<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 MDP32224

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQHQIVQSPARLGLTGPGSPSVQNPTPPRHGHPTSSSSSQSQHQQIQQQPNLLPSSIVAAASSASASAAISSSALLSLLPPLPRAQALLQQMAVLTSKLFEVSPNRALWLSAFRGSLPSFLSSHSLPPPPPLENPNPSSTKEILSQFNSLQTQLFEAVTELQEILDLQDAKQKVAREIKSKDLSLLAFANKLKDAERVLDMLVDDYSDYRKPKRSRTLTESEKEEEEVEDDNDSSSSTTVSSQLKLKDILAYAHKISYTTFAPPEFGAGQAPLRGALPPAPQDEQMRASQLYTFADLDIGLPKTVENMEKKVEALIEPPPPPEAMDISAIHNLLPPNIAVPSGWKPGMPVELPRDLLLPPPGWKPGDPVVLPPLESIAAPRAADQQYMRPPQGLHRPPDVIQVRAVQLDILEDDDSSDYSSDDASSDDED
Length431
PositionMiddle
OrganismCapsella rubella
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Brassicales> Brassicaceae> Camelineae> Capsella.
Aromaticity0.04
Grand average of hydropathy-0.456
Instability index69.54
Isoelectric point4.82
Molecular weight46845.18
Publications
PubMed=23749190

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

>MDP32224
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.17|      16|      16|     339|     354|       1
---------------------------------------------------------------------------
  339-  354 (34.68/20.40)	IAV.PSGWKPGMPVELP
  357-  373 (30.49/17.00)	LLLpPPGWKPGDPVVLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     150.40|      40|      53|      62|     102|       2
---------------------------------------------------------------------------
   36-   60 (34.37/12.93)	..........SSSSSQS..............QHQQIQQQPNLLPSSIVA
   62-  102 (58.29/30.98)	ASSASASAAISSSALLSlLPPLP........RAQALLQQMAVLTSKLFE
  113-  157 (57.74/27.07)	AFRGSLPSFLSSHS....LPPPPplenpnpsSTKEILSQFNSLQTQLFE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      38.21|      13|      15|     307|     320|       3
---------------------------------------------------------------------------
  307-  320 (18.69/14.16)	ENME.KKVEALIePP
  324-  337 (19.52/ 9.74)	EAMDiSAIHNLL.PP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     127.61|      43|     181|     196|     243|       4
---------------------------------------------------------------------------
  196-  243 (61.87/47.16)	AERVLDmlvDDYsdYRKPK...RSRTLTESEKEEEEVEDDNDSS..SSTTVSS
  380-  427 (65.74/37.05)	APRAAD...QQY..MRPPQglhRPPDVIQVRAVQLDILEDDDSSdySSDDASS
---------------------------------------------------------------------------




































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 MDP32224 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) PVELPRDLLLPPPGWKPGDPVVLPPLESIAAPRAADQQYMRPPQGLHRPPDVIQVRAVQLDILEDDDSSDYSSDDASSDDED
2) RKPKRSRTLTESEKEEEEVEDDNDSSSSTTV
3) VQSPARLGLTGPGSPSVQNPTPPRHGHPTSSSSSQSQHQQIQQQPNLLP
350
211
7
431
241
55










Molecular Recognition Features






MoRF SequenceStartStop




1) RPPQGLHRPPDVIQVRAVQLDILEDDDSSDYSSDDA
390
425