<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 MDP25806

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMDSEISLKKLIKVSIKKKSPPKVFLDLVKQWLEKGDRSDNEILESLIELHPSLISEQEQKSLQLHYAIQLACSSLDEHRRFMKLLPQSTLDSQRDYILYLRNNLKSLFSENMMREFINGTFVEYSKGICERMRSNLSATLKRLWTYILFLWGTIIDHYDSFITVPVFKDLGIHIVGTLKDLGDSNMLAYFSNKANSILNPSELHKDVHLPIATQKHKTEVPSIASMKRALALNGSSKKIQHYFKFKRFIWLNSRFRLWESNDVVEKYFSFFKISTQKIEDVIKEIFSAFFGGITTAIHSHEDAFVIFNWKTFIVSRLPQVLKESKVVHNQTIPENIEKMILSEMHQYNDEVITKMTVGGMKDKPFDLRKQFLKSCVYTRVISLDAMLKIFPEETENVSPALITHEREQLAHVESLSSDINSRLLDINTELTSLEESKLIETFQNIPSSNIIFSIMKQQQLCKSTHRAIDVLIREKSCEKLSRLILALANVLPVANYIFYNDEKGPWGILDKLISFLDGESFGVDADDSSFQDTYAHFGILLAGVILLTSNFGIDFDNVCIETSYTVTYINRIFFRSAGDMTDRFEGEDEQEKNIVQNYYNLMGAWLNALFDVNNEGLSDDLIKSVGVKQIYK
Length632
PositionTail
OrganismClavispora lusitaniae (strain ATCC 42720) (Yeast) (Candida lusitaniae)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Metschnikowiaceae> Clavispora.
Aromaticity0.10
Grand average of hydropathy-0.181
Instability index49.97
Isoelectric point6.14
Molecular weight72867.92
Publications
PubMed=19465905

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
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

>MDP25806
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      96.69|      32|     110|     313|     346|       1
---------------------------------------------------------------------------
  313-  346 (52.44/38.21)	IVSRLPQV......LKESKVVHN.QTIPENieKMILSEMHQ
  419-  457 (44.25/26.19)	INSRLLDInteltsLEESKLIETfQNIPSS..NIIFSIMKQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      98.64|      26|     113|     142|     168|       2
---------------------------------------------------------------------------
  120-  139 (26.20/14.83)	.....TFVEYSKG.ICERMRSNLSAT
  140-  165 (48.27/30.25)	LKRLWTYILFLWGTIIDHYDSFITVP
  167-  184 (24.17/14.73)	FKDLGIHIV...GTLKDLGDS.....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      93.72|      27|      28|     499|     526|       4
---------------------------------------------------------------------------
  499-  526 (45.58/35.68)	YNDEKGPWGILDKLISFLDGeSFGVDAD
  530-  556 (48.14/32.79)	FQDTYAHFGILLAGVILLTS.NFGIDFD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.32|      15|      16|     261|     275|       5
---------------------------------------------------------------------------
  261-  275 (27.88/17.30)	NDVVEKYFS.FFK.IST
  279-  295 (18.44/ 9.02)	EDVIKEIFSaFFGgITT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.63|      11|     353|     239|     255|       7
---------------------------------------------------------------------------
  226-  236 (18.17/16.38)	MKRALALNGSS
  245-  255 (21.46/ 6.57)	FKRFIWLNSRF
---------------------------------------------------------------------------




































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 MDP25806 with Med5 domain of Kingdom Fungi
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