<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 MDP02872

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMRFGDVFSRYHPPQIEESIRRAQPTIEFIFAATEESIFVHAIISSKHIRTLSTGDIEKVLEHSSNNTSYLLPVIISPHGMCGKLTGCCPNDLVKQVYFSNSGKIGLPHRTSQSSVCQLRGQNCYVKVSLGCSKSRGDKPLNPNPDYIRNLPKHQSTEAYAMGRVDQKGPLDLLSVHEKTFIYPPEAVLVPVLQTSFARSSLRRFWLQNWIGPSLAGSSFFRHCFCSDGNLDILEKSWAEFSGIHTQHCYNSSSNSNNSSISSLSSSSSDSVTTGARDLEADADSSCRQSGLSSNDQMETDCLKLGSKRPRIGMTESYGQAGVGNDQIGSNWDWDDDDRGIVMDIQSLLSEFGDFGDFFENDVLPFGEPPGTAESSAIMFGASDCGDVGSSPAGVMDTSDQMLLPVGLPSFDSFNPPLPLVTEEFLSKSQEVTNSAVTSGPSNQTPASSTGEFDHLMKAEALMTFAVEYGAVETPASDSSSVFRNPYLPKSRKVESSNSSQSNYKYAATPPSFPCFGGLDEKTGMPMNLKAHPGGHDSNSMLQLKKYYTHVETREERYGRRLLTHNDSNATNEMSGTSQFGNLYSIKSDKSASRKMTQGVFGGERILLSMKTVLGTEVECSMFQASMLRMRHILLSPTSPATINLSRPTASSVLNQLPDDPSTMADNLSSRYEVKKESIPFKSAGDIDGVMLDGHLNAPVGVWRTVGAPKVSKLATSSIEASPSLTHNLYNEESMLSYGQSQPLQELLDGIPLLVQQATSFVDLALDADGGDCPYSWLALQEHWRRGFCCGPSMVHAGCGGTLASCHSLDIAGVELVDPLSANIHASSVISLLHSDIKSALKSAFGSLDGPLSVTDWCRGRGQSGDVGASADGSSTESNISECRDSSSTVTLSVGEAVSPSQTSVGGSSYLKDGGKVDETSQRRLNQETSGSELEQQQSSRLRSTLFVLPSPALLVGYQDDWLKTSGNSLQLWEKAPLEPYALPKPINYSVICPDIDPLTSAAADFFQQLGIVYETCKLGTHSPQSLGNQMEIDSGKWFSSGFVLLDCPQSMKIESSNASLLGSISDFFLSLSNGWDMTCYLKSLSKALKALKIGQFLFTNQKEGISSPCLVIYVVCPFPEPTAVLKTVIESSIAVGSIILPSDRDKRSLLHSQIGKALSSSAAADEASVSNIPVVSGFSVPKVVVQIVTVDAIFRVTSPPFNELIILKEMAFTVYNKARRISRGSMNDLALSSSLSRSHSVLTPMTSIPTMWKDSVGSRIPGSSIPREGEIDSSLRGGAWENSWQTRTGGLSCDPNRNGDFFYPDEVRYMFEPLFILAESGSLEHGVSPTAFGNSTSETSKIVSDESGGGFMQAANSVGSTDPGSGSQHVGLEPDGLDSSNQKIPSLHCCYGWTEDWRWLVCIWTDARGELLDCNIFPFGGISSRQDTKGLQCLFVQVLQQGCHILQACTSSDTGVVKPRDFVITRIGSFYELEYLEWQKAIYSVGGSEVKKWPLQLRRSVPDGMPANTNGTSLDQQEMSLIQERTLPSSPSPLYSSHTKASFMKGGLGQPAARKQLLSGQTLVDNSRGLLQWVQSISFVSVSVDHSLHLVLQADSPSSGTHSGTGPGQSSYIEGFTPVKSLGSTSASYMLIPSPSMRFLPPTPLHLPTCLTAESPPLAHLLHSKGFAIPLSTGFVVSKAVPSMRKDYRNHPKEEWPSVLSISLIDYYGGNKVTQDKVIRGTAKQAGRTPSSESRDSEIDNHLILASIAAELHALSWMTVSPGFLDRRTALPFHTDMVLRLRRLLHFAEKELSGQPDKSQV
Length1801
PositionKinase
OrganismGossypium raimondii (New World cotton)
KingdomViridiplantae
LineageEukaryota> Viridiplantae> Streptophyta> Embryophyta> Tracheophyta> Spermatophyta> Magnoliopsida> eudicotyledons> Gunneridae> Pentapetalae> rosids> malvids> Malvales> Malvaceae> Malvoideae> Gossypium.
Aromaticity0.07
Grand average of hydropathy-0.260
Instability index51.06
Isoelectric point5.62
Molecular weight195103.21
Publications
PubMed=23257886

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

>MDP02872
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     226.60|      73|     839|     672|     752|       1
---------------------------------------------------------------------------
  672-  752 (103.84/73.14)	EVKKESIPFKSAGDiDGvmLDGHLNapvGVwrTVGAPKVSKLATSSIEASPSLTHNLYNEESMLSYGQSQPL..QELLDGIPL
 1489- 1563 (122.76/63.37)	EVKKWPLQLRRSVP.DG..MPANTN...GT..SLDQQEMSLIQERTLPSSPSPLYSSHTKASFMKGGLGQPAarKQLLSGQTL
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     289.21|      93|     839|      44|     146|       2
---------------------------------------------------------------------------
   44-  146 (149.32/96.72)	SSKHIrTLSTGDIEKVLEHSSNNTSYLlpviisPHGmcGKLTGCCPNDLVKQVYFS.....NSGKIGLPHRTSQSSVCQLRGQNCYVKVSlGCSKSRGDK.PLN....PNP.DY
  885-  988 (139.89/69.80)	SSSTV.TLSVGEAVSPSQTSVGGSSYL......KDG..GKVDETSQRRLNQETSGSeleqqQSSRLRSTLFVLPSPALLVGYQDDWLKTS.GNSLQLWEKaPLEpyalPKPiNY
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     342.82|     148|     750|     362|     598|       3
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  436-  520 (84.35/162.44)	.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................VTSGPSNQTPASSTGEFDHLMKAEALMTFAVEYGAVETPASDSSSVFrNPY..LPKSRKvESSNSSqsnykyaaTP.PSFPCFGGLDE
  521-  598 (84.37/36.51)	KTGMPMN.LKAHPGGHDSNSMLQLKKYYTHvetrEERYG.RRLLTHNDSNATNEMSGTSQFGNLYSiKSDKSASRKMTQG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 1196- 1273 (85.95/26.57)	................................................................................vfggerillsmktvlgtevecsmfqasmlrmrhillsptspatinlsrptassvlnqlpddpstmadnlssryevkkesipfksagdidgvmldghlnapvgvwrtvgapkvsklatssieaspslthnlyneesmlsygqsqplqelldgipllvqqatsfvdlaldadggdcpyswlalqehwrrgfccgpsmvhagcggtlaschsldiagvelvdplsanihassvisllhsdiksalksafgsldgplsvtdwcrgrgqsgdvgasadgsstesnisecrdssstvtlsvgeavspsqtsvggssylkdggkvdetsqrrlnqetsgseleqqqssrlrstlfvlpspallvgyqddwlktsgnslqlwekaplepyalpkpinysvicpdidpltsaaadffqqlgivyetcklgthspqslgnqmeidsgkwfssgfvlldcpqsmkiessnasllgsisdfflslsngwdmtcylkslskalkalkigqflftnqkegisspclviyvvcpfpeptavlktviessiavgsiilpsdrdkrsllhsqigkalsssaaadeasvsnipvvsgfsvpkvvvqivtvdaifrVTSPPFNELIILKEMAFTVYNKARRISRGSMNDLALSSSLSRSHSVL.TPMtsIPTMWK.DSVGSR........IPgSSIPREGEIDS
 1276- 1350 (88.15/26.70)	RGGAWENsWQTRTGGLSCDPNRNGDFFYPD....EVRYMfEPLFILAESGSLEHGVSPTAFGNSTS.ETSKIVSDESGGG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     309.69|      97|     579|     201|     301|       4
---------------------------------------------------------------------------
  201-  301 (165.70/112.24)	LRRFWLQNW.IGPSL..AG.SSFFRHCFCSD.GNLDILEKSWAefsGIHTQHCYNSSSNSNNSSISSLSSSSSD..SVTTGARDLEADADSSCRQSGlSSNDQMETDC
  779-  882 (143.99/86.53)	LQEHWRRGFcCGPSMvhAGcGGTLASCHSLDiAGVELVDPLSA...NIHASSVISLLHSDIKSALKSAFGSLDGplSVTDWCRGRGQSGDVGASADG.SSTESNISEC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     210.69|      63|    1226|     335|     419|       5
---------------------------------------------------------------------------
  340-  414 (102.06/79.12)	IVMDIQSLLSEFGDF....GDFFENDVLPFGEPPGTAESSAImfgasDCGDVGSSPAGVMDTSDQMllpvglpSFDSFN
  991- 1057 (108.63/44.64)	ICPDIDPLTSAAADFfqqlGIVYETCKLGTHSPQSLGNQMEI.....DSGKWFSSGFVLLDCPQSM.......KIESSN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      69.90|      22|     462|    1156|    1181|       6
---------------------------------------------------------------------------
 1156- 1181 (31.10/24.38)	KALSSSAaadeASVSNIPVVSGFSVP
 1620- 1641 (38.81/21.01)	KSLGSTS....ASYMLIPSPSMRFLP
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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 MDP02872 with Med13 domain of Kingdom Viridiplantae
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