<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 MDP25844

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMENENFYKLALRCADRQIASGDFLNFYKEFYNEKFSAKMENEDTPNESKVLEVSNLLASECIRLLSFEKSLILANYVVEMVFVNYNSDLVHAFLPQLYYITNSNMLIHFFAQSSAFFSKLSDKLVMDQLNKDLSTYVIPSILNVDVTTIGNDLVVAICKFLLLMMNFINGNVVLSSDRSRDNLNALLNRLSKVNKLLHKKVQQQADAKLIFKNAKNNVFPLESAVQEFVSSPSITSPQFEPSPISNAKAQASGGATVSGAKYQDIKLVRYYKNIWLNNKIINWGPIDSDFLSRYASIATSAFQGVTYSPQSTDSILQDLIETSFTCFAQFVNNKQYHQLNSNFNLLERQWMVFICKHLPLLILENGSGNSHTVPQALESIDDKVVKAIRTYYSEKDDMKGRNEDLFDDYPSNNLDIRHEFIKNLVSLGLQSPTLLNDYLREDQMIDTRTLLTTDDLIVTNSQGVQELVKDFKHFLTNSLDSLEPEVLINDSNDNADGLQQIFHNFENIPPTKQREISNILIDILQHALENLEFDRIAKICSVLSFNFSHSLTTILSFSSPTKICEMLIKFVDVSWDKFVEPRCKELVESEYDTMNFFLSFSCSILLLIVIWQTYDFSLVDVVLQSSESNTENSFVISYISKLPEIPDVFLLDPKNSLDQEMRTKSHQVVQNWLRDLFVNGSISDDLLQSVDLKQLAVLVPFIFKQVLLTLEVGAIEDVSNLVGGLEYFLQPFMLIGLVKIVYWLEQYLYSLKSENLDEGLLEKLLTLLNSIFNPQALNEDSKLFHSSLLRLNAVRLLRVLRQFRSQSQSNYGIYSTESSGHPKLELLIERLLSALNVSPTYNLDPRVITTENIYSQKQVGYGRFLILNENPINKIMTNQINSFWNLHSSTYYNLDYLKEVINLVSPRVFLQDVLATLEYKLDTYGVAGTRNKIAAVESEHVMDYLFYFLVLYDVRSQVDAVSLLQVMDGNSESPIVKEEMQMKTTEVAPKAEVSQDDDFDMLFGEPETNVTGVDKENQSTNVESKPTESKYNLTATLERHSFGLIIHEMKQECNEALSTGDISKDVCDKITKYHEKYVYLLKTCVF
Length1086
PositionTail
OrganismZygosaccharomyces rouxii (strain ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229) (Candida mogii)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Saccharomycetaceae> Zygosaccharomyces.
Aromaticity0.10
Grand average of hydropathy-0.130
Instability index39.98
Isoelectric point4.93
Molecular weight124134.95
Publications
PubMed=19525356

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

>MDP25844
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      97.83|      33|      64|     747|     782|       1
---------------------------------------------------------------------------
  747-  782 (47.50/32.90)	Y.LYSLKSENLD..EGLLEKLLTLLNsiFNPqALNEDSK
  811-  846 (50.33/25.58)	YgIYSTESSGHPklELLIERLLSALN..VSP.TYNLDPR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      82.75|      25|      60|     918|     946|       2
---------------------------------------------------------------------------
  918-  946 (38.31/43.06)	EYKLDTYGVAGTrnkiAAVESEHVMDYLF
  979- 1003 (44.44/36.50)	EMQMKTTEVAPK....AEVSQDDDFDMLF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     102.95|      30|     344|     330|     392|       3
---------------------------------------------------------------------------
  142-  171 (52.55/18.50)	LNVDVTTIGNDLVVAICKFL.LLMMNFINGN
  339-  369 (50.40/58.54)	LNSNFNLLERQWMVFICKHLpLLILENGSGN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      91.41|      32|      63|     211|     245|       4
---------------------------------------------------------------------------
  211-  245 (53.83/47.94)	FKNA..KNNVF...PLESavqEFVSS.PSITSPQFEP...SPIS
  271-  311 (37.59/24.77)	YKNIwlNNKIInwgPIDS...DFLSRyASIATSAFQGvtySPQS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      85.37|      18|      22|     526|     547|       5
---------------------------------------------------------------------------
  503-  520 (29.23/10.44)	HNFEN.IPPTKQREISNIL
  526-  543 (30.18/11.13)	HALEN.LEFDRIAKICSVL
  549-  567 (25.97/14.97)	HSLTTiLSFSSPTKICEML
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.26|      15|      15|      79|      93|       6
---------------------------------------------------------------------------
   79-   93 (26.10/13.27)	EMVFVNYNSDLVHAF
   96-  110 (27.16/14.07)	QLYYITNSNMLIHFF
---------------------------------------------------------------------------




































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 MDP25844 with Med5 domain of Kingdom Fungi
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