<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 MDP06905

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMKAAQGGAEEAEKLNKMSSLLERLHAKFNQNRPWTETVKLVRQVMEKRVVMNSGGHQHLVSCLETLQKALKVSSLPAMTDRLESIARQNGLGSHLSANGTECYITSDMFYVEVHLDSTGLLCDVKVAHHGENPVSCPELVQHLREKNFDEFSKHLKGLVNLYKLPGDNKLKTKMYLALQSLELDLIKMASMYWQATNASPLDKILHGSVGYLTPRSGGHLMNLKYYISPYDLFEDGTRAPIALHDNNVPRSLGLNVSVTIEGTLAMYKLPIAPLIMGSHPVDNKGTPSFSSVTSANSVDLPACFFLKFPRPIPVSQAFIQKLQSCTGIPLFDTPPAFVPLYELITQFELSKETDSVPLNHNMRFYAALPGQQHCYFLNKDAPLPDGRSLQGTLISKIAFQHPGRVPLILNLIRHQVAYNTLIGSCVKRTVLKEDSPGILQFEVCPLSDSCFSVSFQHPVNDSLVCVVMDVQDSTHVNCKLYKGLSDALICTDDFIAKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNLPPASSPGYGMTTGSNPMSGTTTPTNTFPGGPITTLFNMSMSMKERHDSVGHGEDFSKVSQNPILTSLLQITGNVGSAIGSSPTPPHHTPPPVSSPASNTKNHPMLMNLLKDNPPQDFSTLYGSSPLERQNSSSGSPRMEMGPGGNKQKKKKSRIPADKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADTLDTPHITPAPSQCSTPPTTYPQSIPHPQPSIQRMVRLSSSDSIGADVTDILSDIAEEASKLPSTNDDCPPIGTPVRDSSSSGHSQSALFDPDVFQTNNSENPYTDPADLIADAAVSPNSDSSNHFFPDGVDFNPDLLNSQSQSGFGEEYFDESSQSGDADDFKGYAPQPLSTLGVQVLGGDGGENKFKGSSQADTVDFSIIASASKALGSSDIMEHHSGSQSPLLSTGDLGKEKPQKRVKEGNGSGSSLSGPGLDGKPGKRSRTPSSDGKSKEKLPKRKKADTEGKSPSHSTSNRPFTPPASTGKIKSSKSEGSSGSKMSSSLYSSQGGSGSGQSKSSAQSVGKPGSSPITKHGLSSSSGDLQGVLTSLPLQ
Length1104
PositionMiddle
OrganismAlligator mississippiensis (American alligator)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Crocodylia> Alligatoridae> Alligatorinae> Alligator.
Aromaticity0.06
Grand average of hydropathy-0.454
Instability index51.42
Isoelectric point6.44
Molecular weight118800.43
Publications
PubMed=22293439

Function

Annotated function Component of the Mediator complex, a coactivator involved in the 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:RU364059
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

>MDP06905
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.52|      12|      17|     849|     863|       2
---------------------------------------------------------------------------
  849-  860 (23.54/ 8.14)	PNSDSSNHFFPD
  889-  900 (17.98/ 7.56)	GDADDFKGYAPQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             6|     626.71|     109|     109|     536|     644|       3
---------------------------------------------------------------------------
  283-  424 (90.57/40.89)	NKG..TPSFSSVTSANSVDLP............................................................acfflkfprpipvsqafiqklqsctgiplfDTP....PAFV.PLYELitqfelskETDSVPL....NHNMRFYAAL.PG..QQHC.YFLNKDAPLPD.G..R...........S..............................L.QG..TLI.SKI.......AfQH.......................pgrvPLILNLIrhQVAYN..T.......................LIGS....
  426-  518 (64.07/26.44)	..........................................V....................................KR..............................TVL....KEDS.PGI.L........QFEVCPL....SDSCF.SVSF.QH...PVNdSLVCVVMDVQDsT..HvncklykglsDA..............................LICT..DDFiAKV.......V.QR.........................cmSIPVTMR.................................AIRRKAET
  519-  625 (167.66/82.93)	IQA..DTPALSLIAETVE..................dM....V....................................KK..............................NLP....PASS.PGYGM........TTGSNPM....SGTTTPTNTF.PG..GPIT.TLFNMSMSMKE.R..H..........DS..............................VGHG..EDF.SKV.......S.QN...........................PILTSLL..QITGNVGS.......................AIGSSPTP
  626-  742 (118.81/56.29)	PHH..TPPPVSSPASNTKNHP................MlmnlL....................................KD..............................NPP....QDFS.TLYG............SSPLerqnSSSGSPRMEMgPG..GN.......KQKKKKS.RipA..........DK..............................PKHQteDDF.QRElfsmdvdS.QN...........................PIF.D.V..NMTADTLD.......................TPHITPAP
  743-  946 (83.17/36.85)	SQC..STPPTTYPQSIPHPQPsiqrmvrlsssdsigaD....V....................................TD..............................ILSdiaeEASKlPS...........TNDDCPP....IGTPVRDSSS.SG..HSQS.ALFDPDVF..Q.T..N..........NSenpytdpadliadaavspnsdssnhffpdgVDFN..PDL.LN........S.QSqsgfgeeyfdessqsgdaddfkgyapqPLSTLGV..QVLGGDGGenkfkgssqadtvdfsiiasaskALGSSDIM
  947- 1083 (102.44/47.36)	EHHsgSQSPLLSTGDLGKEKP......................qkrvkegngsgsslsgpgldgkpgkrsrtpssdgksKE..............................KLP....KRKK.AD...........TEGKSPS....HSTSNRPFTP.PAstGKIK.SSKSEGSSGSK.M..S..........SS..............................LYSS..QGG.SGS.......G.QS..............................KSSA..Q...SVGK.......................P.GSSPIT
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      94.12|      30|      48|     147|     176|       4
---------------------------------------------------------------------------
  147-  165 (24.83/10.89)	..................................NFD.EFSKHLKGLVNLYKLP
  166-  214 (36.91/19.40)	GDNKLKTKMYL...alqsleldlikmasmywqatNAS.PLDKILHGSVG.YLTP
  217-  270 (32.38/16.21)	GGHLMNLKYYIspydlfedgtrapialhdnnvprSLGlNVSVTIEGTLAMYKLP
---------------------------------------------------------------------------




































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 MDP06905 with Med1 domain of Kingdom Metazoa


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) ALGSSDIMEHHSGSQSPLLSTGDLGKEKPQKRVKEGNGSGSSLSGPGLDGKPGKRSRTPSSDGKSKEKLPKRKKADTEGKSPSHSTSNRPFTPPASTGKIKSSKSEGSSGSKMSSSLYSSQGGSGSGQSKSSAQSVGKPGSSPITKHGLSSSSGDLQGVLTSLPLQ
2) KNLPPASSPGYGMTTGSNPMSGTTTPTNTFPGGPITTLFNMSMSMKERHDSVGHGEDFSKVSQNPILTSLLQITGNVGSAIGSSPTPPHHTPPPVSSPASNTKNHPMLMNLLKDNPPQDFSTLYGSSPLERQNSSSGSPRMEMGPGGNKQKKKKSRIPADKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADTLDTPHITPAPSQCSTPPTTYPQSIPHPQPSIQRMVRLSSSDSIGADVTDILSDIAEEASKLPSTNDDCPPIGTPVRDSSSSGHSQSALFDPDVFQTNNSENPYTDPADLIADAAVSPNSDSSNHFFPDGVDFN
3) QSQSGFGEEYFDESSQSGDADDFKGYAPQPLSTLGVQVLGGDGGENKFKGSSQAD
939
539
872
1104
865
926










Molecular Recognition Features






MoRF SequenceStartStop




1) ADDFKGYAP
2) AQSVGKPGSSPITKHGL
3) FGEEYFDES
4) MSSSLY
5) SKEKLPKRKKAD
891
1071
877
1051
1003
899
1087
885
1056
1014