<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 MDP27997

Description Mediator of RNA polymerase II transcription subunit 5
SequenceMSEVSLHKLVTKAINQRLPSKSFISLINQFNVKQPIHDNQYIHDLLELDNTPTLKQQRINETKILQIIELSLSSSRQCHQFWKNLGKLDNNVQVRYLTKINKTLLHCSKYDRDLLKQLINTEFIDYSLDYLNKLHDKTFTTSQKQVVNHIIFIVGSIIDNKLVKSEQENILPIQNFIIKLITILKNLKLGKLLSFLLLKSKTILTSDQIEHLSHSKIIKHDLQVQVKTEDNVINYTSIASLSITTLSTEKQSDFYKTKRTFWLIKIIGNFEFDNIANMFVNFMPSGSSPYTLVYEFIQTFITCYDLLKHGDFRRFNLKNFLVTRVPSILGFFKISDEDIQTVVENVFADHTELKNDFTKSLALNRMLPTDKYPNDVTIPELNLRQRFNEKLLNINSEFTSLEESGLIEFMHALPNDLQYSKSHQLELSSIIVEIINDLISGKDFEKLNRILLCIMNNIELLNLIMFNCERAYSVLYQLIDFIDSTQFNIDDDDENFQDTFTYFGVTVLAIILIVHHFKLDYSFSIKNSFILDYINNFYYGLCDNLTNQETDDEEQIVNYNNLLTDWINALFDDNNDGLSDELIKSVNIKQIYKLIPIVYQQAIIATSSGKLGYASLTNGLDYLSQLFLIPSTVSLISWLVKELNLLQKLEADNAHLKVLSEIIKSNTSGNSQEISVLIFKIILNIHGNNIYKTITKFKEWEGIPIAKEIITAVGTYNSETAISKDLNVCETIKLQLLNKGTTLPIDFIIEYIEKNKAQVIWFLIYEVYNFQKSNDEELKYFINLMVYLIIIYSPSTKALQGVGVENGTIGVTDKFVLTIQDHYSSIFDTKLEPKEEDLDMLNDDLFNDLPNTSSTSQKLLKLNSEISFKKSLLGEFSKIKSDNHSLFEKSIKILNDKILDELNKI
Length905
PositionTail
OrganismSpathaspora passalidarum (strain NRRL Y-27907 / 11-Y1)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Debaryomycetaceae> Spathaspora.
Aromaticity0.10
Grand average of hydropathy-0.108
Instability index32.79
Isoelectric point5.47
Molecular weight104539.86
Publications
PubMed=21788494

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

>MDP27997
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      63.99|      22|     112|     117|     160|       1
---------------------------------------------------------------------------
  135-  160 (28.11/16.72)	HDKTFTTSQKQVVNHIIFivgSIIdN
  415-  436 (35.88/33.72)	NDLQYSKSHQLELSSIIV...EII.N
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     122.09|      34|      39|     268|     301|       2
---------------------------------------------------------------------------
  268-  301 (63.02/38.28)	GNFEFDNIANMFVNFMPSGSSPYTLVYEFIQTFI
  310-  343 (59.07/35.45)	GDFRRFNLKNFLVTRVPSILGFFKISDEDIQTVV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      80.08|      22|      32|     527|     548|       3
---------------------------------------------------------------------------
  527-  548 (40.97/24.71)	NSFILDYINNFYYGLCDNLTNQ
  560-  581 (39.11/23.22)	NNLLTDWINALFDDNNDGLSDE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     114.43|      35|      39|      15|      50|       5
---------------------------------------------------------------------------
   15-   50 (55.19/38.72)	NQRLPSKSFISLInQFNVKQPIHDNQYIHDLLELDN
   56-   90 (59.25/37.01)	QQRINETKILQII.ELSLSSSRQCHQFWKNLGKLDN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     124.54|      40|     221|     643|     682|       7
---------------------------------------------------------------------------
  643-  682 (62.71/37.15)	LNLLQKLEADNAHLKVLSEIIKSNTSGNSQEISVLIFKII
  860-  899 (61.83/36.52)	LKLNSEISFKKSLLGEFSKIKSDNHSLFEKSIKILNDKIL
---------------------------------------------------------------------------




































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 MDP27997 with Med5 domain of Kingdom Fungi
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