<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 MDP03421

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMPEFPSPSSPAGGGRRRTLNNADNKPDLHGTMNDPYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVDPRAVVLHGREPHGEQGGGGATGERGHSRSRAERTGHHHRPLLLRFKPAASRRPLPPPTEQLLRWNPNLLYLISQIEGELQNVSWFQFLPVEPDPSTASERSSKAEQKDALNNIVLSAHLHLQSEGFLSTWTNSFVGPWDPSQGEHNPVVSNGLWVAPGNLEEVAAALCQALRNSLERRAQPTIEFVFAATEEAIFVHVIISARYVRNLCSDDIEKVLTHSPRSVGEGLPVIVAPSGMLGRLVGCCPSDLVRQVYSSKLSAATLPGFTQPTMCQLRGQSYYVEVALGFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLESADSVPVLERTFIYPPEAVMVPMVHQAFVRFSSKRMCSQACVGNSSWEGWPFWNFSPSSYFRNSSCLGSSRGLGVNSNFLRLRRQKNSNYNSMASSISSVSSTSNGSEHAVAAEGGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCSWGWDEEGVAMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLVIPGPDCGDATFTDSPSTAMDIPEQRFSPVGLSSLEVFNHQTVAPIHDVVSKVQEPQKDIASPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGETPTSLFTNPYQPRSIKPGSSSFNSRVYSYDAAQSSQMESGEDKPEKSVRLASGNLSRDIGSSNLYTVVQVGKKESDKGLKNTDIQSGKEEASRPISGETSLDSSVVSQRKSDSMFNAGYFLLSMKTALATEMECIKFQAAMCRIRHTLLSLSSKASSELKSALSSLVHTDVSNKLDLVPKYDIKRKENIPARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGTCHSKDCAGVDLVDPLSAEVSDSSVISLLQSDIKAALKTAFANMDGPLLVTDWCRGRSNAAEYASMGDAYSFQHPTGDIRESSSSISIGGDSMSPPQSSHVISNDRGTSELEHHRGYHRVRPTVAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTSAATDFFLQLGTIYEVCKLGTHSPQNSGGQMELSPGKYLSSGLVLTECPDQVKIGNGHSSSISSTSEYLQALSRNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFPEPSAVLETLVECSVALGSVMLSPERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTVETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSSGMESSKSGVDASGSGIYSSISGGGSDSGASASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGEGNQTSSGPSSYLEGFTPVKSIGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRKDSARLANEDRPSVLSVSIIDHYGGSIAAVQEKMSRGSGKQTRNFTQEAAGRDHETEMHNVLEAVAAELHSLSWMTVSPVYLERRSALPSHCDMVLRLRRLLHYADRHLSQSTEKGDVA
Length2002
PositionKinase
OrganismOryza glumipatula
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza.
Aromaticity0.07
Grand average of hydropathy-0.318
Instability index57.26
Isoelectric point5.92
Molecular weight217343.08
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

>MDP03421
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.65|      18|      37|     639|     657|       1
---------------------------------------------------------------------------
  639-  657 (28.23/19.42)	PSTAMDIPEQRFSPVgLSS
  679-  696 (30.42/15.94)	PQKDIASPTSSQSVV.LSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     161.41|      40|      57|     987|    1027|       2
---------------------------------------------------------------------------
  987- 1027 (69.89/41.33)	FVDiALDMDDGDGSFFWLSLDEQK...RRGF.SCD.PSMVHAGCGG
 1042- 1086 (54.27/27.43)	LVD.PLSAEVSDSSVISLLQSDIKaalKTAFaNMDgPLLVTDWCRG
 1488- 1513 (37.25/16.25)	............SSVTWDNSWPGR...AGGF..MD.PNKIPDVC..
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      73.58|      20|     508|     942|     961|       3
---------------------------------------------------------------------------
  942-  961 (37.53/22.98)	PKGPTHLESFSAKTYTGTSQ
 1430- 1449 (36.05/21.74)	PKAISTSDMFQSPAYMGRSQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     153.04|      49|     508|     710|     789|       4
---------------------------------------------------------------------------
  735-  788 (69.73/92.63)	QPRSIkPGSSsfnSRVYSyDAAQSSQMES..GEDKPEKSVRLASGNLSRDIGSSNL
 1718- 1768 (83.31/36.56)	QDRNM.PSSP...SPLYS.PHAKSSFMKGalGQSGNKKQILVEQAGMDSSKGSLHL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     113.15|      36|     611|     589|     627|       5
---------------------------------------------------------------------------
  589-  627 (57.42/47.87)	DINLLISEFGDFsdFFQ....EEELDFG..EPPGTAESHSLViPG
 1203- 1244 (55.73/35.15)	DIEMLTSAATDF..FLQlgtiYEVCKLGthSPQNSGGQMELS.PG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      74.62|      24|      59|    1769|    1797|       6
---------------------------------------------------------------------------
 1769- 1797 (33.84/42.22)	VRSISLVAISqDHSLHL.TCqadlLTRPTP
 1830- 1854 (40.78/30.53)	VPSPSMRYLS.PATLQLpTC....LTSESP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     310.06|      97|    1551|       8|     114|       7
---------------------------------------------------------------------------
    8-  114 (150.37/148.34)	SSPAGGG.....RRRTL...NNADNKPDLHGTMNdpYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVdprAVVLHgrepHGEQGGGGATgERGHSRSR...AERTG
 1556- 1663 (159.69/121.54)	SSISGGGsdsgaSASALlegSDNDNAASLHCCYG..WTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLF...IQILQ....HGCQIMSSAP.ESSNTRPRdviITRIG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     185.13|      60|    1551|     365|     424|       8
---------------------------------------------------------------------------
  365-  424 (102.26/82.36)	GFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLE..SAD.......SV.PV.LERTFIYPPEAVMV
 1908- 1978 (82.87/64.88)	GSIAAVQEKMSRGSGKQTRNFTQEAAGRDHETEMHNVLEavAAElhslswmTVsPVyLERRSALPSHCDMV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     105.90|      35|      59|    1315|    1354|      12
---------------------------------------------------------------------------
 1315- 1354 (52.71/40.39)	SGPCTVIyVVCPFPEPSAVLETL.VECSVALGsvmlSPERE
 1376- 1411 (53.19/27.90)	SSASNVV.MLSGFSIPKLVLQIVtVETLLRLH....KPNNE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.86|      22|      22|     431|     452|      19
---------------------------------------------------------------------------
  431-  452 (43.32/24.23)	FVRFS.SKRMCSQACVGNSSWEG
  455-  477 (38.54/20.70)	FWNFSpSSYFRNSSCLGSSRGLG
---------------------------------------------------------------------------




































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 MDP03421 with Med13 domain of Kingdom Viridiplantae
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