<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 MDP04335

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMNCELILKKDFTNDIIELDKKMSSLFETVFKKKDEPDENKKENFKSLVNDISKIEIGIIQKLKSVPCIDKTQKKIKRMKSEIAKYDKAILKTEAGLYRIYGAVTNSLSIAQEKLSELKKSQQQQNTKNDILDISKSLTKNYSIAAPPFWKPEDYVKPFPTGVQFVRGCLKHNIPLKDISRRRILRNPTINTISNIRNLQQNDKMYSSLSNQQRQSNSMQQANYNLQNSNYKNLNKSYQSPKNQKGYMTQQRGSYQNFLQRSINPQHHYSQVGNRVNKMPYQHDQNRYPGDGQVGTKRFLTKPGQSDIHQSPGISKRTPSTANVQMKPQRLPSYSSYLQKTEDGTTFKKAKKLKVGRNMRILPWSSFIDPYYKGYETSTSDDSDELNSEEEKEITTKYYAKKAGPSVELPVERTDSPDTSRHMNYL
Length425
PositionMiddle
OrganismStrongyloides venezuelensis (Threadworm)
KingdomMetazoa
LineageEukaryota> Metazoa> Ecdysozoa> Nematoda> Chromadorea> Rhabditida> Tylenchina> Panagrolaimomorpha> Strongyloidoidea> Strongyloididae> Strongyloides.
Aromaticity0.08
Grand average of hydropathy-1.034
Instability index54.41
Isoelectric point9.69
Molecular weight49147.15
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

>MDP04335
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.90|      19|      29|     194|     212|       1
---------------------------------------------------------------------------
  194-  212 (34.21/18.22)	NIRNLQ.QN.DKMYSSLSNQQ
  224-  244 (25.69/11.97)	NLQNSNyKNlNKSYQSPKNQK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     136.81|      34|      80|     247|     280|       2
---------------------------------------------------------------------------
  247-  280 (62.15/38.07)	MTQ.QR.GSYQNFLQRSIN....PQHHYSQ.VGNRVNKMPY
  288-  316 (27.98/13.21)	PGDgQV.GT.KRFLTKPGQ....SDIHQSPgISKR......
  325-  363 (46.69/26.82)	MKP.QRlPSYSSYLQKTEDgttfKKAKKLK.VGRNMRILPW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     160.84|      52|      79|      40|      99|       3
---------------------------------------------------------------------------
   40-   99 (73.58/67.81)	KKENFKSLVNDISKieigiiqKLK.....SVPCIDKTQKKIKRMKSEIaKYDKAILKTEAGLYRI
  122-  178 (87.26/59.25)	QQQNTKNDILDISK.......SLTknysiAAPPFWKPEDYVKPFPTGV.QFVRGCLKHNIPLKDI
---------------------------------------------------------------------------




































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 MDP04335 with Med4 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) QQNDKMYSSLSNQQRQSNSMQQANYNLQNSNYKNLNKSYQSPKNQKGYMTQQRGSYQNFLQRSINPQHHYSQVGNRVNKMPYQHDQNRYPGDGQVGTKRFLTKPGQSDIHQSPGISKRTPSTANVQMKPQRLPSYSSYLQKTE
2) YETSTSDDSDELNSEEEKEITTKYYAKKAGPSVELPVERTDSPDTSRHMNYL
199
374
341
425










Molecular Recognition Features






MoRF SequenceStartStop




1) EKEITTKYYAKK
2) RHMNYL
3) RNMRILPWSSFIDPYYKGYET
390
420
356
401
425
376