<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 MDP04439

Description Mediator of RNA polymerase II transcription subunit 6
SequenceMDDALATEGNQDIENDLDDILSPPGTDMTRICFRDQLWLNSYPLNCILVFDYFALSPFYDVTCNNELLRSRSQSIHPFDISHLSKMTGNEYVLTRIKEPNLFVLRKQMRYGPDRVIPQLMYYILDGSIFQAPQLCNLLYSKIEKTIHHLSQGFTIVSKLEKINCDDSEEESIDKKVKNVKKPIELKKLSAVNDIHTTLLRKVKLCIQWMRKTTGTCRLFRPSDEEEENKKKKKKKKNSKIDIDQLFSKELEDLYKPFLIQSPSTSSSSQATRATPKQVTGLFSDDASRFKKRINKKQKRIVTQVPADGLSTDFWSWRKYGQKPIKGSPYPRGYYRCSSSKECEARKQVERCPSDPSLLLVTYAAEHNHPIPPHRNSLSGSTRINKLTTASSFHIHRPL
Length398
PositionHead
OrganismZostera marina (Eelgrass)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Zosteraceae> Zostera.
Aromaticity0.08
Grand average of hydropathy-0.656
Instability index51.83
Isoelectric point9.31
Molecular weight45929.16
Publications
PubMed=26814964

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. 
GO - Cellular Component
core mediator complex	GO:0070847	IBA:GO_Central
mediator complex	GO:0016592	IBA:GO_Central

GO - Biological Function
DNA-binding transcription factor activity	GO:0003700	IEA:InterPro
sequence-specific DNA binding	GO:0043565	IEA:InterPro
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

>MDP04439
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      91.59|      32|      58|     166|     223|       1
---------------------------------------------------------------------------
  166-  199 (44.70/78.22)	DSEEESIDKKVKNVKkpIELKKL..SAVNDIHTTLL
  225-  258 (46.89/20.19)	EEENKKKKKKKKNSK..IDIDQLfsKELEDLYKPFL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      75.09|      23|      68|     261|     284|       2
---------------------------------------------------------------------------
  261-  284 (35.69/28.88)	SP.....STSSSSQATRATpKQVTGLFSD
  327-  354 (39.40/26.09)	SPyprgyYRCSSSKECEAR.KQVERCPSD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.89|      14|      68|      67|      85|       4
---------------------------------------------------------------------------
   67-   85 (18.91/19.53)	LLRSR.SQSIHpfdisHLSK
  137-  151 (20.98/ 9.57)	LLYSKiEKTIH.....HLSQ
---------------------------------------------------------------------------




































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 MDP04439 with Med6 domain of Kingdom Viridiplantae
Unable to open file!