<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 MDP12246

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMWTNVFKIGGLHQISWFQFLPHESDVSSLVDKSVKLDKKDAATWLVLSSHLQLQKEGFLSTWTNSFVGPWDPSQGLHNPDEKIKLWLFSPGQHSSVVEKAQSAVSKLRVLASGLWVAPGDSEEVAAALSQALRNCMERKLRGLSYVRYGDVFTKHHPFSQNEELFRKGQPVVEFIFSATEEAIFVHVIISAKLIRALSSGDIDKISEDTSNVSGERLPVIVSPHGMRGRLTGCCPADLVKQVYLSSCKFSASNGIVGLPCNVSRSGYQLKGQNCYVEVSLGCTTPGNNNIKESSRMLIYPPEAILVPVVQTACARSSLKRFWLQNWIGPSLSFTSSFMHCFDFSSDAKVNSTDGSWLDANIMRSNRQYNSSSNSNSSSVSSVSTSSSDSDYKTSGAGDLEADADSLMCRPSGLSSVDQSRNDNLKTGFKRSRTGISESFSQAGAVINPSTSDYASMEVNNSAITGGNDQIGLQWGWDDDDRGVGMDIQALLSEFGDFGDFFENDVLPFGEPPGTAESQALMYPAADSADVGSSPCPSMMDVKDQMLLPVGFPSFDSFNQPPPPASLDDSLSKHQEVIKSTAVAYQVNNSSAAIAGEFDHLIKAEALMTFAPEYGAVETPTGEKSHLIFRNPYLPKSREVDTSNSSSDSYVYSATPPLSPYFDACEEKSGVTVNLKTGSGRRDTSSIIQSKRYYTHIESGKEKNDGKLSGSDHSCATREAQVEQSPFYGFNSTNSVKSIHNKTEKANEALLKADSFGQSMKTVLATEVECLMCQAFMCKIRHTLLSSSSYLPVGASRMSGSTIINQPQGEAVVTVDNMSSKSEMKKKEIIPVRIAGDIDGGLLDGTLNAQVGVWRSVGVSKGMKQPSSALEACHSVQHNSFIEESMLAYGLRQPLQELLDGVALLVQQATSLVDVALDADNNDGPYGWLTLQEQWRRGFSCGPSMVHAGCGGVLASCHSLDIAGVELIDPLSADVQASFALTLLQNDIKTAMKSAFGTMEGPLSVVDWCKGRSQSNDGGISGDGFSAESTASASECRDSSSTISFSVGEPISPSQSSAGGSSLKDGIRVDEASERRLSQDTCLSESEQLPGSRLRPTLSAVPYPAILVGYQDDWLKTSPSSLQLWEKAPFEPYAMPKHMSYYVVCPDINALTTAATDFFQQLGTVYETCKLGTHSPQCMGNEMEIDSGKNVSSGFVLIDCPQSMKIDSSSTSMLGSISDYFLSLSNGWDLESYLKSLSKVLRNLKLSSCMTMNPKEGSTGPCTVIYVVCPFPEPLAVLQTVVESSIAVGSVVLSSDKERRSTLQNQVGKALSYSAAVDESLSNVLTLSGFCIPKLVLQIVTVDAIFRVTSPALSELLVLKEIAFTVYNKARRISRGSSSDMVQSSSMSGRSHPVLMQMTSPVPGMWKDCVGPRSIGTSLQREAELDASLRSGSWDNWQISRGGSLGCDPNRIGDFSFQDEVRYLFEPLYILAEPGSLDRGLSFPMSGNLMAESSKLLLDDGTSGNFMQSSASSGGGDTGPNTQSETSEPDGFGSAHQKSLPSLHCCYGWTEDWRWLVCIWTDSRGELLDNYIYPFGGISSRQDTKGLQSLFVQILQQGCQILQACPPEAANAKPRDFVIARIGSFFELECQEWQKALYAIGGSEVKKWSLQLRRSVPDGMSASSNGTSLQQQEIGLIQERALPSSPSPLYSPHSKVSSFMKGGMGQPSTRKQLIGGQGMVDNSRGLLQWVQSISFVSVSIDHSLQLMFQADIVSHGTSQSSGVLSQPGYLEGYTPVKSLGSTSNSYILIPSPNMRFLPPVGLQLHTCLTAESPPLAHLLHSKGCAIPLSTGFVVSKAVPTMRRDARSISKEEWPSVLSVSLVDYYGGSNIIQEKFFKGVGKVGGRGTSSETRDVEIETHLILENIAAELHALSWMTVSPAYLERRSALPFHCDMVLRLRRLLHFADKEVSRQPEKTQV
Length1957
PositionKinase
OrganismNicotiana tabacum (Common tobacco)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> asterids> lamiids> Solanales> Solanaceae> Nicotianoideae> Nicotianeae> Nicotiana.
Aromaticity0.08
Grand average of hydropathy-0.228
Instability index54.19
Isoelectric point5.43
Molecular weight212081.53
Publications
PubMed=24807620

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	IBA:GO_Central

GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP12246
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     202.77|      65|      78|     922|     988|       2
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  922-  988 (106.63/62.21)	DGPYG...WLTLQEQWRRGFSCGPSMvHAGCGGVLASCH.SLDIAGVELIDPLSADvQASFALTLLQNDIK
  999- 1067 (96.14/49.13)	EGPLSvvdWCKGRSQSNDGGISGDGF.SAESTASASECRdSSSTISFSVGEPISPS.QSSAGGSSLKDGIR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.56|      22|      79|    1223|    1254|       3
---------------------------------------------------------------------------
  110-  136 (29.65/ 7.41)	LASGlWvapgDSEEVAAALSQALRN.....CM
 1223- 1249 (35.91/35.72)	LSNG.W....DLESYLKSLSKVLRNlklssCM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     286.84|      86|     122|    1375|    1469|       5
---------------------------------------------------------------------------
 1375- 1469 (144.91/111.30)	GSSSDMVQSSSMSGRSHpvlmqmtsPVPGMWKDCVGPRSIGTSLQRE.AELDASL.RSGSWD....NWQISRGGSLGCDPNRIGDFSFQDEVRYLfEPLYI
 1500- 1591 (141.93/89.13)	GTSGNFMQSSASSGGGD........TGPNTQSETSEPDGFGSAHQKSlPSLHCCYgWTEDWRwlvcIWTDSRGELLDNYIYPFGGISSRQDTKGL.QSLFV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     124.54|      35|      39|     492|     527|       7
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  492-  527 (60.80/39.89)	SEFGDFGDFFENDVLPFGEPPGTAESQAlMYPAA..DS
  533-  569 (63.75/37.74)	SPCPSMMDVKDQMLLPVGFPSFDSFNQP.PPPASldDS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     289.13|      81|    1158|     616|     698|       8
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  382-  433 (37.32/17.07)	.......................VSTSSSDSD.YKT.....................SGAGDLEADADSlmC...RPSGLSSvdqsrndNLKTGFKRSRT...............
  616-  698 (138.47/97.82)	VETPTGEKSHLIFRNPYLPKSREVDTSNSSSDSYVY.....................SATPPLSPYFDA..C..EEKSGVTV.......NLKTGSGRRDTSSIiqSKRYYTHIES
 1752- 1857 (113.35/73.36)	VSHGTSQSSGVLSQPGYLEGYTPVKSLGSTSNSYILipspnmrflppvglqlhtcltAESPPLAHLLHSkgCaiPLSTGFVV.......SKAVPTMRRDARSI..SKEEWPSVLS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     339.60|     108|     951|     146|     269|      11
---------------------------------------------------------------------------
  146-  269 (156.91/122.51)	VRYGDVFTKHHPFSQneELFRKGqPvvefiFS..ATEEAIFVHVIISAklIRALSSGDIDKISEDTSNVSGERLPViVSPHGMRGRLTGCCPADLVKQVYLSSCKF.....SASNGIVGlpcnvSRSGYQL
 1107- 1221 (182.69/102.01)	VGYQDDWLKTSPSSL..QLWEKA.P.....FEpyAMPKHMSYYVVCPD..INALTTAATDFFQQLGTVYETCKLGT.HSPQCMGNEMEIDSGKNVSSGFVLIDCPQsmkidSSSTSMLG.....SISDYFL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      91.66|      29|     127|     439|     470|      18
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  439-  470 (46.38/38.19)	FSQAGAVINPSTSDYasmEVNNS..AITGGNDQI
  570-  600 (45.28/28.75)	LSKHQEVIKSTAVAY...QVNNSsaAIAGEFDHL
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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 MDP12246 with Med13 domain of Kingdom Viridiplantae
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