<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 MDP03140

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMPEFPSPSSPAGGGRRRTLNNADNKPDLHGTMNDPYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVDPRAVVLHGREPHGEQGGGGATGERGHSRSRAERTDPTTTAPFFSGSNRRQVADLFRRPPSSFSDVFGMLIRDPRCYVYSCIGYLKVDIFDRSHFCLFLIEKANNVTAKCNNSLKKSLIVHAIGLACVKKGELQNVSWFQFLPVEPDPSTASERSSKAEQKDALNNIVLSAHLHLQSEGFLSTWTNSFVGPWDPSQGEHNPVVSNGLWVAPGNLEEVAAALCQALRNSLERRAQPTIEFVFAATEEAIFVHVIISARYMRNLCSDDIEKVLTHSPRSVGEGLPVIVAPSGMLGRLVGCCPSDLVRQVYSSKLSAATLPGFTQPTMCQLRGQSYYVEVALGFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLESADSVPVLERTFIYPPEAVMVPMVHQAFVRFSSKRMCSQACVGNSSWEGWPFWNFSPSSYFRNSSCLGSSRGLGVNSNFLRLRRQKNSNYSSMASSISSVSSTSNGSEHAVAAEGGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCSWGWDEEGVAMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLVIPGPDCGDATFTDSPSTAMDIPEQRFSPVGLSSLEVFNHQTVAPIHDVVSKVQEPQKDIASPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGETPTSLFTNPYQPRSIKPGSSSFNSRVYSYDAAQSSQMESGEDKPEKSVRLASGNLSRDIGSSNLYTVVQVGKKESDKGLKNTDIQSGKEEASRPISGETSLDSSVVSQRKSDSMFNAGYFLLSMKTALATEMECIKFQAAMCRIRHTLLSLSSKASAELKSALSSLVHTDVSNKLDLVPKYDIKRKENIPARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGMCHSKDCAGVDLVDPLSAEVSDSSVISLLQSDIKAALKTAFANMDGPLLVTDWCRGRSNAAEYASMGDAYSFQHPTGDIRESSSSISIGGDSMSPPQSSHVISNDRGTSELEHHRGYHRVRPTVAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTSAATDFFLQLGTIYEVCKLGTHSPQNSGGQMELSPGKYLSSGLVLTECPDQVKIGNGHSSSISSTSEYLQALSRNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTANSSNMITLIIHAERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTVETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSSGMESSKSGVDASGSGIYSSISGGGSDSGASASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGEGNQTSSGPSSYLEGFTPVKSIGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRKDSARLANEDRPSVLSVSIIDHYGGSIAAVQEKMSRGSGKQTRNFTQEAAGRDHETEMHNVLEAVAAELHSLSWMTVSPVYMERRSALPSHCDMVLRLRRLLHYADRHLSQSTEKGDVA
Length2036
PositionKinase
OrganismOryza barthii
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza.
Aromaticity0.07
Grand average of hydropathy-0.314
Instability index55.61
Isoelectric point6.06
Molecular weight221159.47
Publications









Function






Annotated function

Component of the Mediator complex, a coactivator involved in
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

>MDP03140
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.52|      16|      18|     983|     998|       1
---------------------------------------------------------------------------
  983-  998 (31.20/16.55)	LENVGVWKPVGTPKG.P
 1001- 1017 (24.32/11.28)	LESFSAKTYTGTSQGlP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     175.46|      54|     508|    1062|    1115|       2
---------------------------------------------------------------------------
 1062- 1115 (101.16/60.77)	QKRRGFSCDPSMVHAGCGGI...LGMCHSK...DCAGVDLVDPLSAEVSDS..SVISLLQ.SD
 1549- 1611 (74.30/42.36)	QDDRKYAFEPLFILAEPGSVdysSGMESSKsgvDASGSGIYSSISGGGSDSgaSASALLEgSD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.07|      20|      36|     649|     669|       3
---------------------------------------------------------------------------
  649-  669 (34.68/24.33)	EFGD..FSDfFQEEELDFGE....PPG
  682-  707 (29.40/14.97)	DCGDatFTD.SPSTAMDIPEqrfsPVG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     177.35|      60|     508|     223|     290|       4
---------------------------------------------------------------------------
  223-  290 (82.73/77.68)	EPDPSTASERSSkaeQKDALNNiVLSAHLhLQSEGFLsTWTNSFVGpWDPSQGEhNP..VVSNGLW...VAPG
  731-  795 (94.62/56.50)	EPQKDIASPTSS...QSVVLSS.GRSSHL.TRAEALL.TYAPEYAA.IEISTGE.TPtsLFTNPYQprsIKPG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      91.59|      31|     508|     924|     957|       5
---------------------------------------------------------------------------
  924-  957 (36.68/35.15)	TLLSLsSKASAELkSALSSLVHTdVSNKLDLVPK
 1435- 1465 (54.92/35.00)	TLLRL.HKPNNEL.AVLKDMAFT.VYNKARRIPK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     352.90|     109|    1049|      68|     181|       6
---------------------------------------------------------------------------
   68-  181 (179.83/113.21)	HALVKIAAAIVD.PRAVV..LHGREPHGEQGGGG.......ATGERGHSRSRAERTDPTTTAPFFSG..SNRRQVADLFRRppSSFSDVFGMLIRDPRCYVYscIGYlKVDIFDRSHFCLFLIEKA
 1117- 1237 (173.07/94.12)	KAALKTAFANMDgPLLVTdwCRGRSNAAEYASMGdaysfqhPTGDIRESSSSISIGGDSMSPPQSSHviSNDRGTSELEHH..RGYHRVRPTVAVLPLPSLL..VGY.QDDWLKTSANCLSLWEKA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     235.50|      70|     609|    1251|    1327|       8
---------------------------------------------------------------------------
  344-  391 (61.56/33.07)	............................DIEKVLTHSPRSVGEGLPVivAPSGML..GRLVGCCPSDL.VRQVYSSKLS
 1251- 1324 (113.18/98.75)	YALCPDIEM.LTSAATdFflQLGT..IYEVCKLGTHSPQNSGGQMEL..SPGKYLSSGLVLTECPDQVkIGNGHSSSIS
 1861- 1910 (60.76/36.19)	YLLVPSPSMrYLSPAT.L..QLPTclTSESPPL.AHLLHSKGTAIPL..AMG.YVVS......................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.85|      14|    1022|     492|     505|      12
---------------------------------------------------------------------------
  492-  505 (28.42/12.46)	MCSQACVGNSSWEG
  517-  530 (25.43/10.42)	FRNSSCLGSSRGLG
---------------------------------------------------------------------------




































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 MDP03140 with Med13 domain of Kingdom Viridiplantae
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