<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 MDP22237

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMSSCFVPNGASLEDCHSNIFCLADLTGIKWRRFVWQGPTSSPILFPFTEEDPILYSFSRCLAADVLSVWRRHHTQGRRELWLFWWGDDPSFAELIHNELSSEEDGEWESGLSYECRTLLFKAIHNLLERCLMNRGFVRIGKWFVKPYQKEEKIINKSEHLSCAFTFFVHGDSNVCTSVEIAQHQPLQRLSEEHLSLAQQSSNPLQVILSPYGLNGTLTGQAFKMSDHPTQKLIEEWRQFYPISPNPKEVQEDKMEDSDWEDDSLAAVEVLVAGVRMVYPSCLVLLPLLDLPTVVSQGSSNTPGSQCVAPQGQAAHKDPAMSSVTLTPPTSPEEAHTDYRPAQRWLKLSSASDCYNSNNSLHGGKIPRGLASQMVESVWQEYNTNRTGNKRKFTTLTNGAVEEESDKTAVWNFVEPAHRPPCNCSRHKNLKQRCSSTSGHPSSSGQPAQPPTKHKLSEKMEKGEKQQRRPQTPFHHRNSVSEELSLEPQTPRLCSRPQEESSYPSLHHVDTVPKAPMLHTHSLLTDLGSPPPPPLSPHPCDHVESDMTPGGMKTCSTPIHQPLYPPSVEPCLVPQKGSSGESPLESMPMPLPFPPAYNESMEPTVFVGSAVNPSEDSSHNPWRYFNLPRRKDSNFVTPQLPVDKIREDCWGGTESLVSVTETMCDSTQPLKVSQELVRTYAQRRNSHLVSISGDDEHGEEPDPYAFVEGDEEFSFIEKRDKAAAEKEGGKKHKLDEGAGTDDGQGPSGSKPLSSTSLIHENDLAVSYSDLDKIFNSDEDELAPGSKRAGIVTEGKFGSKETKPASIDQLSGLSSVDLHVMFPTPPSAENQGYSPMNSGSKDGLETGTGLTLLDGSQLNSHFKMEVEEGFCSPKPSEIKDFSFVYKPETCQSFIGCSMYAPLKTLPSRCLLPVKLPGDCVYTPSWTMGKMDLMPQVSNVNLLIKDGNLPSVEPDYSQTYTPQTHTPFLAGSAPPSNSGTGILPSPATPRFSVPTPRTPRTPRTPRGPSSVQGSLKYDNSDLYSPASTPSTCRPLSSVEPATVPSIPEAHSLYVTLILSESVMNLFKDCNFDSCCVCVCNMNIRGADVGVYLKDNGDAQYTCTCGFSAVTNRRFGQSAGLFLEDELDVVGRGSDAGRDTERCFDELRLSTTHKGGGLKEKYPDELILLLQDQCTNPLAQIAGVDSSKPRSTLSSFLRVEERDCYNDCYMALEHGRQFMDNMSGGKVDETLVKSTCLHQWPKSKSADISKLFSQEVLRVLLSLQPVLQDTIQKKRSVRSWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPVPTFLVGYEHDFVVLSPFALPYWEKLLLDPYGSQRDVGYVVICPDVEALLRGARSFFKDLSAMYEACQLGQHRPISKSHPEGIVTVGSTEGSNVAEQPLSDWFLNLAAREGNNEAFNRLKLFAQVFRCDLAPYLSEQSLDSSLLSQRNSTPASSSSSSSSPQTSNTSSGLQSTNTTSTGSAQPSQVNSTTPSSASLGSQTIGAMASSKPSMYSPFGSAGTQGNATQNGPQINSQGGAGHTENGSSQPQVSAETPESTMERDKVGKPTDGDSHAVSYPPAIVVYIVDPFSYEDADREVHSSTFTLGLLRCYMEMLPFLPAHIRNVVSVQIVPCQYLLQPVHSGERHLYSQHLKSLAFSVYTQCRRPLPTSTNFKTLTGFGPGLAIDTALKNPERPECLRLYTPPFILAPVKDKQTELGETFGEASQKYNVLFVGYCLSHDQRYLLASCTDQHGELLETCIISIDVPNRARRKKGSARRVGLQKLWEWCVGLVQLTSLPWRVVIGRLGRMGHGELRDWSILLSRRNLQSLSKRLKEMCKMCGISAADTPSILSACLVAMEPQGSFVIMPDSVSTGSVFGRSTTLNMQTSQLSTPQDTSCTHILVFPTSAMVQVNTNTSEPIDINFNPINPDGSDGMGFLDLFGNDMDHDMDPDLINILPNSPTTSPVHSPSGHYHQGGDGGKGPSADRMESHEEALNILQQPMALGYFISTAKAGPLPDWFWSACPEAQNQCPLFLKASLHLHVSSVQSDEFLHSKHSHPLDSNHTSDVLRFVLEQYNALSWLTCDPATQDRRSCLPVHFVVLTQMYNFIINMI
Length2118
PositionMiddle
OrganismOryzias latipes (Japanese rice fish) (Japanese killifish)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Actinopterygii> Neopterygii> Teleostei> Neoteleostei> Acanthomorphata> Ovalentaria> Atherinomorphae> Beloniformes> Adrianichthyidae> Oryziinae> Oryzias.
Aromaticity0.08
Grand average of hydropathy-0.447
Instability index53.81
Isoelectric point5.61
Molecular weight233261.64
Publications
PubMed=17554307

Function

Annotated function Component of the Mediator complex, a coactivator involved in 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	IBA:GO_Central

GO - Biological Function
transcription coregulator activity	GO:0003712	IBA:GO_Central

GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central









Interaction





Binary Interactions











Repeat regions





Repeats

>MDP22237
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             6|     221.77|      36|      37|    1485|    1520|       1
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  527-  550 (35.31/ 9.97)	............GSPP........P......PPLSP....HPCDHVES.DMTPGG..
  983- 1006 (35.94/10.27)	PATP.......rFSV.........PTPRTPRTPRTP....R.............GPS
 1007- 1045 (38.24/11.37)	.SVQ........GSLKydnsdlysP....ASTPSTC....RPLSSVEP.ATVPSIPE
 1485- 1516 (49.28/16.64)	............GSAQ........PSQVNSTTPSSA....SLGSQTIG.AMASSKPS
 1517- 1536 (29.90/ 7.39)	MYSP.......fGSA.........GTQGNAT.....................QNGPQ
 1537- 1583 (33.10/ 8.92)	INSQggaghtenGSSQ........P.QVSAETPESTmerdKVGKPTDGdSHAVSYP.
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      89.97|      27|      36|      30|      64|       2
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   21-   57 (38.01/30.15)	CLA.DltgikWRRFVWQGPtSSPILFpFTEEDPilySF
   60-   91 (51.95/23.15)	CLAaD.vlsvWRRHHTQGR.RELWLF.WWGDDP...SF
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      93.64|      27|      41|     179|     206|       3
---------------------------------------------------------------------------
  179-  206 (41.95/32.46)	EIAQHqPLQRLSEEHLSLAQQSSNPLQV
  223-  249 (51.69/35.52)	KMSDH.PTQKLIEEWRQFYPISPNPKEV
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|     135.84|      30|      32|     563|     594|       4
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  563-  592 (58.48/22.33)	YPPSVEP....CLVPQKGS...SGE.SPLESMPMPLPF
  596-  623 (51.04/21.34)	YNESMEP....TVFV..GS...AVN.PSEDSSHNPWRY
  947-  981 (26.33/ 6.71)	..PSVEPdysqTYTPQTHTpflAGSaPPSNSGTGILP.
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             3|      57.31|      15|      17|    1109|    1123|       5
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 1109- 1123 (25.82/17.39)	RRFGQSAGLFLE...DEL
 1128- 1143 (16.46/ 7.80)	R..GSDAGRDTErcfDEL
 1156- 1169 (15.03/ 6.35)	EKYPDELILLLQ...DQ.
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---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     536.38|     178|     382|    1242|    1453|       6
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 1245- 1453 (276.49/269.78)	SKLFSQEVLRVLLSLQPVLQDTIQKKRSVRSWGVQ...GPL......TWQQFHKMAGRGSYgtDESPEPLPVPT.F..LVG......................YEHDFvVLSPfaLPYWEKLLLDPYGSQR...DVGYVVICpdveaLLRGARSFF....KDLSAMYEACQLGQHRPISKSHPEGivtvgstEGSNVAEQPLSDWFLNLaaregnneafnrLKLFAQVFRC..............DLAPYLSEQSLDSslLSQR
 1605- 1837 (259.89/179.66)	SSTFTLGLLRCYMEMLPFLPAHIRNVVSVQIVPCQyllQPVhsgerhLYSQHLKSLAFSVY..TQCRRPLPTSTnFktLTGfgpglaidtalknperpeclrlYTPPF.ILAP..VKDKQTELGETFGEASqkyNVLFVGYC.....LSHDQRYLLasctDQHGELLETCIISIDVPNRARRKKG.......SARRVGLQKLWEWCVGL............VQLTSLPWRVvigrlgrmghgelrDWSILLSRRNLQS..LSKR
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     101.05|      29|      33|     414|     443|       7
---------------------------------------------------------------------------
  414-  443 (51.57/35.80)	EPAhRPPCNCSRHKNL.....KQRCSSTSGHPSSS
  445-  478 (49.48/28.94)	QPA.QPPTKHKLSEKMekgekQQRRPQTPFHHRNS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      60.09|      17|      34|     733|     749|       8
---------------------------------------------------------------------------
  733-  749 (30.68/17.61)	LDEGAGTDDGQGPSGSK
  769-  785 (29.41/16.52)	LDKIFNSDEDELAPGSK
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     172.91|      54|     846|     306|     378|       9
---------------------------------------------------------------------------
  306-  378 (82.60/79.01)	CVAPQGQAAHKDPAMSSVTLTPPTSPEEaHtdyrpaqrwlklssasDCYNS.............NNSlhGGKIPRGLASQMVESVW
 1170- 1236 (90.31/48.70)	CTNPLAQIAGVDSSKPRSTLSSFLRVEE.R................DCYNDcymalehgrqfmdNMS..GGKVDETLVKSTCLHQW
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      78.51|      25|      32|     631|     658|      11
---------------------------------------------------------------------------
  631-  658 (40.51/41.21)	DSnfvTPQLPVDK..IREDCWGGTESLVSV
  664-  690 (38.00/27.81)	DS...TQPLKVSQelVRTYAQRRNSHLVSI
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      61.17|      18|    1538|     504|     521|      15
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  504-  521 (35.79/23.27)	SLH.HVDTVPKAPMLHT.HS
 2043- 2062 (25.38/14.02)	SLHlHVSSVQSDEFLHSkHS
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     103.51|      33|    1086|     790|     822|      17
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  790-  822 (57.75/37.94)	VTEGK.FGSKETKPASIDQLSGLSSVD.LHVM.FPT
 1876- 1911 (45.76/28.21)	VSTGSvFGRSTTLNMQTSQLSTPQDTScTHILvFPT
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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 MDP22237 with Med13 domain of Kingdom Metazoa
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