<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 MDP27999

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLPYRKQDNQLKPIPRISSSQRLNQPPIQPNGTPPQQAPSTPSAYVSSSLNPIRNLPTTQGNIKSKIRTKEDLQKFEKLPIVAKVNEFETLLNGIADDISKFKDVEIQEKVKRIIEVNDILKSNIEDLNKHRDFSYQVDQLSNENKQLEERAKGILRELIFYRNELKSLPRLPKNEVTPASEVEVQEILKYAMKLAKFTKAPPAMANMPFQIHPNNYIWPAEDALRRGMLAMSSLQGDEIIKQELGGEEEEEEVKKETVDEVMKEETIPKQEQEEIIPRRGSFGYGTTTKKKEEQTDLNLDLFDPDDEYSD
Length311
PositionMiddle
OrganismSpathaspora passalidarum (strain NRRL Y-27907 / 11-Y1)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Debaryomycetaceae> Spathaspora.
Aromaticity0.06
Grand average of hydropathy-0.857
Instability index59.20
Isoelectric point5.17
Molecular weight35748.07
Publications
PubMed=21788494

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

>MDP27999
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.68|      22|      26|      67|      92|       1
---------------------------------------------------------------------------
   71-   92 (35.63/26.22)	EDLQKFEKLPI...VAKVNEFETLL
   97-  121 (30.05/12.64)	DDISKFKDVEIqekVKRIIEVNDIL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.43|      17|      19|     238|     254|       2
---------------------------------------------------------------------------
  238-  254 (28.11/15.38)	DEIIKQELGGEEEEEEV
  260-  276 (29.32/16.33)	DEVMKEETIPKQEQEEI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.45|      19|      26|      13|      37|       3
---------------------------------------------------------------------------
   13-   37 (23.59/25.61)	PIPRISSSqrLNqpPIQpnGTPPQQ
   42-   60 (35.86/16.45)	PSAYVSSS..LN..PIR..NLPTTQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.43|      17|      26|     157|     173|       4
---------------------------------------------------------------------------
  157-  173 (28.71/16.63)	RELIFYRNELKSLPRLP
  186-  202 (27.72/15.86)	QEILKYAMKLAKFTKAP
---------------------------------------------------------------------------




































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 MDP27999 with Med4 domain of Kingdom Fungi


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) DEIIKQELGGEEEEEEVKKETVDEVMKEETIPKQEQEEIIPRRGSFGYGTTTKKKEEQTDLNLDLFDPDDEYSD
2) MLPYRKQDNQLKPIPRISSSQRLNQPPIQPNGTPPQQAPSTPSAYVSSSLNPIRNLPTTQGNIKSKI
238
1
311
67










Molecular Recognition Features






MoRF SequenceStartStop




1) EQEEIIPRRGSFGYGTTTKKKEEQTDLNLDLFDPDDEYSD
2) MLPYRKQDNQLKPIPRI
272
1
311
17