<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 MDP28040

Description Mediator of RNA polymerase II transcription subunit 1
SequenceMKAQGETEESEKLSKMSSLLERLHAKFNQNRPWSETIKLVRQVMEKRVVMSSGGHQHLVSCLETLQKALKVTSLPAMTDRLESIARQNGLGSHLSASGTECYITSDMFYVEVQLDPTGQLCDVKVAHHGENPVSCPELVQQLREKNFDEFSKHLKGLVNLYNLPGDNKLKTKMYLALQSLEQDLSKMAIMYWKATNATPLDKILHGSVGYLTPRSGGHLMNIKYYASPSDLLDDKTASPIILHEKNVPRSLGMNASVTIEGTSAMYKLPIAPLIMGSHPVDNKWTPSFSSITSANSVDLPACFFLKFPQPIPVSKAFVQKLQNCTGIPLFETPPTYVPLYELITQFELSKDPDPLPLNHNMRFYAALPGQQHCYFLNKDAPLPDGQSLQGTLVSKITFQHPGRVPLILNMIRHQVAYNTLIGSCVKRTVLKEDTPGLLQFEVCPLSESRFSVSFQHPVNDSLVCVVMDVQDSTRVSCKLYKGLSDALICTDDFIAKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNLPPASSPGYGMATGNNPMSGTTTPTNTFPGGPITTLFNMSMSIRDRHESVGHGEDFSKVSQNPILTSLLQITGNGGSTIGSSPTPPHHTPPPVSSMAGNTKNHPMLMNLLKDNPAQDFSTLYGSSPLERQNSSSGSPRMEMCSGSNKTKKKKSSRVPPDKSKHQTEDDFQRELFSMDVDSQNPMFDVSMTADALDTPHITPAPSQCSTPPTTYPQPVSHPQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPSTSDDCPPIGTPVRDSSSSGHSQSALFDSDVFQTNNNENPYTDPADLIADAAGSPSSDSPTNHFFPDGVDFNPDLLNSQSQSGFGEEYFDESSQSGDNDDFKGFASQALNTLGMPMLGGDNGETKFKSSGQADTVDFSIISVAGKALGPADIMEHHSGSQSPLMTTGELGKEKTQKRVKEGNGTGASSVSGPGLDSKPGKRSRTPSNDGKSKDKPPKRKKADTEGKSPSHSSSNRPFTPPTSTGGSKSPGSSGRSQTPPGVATPPIPKITIQIPKGTVMVGKPSSHSQYTSSGSVSSSGSKSHHSHSSSSSSSSSASTSGKMKSSKSEGSSSSKLSGSMYSSQGSSGSSQSKNSSQTGGKPGSSPITKHGLSSGSSSTKMKPQGKPSSLMNPSISKPNISPSHSRPPGGSDKLASPMKPVPGTPPSSKAKSPISSGSSGSHMSGTSSSSGMKSSSGSGSSGSLSQKTPPASNSCTPSSSSFSSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTSGPGGEDPMDSQMGVSTNSSNHPMSSKHNMSGGEFQSKREKSDKDKSKVSTSGGSVDSSKKTSESKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGESSGEGLRPQIASSKNYGSPLISGSTPKHERGSPSHSKSPAYTPQNVDSESESGSSIAEKSYQNSPSSDDGIRPLPEYSTEKHKKHKKEKKKVKDRDRDRDKDRDKKKSHSIKPENWSKSPISSDQTLSMTNNPILSADRPSRLSPDFMMGEEDDDLMDVALIGN
Length1581
PositionMiddle
OrganismCricetulus griseus (Chinese hamster) (Cricetulus barabensis griseus)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Mammalia> Eutheria> Euarchontoglires> Glires> Rodentia> Myomorpha> Muroidea> Cricetidae> Cricetinae> Cricetulus.
Aromaticity0.04
Grand average of hydropathy-0.682
Instability index53.47
Isoelectric point8.91
Molecular weight168422.25
Publications
PubMed=21804562

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

>MDP28040
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      64.28|      20|      21|    1085|    1105|       1
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 1085- 1105 (35.06/12.58)	SSGSvSSSGSKSHHSHSSSSS
 1248- 1267 (29.23/ 6.64)	SSGS.GSSGSLSQKTPPASNS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             7|     909.96|     142|     164|    1019|    1182|       2
---------------------------------------------------------------------------
  542-  657 (81.10/14.70)	................................................................................................................................PA.SSP....GYGMATG..................NN..PMSGTTTPTNtfpggpittlfnmsmsirdrhesvghGEDFS.........KVSQNPILTsllQI..TGNGGS....TI..GSS.PTP.PHH..TPPPVSSMAGNTKNHPMLMNllKDNPAQDF
  658-  760 (123.67/28.10)	.......STL.....................YGS....................SPLERQ...........NSS.....................S.GSP......................................RMEMCSG..................SNKTK....KKKSS........................rvPPDKS.........KHQTEDDFQ...RElfSMDVDSQNP.MF..DVS.MTA.DAL..DTPHITPAPSQCSTPPTTYP..QPVSHPQ.
  761-  920 (132.41/29.46)	..PSIQRMVR.....................LSS....................SDSIGPdvtdilsdiaeEASKLPstsddcppiGTPVRDSSSS.GHSQSAlfD...........SDvfQTNNneNPY.TDPAD..LIADAAG..................SPSS.....DSPTN..........................HFFPDgvdfnpdllNSQSQSGFG...EE..YFDESSQ....S..GDN.DDF.KGF..ASQALN..TLGMP....MLG..GDNGETKF
  921- 1083 (166.30/39.91)	.....KSSGQadtvdfsiisvagkalgpadiM.........................EHH...........SGSQ............SPLMTTGEL.GKEKTQ..K...........RV..KEGN..GTG.ASSVS..GPGLDS.........................KP.GKRSR.....tpsndgkskdkppkrkkadteGKSPS.........HSSSNRPFT...PP..TSTGGSKSPGSS..GRS.QTP.PGV..ATPPIPKITIQIPKGTVMVG..KPSSHSQY
 1106- 1236 (199.79/48.86)	SSSSASTSGK.....................MKS....................SKSEGS...........SSSKLS.........GSMYSSQGSS.GSSQSK..N...........SS..QTGG..KPG.SSPIT..KHGLSSG..................SSSTKMKPQGKPSS.................lmnpsiskpNISPS.........HS...RP......P.....GGSDKLASP..MK....PvPG....TPPSSK.....AKSPISSG....SSGSHM
 1237- 1341 (97.09/20.45)	..SGTSSSSG.....................MKSssgsgssgslsqktppasnsC.TPSS...........SS................FSSSGSSmSSSQN...................Q.................HGSSKG..................KS.........PSR..........................NKKPS.........LTAVIDKLK...HG..VVTSG...PGGE..DPM.DSQ.MGV..STNS..............SN..HP......
 1342- 1493 (109.59/24.05)	MSSKHNMSGG.....................EFQ....................SKREKS.........dkDKSKVS.........TSGGSVDSSK.KTSESK..NvgstgvakiiiSK..HDGG..SPSiKAKVTlqKPGESSGeglrpqiassknygspliSGSTPKHERGSPSH..........................SKSPA................YT...PQ..NVDSESES.GSSiaEKSyQNS.PSSddGIRPLPE.......................
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     162.83|      41|      50|     324|     373|       3
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  284-  322 (36.80/30.91)	.....WTPSFSSITsansvdlpaCFFL.KFPQPIPVSKA...F...VQKL...Q..
  331-  373 (69.71/49.03)	ETPPTYVPLYELIT.........QFELsKDPDPLPLNHNM.RF...YAALPGQQhC
  384-  424 (56.32/28.99)	DGQSLQGTLVSKIT..........FQ...HPGRVPLILNMiRHqvaYNTLIGS..C
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     129.85|      44|      64|     153|     197|       5
---------------------------------------------------------------------------
  165-  213 (67.87/42.90)	GDNKLKTKMYLALQSLEQDLSKMAIMYWKATNA....tpldkILHGSVG.YLTP
  216-  269 (61.98/43.34)	GGHLMNIKYYASPSDLLDDKTASPIILHEKNVPrslgmnasvTIEGTSAmYKLP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      60.83|      18|      22|     447|     464|       6
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  447-  464 (33.07/19.93)	ES.RFSVSFQHPVNDSLVC
  471-  489 (27.76/15.50)	DStRVSCKLYKGLSDALIC
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      34.66|      10|     493|    1005|    1014|       7
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 1005- 1014 (17.81/ 8.82)	SKDKPPKRKK
 1495- 1504 (16.85/ 7.90)	STEKHKKHKK
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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 MDP28040 with Med1 domain of Kingdom Metazoa
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