<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 MDP24844

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMVASHLSNSVLVLYRSYPGNPGLKEYLECAIEDGILPLSTFVSTLLQAARSPELDTPTTLDHLCQIALEVQKRSDSQGANSLIPYSESQIVILQTIQDGLALLRTVHTLPISQHHNELASRTEELVRHLLCFASDLSQVSVAQACVSFTDVNDLLNNFRFNLETRQMLESFSILLGLLIGDDAKVAREAQMMQSLQLALGKGDTGGPASDTDVITLGLVHHYLVVILCIDILLRSQMSKVSHRAHEFGAGNTPGVVTLLVYIFRWSSWTPTVFYTQLILSAFIGLTQHPTDCTIWKAFIVGRLPNLISAFEAVVSADHAMVSDWRGGLRSGLVSVFQQHDVIIQCDHTLSEGGGSNIITEENMPSSFTREFLQQFVKLELIDKNMGAQLDPSISKENMSKLSDTHDTSMDFSLYLESRLTPDMVMNDAQSWLDRIWRDAGSHTTFGNFVLKKFSSLVAAVEVESLGQLCKLLYTHAIALDIVALHVKISDLLFHALLFLDSYDCETIGDPQTAVSHLGDVVLFVQYTLAHFQFDTTTFTKDGRSISAAFLKSAFTVYPVEILPPDELLSFNGWFKAIFDSSSEGIEDTILRSTQPKTLLRISATLFSQAIKAASAQKIDKDVLFNGVSYFTGPLLNWTLVGVIKALSQEILLKGLSAHIHIEILQTLVLSSSCPQPVLALCSPQILRLLSELGNGATTSMIDIDVWAMQRAVRNASGSKADNDPNSRVQIWQQDPQRALQNVFLQARSHKTPVLDVERCLRMIPVTKFLQIMWMELFESAKLGEMESCKRIATFVLTMPRCSNVPPLLPIFMHLVLPSLIAAADRQQAQEQNISVELFVAVISSVLSAALHLECAMATVYGNDRVLLGQASSAVARRLAADLGSKRRSPTSQDIVQRLVASQSFTANFPMFIAEL
Length915
PositionTail
OrganismLaccaria bicolor (strain S238N-H82 / ATCC MYA-4686) (Bicoloured deceiver) (Laccaria laccata var. bicolor)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Basidiomycota> Agaricomycotina> Agaricomycetes> Agaricomycetidae> Agaricales> Tricholomataceae> Laccaria.
Aromaticity0.07
Grand average of hydropathy0.180
Instability index46.75
Isoelectric point5.57
Molecular weight100998.13
Publications
PubMed=18322534

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

>MDP24844
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.96|      14|      39|     751|     764|       1
---------------------------------------------------------------------------
  751-  764 (26.78/19.19)	TPVLDVERCLRMIP
  793-  806 (28.19/20.61)	TFVLTMPRCSNVPP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     108.08|      27|      39|     597|     623|       2
---------------------------------------------------------------------------
  597-  623 (42.05/32.03)	TLLRISATLFSQAI..KAASAQKIDKDVL
  638-  664 (32.16/22.61)	TLVGVIKAL.SQEIllKGLSAH.IHIEIL
  699-  723 (33.87/24.24)	SMIDIDVWAMQRAV..RNASGSKADND..
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      35.79|      14|      25|     166|     190|       4
---------------------------------------------------------------------------
  180-  201 (15.31/28.97)	GDDAKVAREaqmmqslqLALGK
  202-  218 (20.47/12.99)	GDTGGPASD.....tdvITLGL
---------------------------------------------------------------------------




































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 MDP24844 with Med5 domain of Kingdom Fungi
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