<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 MDP12247

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMWTNVFKIGGLHQISWFQFLPHESDVSSLVDKSVKLDKKDAATWLVLSSHLQLQKEGFLSTWTNSFVGPWDPSQGLHNPDEKIKLWLFSPGQHSSVVEKAQSAVSKLRVLASGLWVAPGDSEEVAAALSQALRNCMERKLRGLSYVRYGDVFTKHHPFSQNEELFRKGQPVVEFIFSATEEAIFVHVIISAKLIRALSSGDIDKISEDTSNVSGERLPVIVSPHGMRGRLTGCCPADLVKQVYLSSCKFSASNGIVGLPCNVSRSGYQLKGQNCYVEVSLGCTTPGNNNIKESSRMLIYPPEAILVPVVQTACARSSLKRFWLQNWIGPSLSFTSSFMHCFDFSSDAKVNSTDGSWLDANIMRSNRQYNSSSNSNSSSVSSVSTSSSDSDYKTSGAGDLEADADSLMCRPSGLSSVDQSRNDNLKTGFKRSRTGISESFSQAGAVINPSTSDYASMEVNNSAITGGNDQIGLQWGWDDDDRGVGMDIQALLSEFGDFGDFFENDVLPFGEPPGTAESQALMYPAADSADVGSSPCPSMMDVKDQMLLPVGFPSFDSFNQPPPPASLDDSLSKHQEVIKSTAVAYQVNNSSAAIAGEFDHLIKAEALMTFAPEYGAVETPTGEKSHLIFRNPYLPKSREVDTSNSSSDSYVYSATPPLSPYFDACEEKSGVTVNLKTGSGRRDTSSIIQSKRYYTHIESGKEKNDGKLSGSDHSCATREAQVEQSPFYGFNSTNSVKSIHNKTEKANEALLKADSFGQSMKTVLATEVECLMCQAFMCKIRHTLLSSSSYLPVGASRMSGSTIINQPQGEAVVTVDNMSSKSEMKKKEIIPVRIAGDIDGGLLDGTLNAQVGVWRSVGVSKGMKQPSSALEACHSVQHNSFIEESMLAYGLRQPLQELLDGVALLVQQATSLVDVALDADNNDGPYGWLTLQEQWRRGFSCGPSMVHAGCGGVLASCHSLDIAGVELIDPLSADVQASFALTLLQNDIKTAMKSAFGTMEGPLSVVDWCKGRSQSNDGGISGDGFSAESTASASECRDSSSTISFSVGEPISPSQSSAGGSSLKDGIRVDEASERRLSQDTCLSESEQLPGSRLRPTLSAVPYPAILVGYQDDWLKTSPSSLQLWEKAPFEPYAMPKHMSYYVVCPDINALTTAATDFFQQLGTVYETCKLGTHSPQCMGNEMEIDSGKNVSSGFVLIDCPQSMKIDSSSTSMLGSISDYFLSLSNGWDLESYLKSLSKVLRNLKLSSCMTMNPKEGSTGPCTVIYVVCPFPEPLAVLQTVVESSIAVGSVVLSSDKERRSTLQNQVGKALSYSAAVDESLSNVLTLSGFCIPKLVLQIVTVDAIFRVTSPALSELLVLKEIAFTVYNKARRISRGSSSDMVQSSSMSGRSHPVLMQMTSPVPGMWKDCVGPRSIGTSLQREAELDASLRSGSWDNWQISRGGSLGCDPNRIGDFSFQDEVRYLFEPLYILAEPGSLDRGLSFPMSGNLMAESSKLLLDDGTSGNFMQSSASSGGGDTGPNTQSETSEPDGFGSAHQKSLPSLHCCYGWTEDWRWLVCIWTDSRGELLDNYIYPFGGISSRQDTKGLQSLFVQILQQGCQILQACPPEAANAKPRDFVIARIGSFFELECQEWQKALYAIGGSEVKKWSLQLRRSVPDGMSASSNGTSLQQQEIGGMGQPSTRKQLIGGQGMVDNSRGLLQWVQSISFVSVSIDHSLQLMFQADIVSHGTSQSSGVLSQPGYLEGYTPVKSLGSTSNSYILIPSPNMRFLPPVGLQLHTCLTAESPPLAHLLHSKGCAIPLSTGFVVSKAVPTMRRDARSISKEEWPSVLSVSLVDYYGGSNIIQEKFFKGVGKVGGRGTSSETRDVEIETHLILENIAAELHALSWMTVSPAYLERRSALPFHCDMVLRLRRLLHFADKEVSRQPEKTQV
Length1930
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-0.226
Instability index53.61
Isoelectric point5.36
Molecular weight209155.18
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	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

>MDP12247
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     124.54|      35|      40|     492|     527|       1
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  492-  527 (60.80/39.58)	SEFGDFGDFFENDVLPFGEPPGTAESQAlMYPAA..DS
  533-  569 (63.75/37.45)	SPCPSMMDVKDQMLLPVGFPSFDSFNQP.PPPASldDS
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     124.94|      43|      78|     853|     927|       2
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  856-  910 (57.01/81.67)	VGvskGMKQPSS...............ALeaCHSVQHNSFIEESmlaygLRQPLQELLDgvALLVQQATS
 1673- 1730 (67.92/28.18)	IG...GMGQPSTrkqliggqgmvdnsrGL..LQWVQSISFVSVS.....IDHSLQLMFQ..ADIVSHGTS
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     144.65|      44|      86|      69|     113|       3
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   69-  113 (72.76/59.77)	PWDPSQGLHNPDEKIKLWLFSPGQHSSVVEKAQSAvSKLRVLASG
  157-  200 (71.89/53.83)	PFSQNEELFRKGQPVVEFIFSATEEAIFVHVIISA.KLIRALSSG
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     210.72|      65|      78|     922|     988|       4
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  922-  988 (108.35/58.95)	DGPYG...WLTLQEQWRRGFSCGPSMvHAGCGGVLASCH.SLDIAGVELIDPLSADvQASFALTLLQNDIK
  999- 1067 (102.37/49.10)	EGPLSvvdWCKGRSQSNDGGISGDGF.SAESTASASECRdSSSTISFSVGEPISPS.QSSAGGSSLKDGIR
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.97|      12|      31|     377|     388|       5
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  377-  388 (19.70/10.49)	SSVSSVSTSSSD
  411-  422 (21.26/12.06)	SGLSSVDQSRND
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     151.91|      44|     827|     656|     714|       6
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  668-  714 (70.40/65.60)	SGVTVNLKTGSGRRDTSSIIQSKryyTHIESGKEKNDGKLSGSDHSC
 1502- 1545 (81.51/41.64)	SGNFMQSSASSGGGDTGPNTQSE...TSEPDGFGSAHQKSLPSLHCC
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.12|      18|     827|     389|     406|       7
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  389-  406 (31.93/17.94)	SDY..KTSGAGDLEADADSL
 1217- 1236 (29.19/15.72)	SDYflSLSNGWDLESYLKSL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     145.21|      45|    1112|     278|     348|       8
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  289-  333 (84.66/78.64)	NIKESSRMLIYP...................PEAILVPVVQTACARSSL.......KRFWLQNWIGPSLSF
 1242- 1312 (60.55/19.16)	NLKLSSCMTMNPkegstgpctviyvvcpfpePLAVLQTVVESSIAVGSVvlssdkeRRSTLQNQVGKALSY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     119.89|      34|    1112|     624|     657|       9
---------------------------------------------------------------------------
  624-  657 (59.92/37.96)	SHLIFRNPYLPKSREVDTSNSSSDSYVYSATPPL
 1733- 1766 (59.97/38.00)	SGVLSQPGYLEGYTPVKSLGSTSNSYILIPSPNM
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     234.57|      75|     442|    1349|    1428|      12
---------------------------------------------------------------------------
 1349- 1428 (115.99/95.23)	SPALSELLVLKEIAF.............TVYNKARRISRGSSSDMVQSSSMSGRSHPVLMQmTSPVPGMWKdcVGPRsiGTSLQ.REAELDASL
 1784- 1872 (118.58/78.77)	SPPLAHLLHSKGCAIplstgfvvskavpTMRRDARSISKEEWPSVLSVSLVDYYGGSNIIQ.EKFFKGVGK..VGGR..GTSSEtRDVEIETHL
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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 MDP12247 with Med13 domain of Kingdom Viridiplantae
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