTSLPDNMNQFLNPLSGQLFFPWPLEDKIRSGALASNQILLEQGIDPRGYDPVAEEERKRKEEEERKEREEKEKQERAEREREAERQRQERERAIEKQQAEWRRASTAAGASGDAGVGGPPSAKAEKKQFQFTNLDDLDDDDDED
Length327
PositionMiddle
OrganismHypocrea jecorina (strain QM6a) (Trichoderma reesei)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Pezizomycotina> Sordariomycetes> Hypocreomycetidae> Hypocreales> Hypocreaceae> Trichoderma.
Aromaticity0.05
Grand average of hydropathy-0.972
Instability index50.74
Isoelectric point4.86
Molecular weight36761.21
Publications
PubMed=18454138

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

>MDP27606
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      70.83|      21|      21|     244|     264|       1
---------------------------------------------------------------------------
  244-  264 (34.51/15.74)	EEEERKEREEKEKQERAERER
  266-  286 (36.32/16.87)	AERQRQERERAIEKQQAEWRR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.92|      20|      21|     144|     163|       2
---------------------------------------------------------------------------
  144-  163 (38.26/19.59)	PVPDSQTQMAMT.PSAQTPNP
  167-  187 (29.66/13.86)	PAPTNGVAEQQTqASAHTSLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     108.66|      36|      71|       1|      36|       3
---------------------------------------------------------------------------
    1-   36 (62.08/59.11)	MDTYIDSRFERLEKALATLIDS.VTKY..HPS.PIQAEEL
   70-  109 (46.59/42.16)	LDAQIRETLTSLATTRKDLVTTqVTTYpsEPNyPILYEEL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      27.33|      10|      18|     198|     211|       4
---------------------------------------------------------------------------
  198-  211 (11.74/16.41)	SGQLFFpwplEDKI
  218-  227 (15.58/ 6.82)	SNQILL....EQGI
---------------------------------------------------------------------------




































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 MDP27606 with Med4 domain of Kingdom Fungi


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) LNAMAAAAAATNQDSQTPVPDSQTQMAMTPSAQTPNPMQSPAPTNGVAEQQTQASAHTSLPDNMNQFLN
2) SGALASNQILLEQGIDPRGYDPVAEEERKRKEEEERKEREEKEKQERAEREREAERQRQERERAIEKQQAEWRRASTAAGASGDAGVGGPPSAKAEKKQFQFTNLDDLDDDDDED
127
213
195
327










Molecular Recognition Features






MoRF SequenceStartStop




1) RAIEKQQAEWRRASTAAGASGDAGVGGPPSAKAEKKQFQFTNLDDLDDDDDED
275
327