<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 MDP12188

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQNAPHQLLQSPARLGLPTPSSPSVQNPSPPPKFSSQVSQPHQPLQQSNMLTTTTTSSALLPLLPPLSRAQSLLIQMASLASRLFEVSPNRSHWLGAFRGSFPSFLPSGTPVPQDSFPSSSKEILSVFTSLQTQLFEAVAELQEILDLQDEKQKVIREIRSKDSSILAFANKLKEAERVLDMLVDDYSDYRRPKRAKLENDTEESSVTTVATQLKLSDILSYAHRISYTTFAPPEFGTGQAPLRGALPPAPQDEQMRASQLYNFSDLDVGLPKTDDGKETIIEPLLEPPAETNPLANIQGLITPNIVVPFGWKPGMPIELPTDLPLPPPGWKPGDPIALPPFDSLPLPPKVEEAPARPVPPPGLPRMPEPIQVRHVQLDIEDDSSDYSSDEASSDSED
Length399
PositionMiddle
OrganismNicotiana tabacum (Common tobacco)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> asterids> lamiids> Solanales> Solanaceae> Nicotianoideae> Nicotianeae> Nicotiana.
Aromaticity0.06
Grand average of hydropathy-0.420
Instability index80.28
Isoelectric point4.73
Molecular weight43683.88
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

>MDP12188
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     146.27|      28|      33|       6|      33|       2
---------------------------------------------------------------------------
    6-   33 (56.12/22.67)	PHQLLQSPARLGLPTPSSPSVQN....PSPPP
   42-   67 (46.32/17.41)	PHQPLQQSNMLTTTTTSSALL......PLLPP
  334-  363 (43.83/16.07)	PGDPIALPPFDSLPLP..PKVEEaparPVPPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      74.13|      25|      37|     235|     268|       3
---------------------------------------------------------------------------
  194-  220 (33.58/ 9.07)	PKRAKLENDTEESSVTtvATQL.KLSDI
  243-  268 (40.55/30.33)	PLRGALPPAPQDEQMR..ASQLyNFSDL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      95.60|      32|      37|     115|     151|       4
---------------------------------------------------------------------------
   69-  101 (47.26/30.01)	SRAQSLLIQMASLASRLFEVSPNRSHWLGaFRG
  120-  151 (48.34/46.66)	SSSKEILSVFTSLQTQLFEAVAELQEILD.LQD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      35.39|      10|     195|     181|     191|       5
---------------------------------------------------------------------------
  181-  191 (15.71/16.78)	LDmLVDDYSDY
  379-  388 (19.68/13.93)	LD.IEDDSSDY
---------------------------------------------------------------------------




































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 MDP12188 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) MLQNAPHQLLQSPARLGLPTPSSPSVQNPSPPPKFSSQVSQPHQPLQQSNMLT
2) PIELPTDLPLPPPGWKPGDPIALPPFDSLPLPPKVEEAPARPVPPPGLPRMPEPIQVRHVQLDIEDDSSDYSSDEASSDSED
1
318
53
399










Molecular Recognition Features






MoRF SequenceStartStop




1) PGLPRMPEPIQVRHVQLDIEDDSSDYS
363
389