<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 MDP32609

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSEATASNISTHYYKLGHLGTVSFYNYVSFTDNDQSLLELELSIRYAHPNILVTYYNKSLYYFTFGHNNVPLETVSRDIELPDLAKDINTDVDLSKDVTGPNPGANNSPSLLANPPKSASSGSTLGAAVDEYLPFASLSLLKSIKKMILFNLSKNGAIKLFGNYCVVARDTINRSILYLDPILFPNGDLLLSMVVKERINLLDSSIIDLKYPSQDAPDINFVIYLIPSGIRCHLFDPTNLVRNFVRKKSAESENLIDLIKLSTGVEYSFNSEEENVWIKLIPNLKHLNNQTSTIAKFIHSVDNKKFILWPWKLCLLQFGKFEEVDEITSPDVTSSQVHPTSNPLDLIGDLIDFNISSNQHHNFAQPSQTLPFSISSVASTGGDAGIGSVDPHTTMEQQPHTLDLNDITTHMVPDLFDLQNPVPSEFFTKEVQDMPPVDGTEVKEDTNQDDVEMDDLFGGSDDEGDDSRNGQNSSKEDLFSDAIKEEPKDALAAGTPAELEKNQLNDLFDISDKEAAPDSGKYSTPAKEPKFKYLDIPKDQMTIKKSSSPDYNDPGAPLPIMPTPIIPVANSVYSTNPPTAAAIGTEGVGLSDDQSSGPYNQPQPKQEIFNSGSSASQIQQKSIFSPILFNPIIKSNIDTKYGKGGKFYVDKEASIGPEEKKKKTFRETSVSGYELPLTKEEDKLPITAQAVGLRKMNNSSLSLAESSMSASSEESDEDEEMPDVISNSPPLRLNTFNDSFGGVPMGNSGGITLNNNPINLSNYNTGGFGSPNSSVIGRFPNIKGESPFSTADLQQTVSPIDYEQSNNQHTPSFPTSQGLQITQSVNNGSGRTSSSDESPVKGISESSNYLPLILRSINVSTIPDIYLLNNLISDQLLPSFTINDDDNDNDLEVMRNNEMFIKAKHLDEFLELIGPNLVFDLGFNQGRSKLSYYMDELVKSKLEENKVFPNSYKVNLIEFLNDQKDYESKDELEDQLDFLDDIANDDDNILNPKSQYKKLKSIEWDALTENTKNKENFEKYKLIVNKLNSSVSTKDEVYFKLPIIKARVLKHNNILNLNNLAINFWKYMNFSPIKSTKHFQVLLISENNGNGTSFLREFLDLLIYNYKECNLGHISKVNLSTVETRPDLENINDGILLVNKDNDQTYNDTYSQINKKLNSLVELIKLDLINKTNNFEFDRPLLLLFVNYNDNLNSTLQISKVFRNLKVSLTNHQLPLVSIFTKIIPGSLIVKQDPFQNWLKVLSNFKLSKLSMNLYNQCPNGSTNKDIVKNTFTQLVKEPPSRIQFKFMSNNFKHSNFNDDIFLHLAYERSIDRNWFSAAWSDPLGVVTFTKSWYCSNKATRNGSGGYGRDTHDVATVCEEIWNKSNELFKKLNDEMNNESSTMGGKKFLVLTRINSIIPDDELIHWKRLSVKHKDISLIVLSVSHSPKLIFQDNRPRFEDTENCGQLDNFFKVFSGSNNSSPTTGGALVTSPNVLSFHSPQQFLNAPGNFLSPQDFVSTAGGAGAGATSAPHGGSNNPDLILHDFGTDVIGIIPKVPLPSFNSPTRLGMKIGYLLKEWMNGSRSTSRPRRSYLVYEVSLLSCSNYWDLDVLMKLILNHYKNLIVLNDILGLRKIDGNISKNESEDDFEQSLEFEASGIVPWHISAVGKSLVYLSHIYVDE
Length1660
PositionKinase
OrganismScheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (Yeast) (Pichia stipitis)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Debaryomycetaceae> Scheffersomyces.
Aromaticity0.09
Grand average of hydropathy-0.428
Instability index39.67
Isoelectric point5.04
Molecular weight185498.99
Publications
PubMed=17334359

Function

Annotated function Component of the SRB8-11 complex. The SRB8-11 complex is a regulatory module of the Mediator complex which is itself involved in regulation of basal and activated RNA polymerase II-dependent transcription. The SRB8-11 complex may be involved in the transcriptional repression of a subset of genes regulated by Mediator. It may inhibit the association of the Mediator complex with RNA polymerase II to form the holoenzyme complex (By similarity). 
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

>MDP32609
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     227.44|      51|      51|     453|     503|       1
---------------------------------------------------------------------------
  419-  460 (49.80/24.84)	...........QNPVPSEFFTKEVQDMPP...VDGTEVKEDTNQddveMDDLFGGS
  461-  511 (81.57/45.89)	DDE.GDDSRNGQNSSKEDLFSDAIKEEPKDALAAGTPAELEKNQ....LNDLFDIS
  512-  541 (34.16/14.47)	DKEaAPDSGKYSTPAKEPKFK..YLDIPKDQM........................
  718-  759 (61.91/32.87)	DEE.MPDVISNSPPLRLNTFNDSFGGVP...MGNSGGITLNNNP....IN......
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      72.43|      21|      97|     830|     851|       2
---------------------------------------------------------------------------
  809-  829 (37.16/21.81)	HTPSFPTSQGLQITQSVNNGS
  831-  851 (35.27/15.47)	RTSSSDESPVKGISESSNYLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     400.05|     118|     413|     943|    1205|       3
---------------------------------------------------------------------------
  857-  978 (64.13/64.90)	.................INVSTI...PDiylLNNlISDQLLpsfTINDDDND............................NDLEVMRN.NEMFIK.AKH...LDEFLEL..IGPNLvfdlgfnqgrsklsyymdelvkskleenkvfpnsykvnlieflndqKDYESKDELEDQLDF
 1100- 1205 (153.40/220.71)	DLLIYNYKECNLGHISKVNLSTVETrPD...LEN.INDGIL...LVNKDNDQTYNDTYSQINKKLNSLVelIKLDLINKTNNFEFDRPLLLLFVNYNDN...LNSTLQISKVFRNL.............................................................
 1519- 1633 (182.53/79.64)	DLILHDFGTDVIGIIPKVPLPSFNS.PT...RLG.MKIGYL...L.....KEWMNGSRSTSRPRRSYLV..YEVSLLSCSNYWDLD.VLMKLILNHYKNlivLNDILGLRKIDGNI..............................................SKNESEDDFEQSLEF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      97.28|      32|     413|     264|     296|       4
---------------------------------------------------------------------------
  207-  243 (42.29/16.26)	IDLKYPSQDApdiNFVIYLIPSgIRcHLFDPTNLVRN
  265-  296 (54.99/29.56)	VEYSFNSEEE...NVWIKLIPN.LK.HLNNQTSTIAK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      34.83|      11|      28|    1042|    1055|       5
---------------------------------------------------------------------------
 1042- 1055 (14.68/17.62)	PIikaRVLKHNNIL
 1072- 1082 (20.15/12.95)	PI...KSTKHFQVL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      77.07|      19|      52|     571|     589|       6
---------------------------------------------------------------------------
  571-  589 (31.84/17.22)	SVYST...NPPTAAAIGTE.GVG
  596-  612 (23.43/10.39)	SGPYN...QPQPKQEIFNS.G..
  622-  644 (21.80/ 9.06)	SIFSPilfNPIIKSNIDTKyGKG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     103.49|      30|     651|      94|     155|       7
---------------------------------------------------------------------------
   98-  127 (55.80/21.41)	VTGPNPGANNSPSLLANPPKSASSG....STLGA
 1469- 1502 (47.69/12.10)	VTSPNVLSFHSPQQFLNAPGNFLSPqdfvSTAGG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     140.43|      43|      44|    1206|    1248|      14
---------------------------------------------------------------------------
 1206- 1248 (74.89/47.88)	KVSLT.NHQLPLVSIFTKIIPGSL..IVKQDPFQNWLKVLS.NFKLS
 1249- 1295 (65.54/40.86)	KLSMNlYNQCPNGSTNKDIVKNTFtqLVKEPPSRIQFKFMSnNFKHS
---------------------------------------------------------------------------




































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 MDP32609 with Med13 domain of Kingdom Fungi
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