<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 MDP25437

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMPEFPSPSSPAGGGRRRTLNNADNKPDLHGTMNDPYYYDCRILVDATPEKSSRKKSTFVRHFSCTSSHALVKIAAAIVDPRAVVLHGREPHGEQGGGGATGERGHSRSRAERTDPTTTAPFFSGSNRRQVADLFRRPPSSFSDVFGMLIRDPRCYVYSCIGYLKGELQNVSWFQFLPVEPDPSTASERSSKAEQKDALNNIVLSAHLHLQSEGFLSTWTNSFVGPWDPSQGEHNPVVSNGLWVAPGNLEEVAAALCQALRNSLERTLRGLSYARFGDVFTKYYPPTRNQNSFRRAQPTIEFVFAATEEAIFVHVIISARYMRNLCSDDIEKVLTHSPRSVGEGLPVIVAPSGMLGRLVGCCPSDLVRQVYSSKLSAATLPGFTQPTMCQLRGQSYYVEVALGFPAATTDKVPESENNQIKKELDSAKDPQLSADEHQKLESADSVPVLERTFIYPPEAVMVPMVHQAFVRFSSKRMCSQACVGNSSWEGWPFWNFSPSSYFRNSSCLGSSRGLGVNSNFLRLRRQKNSNYSSMASSISSVSSTSNGSEHAVAAEGGDLSADADSMACHQSDLPSNIAGSKMVSKRPRSEIPEVSSRAGKESVDNNQGVNGQGRCSWGWDEEGVAMDINLLISEFGDFSDFFQEEELDFGEPPGTAESHSLVIPGPDCGDATFTDSPSTAMDIPEQRFSPVGLSSLEVFNHQTVAPIHDVVSKVQEPQKDIASPTSSQSVVLSSGRSSHLTRAEALLTYAPEYAAIEISTGETPTSLFTNPYQPRSIKPGSSSFNSRVYSYDAAQSSQMESGEDKPEKSVRLASGNLSRDIGSTNLYTVVQVGKKESDKGLKNTDIQSGKEEASRPISGETSLDSSVVSQRKSDSMFNAGYFLLSMKTALATEMECIKFQAAMCRIRHTLLSLSSKASAELKSALSSLVHTDVSNKLDLVPKYDIKRKENIPARLSIDVDHEVYDRSLENVGVWKPVGTPKGPTHLESFSAKTYTGTSQGLPVKRQPIVDLLSAMALIVQQSTSFVDIALDMDDGDGSFFWLSLDEQKRRGFSCDPSMVHAGCGGILGTCHSKDCAGVDLVDPLSAEVSDSSVISLLQSDIKAALKTAFANMDGPLLVTDWCRGRSNAAEYASMGDAYSFQHPTGDIRESSSSISIGGDSMSPPQSSHVISNDRGTSELEHHRGYHRVRPTVAVLPLPSLLVGYQDDWLKTSANCLSLWEKAPLEPYASPKPVTYYALCPDIEMLTSAATDFFLQLGTRLVLTECPDQVKIGNGHSSSISSTSEYLQALSRNWTVKSFVTSLTRVIKDIKLNSSILANQKESTSGPCTVIYVVCPFPEPSAVLETLVECSVALGSVMLSPERERKSFLYSQVAKALNCNASVDESSASNVVMLSGFSIPKLVLQIVTVETLLRLHKPNNELAVLKDMAFTVYNKARRIPKAISTSDMFQSPAYMGRSQSTMMHATSPGPTLWKECLVPRMSGSTLSRETEFDASMRSSVTWDNSWPGRAGGFMDPNKIPDVCVQDDRKYAFEPLFILAEPGSVDYSSGMESSKSGVDASGSGIYSSISGGGSDSGASASALLEGSDNDNAASLHCCYGWTEDWRWLVCIWTDSKGELLDSLIFPFGGISSRQDTKVLQSLFIQILQHGCQIMSSAPESSNTRPRDVIITRIGGFLELEIQEWQKAIYSFGGNEVKKWPVQLRRSIPEGIPSNSNGPALQQQDMGLMQDRNMPSSPSPLYSPHAKSSFMKGALGQSGNKKQILVEQAGMDSSKGSLHLVRSISLVAISQDHSLHLTCQADLLTRPTPGEGNQTSSGPSSYLEGFTPVKSIGSMSASYLLVPSPSMRYLSPATLQLPTCLTSESPPLAHLLHSKGTAIPLAMGYVVSKAVPPVRKDSARLANEDRPSVLSVSIIDHYGGSIAAVQEKMSRGSGKQTRNFTQEAAGRDHETEMHNVLEAVAAELHSLSWMTVSPVYMERRSALPSHCDMVLRLRRLLHYADRHLSQSTEKGDVA
Length2010
PositionKinase
OrganismOryza sativa subsp. indica (Rice)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> Liliopsida> Poales> Poaceae> BOP clade> Oryzoideae> Oryzeae> Oryzinae> Oryza> Oryza sativa.
Aromaticity0.07
Grand average of hydropathy-0.318
Instability index56.38
Isoelectric point5.96
Molecular weight218567.38
Publications
PubMed=15685292

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

>MDP25437
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     521.68|     167|     225|     105|     327|       2
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  105-  293 (252.69/255.01)	HS.RSRAERTdPTTTAPffSGSNRRQV....ADLFRRPPSSFSDVFGMlirdPrCYVYSCIGYLKGELQNVS.WFQFLPVEPDPSTASERSSKAEQKDALNNIVLSA..HLHLQSEGFLSTWTNSFVGPwdPsQGEHNPVVSNGLwvapgnLEEVAAALC.QA.LRNSlerTLRGLSYARFGDvfTKYYPPTRNQNSFR
  335-  511 (268.99/154.44)	HSpRSVGEGL.PVIVAP..SGMLGRLVgccpSDLVRQVYSSKLSAATL....P.GFTQPTMCQLRGQSYYVEvALGFPAATTDKVPESENNQIKKELDSAKDPQLSAdeHQKLESADSVPVLERTFIYP..P.EAVMVPMVHQAF......VRFSSKRMCsQAcVGNS...SWEGWPFWNFSP..SSYFRNSSCLGSSR
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     497.39|     120|     538|    1145|    1265|       4
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 1145- 1265 (206.71/106.79)	DIRESSSSI.SIGGDSMS..PPQSSHVI.....SNDRGTSELEHHRGYHRVR..PTvAVLPL..PSLLVGYQDDWLKTSANCLS.LWEKAPLEPYAS.PKPVTYYALCPDIEMLTSAATDFFLQLGTRLVLTECP
 1564- 1655 (133.80/64.48)	......SSI.S.GGGSDS..GASASALL..egsDNDNAAS...................L.....HCCYGWTEDWRWLV..C...IWTDSKGELLDSlIFPFGGISSRQDTKVLQSLFIQ.ILQHGCQ.IMSSAP
 1677- 1803 (156.88/76.87)	EIQEWQKAIySFGGNEVKkwPVQLRRSIpegipSNSNGPALQQQDMGLMQDRnmPS.SPSPLysPHAKSSFMKGALGQSGNKKQiLVEQAGMD...S.SKGSLH..LVRSIS.LVAISQDHSLHLTCQADLLTRP
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.65|      18|      37|     676|     694|       5
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  676-  694 (28.23/24.34)	PSTAMDIPEQRFSPVgLSS
  716-  733 (30.42/19.95)	PQKDIASPTSSQSVV.LSS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     136.54|      43|     225|     855|     906|       6
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  855-  906 (58.98/68.95)	PISGETSlDSSVVSQRKSDsmFNAgyfllSMKTALAtEMECIKFQAAMCRIR
 1082- 1124 (77.56/54.11)	PLSAEVS.DSSVISLLQSD..IKA.....ALKTAFA.NMDGPLLVTDWCRGR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.32|      15|      17|     819|     835|       7
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  819-  835 (21.51/24.83)	DIGSTNlyTVVQVGKKE
  837-  851 (26.82/20.82)	DKGLKN..TDIQSGKEE
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      87.72|      29|      34|     606|     639|      11
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  606-  639 (44.21/44.93)	QgvngQGRCSWGwDEEGVAMDINLLI..SEFGD..FSD
  642-  674 (43.51/26.71)	Q....EEELDFG.EPPGTAESHSLVIpgPDCGDatFTD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      81.03|      24|     393|     558|     587|      12
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  532-  555 (38.16/25.91)	SMASSISSVSSTSNGSEHAVAAEG
  564-  587 (42.88/20.30)	SMACHQSDLPSNIAGSKMVSKRPR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.82|      18|     950|     951|     970|      14
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  951-  970 (28.13/23.72)	PARLSID.VDHevYDRSLENV
 1903- 1921 (27.69/16.30)	PSVLSVSiIDH..YGGSIAAV
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     217.88|      75|    1330|       4|      93|      15
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    4-   93 (112.04/102.52)	FPSPSSPAgggrrRTLnnADNKPDLHGTMNDP......YYYD..CRIL.VDATPEKSSRKKSTFVRHFSctsshaLVKIAAAIVDPRAVV.LHgrEPHGE
 1335- 1419 (105.84/63.07)	FPEPSAVL.....ETL..VECSVALGSVMLSPererksFLYSqvAKALnCNASVDESSASNVVMLSGFS......IPKLVLQIVTVETLLrLH..KPNNE
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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 MDP25437 with Med13 domain of Kingdom Viridiplantae
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