<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 MDP33401

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMQNAVVLPSPARLGLSTSTPLPLNQNPSPQISIPVPNLPSTSTSSSLPAPPLLHHQTPSTLLSLLPPHPRAQFLVLHLSALTTKLFDVSGNRSSWLASYRGTLPTFLPASTLPQEASSASTTKEILSLISSTQSQLSEAIIELQEALDLEEAKRKLARETHLKDSAMLAFAKKVKQSEQLLGCLVEDYEDYRKPKKRFKPNSQSEDSCDSYLKLSDILSYAHRISYTTFAPPEFGSVQAPPLRGALPPAPQEEQIRASQLYQFADLDVGLPQKEETIKPTLSGIDLVEPMVDVKAIQGLIVPPPMPSGWKPGMPIEIGDVPIVPPGWKPGDPVPLPPVVEVPAGWKPGDAVVLPKHAEETVPMVQKPLVNNAPEPIQVKFVQLDINPDQDDYSSEYSSDVGSSEEDDEE
Length409
PositionMiddle
OrganismAmborella trichopoda
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Amborellales> Amborellaceae> Amborella.
Aromaticity0.05
Grand average of hydropathy-0.315
Instability index64.54
Isoelectric point4.90
Molecular weight44474.07
Publications
PubMed=24357323

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	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

>MDP33401
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     104.37|      17|      17|     326|     342|       1
---------------------------------------------------------------------------
  308-  324 (34.39/13.99)	GWKPGMPIEIGDVPI..VP
  326-  342 (39.69/17.15)	GWKPGDPVPLPPVVE..VP
  344-  362 (30.29/11.55)	GWKPGDAVVLPKHAEetVP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      42.82|      12|      17|      39|      51|       2
---------------------------------------------------------------------------
   39-   51 (20.00/ 9.57)	PSTsTSSSLPAPP
   58-   69 (22.82/ 7.38)	PST.LLSLLPPHP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.72|      18|      18|     237|     254|       3
---------------------------------------------------------------------------
  244-  261 (30.63/14.32)	GALPPA.PQEEQIRASQLY
  264-  282 (24.10/ 9.82)	ADLDVGlPQKEETIKPTLS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      99.59|      29|      90|      99|     127|       4
---------------------------------------------------------------------------
   99-  127 (49.46/32.40)	YRGTLPTFLPASTLPQEASSASTTKEILS
  191-  219 (50.13/32.95)	YRKPKKRFKPNSQSEDSCDSYLKLSDILS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.13|      14|      83|     288|     302|       6
---------------------------------------------------------------------------
  288-  302 (20.84/20.13)	EPmVDVKAIQGLIVP
  374-  387 (26.28/18.92)	EP.IQVKFVQLDINP
---------------------------------------------------------------------------




































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 MDP33401 with Med4 domain of Kingdom Viridiplantae
Unable to open file!