<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 MDP27689

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMSLQDTTKFSNDFITETTTTAADTTTVAANPNTRTTSANHLRASSVSLLAEAVTNGTPSSSEFNRSYDNDSSKDVLSEVRIYDDIITYEKALSRLIDSVDKFKPNLNIAQELIQADKSLFDTLNSFIQYDEIDLHLKALETKASKIDELTQSTLQTLNECHDDLNKLPTLPQIEFELNTILNQRTKINSTILLDYATKLSKFTKIPPTFDKGSIGPNNFIWPAEDSLRRGMLAMASLKADQLTYIPGQAQSMSKEKALPTEVQETQEQTQTQQQDQEEQPRRESFVFSGKNKEEEEETTHTHEDSKRKQEEKDHESGDEDAMDIDLDLFNPDEF
Length334
PositionMiddle
OrganismNaumovozyma dairenensis (strain ATCC 10597 / BCRC 20456 / CBS 421 / NBRC 0211 / NRRL Y-12639) (Saccharomyces dairenensis)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Saccharomycetaceae> Naumovozyma.
Aromaticity0.06
Grand average of hydropathy-0.790
Instability index52.61
Isoelectric point4.54
Molecular weight37776.12
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

>MDP27689
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     202.94|      45|      92|     124|     169|       1
---------------------------------------------------------------------------
   82-  122 (27.80/12.61)	.....YDDIITYEKALSRLIDSVDkfkpnlNIAQELIQADKSLFDT.....
  124-  168 (72.18/41.00)	NSFIQYDEIDLHLKALETKASKID......ELTQSTLQTLNECHDDLNKLP
  169-  203 (39.62/18.11)	....TLPQIEFELNTILNQRTKIN..........STI..LLDYATKLSKFT
  217-  259 (63.33/39.06)	NNFIWPAEDSLRRGMLAMASLKAD......QLTYIPGQAQSMSKE..KALP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      52.53|      15|      15|     290|     304|       2
---------------------------------------------------------------------------
  290-  304 (26.27/15.60)	KNKEEEEETTHTHED
  306-  320 (26.26/15.59)	KRKQEEKDHESGDED
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      49.50|      14|      15|       5|      18|       3
---------------------------------------------------------------------------
    5-   18 (24.94/14.89)	DTTKFSNDFITETT
   23-   36 (24.57/14.57)	DTTTVAANPNTRTT
---------------------------------------------------------------------------




































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 MDP27689 with Med4 domain of Kingdom Fungi
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