<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 MDP00616

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMAGSSSASMRDRVDVCLNEHRFIAYKLLESLSHASSNTTPTILRTTDSLFEAILKKDRVLLQTVKQLNAHQAAQKELDNIKAQIAEKEAKIVQYARELRGGQKAISNVLLKHRRVLSNAKASSTTSHMKPQDIIAYAHKVASTSSAPAGWQPGYPMFGFMPPAPTPEMMRAGVLSRGIIDSIVTKETSSYTSTKRSLDASSAGVPSAVGDVRIGLGISDEEISKLIPPGWKPGDPIDLPAEALVRLRGPSVFAEHGIEVPGHILKAINEQPIPPVYMEQLRAKLDEKTPGHVDKKPRLDDAPDEASSESSSSSDEGSDASDSESEQVPKIRMTLSDSEDDD
Length341
PositionMiddle
OrganismSaprolegnia parasitica (strain CBS 223.65)
KingdomOomycetes
LineageEukaryota> Sar> Stramenopiles> Oomycota> Saprolegniales> Saprolegniaceae> Saprolegnia.
Aromaticity0.04
Grand average of hydropathy-0.459
Instability index48.14
Isoelectric point5.90
Molecular weight36914.23
Publications
PubMed=23785293

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

>MDP00616
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.48|      16|      16|     111|     126|       1
---------------------------------------------------------------------------
  111-  126 (26.24/18.41)	KHRRVLSNA.KASSTTS
  129-  145 (22.24/14.53)	KPQDIIAYAhKVASTSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.94|      16|      16|      30|      45|       2
---------------------------------------------------------------------------
   30-   45 (26.23/17.96)	SLSHASSNTTPTILRT
   48-   63 (24.70/16.53)	SLFEAILKKDRVLLQT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     220.85|      68|     116|     151|     221|       3
---------------------------------------------------------------------------
  151-  221 (109.85/65.76)	QPGYPMFGFMPPAPTPEMMRAGVLSRGIIDSiVTKETSSYTSTkrSLDASSAGVPSAVGDV.RIGLGISDEE
  270-  338 (111.00/58.12)	QPIPPVYMEQLRAKLDEKTPGHVDKKPRLDD.APDEASSESSS..SSDEGSDASDSESEQVpKIRMTLSDSE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      69.78|      19|      19|     225|     243|       4
---------------------------------------------------------------------------
  225-  243 (36.04/21.02)	LIPPGWKPGDPIDLPAEAL
  246-  264 (33.74/19.24)	LRGPSVFAEHGIEVPGHIL
---------------------------------------------------------------------------




































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 MDP00616 with Med4 domain of Kingdom Oomycetes


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) PVYMEQLRAKLDEKTPGHVDKKPRLDDAPDEASSESSSSSDEGSDASDSESEQVPKIRMTLSDSEDDD
274
341










Molecular Recognition Features






MoRF SequenceStartStop




1) DASDSESEQVPKIRMTLSDSEDDD
318
341