<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 MDP32649

Description RNA polymerase II holoenzyme cyclin-like subunit
SequenceMSADFWCSSQRNKWQLSRQSLLEARRKVLLLERKMIQNGLIKDYPNIHYDFNMRIYLHNLLIKLGRRLNIRQVALATAEIYLNRFLTRVSLKEINVYLLVTTCLYVACKIEECPQHIRLIISEARNLWPEYIPHDVTKLAEFEFYLIEEMDSYLFLHHPYKSLIQIRDFLNENSAVFGFTLTDDELQNAWSLVNDSYITDLHLLLPPHIIAVASIYITIVLKKNLSAIRVNSSAVNSNGGPNSMMFNRNPDQNSMHIDDLMILANPSTPGSDLVNNLERTNFHDMKLDEETIKINKFMNFLDHSHINLDEVVEAMQDMINIYVQWNRYNEQGVKKALQVMLLNRQL
Length346
PositionKinase
OrganismScheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (Yeast) (Pichia stipitis)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Debaryomycetaceae> Scheffersomyces.
Aromaticity0.09
Grand average of hydropathy-0.167
Instability index48.89
Isoelectric point6.31
Molecular weight40544.38
Publications
PubMed=17334359

Function

Annotated function Component of the SRB8-11 complex. The SRB8-11 complex is a regulatory module of the Mediator complex which is itself involved in regulation of basal and activated RNA polymerase II-dependent transcription. The SRB8-11 complex may be involved in the transcriptional repression of a subset of genes regulated by Mediator. It may inhibit the association of the Mediator complex with RNA polymerase II to form the holoenzyme complex. The SRB8-11 complex phosphorylates the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (By similarity). 
GO - Cellular Component
mediator complex	GO:0016592	IEA:EnsemblFungi

GO - Biological Function
cyclin-dependent protein serine/threonine kinase regulator activity	GO:0016538	IEA:EnsemblFungi
RNA polymerase II core promoter sequence-specific DNA binding	GO:0000979	IEA:EnsemblFungi

GO - Biological Process
negative regulation of transcription by RNA polymerase II	GO:0000122	IEA:EnsemblFungi
positive regulation of transcription by galactose	GO:0000411	IEA:EnsemblFungi
positive regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle	GO:0010673	IEA:EnsemblFungi









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP32649
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      78.47|      21|      21|     299|     319|       2
---------------------------------------------------------------------------
  285-  299 (15.57/ 7.04)	......MKLDEETIKINKFMN
  300-  320 (35.19/24.56)	FLDHSHINLDEVVEAMQDMIN
  322-  341 (27.72/17.89)	YVQWNRYNEQGVKKALQVML.
---------------------------------------------------------------------------




































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 MDP32649 with CycC domain of Kingdom Fungi
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