<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 MDP08945

Description Mediator of RNA polymerase II transcription subunit 16
SequenceMRGARAGREMAAPDSGRWGECGPRPPGRLGARGGQEPGTLLGAVGMMDLAYVCEWEKWTKSTYCPSLPLACACEAITCLEWDQSGSRLLSADADGQIKCWSMADHLANSWESSVGSQVEGDPIVALSWLHNGVKLALHVEKSGASSFGEKFSRVKFSPSLTLFGGKPMEGWIAVTVSGLVTVSLLKPSGQVLTSTESLCRLRGRVALADIAFTGGGNIVVAAADGSSASPVKFYKVCVSVVSEKCRIDTEILPSLFMRCTTDPNRKDRFPAITHLKFLARDMSEQVLLCASSQTSSLVECWSLRKEGLPVNNIFQQISPVVGDKQPMXLKWRILSATNDLDRVSAVALPKLPISLTNTDLKVASDTQFYPGLGLALAFQDGSVHMVHRLSLQTMAVLYSSAPRSLDEPALKRPRTTGPAVHFKAMQLSWTSLALVGIDNHGKVLSTRILAMKASLCKLSPCTVARVCDYHTKLFLMAITSTLKSLLRPHFLNTPDKSPGDRLAEICAKITDVDIDKVMINLKTEEFVLDMNTLQALQQLLQWVGDFVLYLLVSLPNQVSPEPQPRPLVSLPNQGSPLRPGHSFLRDGTSLGMLRELMVVVRIWGLLKPSCLPVYTATSDTQDSMSLLFRLLTKLWICCRDEGPASEPDEGLVDECCLLPSQLLVPNLDWLPASDGLVSRLQPKQPLRLRFGRAPTLPSSTSTLQLDGLSRAPGQPKIDHLRRLHLGAYPTEECKACTRCGCVTMLKSPNKTTAVKQWEQRWIKNCLCGGLWRRVPLSCP
Length779
PositionTail
OrganismNeotoma lepida (Desert woodrat)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Myomorpha> Muroidea> Cricetidae> Neotominae> Neotoma.
Aromaticity0.06
Grand average of hydropathy-0.023
Instability index48.89
Isoelectric point8.80
Molecular weight85039.00
Publications









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
GO - Biological Process








Interaction





Binary Interactions











Repeat regions





Repeats

>MDP08945
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.88|      10|      15|     551|     560|       1
---------------------------------------------------------------------------
  551-  560 (20.67/11.48)	LVSLPNQVSP
  567-  576 (21.22/11.97)	LVSLPNQGSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.14|      18|      18|     334|     351|       3
---------------------------------------------------------------------------
  334-  351 (29.60/16.93)	LSATN.DLDRVSAVAL.PKL
  353-  372 (22.54/11.37)	ISLTNtDLKVASDTQFyPGL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      85.75|      29|     300|     126|     158|       6
---------------------------------------------------------------------------
  126-  158 (46.79/41.65)	LSWlhngVKLAL.HVEKSGA..SS..FGEKFSRVKFSP
  427-  460 (38.96/24.08)	LSW....TSLALvGIDNHGKvlSTriLAMKASLCKLSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      69.75|      15|      32|     681|     695|       7
---------------------------------------------------------------------------
  659-  672 (20.22/ 9.43)	.PS.QLL.VPNLDWLPA
  681-  695 (28.99/16.93)	QPK.QPL.RLRFGRAPT
  714-  730 (20.55/ 9.71)	QPKiDHLrRLHLGAYPT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      47.11|      13|     301|     298|     310|       8
---------------------------------------------------------------------------
  298-  310 (26.16/16.29)	VECWSLRKEG.LPV
  600-  613 (20.95/11.33)	VRIWGLLKPScLPV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      39.05|      10|      18|      70|      81|       9
---------------------------------------------------------------------------
   70-   81 (17.83/19.07)	ACACEAITCleW
   91-  100 (21.22/14.27)	ADADGQIKC..W
---------------------------------------------------------------------------




































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 MDP08945 with Med16 domain of Kingdom Metazoa
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