<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 MDP00163

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQNIPHQVVQSPARLGLPNPNSPSLQNTNLPKFTSQTPQNHQQQQQQQQSNQLTTPAVSSTLLPLLPPLPRAQSLLIQMASLSSKLFEVSPNRPHWIGAFRGQLPSFLSSQPQPVGAAPQDSSPSSAKEIISQFAALQTQLFEAVAELQQILDLQDAKQKLAREIRSKDSALLAFANKLKETERVLDILVDDYSDYHRQKRTKSSEEDSSTTTIETQIKLTDILSYAHKISYTTFAPPVFGAGQAPLRGALPPAPQEEQMRASQLYNFADLDIGLPKTDEGREGIIEAVVEAEAAAPAKDLLMIPANIVVPSGWKPGMPVELPSDLPILPPPGWKPGDPITLPPLDALAGPARPDEQQLRAGPPPVLGRAPEPIQVRHVQLDIEDDSSDYSSDGGSSSESED
Length403
PositionMiddle
OrganismErythranthe guttata (Yellow monkey flower) (Mimulus guttatus)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> asterids> lamiids> Lamiales> Phrymaceae> Erythranthe.
Aromaticity0.05
Grand average of hydropathy-0.453
Instability index77.40
Isoelectric point4.89
Molecular weight43759.74
Publications
PubMed=24225854

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

>MDP00163
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      70.08|      17|      17|     308|     324|       1
---------------------------------------------------------------------------
  308-  324 (36.59/14.85)	N..IVVPSGWKPGMPVELP
  326-  344 (33.49/13.12)	DlpILPPPGWKPGDPITLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.53|      29|      32|     128|     157|       2
---------------------------------------------------------------------------
  121-  155 (36.87/36.51)	QDsspssAKEIISQFAALqTQLFEAVAELQQILD.L
  156-  190 (36.66/29.82)	QDakqklAREIRSKDSAL.LAFANKLKETERVLDiL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      34.50|      10|      15|     351|     361|       4
---------------------------------------------------------------------------
  351-  361 (15.23/11.56)	GPArPDEQQLR
  369-  378 (19.28/ 9.56)	GRA.PEPIQVR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      60.20|      20|      23|       4|      25|       5
---------------------------------------------------------------------------
    4-   25 (32.27/17.82)	NIPHQVVQSPARLG.LPnpNSPS
  104-  126 (27.93/ 9.64)	QLPSFLSSQPQPVGaAPqdSSPS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.68|      13|      23|      60|      72|       6
---------------------------------------------------------------------------
   60-   72 (23.60/11.42)	SSTLLPLLPPLPR
   84-   96 (24.08/11.79)	SSKLFEVSPNRPH
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      66.01|      18|     192|     192|     209|       7
---------------------------------------------------------------------------
  192-  209 (33.76/25.44)	DDYSDYHRQKRTKSSEED
  386-  403 (32.24/23.97)	DDSSDYSSDGGSSSESED
---------------------------------------------------------------------------




































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 MDP00163 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) QVVQSPARLGLPNPNSPSLQNTNLPKFTSQTPQNHQQQQQQQQSNQLTTPAVSSTL
2) VELPSDLPILPPPGWKPGDPITLPPLDALAGPARPDEQQLRAGPPPVLGRAPEPIQVRHVQLDIEDDSSDYSSDGGSSSESED
8
321
63
403










Molecular Recognition Features






MoRF SequenceStartStop




1) RAGPPPVLGRAPEPIQVRHVQLDIEDDSSDYSS
361
393