<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 MDP09972

Description Mediator of RNA polymerase II transcription subunit 6
SequenceMSATPLPPPGPDGAVALLPPPGTDMTGICFRDQLWLDTYPLDRNLVFDYFALSPFYDITCNNESLRSRQIHPLDMSHLTKMTGMEYLLSEVMEPHLFVIRKQKRESPEKSSPMLAYYILDGSIYQAPQLCNVFASRISRAMHHISKAFTIACSKLEKIGNGYLQNYNYLPPQHTTGKLQQGLCEIAIVITTTKHLDLNKNLKGHTGSATIEHLETEPDAVASESKTQKEAIDLKELKRIDHILSSLKRKIGAAPPPPPYPEGYVPPSAEQEKAPDDVAASEAPPQLDPIIDQGPSKRPRFQ
Length301
PositionHead
OrganismZea mays (Maize)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> PACMAD clade> Panicoideae> Andropogonodae> Andropogoneae> Tripsacinae> Zea.
Aromaticity0.07
Grand average of hydropathy-0.435
Instability index63.02
Isoelectric point6.21
Molecular weight33511.99
Publications
PubMed=19965430

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:RU364143
GO - Cellular Component
core mediator complex	GO:0070847	IBA:GO_Central
mediator complex	GO:0016592	IBA:GO_Central
GO - Biological Function
transcription coactivator activity	GO:0003713	IBA:GO_Central
GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central

Interaction

Binary Interactions











Repeat regions





Repeats

>MDP09972
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      71.63|      17|     246|       1|      20|       1
---------------------------------------------------------------------------
    1-   20 (32.44/20.37)	MSATPLPPPGPDGAVallPP
  250-  266 (39.19/18.44)	IGAAPPPPPYPEGYV...PP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      78.53|      25|      56|     214|     238|       2
---------------------------------------------------------------------------
  214-  238 (41.80/26.29)	ETEPDAV.ASESKTQKE.AIDLKELKR
  271-  297 (36.73/22.31)	EKAPDDVaASEAPPQLDpIIDQGPSKR
---------------------------------------------------------------------------




































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 MDP09972 with Med6 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) SLKRKIGAAPPPPPYPEGYVPPSAEQEKAPDDVAASEAPPQLDPIIDQGPSKRPRFQ
245
301










Molecular Recognition Features






MoRF SequenceStartStop




1) KRIDHILSSLKRKIGAAP
2) PYPEGYVPPSAEQEKAPDDV
3) QLDPIIDQGPSKRPRF
237
258
285
254
277
300