<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 MDP01613

Description Mediator of RNA polymerase II transcription subunit 16 (Fragment)
SequenceAMDLAYVCEWEKKPKSNHCPSIPLVCAWSCRNLIAFTTDLKNEEEKDLTHMVHIIDTEHPWDVYSVNSGHTEVITCLEWDQSGSRLLSADADGHIKCWSMTDHLANSWESTVGSAVEGDPIVALSWLHNGVKLALHVEKSGASNFGEKFSRVKFSPSLTLFGGKPMEGWIAVTISGLVTVSLLKPNGQVLTSTESLCRLRCRVALADVAFTGGGNIVVATSDGSSTSPVQFYKVCVSVVNEKCKIDTEILPSLFMRCTTDPARKDKYPAITHLKFLARDMSEQVLLCASNQNSSIVECWSLRKEGLPVNNIFQQISPVVGDKQPMILKWRILSATNDLDRVSAVALPKLPISLTNTDLKVANDTKFFPGLGLALAFHDGSVHIVHRLSLQMMAVFYGSSSQRPVDEQTIKRQRTAGPLVHFKAMQLSWTSLALAGIDSHGKLSMLRISPSMGHVLDMNMSLRHLLFLLEYCMVTGYDWWDILLHVQPNMVQNLVEKLHEEYMRQNAALQQVLSTRIVAMKASLCKLSSSTIARVCDYHAKLFLIAISCTLKSLLRPHILNTPDKSPGDRLTEVCSKITDIDIDKVMINLKTEEFVLEMTTLQSLQQLIQWVGDFVLYLLASLPNQGSPVRPGHSFLRDGASLGMFRELMVVIRIWGLLKPSCLPVYTATSDTQDSMSLLFRLLTKLWLCCTCCEENHITEPDDTLIDECCLLPSQLLIPNIDWLPINDGIISRLQNKQLVRLQFGKAPGLVGHSVSSQYDAFVRAPGQPKIDHLRRLHLGAYPTEECKSCTRCGCVTMLKSPNKVTAVKQWEQRWIKNCLCGGLWRRMPLSYS
Length833
PositionTail
OrganismCuculus canorus (common cuckoo)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Dinosauria> Saurischia> Theropoda> Coelurosauria> Aves> Neognathae> Cuculiformes> Cuculidae> Cuculus.
Aromaticity0.07
Grand average of hydropathy0.007
Instability index47.38
Isoelectric point7.89
Molecular weight92993.11
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

>MDP01613
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.43|      29|      34|     655|     688|       1
---------------------------------------------------------------------------
  660-  688 (52.93/37.63)	PSCLPVY.TATSDTQ.DSMSLLFR..LLTKL.WL
  691-  724 (36.50/14.33)	TCCEENHiTEPDDTLiDECCLLPSqlLIPNIdWL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     188.30|      52|     139|     454|     508|       2
---------------------------------------------------------------------------
  424-  451 (23.72/ 8.19)	...MQLSWTSL.......ALAGIDSHGKLsmLRISPSM...................
  454-  508 (81.41/59.94)	VLDMNMSLRHLLFLLEYcMVTGYDWWDIL..LHVQPNMvQNLVEKLHeEYMRQNAAL
  595-  642 (83.17/48.16)	VLEMT.TLQSLQQLIQW...VG.DFVLYL..LASLPNQ.GSPVRPGH.SFLRDGASL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      85.28|      30|      36|      87|     120|       3
---------------------------------------------------------------------------
   67-  105 (35.88/32.11)	NSGHTEVITCLEWDQsgsrlLSADADGhIKcwsMTDHLA
  106-  138 (49.40/26.57)	NSWESTVGSAVEGDP..ivaLSWLHNG.VK...LALHVE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     116.14|      39|     139|     163|     205|       4
---------------------------------------------------------------------------
  163-  205 (52.74/49.44)	GKPMEGwIAVTISGLV...TVSLLKpnGQVLTSTESLCRLRCrVAL
  305-  346 (63.39/39.69)	GLPVNN.IFQQISPVVgdkQPMILK..WRILSATNDLDRVSA.VAL
---------------------------------------------------------------------------




































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 MDP01613 with Med16 domain of Kingdom Metazoa
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