<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 MDP27601

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMVDSDERSLRDLLLESADDLEHVVKIIVDTLINRERSVMLKNGESVSNMVKLFDAKQQDIKDLLNRVPEYQEREQLIRTLKGHVEKRDEVIQQVENNLKACEVALTRSCFHANQKVKQVKEAHLRPVNSEVLIKLAHQISAHNSISAPFTWQMGDPSRPFPQETEFRAGHLLNPKLQSSGPQLLPGKNVAQKPLITSPSASSSNGTSAPIRTVGTPLVNSEPTGEYSPRTGYGAVKTPPIQQQVLRGATPNEKQWQNQSAAGATSTQSPYNRISQSPSSSPTLKLKITGLPNRTGTIEQVRELQEVGQMSSDDSNSSDSSDDEVSSKRTGGSNKS
Length335
PositionMiddle
OrganismCaenorhabditis brenneri (Nematode worm)
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Chromadorea> Rhabditida> Rhabditina> Rhabditomorpha> Rhabditoidea> Rhabditidae> Peloderinae> Caenorhabditis.
Aromaticity0.03
Grand average of hydropathy-0.708
Instability index52.76
Isoelectric point7.78
Molecular weight36835.77
Publications









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

>MDP27601
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.29|      20|      23|     185|     205|       1
---------------------------------------------------------------------------
  185-  205 (31.15/20.27)	PGKNVAqKPLITS.PSA..SSSNG
  209-  231 (27.13/12.92)	PIRTVG.TPLVNSePTGeySPRTG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.11|      17|      24|      10|      26|       2
---------------------------------------------------------------------------
   10-   26 (26.10/18.39)	RDLLLESADDLEHVVKI
   36-   52 (27.01/19.27)	RSVMLKNGESVSNMVKL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.72|      24|      31|     125|     148|       3
---------------------------------------------------------------------------
  125-  148 (39.44/25.66)	RPVNSEVLIKLAHQISAHNSISAP
  158-  181 (43.28/28.80)	RPFPQETEFRAGHLLNPKLQSSGP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      62.32|      18|      39|     276|     293|       7
---------------------------------------------------------------------------
  276-  293 (31.66/19.35)	SPSSSPTLKLKITGLPNR
  317-  334 (30.66/18.51)	SDSSDDEVSSKRTGGSNK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      36.34|      11|      14|      53|      63|       8
---------------------------------------------------------------------------
   53-   63 (18.21/11.22)	FDAKQQDIKDL
   70-   80 (18.13/11.15)	YQEREQLIRTL
---------------------------------------------------------------------------




































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 MDP27601 with Med4 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) TWQMGDPSRPFPQETEFRAGHLLNPKLQSSGPQLLPGKNVAQKPLITSPSASSSNGTSAPIRTVGTPLVNSEPTGEYSPRTGYGAVKTPPIQQQVLRGATPNEKQWQNQSAAGATSTQSPYNRISQSPSSSPTLKLKITGLPNRTGTIEQVRELQEVGQMSSDDSNSSDSSDDEVSSKRTGGSNKS
150
335










Molecular Recognition Features






MoRF SequenceStartStop




1) TLKLKITGLPNRTGTIEQVRELQEVG
2) VSSKRTGGSNKS
282
324
307
335