<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 MDP24762

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMSSETVYNLLLNCAERQILASDFLNLYNEFYNEKFATKIENENNEENQSKVVEISESISSDVIKLLNSGNRLLLADYVVQLLFVNYNSDLVQALLPKLYSVSNEFMLVHFFSKSCSYFAKLSDKLIVDQLVKDISRSIIPGVFAMDINIMTNELVISVSKFLQLILNFLPKPIVLASETDKDHLYLLIRRLSQINKLIHRKFSQTLESKMIFKDSKPLFATTATTPFINSPSISSPQFIPSPMVPSKQGPSAEASMKYKDMKLLRYYKNVWLNNKIFNWECTNPDFLSTFSSIVTGLFQFQTSSRLTTDELLTDLIETSFTCFAQFVSNSQYHQTNATFNLLEKLWIIYISKQLPLLILENSTGNPTVVTRALERMDDKIIKAIKSYYAEKNDQRNRNEDLFDDSPSSGLDIRHDFIKSLVMLGLQPPSLINDYLREDQSLDPRTLTSSDALVITNIQGVLEVIRDVNTFVLQTLDSMELENINNSSDVTNNGLKQVFINFETVSPTKQREISNAIVSVIKDSVDQLNFQRLSKICALLCYNFGHSLTTIMLFVKPTTILELLMKFTDISWDQFVVSKSSSMETDYELTSSYLAFGWVTLLLTTISKSYEISLVDIALNSSFLVSKDSFAIQAVSKIYDIPDSFTLSKGGKTDNDEDSQEMRKWFQDLFVNGSLSDSLIQNVDVKKLIDLVPYIFKQVMLGIENGVITDMSRVINGFEYFLQPSMIIGLIRIVYWLEDYLESLKANGIADDIIQKILSVVNSLLAEVSLNSDSRAYHESVLRLNAPNLLKAVRSFRIQTQQNYGIYSSEAQGPPVVESLISKLVLVMNISPVYNIDPRVSVSDNSYSQKQFGYRNFLILSEQPLDKILSNQINSFWSLHSSTYYNIDYLKKLIDIITPKKFFIDVMKTLDYKLSAYGVPNVRNKIRDVDAEHVIDYLFYFMVLHDVNSQQEASEMIMWMDKTLKDADNSAETSTSKTKIPNKAEQQSLPDDDFDMLFGENETSMQGTDEEDAMIVDIETCQNLNNIAVLKKNSFATVLQDTKYLLDAGLVSGDITKEEYEKGCKYHQKYLGLLRTCAF
Length1078
PositionTail
OrganismVanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294) (Kluyveromyces polysporus)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Saccharomycetaceae> Vanderwaltozyma.
Aromaticity0.10
Grand average of hydropathy-0.101
Instability index35.71
Isoelectric point4.98
Molecular weight122827.02
Publications
PubMed=17494770

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

>MDP24762
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     128.30|      42|      55|     543|     596|       1
---------------------------------------------------------------------------
  543-  585 (67.34/62.93)	FGHSLTTIML...FV..KPTTILELLMKFTDISwDQFVVSKSSSMETD
  609-  655 (60.96/30.81)	YEISLVDIALnssFLvsKDSFAIQAVSKIYDIP.DSFTLSKGGKTDND
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      75.29|      24|      54|       1|      26|       2
---------------------------------------------------------------------------
    1-   26 (36.42/26.59)	MSSETVYnlLLNCAERQILASDFLNL
   58-   81 (38.87/22.27)	ISSDVIK..LLNSGNRLLLADYVVQL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     104.38|      35|      55|     100|     136|       5
---------------------------------------------------------------------------
  100-  136 (50.90/40.89)	SVSnEF..MLVHFFSKSCsYFAKLSDKLIVDQLVKDISR
  157-  193 (53.48/33.42)	SVS.KFlqLILNFLPKPI.VLASETDKDHLYLLIRRLSQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      33.38|      11|      55|     759|     769|       6
---------------------------------------------------------------------------
  759-  769 (17.08/ 9.79)	VVNSLLAEVSL
  815-  825 (16.30/ 9.00)	VVESLISKLVL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.26|      20|      56|     209|     228|       9
---------------------------------------------------------------------------
  209-  228 (36.78/23.67)	KMIFKDSKPL............FATTATTP.FI
  255-  287 (27.47/15.81)	SMKYKDMKLLryyknvwlnnkiFNWECTNPdFL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      86.21|      28|     203|     664|     699|      11
---------------------------------------------------------------------------
  664-  699 (45.00/34.30)	WfqdlfvngSLSDSLIQNVD.VKKLIDLV.P.YIFKQVM
  876-  906 (41.21/18.38)	W........SLHSSTYYNIDyLKKLIDIItPkKFFIDVM
---------------------------------------------------------------------------




































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 MDP24762 with Med5 domain of Kingdom Fungi
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