<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 MDP04415

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMVAFLTSVTSKAGFANAMEQKDRILEFCLRSSIPVKQYLPHYTSEEDWKTHFGKKWDLLVERKFKYDPLAILAPGQRIFQRNFDTQSTRSLHETRINSKSHNIHFSHLTIDINARSNRILDTATSKMLQSHLQSPARLGLTNPNSPLIPPNHNPNLKLPSSTTTTTSFSHNSIQPRLSATSSSVLIPRLPPLSRAQCLLLQMSSLASNLFEVCPNPSIWLTAFRGTLPTFFSSPPPLFTVPKLPLVSTTKEVLVLFTSLQTQLFEAVGELQEILNFQDAKDKLSREIRSTNGNLLGFSKRIGETERALDNLMDDYEDYQRLKRRKIGDEEKNEDDGDEDIKGSSFIEVKDILSYAHRISYTTFAPPEYASGQVPLRGALPPAPQDEQMRASQLYRVNELNLGLPKTLLDARDKMTDNVVEHLIEPEPVSFPQINIPPGWRKGMPVDLQLPMGLPPVPPGWKPGDPIPLPPLEQPTLGDIGRIEEKVVVGPPGSVVGSLHPKPAEAIQVKYVQLDINPEDDSSDEYSSGAESSDSED
Length536
PositionMiddle
OrganismZostera marina (Eelgrass)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Zosteraceae> Zostera.
Aromaticity0.07
Grand average of hydropathy-0.454
Instability index60.03
Isoelectric point5.73
Molecular weight59838.19
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. 
ECO:0000256	RuleBase:RU364141
GO - Cellular Component
core mediator complex	GO:0070847	IBA:GO_Central
mediator complex	GO:0016592	IEA:InterPro
GO - Biological Function
cytokinin dehydrogenase activity	GO:0019139	IEA:InterPro
flavin adenine dinucleotide binding	GO:0050660	IEA:InterPro
transcription coregulator activity	GO:0003712	IBA:GO_Central
GO - Biological Process
cytokinin metabolic process	GO:0009690	IEA:InterPro
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central

Interaction

Binary Interactions











Repeat regions





Repeats

>MDP04415
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      67.68|      16|      18|     435|     451|       1
---------------------------------------------------------------------------
  435-  451 (31.33/20.83)	IPPGWRKGMPVDLQlPM
  456-  471 (36.35/20.14)	VPPGWKPGDPIPLP.PL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     153.17|      48|     128|     222|     287|       2
---------------------------------------------------------------------------
  186-  211 (27.79/11.17)	..........................IPRLPPLSRAQCLLLQMSSLASNLFE......................
  223-  287 (70.80/69.17)	FRGTLPtffssPPP.........LFTVPKLPLVSTTKEVLVLFTSLQTQLFEavgelqeilnfqDAKDKLSREI
  375-  418 (54.58/26.86)	LRGALP.....PAPqdeqmrasqLYRVNELNL.GLPKTLL........................DARDKMTDNV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     110.84|      35|      36|     106|     141|       3
---------------------------------------------------------------------------
  106-  141 (55.15/36.62)	SHLtIDINARSNRILDTATSKMLQ.SHLQSPARLGLT
  145-  180 (55.69/32.66)	SPL.IPPNHNPNLKLPSSTTTTTSfSHNSIQPRLSAT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.80|      16|      24|     299|     314|       4
---------------------------------------------------------------------------
  299-  314 (27.06/18.17)	KRIGETERALDNLMDD
  324-  339 (27.75/18.80)	RKIGDEEKNEDDGDED
---------------------------------------------------------------------------




































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 MDP04415 with Med4 domain of Kingdom Viridiplantae


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) IQVKYVQLDINPEDDSSDEYSSGAESSDSED
2) PMGLPPVPPGWKPGDPIPLPPLEQPTLGDIGRIEE
506
450
536
484










Molecular Recognition Features






MoRF SequenceStartStop




1) EAIQVKYVQLDINPE
504
518