<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 MDP28640

Description Mediator of RNA polymerase II transcription subunit 16
SequenceMIELGNQAVSWSKTGLIVYSDKTSTDSNLCMTFLETINGTTWRFHPPKKYTIHPHLYESQNTTSSSNSNGGKYSINAGRSGSPPNYQGSKANRTTNKNCPFFYEITSVHWNNWFNLPGDMLAVCDELGNLTILILGQSLQGPVTMDKLTMLFQDNIYKIHNNPMQLNETSEDSVKCVKKESKKEYPTRISELFWLSSSKPVISSQFCVLDSSINSYRNKVQQIPPYGVFHPPFMKYSCLAVRKNGQIDFWYQFSNSKSHKKISLHLNTAQGKSSNDMDWVEYTNISALNEDQSLLISTYSRLTKVVSFYKLHVNWNITDINNSQLNDPLLSLFHLSDVAVEQIDDEGNLLEFQYLYVISKAPVEKDSAPEILLLYNVLDTGKSIIKRYKLIPTQLNAHYLKILKPDISRLDEQKLKPKHRYTLNCMPEIHLDKKVINIISNILDGFVSIHFEDSTIETYSKTDWKVETERLHHQNRQGKFRDILTSVLSAGFNYPKLPPQSTLEWAIVSPTMCGVLIKQSCKDIPQFISISHENTDDASLDKVNSTAFAFAFVASIHRQLSAEDLSIACKTHLIKISDKDQDRGKECITSLMADIYSFFNITPDAPPELLEKMISSRPVQKTMLLQLELGSSCRHKNVYEMARIIMNLRNVYFAFNGVTRNLQFAIEQLNTISPAQLAGGKLFQTSFTKQDLIHSLIPIAKWLIKFITYLIQEVLILINKGYSSASVSSLVYGVFGARIPRSLLLSILNEIKRVIHLVTKFPENNYPVLNESSKFLKKILSESTVNIEKFETFLVDVNTKFMNLNSKNQSTTREPSLLVKAEIPEDISKISSFLLTYSKNAIISHIDPAQVYFADTSGLRISKDEIFQSSLLHLSQPLDKGLVTDTKSLGPSHQTSRSFSKIEYDGVSYDTFTDNEMTNGSLKRCCRCGCVTRAGYTISEDKTIISTSIKTRRWPTMYARVCICSGYLYELEKAHPEKKESK
Length982
PositionTail
OrganismTetrapisispora phaffii (strain ATCC 24235 / CBS 4417 / NBRC 1672 / NRRL Y-8282 / UCD 70-5) (Yeast) (Fabospora phaffii)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Saccharomycetaceae> Tetrapisispora.
Aromaticity0.09
Grand average of hydropathy-0.291
Instability index42.98
Isoelectric point8.63
Molecular weight111554.40
Publications
PubMed=22123960

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
core mediator complex	GO:0070847	IEA:EnsemblFungi
mediator complex	GO:0016592	IEA:EnsemblFungi

GO - Biological Function
RNA polymerase II activating transcription factor binding	GO:0001102	IEA:EnsemblFungi

GO - Biological Process
negative regulation of transcription by RNA polymerase II	GO:0000122	IEA:EnsemblFungi
positive regulation of transcription by RNA polymerase II	GO:0045944	IEA:EnsemblFungi
regulation of establishment of protein localization to chromosome	GO:0070202	IEA:EnsemblFungi
RNA polymerase II preinitiation complex assembly	GO:0051123	IEA:EnsemblFungi









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP28640
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      86.53|      27|     183|     673|     704|       2
---------------------------------------------------------------------------
  673-  704 (41.22/31.32)	SPAQLAGGKLFQTSftkqdLIHSLIPIAKWLI
  857-  883 (45.31/23.73)	SGLRISKDEIFQSS.....LLHLSQPLDKGLV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     226.02|      56|     183|     262|     317|       3
---------------------------------------------------------------------------
   52-  113 (76.78/40.45)	IHPHLYESQNtTSSSNSNGG..KYSiNAGRSGSPPNYQ.GSKANRTTnkNCP..FFYEItSVHWNnW
  114-  162 (52.12/25.34)	FNL.....PG.....DMLAVcdELG.NLTILILGQSLQgPVTMDKLT..MLFqdNIYKI.HNN....
  262-  317 (97.13/52.92)	ISLHLNTAQG.KSSNDMDWV..EYT.NISALNEDQSLL.ISTYSRLT..KVV..SFYKL.HVNWN.I
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     139.08|      45|      57|     473|     523|       4
---------------------------------------------------------------------------
  473-  523 (71.87/58.39)	HQNRQGKFrdiLTSVLSAGFNY...PKLPPQ.STLEWAIVSPTMcgvLIKQSCKD
  532-  580 (67.21/39.40)	HENTDDAS...LDKVNSTAFAFafvASIHRQlSAEDLSIACKTH...LIKISDKD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      60.65|      20|      55|     369|     388|       5
---------------------------------------------------------------------------
  369-  388 (36.54/21.03)	PEILL.......LYNVLDTGKSI......IKRY
  427-  459 (24.10/11.66)	PEIHLdkkviniISNILDGFVSIhfedstIETY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.05|      14|     610|     354|     367|      13
---------------------------------------------------------------------------
  354-  367 (25.72/18.85)	YLYVISKA.PVEKDS
  967-  981 (21.33/14.28)	YLYELEKAhPEKKES
---------------------------------------------------------------------------




































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 MDP28640 with Med16 domain of Kingdom Fungi
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