<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 MDP12252

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQNAQHQLLQSPARLGLPTPSSPSLQNPTTPPKFSSQLSQHLQPHQQANILTTSTTSSTLLPLLPPLSRAQSLLIQMASLSSRLFEVSPNRSHWLSAFRGSFPSFLPSAAPVPQDSYPSSSKEILSVFTSLQTQLFEAVAELQEILDLQDEKQKVTREIRSNDSAILAFANKLKGAERVLDNLVDDYSDYRRPKRVKLENDIDESSVTTVATQLKLSDILSYAHRISYTTFAPPEFGAGQAPLRGALPPAPQDEQMRASQLYNFANLDVGLPKTDDDKEKIIEPLIEPSADITNLSAIPGLIPPNIIVPSGWKPGMPVELPTDLPLPPPGWKPGDPIALPPVDSLPLPPKVEEAPARPVPPPGLPRMPEPIQVRHVQLDIEDDSSDYSSEASSDSED
Length398
PositionMiddle
OrganismNicotiana tabacum (Common tobacco)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> asterids> lamiids> Solanales> Solanaceae> Nicotianoideae> Nicotianeae> Nicotiana.
Aromaticity0.05
Grand average of hydropathy-0.393
Instability index76.90
Isoelectric point4.84
Molecular weight43468.60
Publications
PubMed=24807620

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
core mediator complex	GO:0070847	IBA:GO_Central
mediator complex	GO:0016592	IEA:InterPro
GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central
GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central

Interaction

Binary Interactions











Repeat regions





Repeats

>MDP12252
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      96.74|      18|      18|     312|     329|       1
---------------------------------------------------------------------------
  236-  252 (27.64/ 9.16)	EFGAGQA.PLRG.A.LPPAP
  312-  329 (38.71/15.91)	GWKPGMPVELPT.D.LPLPP
  331-  350 (30.39/10.84)	GWKPGDPIALPPvDsLPLPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     118.92|      30|      32|       6|      36|       2
---------------------------------------------------------------------------
    6-   33 (46.98/20.05)	..............QHQLLQ.SPAR...LGLPTPSSPSLQNPTTPP
   35-   67 (42.35/18.51)	FS........sqlsQHLQPH.QQAN...I.LTTSTTSSTLLPLLPP
   68-  112 (29.59/ 7.58)	LSraqslliqmaslSSRLFEvSPNRshwLSAFRGSFPSFL.PSAAP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      37.55|      12|      15|     178|     189|       3
---------------------------------------------------------------------------
  178-  189 (21.34/13.99)	ERV.LDNLVDDYS
  195-  207 (16.21/ 9.12)	KRVkLENDIDESS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.85|      15|      19|     273|     289|       6
---------------------------------------------------------------------------
  275-  289 (25.78/18.86)	TDDDKEKIIEPLIEP
  291-  305 (26.07/11.23)	ADITNLSAIPGLIPP
---------------------------------------------------------------------------




































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 MDP12252 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) PVELPTDLPLPPPGWKPGDPIALPPVDSLPLPPKVEEAPARPVPPPGLPRMPEPIQVRHVQLDIEDDSSDYSSEASSDSED
2) QLLQSPARLGLPTPSSPSLQNPTTPPKFSSQLSQHL
318
8
398
43










Molecular Recognition Features






MoRF SequenceStartStop




1) PGLPRMPEPIQVRHVQLDIEDDSSDYS
363
389