<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 MDP28834

Description Mediator of RNA polymerase II transcription subunit 1
SequenceEAEKLNKMSSLLERLHAKYSQNRPWTETIKLVRQVMEKRVVLNSGGHQHLVSCLETLQKALKVSSLPAMTDRLESIARQSGGPGAAAAAPGAAPALINSLGYFITLNLTSSGKFCIVKVVYAAEGPENCPELVQHLREKNFDDFSKHLRGLVNLYKLPGDNKLKTKMYLALQSLELDLQKMAGMYWQATNANPLDKILHGSVGYLTPRSGGLLMNLKYYVSPYDLFEDGTGAPVVLHENSVPRSLGMNVSVTVEGTMAMHKLPIAPLIMGSHPVDSKGTPSFSSITSANSVDLPACFFLKFPRPIPVSRAFIQKLQSCTGIPLFDTAPTFVPLYELITQFELSKEADPLPLNHNMRFYAALPGQQHCYFLNKDAPLPDGRSLQGTLISKIAFQHPGRVPLILNLIRHQVAYNTLIGSCVKRTVLKEDSPGILQFEVCPLSDSCFSVSFQHPVNDSLVCVVMDVQDSSHVNCKLYKGLSDALICTDDFIAKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNLPPASSPGYGMTTGSNPMSGTTTPTNTFPGGPITTLFNMSISMKERHDSVGHGEDFSKVSQNPILTSLLQITGNVGSTIGSSPTPPHHTPPPVSSPASNTKNHPMLMNLLKENPPQDFSTLYGSSPLERQNSSSGSPRMEMGPGGNKQKKKKSRMPADKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADTLDTPHITPAPSQCSTPPATYPQALPHAQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPTSTEDCPPIGTPVRDSSSSGHSQSALFDPDVFQTNSSENPYTDPADLIADAAVSPNSDSSNHFFPDGVDFNPDLLNSQSQSGFGEEYFDESSQSGDTDDFKGYGPQALTNLGVQVLGADGGENKFKGSAPSDTVDFSIIAAASKALGSSDIMEHHSGGQSPLLNTGDLGKEKSQKRVKEGNGSGSAMAGAGIDGKPGKRSRTPSSDGKSKEKLPKRKKQETDGKSPSHSSSNRPFTPPASTGGSKSPGSSGRSQTPPGVATPPIPKITIQIPKGTVTVGKPSSHGQYTSSGSVTSSSSKSHHSHSSSSSSSSSSSTSGKIKSKSEGSSGSKMSSSLYSSQGGSGSGQSKGSAQSVGKPGSSPITKHGLSTGSGSTKMKPQGKPSSLMNPSMSKPNISPSHSRPSGGSDKLASPMKPVPGTPPSSKAKSPISSGSGGSHMSGAGSSSSMKSSSGMGSSGSMSQKPPPSSSSSTASSSSFSSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTSGPGGDDPMDGQMGPSSNSSSHTMSSKHNMSGGEFQGKREKSDKEKSKVSVSGGSVDSSKKNSDSKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGEGGGDGLRPQMASSKSYGSPLISGSTPKHERCSPSHSKSPAYTPQNIDSESESGSSIAEKSYQNSPSSDDGIRPLPDYSAEKHKKHKKEKKKVKDKDRDRERDRDKDRDKKKSHGMKPESWSKSPISADQSLSMASNAILSAERPSRASPEFLIGEEDDDLMDVALIGN
Length1575
PositionMiddle
OrganismTaeniopygia guttata (Zebra finch) (Poephila guttata)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Dinosauria> Saurischia> Theropoda> Coelurosauria> Aves> Neognathae> Passeriformes> Passeroidea> Estrildidae> Estrildinae> Taeniopygia.
Aromaticity0.05
Grand average of hydropathy-0.611
Instability index54.50
Isoelectric point9.03
Molecular weight166494.46
Publications
PubMed=20360741

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

>MDP28834
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.92|      17|      19|    1070|    1087|       2
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 1070- 1087 (25.88/10.14)	SHGQYTSSGSvTSSSSKS
 1088- 1104 (25.03/ 6.34)	HHSHSSSSSS.SSSSSTS
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.67|      18|      19|    1339|    1357|       3
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 1339- 1356 (25.36/ 7.80)	SGGEFQGKREKSDKEKSK
 1429- 1446 (28.31/ 6.12)	SGSTPKHERCSPSHSKSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      58.26|      17|      22|     869|     889|       4
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  869-  887 (24.91/26.47)	GfGEEYFDESSQSgDTDDF
  907-  923 (33.35/15.16)	G.GENKFKGSAPS.DTVDF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             6|     292.29|      47|      52|     956|    1002|       5
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  564-  620 (35.58/ 6.49)	GPITT..LFNMsismkerHDSVGHGedfS.KVS........Q................NPiLTSllqitGN........VGSTIGSSPTP.PH
  794-  853 (45.95/10.89)	..PPI..GTPV.......RDSSSSG...H.SQSalfdpdvfQTN....SS.......ENP.YTD.....PAdliadaavSPNSD.SSNHFFPD
  956- 1002 (72.79/22.29)	GKEKS..QKRV.......KEGNGSG...S.AMA........GAG....ID.......GKP.GKR.....SR........TPSSDGKSKEKLPK
 1010- 1053 (59.91/16.82)	GKSPS..H..........SSSNRPF...T.PPA........STG....GS.......KSP.GSS.....GR........SQTPPGVATPPIPK
 1168- 1216 (39.18/ 8.01)	GKPSSlmNPSM.......SKPNISP...ShSRP........SGG....SDklaspmkPVP.G.................TPPS...SKAKSP.
 1292- 1338 (38.89/ 7.89)	..KPS..LTAV.......IDKLKHG...V.VTS........GPGgddpMD.......GQM.GPS.....SN........SSSHTMSSKHNM..
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      74.50|      23|      24|    1110|    1133|       6
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 1111- 1133 (42.93/15.85)	SEGSSGSKMSSSLYSSQGGSGSG
 1455- 1477 (31.57/ 6.46)	SESESGSSIAEKSYQNSPSSDDG
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     145.65|      34|     110|     528|     563|       7
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  528-  561 (62.25/21.96)	DMVKKNLPPASSPGYGMTTGSNPMSGTTTPTNTF
  641-  674 (49.72/15.34)	NLLKENPPQDFSTLYGSSPLERQNSSSGSPRMEM
 1249- 1277 (33.68/ 8.98)	...QKPPPSSSSSTASSSSFSSSGSSMSSSQN..
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      46.90|      14|      30|     232|     246|       8
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  232-  246 (20.85/14.73)	APVVLHENSVPrSLG
  265-  278 (26.05/13.57)	APLIMGSHPVD.SKG
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---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     122.61|      28|      52|     348|     375|       9
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  320-  346 (36.14/24.39)	GIPLF...DTAPTFVPLYELITQF...ELSKEA.
  348-  375 (54.51/41.18)	PLPLN...HNMRFYAALPGQQHCY...FLNKDAP
  399-  429 (31.96/20.56)	PLILNlirHQVA.YNTLIGS..CVkrtVLKEDSP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     104.46|      30|      52|     686|     719|      10
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  686-  715 (55.46/28.14)	SRMPADKPK..HQTEDDFQRELFSMDVDSQNP
  739-  770 (48.99/24.87)	STPPATYPQalPHAQPSIQRMVRLSSSDSIGP
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      36.51|      10|      84|    1281|    1290|      13
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 1281- 1290 (19.03/ 9.60)	SSKGKSPSRN
 1366- 1375 (17.48/ 8.00)	SSKKNSDSKN
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.24|      16|      19|    1483|    1498|      15
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 1483- 1498 (26.97/18.26)	DYSAEKHKKHKKEKKK
 1503- 1518 (27.27/18.54)	DRDRERDRDKDRDKKK
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.05|      11|      20|    1135|    1145|      16
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 1135- 1145 (19.61/ 8.60)	SKGSAQSVGKP
 1156- 1166 (20.45/ 9.34)	STGSGSTKMKP
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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 MDP28834 with Med1 domain of Kingdom Metazoa
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