<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 MDP01835

Description Mediator of RNA polymerase II transcription subunit 1 (Fragment)
SequenceEAEKLNKMSSLLERLHAKYSQNRPWTETMKLVRQVMEKRVVLNSGGHQHLVSCLETLQKALKVSSLPAMTDRLESIARQSGLGSHLSANGTECYITSDMFYVEVQLDPTGLLCDVKVAHHGENPVSCPELVQHLREKNFDEFSKHLRGLVNLYKLPGENKLKTKMYLALQSLELDLQKMAGMYWQATNANPLDKILHGSVGYLTPRSGGLLMNLKYYVSPYDLFEDGTGAPVILHENNVPRSLGMNVAVTVEGTMTMHKLPIAPLIMGSHPVDSKGTPSFSSITSANSVDLPACFFLKFPRPIPVSRAFIQKLQSCTGIPLFDTPPTFVPLYELITQFELSKEADPLPLNHNMRFYAALPGQQHCYFLNKDAPLPDGRSLQGTLISKIAFQHPGRVPLILNLIRHQVAYNTLIGSCVKRTVLKEDSPGILQFEVCPLSDSCFSVSFQHPVNDSLVCVVMDVQDSTHVNCKLYKGLSDALICTDDFIAKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNLPPASSPGYGMTTGSNPMSGTTTPTNTFPGGPITTLFNMSISMKERHDSVGHGEDFSKVSQNPILTSLLQITGNVGSTLGSSPTPPHHTPPPVSSPASNTKNHPMLMNLLKENPPQDFSTLYGSSPLERQNSSSGSPRMEMGPGGNKQKKKKSRVPADKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADTLDTPHITPAPSQCSTPPATYPQALPHAQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPPSTEDCPPMGTPVRDSSSSGHSQSALFDPDVFQANSSENPYTDPADLIADAAVSPNSDSSNHFFPDGVDFNPDLLNSQSQSGFGEEYFDESSQSGDTDDFKGYASQALTNLGVQVLGADGGENKFKGSNPSDTVDFSIIAAASKALGSSDIMEHHSGGQSPLLNTGDLGKEKSQKRVKEGNGSGSAMAGAGIDGKPGKRSRTPSSDGKSKEKLPKRKKQETDGKSPSHSSSNRPFTPPASTGGSKSPGSSGRSQTPPGVATPPIPKITIQIPKGTVTVGKPSSHGQYTSSGSVTSSSSKSHHSHSSSSSSSSSSSTSGKIKSKSEGSSGSKMSSSLYSGQGGSGSGQSKGSAQSVGKPGSSPITKHGLSTGSGSTKMKPQGKPSSLMNPSMSKPNISPSHSRPSGGSDKLASPMKPVPGTPPSSKAKSPISSGSGGSHMSGTGSGSSMKSSSGMGSSGSMSQKPPPSSNSSTASSSSFSSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTSGPGGDDPMDGQMGPSSNSSGHAMSSKHNMSGGEFQGKREKSDKEKSKVSVSGGSGDSSKKNSDSKSVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGEGGGDGLRPQMASSKSYGSPLISGSTPKHERCSPSHSKSPAYTPQNIDSESESGSSIAEKSYQNSPSSDDGIRPLPEYSAEKHKKHKKEKKKVKDKDRDRERDRDKDRDKKKSHGMKPESWSKSPISAEQPLSMAGSAILAAERPSRASPEFLIGEEDDDLMDVALIGN
Length1573
PositionMiddle
OrganismManacus vitellinus (golden-collared manakin)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Archelosauria> Archosauria> Dinosauria> Saurischia> Theropoda> Coelurosauria> Aves> Neognathae> Passeriformes> Pipridae> Manacus.
Aromaticity0.04
Grand average of hydropathy-0.634
Instability index54.30
Isoelectric point8.89
Molecular weight166722.69
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

>MDP01835
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             8|     382.28|      49|      50|    1184|    1232|       1
---------------------------------------------------------------------------
  763-  804 (42.24/ 8.53)	SDSIGPDVTDILSDIAE...EASKLPPS.....TEDC.PPM.......GTP.V........RDSS...SS
  985- 1038 (40.28/ 7.77)	SRTPSSDGKSKEKLPKRkkqETDGKSPS....hSSSN.RPFTppASTGGSK.SPG......S.SG...RS
 1097- 1133 (47.49/10.58)	SSSSTSG...KIKSKSE...GSSG.........SKMS.SSLY..SGQGGS............GSG...QS
 1135- 1170 (38.23/ 6.97)	.......GS...AQSVG...K.PGSSPI.....T..K.HGLS..TGSGSTK.MKP......QGKP...SS
 1184- 1232 (91.89/27.89)	SHSRPSGGSDKLASPMK...PVPGTPPS.....SKAK.SPIS..SGSGGSH.MSG......TGSG...SS
 1236- 1269 (48.51/10.98)	SSGMGSSGS....MSQK...P....PPS.....SNS..STAS..SSSFSS.............SG...SS
 1271- 1332 (36.54/ 6.31)	SSSQNQHGSSKGKSPSR......NKKPSltaviDKLKhGVVT..SGPGGDDpMDGqmgpssNSSGhamSS
 1453- 1495 (37.10/ 6.53)	SESE.SGSS..IAE..K...SYQNSPSS.....DDGI.RPLP..EYSAEKH.KKH......KKEK...K.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      48.63|      13|      20|     527|     539|       2
---------------------------------------------------------------------------
  527-  539 (23.45/ 9.69)	MVKKNLPPASSPG
  549-  561 (25.18/10.98)	MSGTTTPTNTFPG
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             6|     376.40|      61|     116|     575|     635|       3
---------------------------------------------------------------------------
  575-  635 (104.17/53.70)	KERHDSVG..HGED.FS.KV.SQNPILTSLLQITGNVGSTLGSSPTPPHHT...PPPV.S.S..PASNTKNHP
  642-  682 (50.84/21.55)	KE.NPP......QD.FS.T...........L.........YGSSPLERQNSssgSPRM.EmG..PGGNKQKKK
  690-  752 (82.69/40.75)	KPKHQTEDdfQREL.FSmDVdSQNPIF.D.VNMTADTLDTPHITPAPSQCS...TPPA.T.Y..PQALPHAQP
  822-  866 (48.79/20.31)	.....................SENP.YTDPADLIADAAVSPN.SDSSNHFF...PDGV.D.FnpDLLNSQSQS
  869-  893 (26.40/ 6.81)	GE..........EY.FD.ES.SQSG.DTDDFK..GYASQAL................................
  904-  960 (63.51/29.18)	.......D..GGENkF..KG.S.NPSDTVDFSIIAAASKALGSSDIMEHHSggqSPLLnT.G..DLGKEKSQK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     125.15|      31|     108|    1410|    1446|       4
---------------------------------------------------------------------------
  255-  281 (43.89/17.89)	MTMHKLPIAPL.IMGSHP.VDSKGTPSFS.....
 1415- 1446 (55.23/42.73)	MASSKSYGSPL.ISGSTP.KHERCSPSHSkSPAY
 1531- 1556 (26.03/ 8.07)	.....SAEQPLsMAGSAIlAAER..PSRA.SPEF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      76.52|      18|      18|    1380|    1397|       5
---------------------------------------------------------------------------
 1353- 1367 (23.25/ 9.69)	SKVSVS...GGSGDSSKK
 1380- 1397 (30.36/15.59)	AKIIISKHDGGSPSIKAK
 1401- 1414 (22.91/ 9.41)	QK....PGEGGGDGLRPQ
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      76.19|      23|      24|     434|     456|       6
---------------------------------------------------------------------------
  434-  456 (42.85/24.57)	VCPLSDSC.FSVSFQHPVNDSLVC
  458-  481 (33.34/17.57)	VMDVQDSThVNCKLYKGLSDALIC
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      51.55|      14|      31|     282|     295|       7
---------------------------------------------------------------------------
  282-  295 (25.13/12.93)	SITSANSVDLPACF
  315-  328 (26.42/14.01)	SCTGIPLFDTPPTF
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      80.87|      17|      17|    1059|    1075|       8
---------------------------------------------------------------------------
 1040- 1055 (23.24/ 7.93)	TPPGVATPPIPKITIQ.
 1056- 1072 (29.45/12.34)	IPKGTVTVGKPSSHGQY
 1073- 1089 (28.18/11.44)	TSSGSVTSSSSKSHHSH
---------------------------------------------------------------------------




































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 MDP01835 with Med1 domain of Kingdom Metazoa
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