<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 MDP29961

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMSAGDVSLETLVKVCLKKRATSQVFLSLFKQLNHKQEVGVEDLVGLLKTRQEFDPLEVVYLTSASLGDQSSNLRLAKLLENLGIATEENQYLILNSLTNTSRDDHFKSQFPFNSFEISAILTSLSSYFKNLLENQQKQLIIFESICYFLNVLFEIIPFEISPLSPEQNELLTIIIGEIKHQGNHHLAETLESNIHKSLKKSNNRQSISNPSSSGSSNASITSTSSHTSHLSFLKTNKLPKFIWLNSVIQNWETSSDKFLSAFSQFVKVKTNQNILNELINTSFECITVVLQSRDSSDLFIKNWKLFFTKKLPILIKSLNLKNIESLLINALNLIDPKIFKTIKLISSDGDNNNLGDQNDDMFSSFPSTNTDIRHDFLRSCIALKLLPSTAFNTILKEDSNAENRPLLENDDALDLDGHVIDLQTRLNQTLIDINPEFIPLEDSGLLEFLNSIEQFEGTKQFEISKLILDTIYKFIEEDDFQHFYRLALGLGLSEGALHSIIFQISPEVLIKPIMKFLDDWEISNDDSNFQDLYSSFGVVLLLFLLIIKKYNISLNQLLLMKDNKSSFCIKFLINLGSLKQFESNDNINHEQSELINGWINALFDSGGISDDLMRLSTVQECFQLFPLIFQHAFIGVKKNLVDLDTVKGGLEYFLQPFLLSTIVGILSWCENYFWKNQDLELLVSLIKNLINPMDLSGDSIHIHKFVMLIYGKNLYEILSTLQRTQSINIDSSILTNLQTNWDHSYNTNTSNTHKTFNFFEINTSPVFNKFLKNGIIDKNSKKIENQSSPLLQFHNQFQSLINWNNQQSSVIISNYDYQNLSILTQIIDEDIIIDYFLGQILESQSLNSKSFHLTLELSTYLLTVQIIDSIKTKDYILNSLKSGELMEQISIESIKPFYKILSTLIQKKKSIEHDNDEINKEIFKIFYNQFIECIHNFIPLKE
Length942
PositionTail
OrganismWickerhamomyces ciferrii (strain F-60-10 / ATCC 14091 / CBS 111 / JCM 3599 / NBRC 0793 / NRRL Y-1031) (Yeast) (Pichia ciferrii)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Phaffomycetaceae> Wickerhamomyces.
Aromaticity0.10
Grand average of hydropathy-0.106
Instability index43.95
Isoelectric point5.21
Molecular weight107934.95
Publications
PubMed=23193139

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
transcription coregulator activity	GO:0003712	IEA:InterPro

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









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP29961
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     168.75|      44|     180|      46|     101|       1
---------------------------------------------------------------------------
   46-   89 (67.73/27.29)	LLKTRQEFDPLE....VVYLTSASLG.DQSSNLRLAKLLENLGIATEEN
  232-  273 (61.91/23.93)	FLKTNKL..P.K....FIWLNSVIQNwETSSDKFLSAFSQFVKVKTNQN
  430-  466 (39.11/10.77)	LIDINPEFIPLEdsglLEFLNSIEQF.EGTKQFEISKL...........
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     196.93|      58|     185|     639|     730|       2
---------------------------------------------------------------------------
  104-  141 (44.53/14.28)	DHFKSQFPF..N......SFEISAILTSLS...SYFknlLENQQKQLII......................
  147-  196 (59.41/18.03)	........YFLNvlfeiiPFEISP....LS..PE......QNELLTIIIGEIKHQGNHhLAETLES.NIHK
  644-  704 (92.98/86.33)	DTVKGGLEYFLQ......PFLLSTIVGILSwcENYF...WKNQDLELLVSLIKNLINP.MDLSGDSiHIHK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.01|      19|     185|     712|     730|       3
---------------------------------------------------------------------------
  712-  730 (34.07/21.90)	KNLYEILSTL.QRTQSINID
  895-  914 (30.94/19.14)	KPFYKILSTLiQKKKSIEHD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      36.87|      11|      58|     517|     528|       4
---------------------------------------------------------------------------
  517-  528 (17.41/12.85)	LDDWEiSNDDSN
  578-  588 (19.46/ 9.20)	LKQFE.SNDNIN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      72.05|      21|      55|     339|     359|       5
---------------------------------------------------------------------------
  339-  359 (36.25/20.25)	FKTIKLISSDGDNNNLGDQND
  391-  411 (35.80/19.90)	FNTILKEDSNAENRPLLENDD
---------------------------------------------------------------------------




































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 MDP29961 with Med5 domain of Kingdom Fungi
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