<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 MDP15977

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMLQNVPHQLLQSPARLGLPTPSSPSLQNPNPAPKFSSQVSQPHQQANILTTPTTSSTLLPLLPPLSRAQSLLIQMASLASRLFEVSPNRSHWLSAFRGSLPSFLPPAAPVPQDSCPSSSKEILSVFTSLQTQLFEAVAELQEILDLQDEKQKVTREVRSKDSSILAFANKLKETECVLDMLVDDYSTYCRPKRTKLENDTEESSATTVASRLKLSDILSYAHRISYTTFAPPEFGAGLASLRGALPPAPQDEQMRASQLYNFADLDVGLPKADEAKKIVEPLIEPLAETNPLANLSAIPGLVPPNIVVPSGWKPGMPVELPTDLPLPPPGWKPGDPIALPPMDSLSLPPKAEEAPGRPVPPAGLPRMPEPIQVRHVQLDIEDDSSDYSSDDASSDSED
Length398
PositionMiddle
OrganismCapsicum chinense (Scotch bonnet) (Bonnet pepper)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> asterids> lamiids> Solanales> Solanaceae> Solanoideae> Capsiceae> Capsicum.
Aromaticity0.05
Grand average of hydropathy-0.328
Instability index77.14
Isoelectric point4.80
Molecular weight43093.41
Publications
PubMed=29089032

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

>MDP15977
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     108.78|      34|      39|     291|     329|       1
---------------------------------------------------------------------------
   70-  111 (46.82/13.18)	SLliqmASLASRLFEVSPN...RSHWlsafRGSLPSFLPPAAPVP
  291-  327 (61.97/30.38)	PL....ANLSAIPGLVPPNivvPSGW....KPGMPVELPTDLPLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      80.30|      23|      33|       6|      31|       2
---------------------------------------------------------------------------
    6-   31 (36.98/26.36)	PHQllQSPArLGLPTPSSPSLQNPNP
   42-   64 (43.33/21.13)	PHQ..QANI.LTTPTTSSTLLPLLPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      75.73|      25|      51|     148|     174|       3
---------------------------------------------------------------------------
  148-  172 (39.73/28.20)	DEKQKVTREVRSK......DSSILAFANKLK
  183-  213 (35.99/18.71)	DDYSTYCRPKRTKlendteESSATTVASRLK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      38.95|      11|      22|     238|     248|       4
---------------------------------------------------------------------------
  238-  248 (19.33/ 9.32)	LASLRGALPPA
  262-  272 (19.62/ 9.57)	FADLDVGLPKA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.45|      11|      19|     333|     348|       6
---------------------------------------------------------------------------
  333-  348 (15.51/16.60)	PGDPIalPPMdslSLP
  355-  365 (24.94/10.37)	PGRPV..PPA...GLP
---------------------------------------------------------------------------




































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 MDP15977 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) LLQSPARLGLPTPSSPSLQNPNPAPKFSSQVSQPHQQANILTTPT
2) PVELPTDLPLPPPGWKPGDPIALPPMDSLSLPPKAEEAPGRPVPPAGLPRMPEPIQVRHVQLDIEDDSSDYSSDDASSDSED
9
317
53
398










Molecular Recognition Features






MoRF SequenceStartStop




1) VPPAGLPRMPEPIQVRHVQLDIEDDSSDYS
359
388