<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 MDP33009

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMDKFIDVRFDRVEKALVTLIDSIAKYNPSPALAEDLLAADRELNSGLEQLQTHQNNHLRILALRDDVAALDGQIKSTLLALAARRRDILQTPATEFPEDSVNRTIRDETKHYPFTYDELMSYARRISRNTVPGPGQTDGSEFFAQFGGPIPATGAGDGGSAPETAAPTPAAAPTPGAIPAGPASAGVNGAVGTPVGGGGAPASQSGTPGGAGGTGPGTGTGTAAPTPAPFASSGGAPPPATNVPNVLPDDLKNYIAPTAGTVFSPWPAPDLMMHGGLRALHAVTESACRDKHIALPHLQEPPPKTQAQAQAQTQAQASVPPLRIRFVSLEEQEEQERLRAQREAEEREEREERQRQMEEAAAAAAGAGAGAHASSNMGGSYGHAPAAAPAPAQFASTLDMEDDD
Length404
PositionMiddle
OrganismSporothrix schenckii (strain ATCC 58251 / de Perez 2211183) (Rose-picker's disease fungus)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Pezizomycotina> Sordariomycetes> Sordariomycetidae> Ophiostomatales> Ophiostomataceae> Sporothrix.
Aromaticity0.04
Grand average of hydropathy-0.459
Instability index59.85
Isoelectric point4.93
Molecular weight41880.82
Publications
PubMed=24855299

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

>MDP33009
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      49.43|      14|      18|      96|     113|       2
---------------------------------------------------------------------------
  100-  113 (25.34/20.33)	SVNRTIRDETKHYP
  121-  134 (24.09/ 7.91)	SYARRISRNTVPGP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      45.43|      12|      18|     238|     249|       3
---------------------------------------------------------------------------
  238-  249 (24.14/13.15)	PPATNV..PNVLPD
  257-  270 (21.29/10.67)	PTAGTVfsPWPAPD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      92.74|      29|      30|      31|      59|       5
---------------------------------------------------------------------------
   31-   59 (47.59/38.04)	ALAEDLLAADRELNSGLEQLQTHQNNHLR
   62-   90 (45.14/35.67)	ALRDDVAALDGQIKSTLLALAARRRDILQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     137.34|      27|      55|     153|     179|       6
---------------------------------------------------------------------------
  153-  179 (52.49/20.34)	TGAGDGGSAPE....TAAPTPAAAPTPGAIP
  207-  237 (49.23/18.61)	TPGGAGGTGPGtgtgTAAPTPAPFASSGGAP
  376-  396 (35.62/11.37)	NMGGSYGHAP.....AAAPAPAQFAS.....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      63.24|      15|      17|     330|     344|       7
---------------------------------------------------------------------------
  299-  311 (16.44/ 6.47)	..QEPPPKTQAQAQA
  330-  344 (24.29/13.17)	EEQEEQERLRAQREA
  346-  360 (22.51/11.65)	EREEREERQRQMEEA
---------------------------------------------------------------------------




































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 MDP33009 with Med4 domain of Kingdom Fungi


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) ARRISRNTVPGPGQTDGSEFFAQFGGPIPATGAGDGGSAPETAAPTPAAAPTPGAIPAGPASAGVNGAVGTPVGGGGAPASQSGTPGGAGGTGPGTGTGTAAPTPAPFASSGGAPPPATNVPNVLPDDLKNYIAPTAGTVFSPWPAPDLMMHGGLRALHAVTESACRDKHIALPHLQEPPPKTQAQAQAQTQAQASVPPLRIRFVSLEEQEEQERLRAQREAEEREEREERQRQMEEAAAAAAGAGAGAHASSNMGGSYGHAPAAAPAPAQFASTLDMEDDD
123
404










Molecular Recognition Features






MoRF SequenceStartStop




1) LRIRFV
2) TLDMEDD
322
397
327
403