<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 MDP29887

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMTNESLYSLAVKCSQRQLSSGEFLNLYKEFYNEKLASEAGSVDDDSEPPSNAESKTTATTICTQMAQEFTKIFKEQHNLILIDYLIEILFVNYNPDLIHLFLPLLKTVSTGDGNNDNLLIHFLSKLSAYFVQLRDKLVGDQLVKDLPGVIIPNLLEIQYGNNNELSVALAKCLLVLLKYPSNVLTIESVSCRDNAHHLLSKLSDISRLVYKKLLHTLDNKVNFKDSNGLTKDVSGQEPSSIYSPSITSPQFISSPLFSMKTPSLPNNKDGTVSTMKYKDMKLFRYYKNIWLNNKIMNWEMIGSEFLSKYNSISSTLFPESADGNHVTVPNVDMLLIDLIETSFTCFAQYVSNKQYHRTNSNLNLLERQWIIFISKHLPILLLNHSSKNPQIVTTALEQIDPKVIKAITSYYSEKDDMRVRNDDLFDDFSSTSFDVRHDFIKSLVSLGLQPPTLINEFLREDQAVDPKSLPVTDDLVITTSQGTQETVGDIQSFIISSLDSLELENICSDDVNSESDIPHSNVRSSISGDSFNGIHQILQNNETIPPTKMKEISTVIFELLKDAIAVGNHSRISKICALLCFNFNHSLIAFFSFQSPQGIIEDLLHFVDKVWPNSSHSSKDDNTAPDESNDLFLSFSWALLLLTSINKNIGISLVDVALKSSLDIPLEDSFTIKFIDQLTEIPDDYSIEPQNRTLPEVQTQSHKLVRNWLSDLFINGSLSDQLTQNTDAKQLATLLPFILKQVLYALECNVVTDMNNVIGGFEYFLQPFMIVGLIKIVFWLEKYLSYLNNEPELVELTQKVLVIMNSLLNPTTLNEDSRTFHCAALRLNAIPLLKMLRKFCVPQTQTEYGVYSSDTQEPPMVESLIKKLISVINFAPVYNMDPRIVSTDNIYLQQKPIGYGKLQILNENPIDKIMTNQINSFWNLHSSTYYNIDFLNEIIKLITPKKFFFDVLNTLTYKISVYGVPAARNKMSTVDSDHVIDYLFYFLVLHDCESQVDAGYMVQLLSGNLEIDNSAIKPKKDLVKAKEQPADDLVGVPKSEIAQDDDFVMLFGENDTSSHNMNDDMQDVHFESSEDDEVKKLQKFYALKKDSFGVILYQLKLVHDAAVKDGDLSKTEYEKFNKHYEKYLSMLKTFIF
Length1136
PositionTail
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.
Aromaticity0.09
Grand average of hydropathy-0.161
Instability index38.01
Isoelectric point5.00
Molecular weight129009.61
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
mediator complex	GO:0016592	IEA:EnsemblFungi

GO - Biological Function
transcription coregulator activity	GO:0003712	IEA:InterPro

GO - Biological Process
histone H3 acetylation	GO:0043966	IEA:EnsemblFungi
regulation of transcription by RNA polymerase II	GO:0006357	IEA:EnsemblFungi
transcription by RNA polymerase II	GO:0006366	IEA:EnsemblFungi









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP29887
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.80|      17|      49|      13|      32|       1
---------------------------------------------------------------------------
   13-   32 (27.13/26.51)	CSQrqlSSGEFLNLYKEFYN
   62-   78 (32.67/22.06)	CTQ...MAQEFTKIFKEQHN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     116.77|      39|      49|      81|     125|       2
---------------------------------------------------------------------------
   81-  125 (51.42/43.57)	LIDYLIEILFVNynpDLIHLFLPLLKTVSTgdGNNDNLLIHfLSK
  133-  171 (65.35/34.56)	LRDKLVGDQLVK...DLPGVIIPNLLEIQY..GNNNELSVA.LAK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      92.01|      30|      49|     579|     608|       3
---------------------------------------------------------------------------
  579-  608 (55.48/34.40)	LCFNFNHSLIAFFSFQSPQGI..............IED..LLHFVD
  631-  676 (36.52/20.07)	LFLSFSWALLLLTSINKNIGIslvdvalkssldipLEDsfTIKFID
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     135.60|      45|      66|     789|     836|       4
---------------------------------------------------------------------------
  789-  836 (67.28/48.42)	NEPELVE.LTQKVLVIMNslLNPtTLNEDSRTFHCAALRLNAIPL....LKML
  856-  905 (68.32/39.54)	QEPPMVEsLIKKLISVIN..FAP.VYNMDPRIVSTDNIYLQQKPIgygkLQIL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     153.66|      39|      42|    1007|    1047|       8
---------------------------------------------------------------------------
  465-  500 (40.29/21.79)	.....DPKSLPVTDDL..VITTSQGTQETV.GdIQSFIISSLDS.
 1007- 1047 (57.85/41.70)	GnlEIDNSAIKPKKDL..VKAKEQPADDLV.G.VPKSEIAQDDDF
 1052- 1092 (55.52/33.79)	G..ENDTSSHNMNDDMqdVHF.ESSEDDEVkK.LQKFYALKKDSF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      89.73|      31|      72|     190|     221|      10
---------------------------------------------------------------------------
  190-  214 (34.19/21.09)	...............................................SCRD.NAHHLLS..KLSDISRLVYKKLL
  216-  289 (26.63/16.97)	TLDNKVnfkdsngltkdvsgqepssiyspsitspqfissplfsmktpSLPN.NKDGTVStmKYKDMKLFRYYKNI
  290-  313 (28.91/12.90)	WLNNKI.........................................MNWEmIGSEFLS..KYNSIS........
---------------------------------------------------------------------------




































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 MDP29887 with Med5 domain of Kingdom Fungi
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