<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 MDP27630

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMDKELDGRFERLEKALATMIDSLSKNNPSTKLAQDLVAAEAELLEGLKLLEAHQNNHARIQQLRQSTEQADAQIKDIISSLWKMRQELTSVQTSPIPKGAKFQFTTGELLDFARRISRNTLPPPGVTNGVNMTPAAARHSQQPSSVEPEDSFRVTSQSQTQTPNTSFNVSFNGTLVDTPGPFNNNSTPIPNAGPANSQNPHTELPEHLKLATNPLHGASFFPWPSVEQVRSGALGAYQLLVDKGIDPRGYDPEFEEQRRKDAEREAEERAKQEREEAERRAREEAERIARQRELERQRARESMAAAAEEGRRDSVVGGPAAGKPKQFTFLGGDDDDDDDDD
Length341
PositionMiddle
OrganismChaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Pezizomycotina> Sordariomycetes> Sordariomycetidae> Sordariales> Chaetomiaceae> Chaetomium.
Aromaticity0.05
Grand average of hydropathy-0.927
Instability index44.28
Isoelectric point5.08
Molecular weight37875.23
Publications
PubMed=21784248

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

>MDP27630
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      73.47|      19|      20|     264|     282|       1
---------------------------------------------------------------------------
  246-  261 (22.15/ 8.04)	...DPRGYDPEFEEQRRKD
  264-  280 (22.11/ 8.02)	REAEERAKQEREEAERR..
  282-  300 (29.21/12.41)	REEAERIARQRELERQRAR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     130.65|      26|      28|     172|     198|       2
---------------------------------------------------------------------------
  120-  141 (28.03/ 9.94)	TL.PPPGVT...NGvNMTP...AA....ARHSQ.
  146-  172 (27.29/12.25)	..VEPEDSFrvtSQ.SQTQTPNTS....FNVSFN
  174-  199 (47.35/28.34)	TLVDTPGPF...NN.NSTPIPNAG....PANSQN
  200-  228 (27.96/ 9.89)	PHTELPEHL...KL.ATNPLHGASffpwPSVEQ.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.14|      19|      28|      25|      43|       3
---------------------------------------------------------------------------
   25-   43 (29.83/14.75)	KNNPS..TKLAQDLVAAEAEL
   54-   74 (27.31/13.05)	QNNHAriQQLRQSTEQADAQI
---------------------------------------------------------------------------




































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 MDP27630 with Med4 domain of Kingdom Fungi


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) ARRISRNTLPPPGVTNGVNMTPAAARHSQQPSSVEPEDSFRVTSQSQTQTPNTSFNVSFNGTLVDTPGPFNNNSTPIPNAGPANSQNPHTELPEHLKLATNPLHGASFFPWPSVE
2) LVDKGIDPRGYDPEFEEQRRKDAEREAEERAKQEREEAERRAREEAERIARQRELERQRARESMAAAAEEGRRDSVVGGPAAGKPKQFTFLGGDDDDDDDDD
113
240
227
341










Molecular Recognition Features






MoRF SequenceStartStop




1) GRFER
2) RIARQRELERQRARESMAAAAEEGRRDSVVGGPAAGKPKQFTFLGGDDDDDDDDD
7
287
11
341