<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 MDP06887

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSSCFVPNGASLEDCHSNLFCLADLTGIKWKRYVWQGPTSAPILFPVTEEDPILSSFSRCLKADVLSVWRRDQRPGRRELWIFWWGDDPNFADLIHHDLAEEEDGVWENGLSYECRTLLFKAVHNLLERCLMNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEISQHQPVYLLSEEHLTLAQQSNSPFQVILSPFGLNGTLTGQSFKLSDSSTKKLIGEWKQFYPITSNLKEGSEEKQEEMDWEDDSLAAVEVLVAGVRMVYPACFVLVPQTDIPAPSTVGASHCSTTCLGVHQVPATTRDPAMSSVTLTPPTSPEEVQTAVDAQSAQKWVKFSSVSDGFSSDSTSHHGGKIPRKLANQVVDRVWQECNMNRAQNKRKYSATSNGLCDEETADKVASWDFVEATQRTNCNCSRHKNLKPRNSGQQGQAPPASQQQQAAPKHKTNEKQDKGDKPQKRPLTPFHHRVSISDDVAMEAESASQRLVITAPDSQSQHFYQMPTPDPLVPSKAMEDRIDGLSQSFPAQFPEVIEPTIYIGTAVNLEEDEADNTWKYYKVPKKKDVEFLPPPLPCDKFRDDPVVPAGQENLTSVTELMVQCRKPLKVSDELVQQYQSKNQYLAAVVSETDQEPEIDPYAFVDGDVEFLFPDNKKERQNNERETGKKHKAEDGTPNVTVLSHEGKDAMSLFSPSVKPEQRTAAHARTASTSLIHETDLVVSYTDLDNLFNSDEDELTPGSKRTVNGSDDKPNCKESKTGNLDPLSCISTADLHKIMDTTLGGTVLEGNSSSIGAQFRIEVDEGFCSPKPSEIKDYSYVYKPENCQALVGCSMFAPLKTLPSQCLPSIKLPEECIYRQSWAVGKLELLPPGPAMPFIKEGDGSTMDQEYGPAYTPQTHTPFGMPPNSAPPSNSGAGILPSPSTPRFPTPRTPRTPRTPRGGGGPASAQESVMNLFKDCNFDSCCICVCNMNIKDELDILGRNTEGGKEAEKRFEALRATSVEHADQDPIPKVGAVSNLVRVEERDCCNDCYLALEHGRQFMDNMSGGKVDEALVKSTCLHHWSKRNVVDVSMQCSQDILRMLLSLQPVLQDAIQKKRTVRSWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLLGYDYDFLVLSPFALPYWERLMLEPYGSQRDVAYVVVCPENEALLNGAKSFFRDLTAIYESCRLGQHRPICKLLPDGIMRVGSTASKKLSEKLVAEWFSQAANANNEAFSKLKLYAQVCRYELGPYLASQPLDSSLLSQINLVPPTSQSVSTQPQAAATTTNSTLTTTAASSSSTNIGSGLSANKPSSFPPFSSMNSTTSASLPTQATTVQNGQPGGQQQQATLQAAGIPGEASSAPAQPHPEVSESTMDRDKVGVPTDGDSHAITYPPAIVIYIIDPFTYERKDENSSSSSVWTLGLLRCFMEMVQILPSSIRNIVSVQIVPCQYLLQPVKHEDRQIYTQHLKSLAFSAFTQCRRPLPTSTNVKTLTGFGPGLAMETALKSPDRPECIRLYTPPFILAPVKDKQTELGETFGEAGQKYNVLFVGYCLSHDQRWLLASCTDLYGELLETCIINIDVPNRARRKKGSARRLGLQKLWDWCLGLVQMSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCGISAADSPSFLSACLVAMEPQGSFIIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTSCTHILVFPTSASVQVASSTYTTENLDLAFNTNNDGADGMGIFDLLDTADELDPDIINILPASPTGSPVHSPGSHYPHGGDMGKGQSTDRLLSTESHDEVTNILQQPLALGYFVSTAKAGPLPDWFWSACPQAQNQCPLFLKASLHLHVPSVQSDELLHSKHSHPLDSNQTSDVLRFVLEQYNALSWLTCDPATQDRRSCLPVHFVVLNQLYNFIMNML
Length1951
PositionMiddle
OrganismAlligator mississippiensis (American alligator)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Crocodylia> Alligatoridae> Alligatorinae> Alligator.
Aromaticity0.07
Grand average of hydropathy-0.413
Instability index50.25
Isoelectric point5.51
Molecular weight215621.94
Publications
PubMed=22293439

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. 
ECO:0000256	RuleBase:RU364134
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

>MDP06887
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|    1004.24|     376|     514|     786|    1298|       1
---------------------------------------------------------------------------
  786- 1134 (406.94/490.45)	DTTLGGTVLEGNSSSIGAqfrievdeGFCSPKPSEIKDYSYVYKPEN....CQALVgCSMFAPLKTLPSQCLPSIKLPEEciyrQSWAvgklellppgPAMPFiKEGDGSTMDQE..............YGPAYTPQTHTPFGM...PPNSAPPSNSGAGILPSPSTPRFPTPRTPRTprtprggggpasaqesvmnlfkdcnFDSCCICVCN...MNIKDElDILGRNTEGGKEAEKRFEALRATSVEHADQDPIPKVG...AVSNLVRVEERDCCNDCY.....LA......LEHGRQFMDnmSGGKVDEALVkSTCLHHwSKRNVVdvsMQCSqDILRMLLSLQPVLQD....AIQKKRTVRSWGVQ............GPLTWQqfhKMAGR.GSYGTDE......................................................................................................................................................................
 1206- 1295 (24.29/291.89)	....................................................................................................................................................................................................................................................................................................................................................................................................................speplpiptfllgydydflvlspfalpywerlmlepygsqrdvayvvvcpeneallngaksffrdltaiyeSCRLGQH..RPICKLLPDGIMRVGSTASKK...LSEKLVAEWFSQAANANNEAFSKLKLYAQVCRYELGPYLASQPLDSSlLSQInLVPPTSQSV
 1307- 1746 (573.02/-8.00)	NSTLTTTAASSSSTNIGS........GLSANKPSSFPPFSSMNSTTSaslpTQATT.VQNGQPGGQQQQATLQAAGIPGE....ASSA..........PAQPH.PEVSESTMDRDkvgvptdgdshaitYPPAIVIYIIDPFTYerkDENSSSSSVWTLGLLRCFMEMVQILPSSIRN.........................IVSVQIVPCQyllQPVKHE.DRQIYTQHLKSLAFSAFTQCRRPLPTSTNVKTLTGFGpglAMETALKSPDRPECIRLYtppfiLApvkdkqTELGETFGE..AGQKYNVLFV.GYCLSH.DQRWLL...ASCT.DLYGELLETCIINIDvpnrARRKKGSARRLGLQklwdwclglvqmSSLPWR...VVIGRlGRIGHGE...................................................................lkdwSCLLSRRnlQSLSKRLKDMCRMCGISAADSpsfLSACLVAMEPQGSFIIMPDSVSTGSVFGRSTTLNMQTSQLNTPQDTS.CTHI.LVFPTSASV
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     423.62|     142|     234|     354|     521|       4
---------------------------------------------------------------------------
  365-  521 (210.35/196.43)	GGKIPRKLANQVVD.....RVWQECnMNRAQNKRKYSATSNGLCDEEtaDKVASWDFVEA.TQRTNCNCSRHKNLKPRNSGQQGQAPPASQQQQAApKHKTNEKQ...DKGDKPQKRplTPFHHRvSISDDVAMEAEsasqrLVITAPDsqSQHFYQmPTPDPLVP
  597-  747 (213.27/133.09)	GQENLTSVTELMVQcrkplKVSDEL.VQQYQSKNQYLAAVVSETDQE..PEIDPYAFVDGdVEFLFPDNKKERQNNERETGKKHKAEDGTPNVTVL.SHEGKDAMslfSPSVKPEQR..TAAHAR.TASTSLIHETD.....LVVSYTD..LDNLFN.SDEDELTP
---------------------------------------------------------------------------




































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 MDP06887 with Med13 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) FPDNKKERQNNERETGKKHKAEDGTPNVTVLSHEGKDAMSLFSPSVKPEQRTAAHARTAST
2) GSPVHSPGSHYPHGGDMGKGQSTDRLLSTESH
3) ILGRNTEGGKEAEKRFEALRATSVEHADQD
4) NCNCSRHKNLKPRNSGQQGQAPPASQQQQAAPKHKTNEKQDKGDKPQKRPLTPFHHRVSISDDVAMEAESASQRLVITAPDSQSQHFYQMPTPDPLVPSKAMEDRIDGLSQSFP
5) PAMPFIKEGDGSTMDQEYGPAYTPQTHTPFGMPPNSAPPSNSGAGILPSPSTPRFPTPRTPRTPRTPRGGGGPASAQ
6) VPPTSQSVSTQPQAAATTTNSTLTTTAASSSSTNIGSGLSANKPSSFPPFSSMNSTTSASLPTQATTVQNGQPGGQQQQATLQAAGIPGEASSAPAQPHPEVSESTMDRDKVGVPTDGD
659
1798
986
424
880
1288
719
1829
1015
537
956
1406










Molecular Recognition Features






MoRF SequenceStartStop




NANANA