<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 MDP27679

Description Mediator of RNA polymerase II transcription subunit 16
SequenceMSLIGQHPVSWSKNGVIAYADPHSPDANLRITFLETINGINWRFHPPTKYILHPQLHEPQFSHSYTLNTAPSASEHSNSMTSSTIGLHPTPTRTVTTANTTTVSSIPPSAGTSVHSKGNPQFFYSITGVYWNNWLSLPGDMLAVCDELGNLTMMIAGQQPNGANTFERLTMLFQDNVYKIYNHVMSLKPSTSIPLITEKFERKHTKKEYNTTIMDFEWLSATKITMAAKFCALDTTSNTYKNKLQQIPPYGVFHPAFMKYACLGIRKNGQINFWYQFSNSKDHKKITLQLHTSVNQRTKELDWLTFAKITPIVEDQCMLISTYSKLTNKLIFYELHVNWNVNATKPTALNDPTVKIQQILETTIDPVDNEGNPLKLSNIHIMSKTPTENDPSPEILLVYDIMGSRKTLVKRYKLVRTQLPLDFVSILKSENNSGGGQYLRSNRYNFIHQVDLPLEKRVKQVTTELINGFITFYFEDGTTIVYNQGDWKVETERLLNQPLSGNYNNLVTSMLSVNFQFPKLPNLSAIEWVRVSPSLTGIIAKIANKSTPQYFPLMKHDVTDTSKDDLNATAFAFAYVIGTYRQLSAEDLTITCKTHLMQIAKLDENRAKNFVMLIVARIYTFLNVSLDPPKEIMDKFLTGRQFQRITLFQLELGTCFDGSNLDEMARLLLNLKSAHFAFNGVSRNLHFAIEQINTTNAAQQLASGKTFQTVFSKQDLIYSLIPIAKWFVKFITYMIQELLILINNPPNKENTLVIGVFGSKVSRMLILLILVEIKKIVQIITKFPENTYPVLNESSYYLRTVLSDSPVNFEKFETFLVDVNNKFSAYNEQQQKLNPQSQSTQMLRECSLLVRAEVLPEFSKIGEFLLAYSNNVLISHVDAARVYFCDTSGLRISSTELFRPEYCKLLQPLEKGLVIDPDDNPILPLNPGRFSPMVYDGISYDRFTKQEVSEEKIKRCARCGCVTRAGYVVSNDKTITSTIITTKRWPSMYTRNCTCSGMLYELRI
Length1004
PositionTail
OrganismNaumovozyma dairenensis (strain ATCC 10597 / BCRC 20456 / CBS 421 / NBRC 0211 / NRRL Y-12639) (Saccharomyces dairenensis)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Saccharomycetaceae> Naumovozyma.
Aromaticity0.10
Grand average of hydropathy-0.213
Instability index33.44
Isoelectric point8.82
Molecular weight114290.09
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

>MDP27679
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      71.46|      20|      59|      46|      66|       1
---------------------------------------------------------------------------
   46-   66 (36.84/26.48)	PPTKYI.LHPQlHEPQFSHSYT
  107-  127 (34.62/20.06)	PPSAGTsVHSK.GNPQFFYSIT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.42|      12|      34|     411|     422|       2
---------------------------------------------------------------------------
  411-  422 (21.55/15.08)	RYKLV.RTQLPLD
  443-  455 (17.87/11.10)	RYNFIhQVDLPLE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     128.80|      39|      83|     204|     244|       3
---------------------------------------------------------------------------
  204-  244 (65.03/48.73)	HTKkeYNTTIMDFEWLSATKIT.MAAKFCALDTTSNTYKNKL
  291-  330 (63.77/41.62)	HTS..VNQRTKELDWLTFAKITpIVEDQCMLISTYSKLTNKL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      84.95|      27|      35|     723|     751|       4
---------------------------------------------------------------------------
  723-  751 (42.48/32.82)	IAKWFVKFITYMIQELLILINNPPnkENT
  761-  787 (42.46/26.23)	VSRMLILLILVEIKKIVQIITKFP..ENT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      43.87|      12|      36|     345|     356|       5
---------------------------------------------------------------------------
  345-  356 (21.23/11.58)	KPTALNDPTVKI
  384-  395 (22.65/12.84)	KTPTENDPSPEI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     167.23|      54|      63|     591|     645|       6
---------------------------------------------------------------------------
  591-  645 (86.70/47.05)	TC..KTHLMQIAKLDEN.RAKNFVMLIVARIYTFLNVSLDpPKEIMDKFLTGRQFQRI
  654-  710 (80.53/39.64)	TCfdGSNLDEMARLLLNlKSAHFAFNGVSRNLHFAIEQIN.TTNAAQQLASGKTFQTV
---------------------------------------------------------------------------




































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 MDP27679 with Med16 domain of Kingdom Fungi
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