<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. 
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
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.52|      12|      17|     849|     863|       2
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  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
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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 MDP06905 with Med1 domain of Kingdom Metazoa
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