<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 MDP01565

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMKAQGETEESEKLSKMSSLLERLHVKFNQNRPWSETVKLVRQVMEKRVVMSSGSHQHLVSCLETLQKALKVTSLPAMTDRLESIARQNGLGSHLSASGTECYITSDMFYVEVQLDPAGQLCDVKVAHHGENPVSCPELVQQLREKNFDEFSKHLKGLVNLYNLPGDNKLKTKMYLALQSLEQDLSKMAIMYWKATNAGPLDKILHGSVGYLTARSGGHLMNLKYYASPSDLLDDKTASPIILHENNVPRSLGMNALVTIEGTSAMYKLPIAPLIMGSHPADNKWTPSFSSVTSANSVDLPACFFLKFPQPIPVSRAFVQKLQNCTGIPLFENQPTYIPLYELITQFELSKDPDPMPLNHNMRFYAALPGQQHCYFLNKDAPLPDGRSLQGTLVSKITFQHPGRVPLILNMIRHQVAYNTLIGSCVKRTILKEDSPGLLQFEVCPLSESRFSVSFQHPVNDSLVCVVMDVQDSTHVSCKLYKGLSDALICTDDFIAKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNLPPASSPGYGMTTGNNPMSGTTTPTNTFPGGPITTLFNMSMSIKDRHESVGHGEDFSKVSQNPILTSLLQITGNGGSTIGSSPTPPHHTPPPVSSMAGNTKNHPMLMNLLKDNPAQDFSTLYGSSPLERQNSSSGSPRMEMCSGINKTKKKKSSRLPPDKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADTLDTPHITPAPSQCSTPPTTYPQPVPHPQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPSTSDDCPPIGTPVRESSSSGHSQSALFDSDVFQTNNNENPYTDPADLIADATGSPSSDSPTNHFFPDGVDFNPDLLNSQSQSGFGEEYFDESSQSGDNDDFKGFASQALNTLGVPMLGGDNGETKFKGNSQADTVDFSIISVTGKALGPAELMEHHSGSQSPLLTTGDLGKEKTPKRVKEGNGTTNSSLSGPGLDSKPGKRSRTPSNDGKSKDKPPKRKKADTEGKSPSHSSSNRPFTPPTSTGGSKSPGSSGRSQTPPGVATPPIPKITIQIPKGTVMVGKPSSHSQYTSSGSVSSSGSKSHHSHSSSSSSSSSASTSSKMKSSKSEGSSSSKLGSSVYSSQGSSGSSQSKNSSQSGGKPGSSPITKHGLSSGSGSTKMKPQGKPSSLMNPLSKPNISPSHSRPPGSSDKLASPMKPVPGTPPSSKAKSPISSGSGGSHMSGTSSSSGLKSSSGLGSSGSLSQKTPPSSNSCTASSSSFSSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTSGPGSEDAMDGQMGVSTNSSSHLMSSKHNISGGEFQGKREKSDKDKSKVSTSGGSVDSSKKTSESKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGESSGEGLRPQMTSSKNYGSPLISGSTPKHERGSPSHSKSPAYTPQNLDSESESGSSIAEKSYQNSPSSDDGIRPLPEYSTEKHKKHKKEKKKVKDRDRDRDKDRDKKKSHSIKPESWSKSPISSDQSLSMTSNTILSADRPSRLSPDFMIGEEDDDLMDVALIGN
Length1580
PositionMiddle
OrganismFukomys damarensis (Damaraland mole rat) (Cryptomys damarensis)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Hystricomorpha> Bathyergidae> Fukomys.
Aromaticity0.04
Grand average of hydropathy-0.670
Instability index53.99
Isoelectric point8.88
Molecular weight168431.23
Publications









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

>MDP01565
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
            10|     921.29|     104|     104|    1114|    1217|       2
---------------------------------------------------------------------------
  596-  685 (77.79/17.16)	.......................S...K.V..SQNPIL..TS......LLQITG.NGGSTIG..SSPT...........P...PHhtppP..........VSSMAGNTK.NHPM...........LMN.L...LKD.N...P......AQ.DF...STLY.GSSplerqnSS...SGSPrMEMCSGIN
  688-  794 (86.84/20.03)	KKKKSSrlppdKPKHQTEDDF.QR...E.LFSMD.......V......DSQN..............PIfdvnmtadtldT...PH...............ITPAPSQCS.TPPT.T....YPQ.PVPHP.....QP.S...IqrmvrlSS.SD...SIGP.DVT......DI...LSDI.AEEASKLP
  805-  909 (94.79/22.55)	TPVRES.....SSSGHSQSALfDS...D.VFQTNNNENpyTD......PADLIA.DATGSPS..SDSP...........T...NH....F..........FPDG...VD.FNPD...........LLNSQ...SQS.G...F......GE.EYfdeSSQS.GDN......DDfkgFASQ.ALNTLGVP
  918- 1009 (72.15/15.37)	TKFK............GNSQA.DTvdfS.IISVTGKAL..GP......AELMEH.HSGSQ.....SPL...........L...TT....GdlgkektpkrVKEGNGTTN...............S...SL...SGP.G...L....dsKPgKR...SRTP.SND......GK.....SK.DK.....P
 1010- 1089 (93.55/22.16)	PKRKKA.....DTEGKSPSHS.SS...NrPFTPPTSTG..GS......KSPGSSgRSQTPPGvaTPPI...........P...KI....T..........IQIPKG.TV.M..V.G....KPS.S...........................H...SQYT..SS.....................GSV
 1114- 1217 (187.72/52.04)	SKMKSS.....KSEGSSSSKL.GS...S.VYSSQGSSG..SS......QSKNSS.QSGGKPG..SSPI...........T...KH....G..........LSSGSGSTK.MKPQ.G....KPS.SLMNPL...SKP.N...I......SP.SH...SRPP.GSS......DK...LASP.MKPVPGTP
 1220- 1265 (65.77/13.34)	SK...A.....KSPISS.................GSGG..SH......MSGTSS.SS................................G..........LKSSSG.......L.G....SSG.SL.........................SQ...KTPP..SS.......................N
 1266- 1373 (104.40/25.60)	SCTASS.....SS..FSSS...GS...S.MSSSQNQHG..SS......KGKSPS.RN.KKPS..LTAV...........IdklKH....G.........vVTSGPGSEDaMDGQmGvstnSSS.HLMS.....SKH.N...I......SG.GE...FQGKrEKS......DK...DKSK.VSTSGGSV
 1375- 1459 (82.09/18.52)	SSKKTS.....ESKNV..................GSTG..VA......KIIISK.HDGGSPS.iKAKV...........T.lqKP....G..........ESSGEG....LRPQ.M....TSSkNYGSPLisgSTP.KherG......SP.SH...S..............K.....SP.AY....TP
 1460- 1541 (56.19/10.30)	QNLDS............................ESESG..SSiaeksyQNSPSS.DDGIRPL..PEYS...........T...EK....H..........KKHKKEKKK.VKDR.D....RDR.DKDRDK...KKShS...I......KPeSW...SKSP.ISS......DQ................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     136.12|      44|     340|     101|     150|       3
---------------------------------------------------------------------------
  101-  150 (67.78/60.51)	CYITSDMFYVEVQlDPAGQ..LC...DVKVAHHgenpVSCpELVQQLREK..NFDEF
  443-  493 (68.34/41.48)	CPLSESRFSVSFQ.HPVNDslVCvvmDVQDSTH....VSC.KLYKGLSDAliCTDDF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     131.90|      40|      50|     328|     373|       4
---------------------------------------------------------------------------
  328-  373 (65.63/53.96)	PLFENQPTYIPLYELITqFelsKDPDPMPLNHNM.RF...YAALPGQqhC
  381-  424 (66.27/37.33)	PLPDGRSLQGTLVSKIT.F...QHPGRVPLILNMiRHqvaYNTLIGS..C
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     166.16|      44|      64|     153|     197|       5
---------------------------------------------------------------------------
  153-  197 (70.46/47.32)	HLKGLvNLYNLPG...DNKLKTKMYLALQSLEQ.DLSKMAIMYWKATNA
  218-  264 (66.41/40.09)	HLMNL.KYYASPSdllDDKTASPIILHENNVPR.SLGMNALVTIEGTSA
  279-  306 (29.29/12.84)	...........PA...DNKW.TPSFSSVTSANSvDLP..ACFFLK....
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.03|      17|      20|     541|     558|       6
---------------------------------------------------------------------------
  541-  558 (30.58/20.35)	PPASSPGYGMTTGNNpMS
  563-  579 (34.45/17.92)	PTNTFPGGPITTLFN.MS
---------------------------------------------------------------------------




































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 MDP01565 with Med1 domain of Kingdom Metazoa
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