<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. 
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

>MDP28834
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      50.92|      17|      19|    1070|    1087|       2
---------------------------------------------------------------------------
 1070- 1087 (25.88/10.14)	SHGQYTSSGSvTSSSSKS
 1088- 1104 (25.03/ 6.34)	HHSHSSSSSS.SSSSSTS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      53.67|      18|      19|    1339|    1357|       3
---------------------------------------------------------------------------
 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
---------------------------------------------------------------------------
  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
---------------------------------------------------------------------------
  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
---------------------------------------------------------------------------
 1111- 1133 (42.93/15.85)	SEGSSGSKMSSSLYSSQGGSGSG
 1455- 1477 (31.57/ 6.46)	SESESGSSIAEKSYQNSPSSDDG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     145.65|      34|     110|     528|     563|       7
---------------------------------------------------------------------------
  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
---------------------------------------------------------------------------
  232-  246 (20.85/14.73)	APVVLHENSVPrSLG
  265-  278 (26.05/13.57)	APLIMGSHPVD.SKG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     122.61|      28|      52|     348|     375|       9
---------------------------------------------------------------------------
  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
---------------------------------------------------------------------------
  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
---------------------------------------------------------------------------
 1281- 1290 (19.03/ 9.60)	SSKGKSPSRN
 1366- 1375 (17.48/ 8.00)	SSKKNSDSKN
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.24|      16|      19|    1483|    1498|      15
---------------------------------------------------------------------------
 1483- 1498 (26.97/18.26)	DYSAEKHKKHKKEKKK
 1503- 1518 (27.27/18.54)	DRDRERDRDKDRDKKK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      40.05|      11|      20|    1135|    1145|      16
---------------------------------------------------------------------------
 1135- 1145 (19.61/ 8.60)	SKGSAQSVGKP
 1156- 1166 (20.45/ 9.34)	STGSGSTKMKP
---------------------------------------------------------------------------




































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


     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) ALGSSDIMEHHSGGQSPLLNTGDLGKEKSQKRVKEGNGSGSAMAGAGIDGKPGKRSRTPSSDGKSKEKLPKRKKQETDGKSPSHSSSNRPFTPPASTGGSKSPGSSGRSQTPPGVATPPIPKITIQIPKGTVTVGKPSSHGQYTSSGSVTSSSSKSHHSHSSSSSSSSSSSTSGKIKSKSEGSSGSKMSSSLYSSQGGSGSGQSKGSAQSVGKPGSSPITKHGLSTGSGSTKMKPQGKPSSLMNPSMSKPNISPSHSRPSGGSDKLASPMKPVPGTPPSSKAKSPISSGSGGSHMSGAGSSSSMKSSSGMGSSGSMSQKPPPSSSSSTASSSSFSSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTSGPGGDDPMDGQMGPSSNSSSHTMSSKHNMSGGEFQGKREKSDKEKSKVSVSGGSVDSSKKNSDSKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGEGGGDGLRPQMASSKSYGSPLISGSTPKHERCSPSHSKSPAYTPQNIDSESESGSSIAEKSYQNSPSSDDGIRPLPDYSAEKHKKHKKEKKKVKDKDRDRERDRDKDRDKKKSHGMKPESWSKSPISADQSLSMASNAILSAERPSRASPEFLIGEEDDD
2) KNLPPASSPGYGMTTGSNPMSGTTTPTNTFPGGPITTLFNMSISMKERHDSVGHGEDFSKVSQNPILTSLLQITGNVGSTIGSSPTPPHHTPPPVSSPASNTKNHPMLMNLLKENPPQDFSTLYGSSPLERQNSSSGSPRMEMGPGGNKQKKKKSRMPADKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADTLDTPHITPAPSQCSTPPATYPQALPHAQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPTSTEDCPPIGTPVRDSSSSGHSQSALFDPDVFQTNSSENPYTDPADLIADAAVSPN
3) QSQSGFGEEYFDESSQSGDTDDFKGYGPQAL
932
532
865
1566
843
895










Molecular Recognition Features






MoRF SequenceStartStop




1) FGEEYF
2) IPKITIQIPKGT
3) IRPLPDYSAEKHKKHKKEKKKVKDKDRDRE
4) MSSSL
5) NKKPSLTAVIDKLKHGVV
6) SIKAKVTLQK
7) SPEFLIGEEDDDLMDVALIGN
8) VAKIIISKH
9) YGSPLI
870
1051
1478
1119
1290
1395
1555
1381
1423
875
1062
1507
1123
1307
1404
1575
1389
1428