<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 MDP33685

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMESEKRVPADKDSPAKSLITALHLKYVEKPWSETINLVCRCMEKRKKDSNVPSKQLLDCLERLHKALNATSFTDMVTRLEIIAKHKGLGSHLSPSEDVCYITSDIFYLEVLFQPAGEVADVKVAHHGEAPVSSEMLCNLLRLKNFEEFGKELEGLSSLFNTSGDSETNMKMFSALQFVEKDLLKMFQIPRPVSSGDPWLDNVLHGRIGNVTPRNNGIRYPMSIEYYISPYDLLEEKMKPESRSCGNKVFVTAEVTNTIQRLPSASVIADSPQMTNEGFPVHATLDDLVSMELSACLFLKFPRPVPILSCFIEEFHRLTAGISVSEDLKQVPFYELLMKTKMNVTTWGSDSCCFLVTLPGHHRQGYVISQQWWLKPWEGALVHKIPFTHPGHVPSLLSLLRHQTAFSTLIASCVTGNEQALHLSMLNELDFHFEILPYTGTSFSLSFQHPVTGSMASLFVNVVDSNHISCKLFPPEVPDPSIDDWISKVMKRCMSIPVTMRAIFRKIASRETPTASETGAAPENTSEITATTSSSLPIAQENTQSANHCPGALVMFFLQNL
Length560
PositionMiddle
OrganismLepisosteus oculatus (Spotted gar)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Actinopterygii> Neopterygii> Holostei> Semionotiformes> Lepisosteidae> Lepisosteus.
Aromaticity0.08
Grand average of hydropathy-0.121
Instability index50.63
Isoelectric point6.00
Molecular weight62600.33
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	IBA:GO_Central

GO - Biological Function
retinoic acid receptor binding	GO:0042974	IBA:GO_Central
thyroid hormone receptor binding	GO:0046966	IBA:GO_Central
transcription coregulator activity	GO:0003712	IBA:GO_Central
vitamin D receptor binding	GO:0042809	IBA:GO_Central

GO - Biological Process
cellular response to thyroid hormone stimulus	GO:0097067	IBA:GO_Central
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP33685
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.61|      16|     117|       6|      29|       2
---------------------------------------------------------------------------
    6-   22 (22.44/27.74)	RvPADKDSPAKSLITAL
   45-   60 (28.17/11.16)	R.KKDSNVPSKQLLDCL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     132.87|      38|      41|     309|     347|       4
---------------------------------------------------------------------------
  309-  347 (62.71/40.93)	CFIEEFH.RLTAGISVSEDLKQVPFYELLMKtKMNVTTWG
  352-  390 (70.15/41.85)	CFLVTLPgHHRQGYVISQQWWLKPWEGALVH.KIPFTHPG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.51|      18|     169|     279|     305|       5
---------------------------------------------------------------------------
  283-  304 (25.38/30.21)	TLDDLVSMELSACLFLkfprPV
  480-  497 (34.13/10.79)	SIDDWISKVMKRCMSI....PV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     117.16|      34|      36|     403|     436|       6
---------------------------------------------------------------------------
  403-  436 (57.81/32.20)	TAFSTLIASCVTGNEQALHLSMLNELDFHFEILP
  440-  473 (59.35/33.22)	TSFSLSFQHPVTGSMASLFVNVVDSNHISCKLFP
---------------------------------------------------------------------------




































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 MDP33685 with Med1 domain of Kingdom Metazoa
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