<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 MDP00511

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMRGRLSGCSPNDLVKQVYFSGSGKIRTFNGFIGLPYHPSQGSGCQLWGQNCYVKVTLGCSKSGSDKALNSNANIRNLPKHHPTEASAAGRDDQKGSLDLLSVLEKTFIYPSEAVLVPVLQTSFARSSLRRFWLQNWIGPSLAASSLLRHCDGNIDSMERSWVEFSGIHTQHCYNSSSNSNNSSISSISSSSSDSVTTGARDLEADADSSCRQSGLSSNDQMEIDCLKMGSKRPRIGITESYGQAITVTNASSQDAYKSNIGSMEVNHSAITAVGNDQIGSNWDWDDDDRGIVMDIQSLLSEFGDFGDFFENDVLPFGEPPGTAESSAIMFAAPDCGDAGSSPAGVMDVSDQMLLPVCLPSFDSFTPHPPVAIEECLSKSQEVTSSAVTSGPLNHTLASSTGEFDHLMKAEALMTFATEYGAVETPASDSSSIFKKPYLPKSHKAESSNSSPNNYIYGATPPSSPCFDGLDEKTGMPMNLKAYPGGHDLSATYQLKKYYTPVETRKERYDGKLLTHNDSSVTNEVSGTSQFANFNSMNAVKSADRKMTQGICGKEHILLSMKTVLATDVECAMFQASMLRMRHILLSPMSLATISLSRPAGRSVLNHLPGDPSSMTDNVSSRYEVKKKESIPVRIAGDIDGGMLDGHLNAPVGVWRTVGVPKVSKPAASPSIEASPSLTHNSFNEDSILSYGQRQPLQELLDGIVLLVQQATSFVDLVLDADCGDGPYSWLALQEHWRRGFCCGPSMVHAGCGGTLASCHSLDIAGVELVDPLSANIHASSVISLLHSDIKSALKSAFGNLDGPLSVTDWCKGRGQSGDVGASADGSSAESNTNECRDSSTTVTHSVGEAMSPSQTSVGGSSVLKVTGALDGGKVEETSQRRLNQEISGSESEQQQCTRLRPTLFVLPSPAILVGYQDDWLKTSANSLQLWEKAPLEPYALPKPIIYSVICPDIDPLTSAAADFFQQLGTVYETCKLGTHSPQSLGNQMEMDSGKWSSSGFVLLDCPQSMKIESSNASLLGSISDYFLSLSNGWDLACYLKSLSKALKALKLSQFLSTNQKEGISGPCMVIYVVCPFPEPTAVLKTVVESSIAIGSIILPSDRERRSVLYSQVGKALSSSAAADEASISNIPVVSGFSVPKLVLQIVTVDAIFRVTSPPFNELVILKETAFTIYNKARRISRGSTNDVSLSSSLSSRPHSVLTPMTSIPGMWKDCVGSRIPGSSLPREGEIDSSLRGGAWDNSWQTSRAGGLSCDPNRNGDFFYQDEVCYMFEPLFILAESGSVEHGISPTAFGNSTSETSKTVSDESSGAFMQTANSAGSIDPGSGSQLDGSESDGVSSGNNKTPSLHCCYGWTEDWRWLVCIWTDARGELLDCDIFPFGGISSRQDTKGLQCLFVQVLQQGCQILQTCASPDTGVVKPRDFVITRIGNFYELEYLGISVCSFCDSLHFIFLLVRKLLSIALLQFCLSVTVTCCVLQYKLCFSFYVVLFLQL
Length1492
PositionKinase
OrganismTheobroma cacao (Cacao) (Cocoa)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Malvales> Malvaceae> Byttnerioideae> Theobroma.
Aromaticity0.07
Grand average of hydropathy-0.158
Instability index47.85
Isoelectric point5.15
Molecular weight160419.66
Publications
PubMed=23731509

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

>MDP00511
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     184.86|      50|     386|     308|     360|       1
---------------------------------------------------------------------------
  192-  226 (34.02/ 9.26)	..................SDSVTTGARDLeADADSScrQSG.LSSNDQMEID.CL
  308-  358 (86.74/46.25)	FFENDVLPFGEP.PGTAESSAIMFAAPDC.GDAGSS..PAGVMDVSDQMLLPvCL
 1262- 1306 (64.10/27.66)	FYQDEVCYMFEPlFILAESGSVEHGISPT.AFGNST..SETSKTVSDE.......
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      77.71|      21|     301|     997|    1037|       2
---------------------------------------------------------------------------
  430-  450 (38.73/ 7.68)	SSIFKKPYLPKSHKAESSNSS
  997- 1017 (38.97/42.20)	SSGFVLLDCPQSMKIESSNAS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      72.45|      23|      25|     535|     559|       3
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  535-  557 (41.16/28.79)	SMNAVKSADRK..MTQ.GICGKEHIL
  559-  584 (31.29/26.82)	SMKTVLATDVEcaMFQaSMLRMRHIL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      57.53|      14|     492|     718|     744|       4
---------------------------------------------------------------------------
  728-  744 (28.70/30.84)	SWlalQEHWRRGFCCGP
 1242- 1255 (28.83/ 6.20)	SW...QTSRAGGLSCDP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     277.78|      89|     365|     745|     872|       5
---------------------------------------------------------------------------
  256-  307 (73.03/26.84)	YKSNIGSMEVN...HSAIT.....AVGN.DQIGSNWDW.....DDDDRGIVMDIQSLLSEFGDFGD......................................
  772-  872 (131.59/80.78)	LSANIHASSVIsllHSDIKsalksAFGNlDGPLSVTDWckgRGQSGDVGASADGSSAESNTNECRDSSTTVTHSVGEAMSPSQTSVGGSSVLK...VTGALDGG
 1181- 1237 (73.16/22.01)	.........................................RGSTNDVSLSSSLSS......RPHSVLTPMTSIPGMWKDCVGSRIPGSSLPRegeIDSSLRGG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      59.65|      18|     649|     750|     771|       6
---------------------------------------------------------------------------
  750-  771 (22.86/26.97)	GCgGTLASCHSLDiAGVelVDP
 1402- 1419 (36.79/21.62)	GC.QILQTCASPD.TGV..VKP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     142.08|      46|     488|     586|     631|       7
---------------------------------------------------------------------------
  586-  631 (80.41/46.43)	SPMSLATISL.SRPAGRSVLNHLPG...DPSSMTDNVS.SRYEVKKKESIP
 1089- 1139 (61.67/33.84)	SSIAIGSIILpSDRERRSVLYSQVGkalSSSAAADEASiSNIPVVSGFSVP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.95|      18|     310|    1020|    1037|       8
---------------------------------------------------------------------------
 1020- 1037 (37.20/19.57)	GSISDYFLSLSN.........GW..D...LAC
 1331- 1362 (19.76/ 6.93)	GSESDGVSSGNNktpslhccyGWteDwrwLVC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.75|      16|     487|     511|     526|       9
---------------------------------------------------------------------------
  511-  526 (28.25/18.46)	KLLTHNDSSVTNEV...SG
  975-  993 (25.50/15.82)	KLGTHSPQSLGNQMemdSG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      79.31|      23|      41|      20|      42|      11
---------------------------------------------------------------------------
   20-   42 (45.26/26.43)	SGSGKIRTFNGFI.GLP.YHPSQGS
   62-   86 (34.05/18.10)	SGSDKALNSNANIrNLPkHHPTEAS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      70.59|      19|     509|     139|     157|      13
---------------------------------------------------------------------------
  139-  157 (35.58/22.72)	PSLAASSLLRHCDGNIDSM
  669-  687 (35.01/22.22)	PSIEASPSLTHNSFNEDSI
---------------------------------------------------------------------------




































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 MDP00511 with Med13 domain of Kingdom Viridiplantae
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