<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 MDP31724

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMFPHKKNDPLKSLPISRVGSSQRLNQHISSIPSTPNYVASSLNPVRNLPVSSGSIKSKITTKAALDKFEQLPIVKQVGAFEDTLNAISDNISQFKEGQLHANVEKIIAINDDLKSKIEELDRHRRLGENIKELEAESSNLDNTSKYILKELISYRNELRALPRLPASASKGSGDTVEIEDILKYAMKLAKFTKAPATSASMPFQIHPNNYVWPAEDALRRGMLAASSLNPDEIIANELGTTEEEKIQEKKDEQVKKADKQQDTGIRRGSFGDYGSSSSGKKKEEQSAQLDLDLFDSEDEFSD
Length302
PositionMiddle
OrganismScheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (Yeast) (Pichia stipitis)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Debaryomycetaceae> Scheffersomyces.
Aromaticity0.05
Grand average of hydropathy-0.694
Instability index52.19
Isoelectric point5.72
Molecular weight33544.22
Publications
PubMed=17334359

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 (By similarity). 
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

>MDP31724
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      79.18|      27|      29|      98|     124|       1
---------------------------------------------------------------------------
   98-  124 (44.92/26.50)	QLHANVEKIIA..INDDLKSK..IEELDRHR
  125-  155 (34.26/18.80)	RLGENIKELEAesSNLDNTSKyiLKELISYR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      35.99|      11|      29|     248|     258|       2
---------------------------------------------------------------------------
  248-  258 (18.03/12.42)	EKKDEQVKKAD
  280-  290 (17.96/12.34)	KKKEEQSAQLD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.81|      13|      29|     157|     169|       3
---------------------------------------------------------------------------
  157-  169 (22.39/10.78)	ELRALPRLPA.SAS
  187-  200 (17.42/ 7.20)	KLAKFTKAPAtSAS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.95|      12|      33|       8|      20|       4
---------------------------------------------------------------------------
    8-   20 (18.15/14.35)	DPLKSLPISRvGS
   43-   54 (22.80/13.30)	NPVRNLPVSS.GS
---------------------------------------------------------------------------




































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 MDP31724 with Med4 domain of Kingdom Fungi


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) DEIIANELGTTEEEKIQEKKDEQVKKADKQQDTGIRRGSFGDYGSSSSGKKKEEQSAQLDLDLFDSED
231
298










Molecular Recognition Features






MoRF SequenceStartStop




1) LKSLPISRV
2) MFPHKKN
3) QVKKADKQQDTGIRRGSFGDYGSSSSGKKKEEQSAQLDLDLFDSEDEFSD
10
1
253
18
7
302