<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 MDP29889

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMAPAVERHEGNLAVSAGHKRASSVSLLQEGTDAAALAEDLKKVRIYSGIVEYEDTLAALVESVDSYKPDMAVAQRLVDADKELFASLDKFKEYDEISTRLGELKGKSTALDTKTRDILEKLNECHDELNKLPYLEQVQFEMDTILEQREKINSSELLDYATKLSKFTRIPPTFDKGSIGPNNFIWPAEDALRKGMLAIAALHSRELTRIPGQDDAEDKKKQTEKPDVPEPAPVTEERRSSFVFGDTSTADDQKSSSAHSDHDDDDAMDLDLDLFNPDEF
Length279
PositionMiddle
OrganismKazachstania naganishii (strain ATCC MYA-139 / BCRC 22969 / CBS 8797 / CCRC 22969 / KCTC 17520 / NBRC 10181 / NCYC 3082) (Yeast) (Saccharomyces naganishii)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Saccharomycetaceae> Kazachstania.
Aromaticity0.06
Grand average of hydropathy-0.651
Instability index35.90
Isoelectric point4.60
Molecular weight31136.22
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:InterPro

GO - Biological Function
RNA polymerase II core promoter sequence-specific DNA binding	GO:0000979	IEA:EnsemblFungi
transcription coregulator activity	GO:0003712	IEA:InterPro

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IEA:InterPro
transcription by RNA polymerase II	GO:0006366	IEA:EnsemblFungi









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP29889
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     125.84|      43|      44|       6|      49|       1
---------------------------------------------------------------------------
    6-   49 (64.37/41.16)	ErHEGNLA..VSAGHKRASSVSLLQEGTDA.AALAEDLKKVRIYSGI
   51-   96 (61.47/35.06)	E.YEDTLAalVESVDSYKPDMAVAQRLVDAdKELFASLDKFKEYDEI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.73|      15|      38|     156|     170|       2
---------------------------------------------------------------------------
  156-  170 (26.69/18.52)	LLDYATKLSK.FTRIP
  195-  210 (22.04/14.23)	MLAIAALHSReLTRIP
---------------------------------------------------------------------------




































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 MDP29889 with Med4 domain of Kingdom Fungi
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