<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 MDP00457

Description Mediator of RNA polymerase II transcription subunit 13
SequenceMAENVSCYALLKHPPTALPKGANSTECHLLFISADSGFVTTVSSVLPAQESAMGVTNSPKHSGKKLTNQVVHQAWKECYLNQLQHKYSGPSSVTPKKEAPNGVPTWDFTDPEERAPCSCSRLKQQKQQQQTNTSSANPPSGANPTPSSGPALPPPSLPKHKATDKPEKADKQPKRAAAMTPFHHRLSVGQEACLEQDSSGGSQLGLVSLDPPLDPMPSCKYPKPLSAGRKAPESLLHSPVSPLPPTLSPHPRGGQDPEVLNTSLGMAPFPDGASGMGGMEPSETALYAAPLGPREREAGAGWWRGFRTPRADKAGFRPPELPSDRVEVKTETQATEGVALKRLFMQTQKRFKISEECVRAHIQTLGLLHQPGDPGDDPYDFKEGDIEYSFPTSKRLKGQGRDPNKRGPKGEEISNGALPDGKDAMSIFSSAPKADDDSPQEDDAAAKAQNPSLTRETDLVVLISDLENIFDEDEEELRTACPNQHTARVLVSGSEDRREGRVAVPYPSTVADLQRMFPTPPSLEQHPAFSPIMTYRDTPSQEPPAPSVGSDHPLGPLSSTQLQEYRMEVEEGMASPKPEDIKDFSFVYRVPSVQPQMGCSMFAPLRTLPSQCLPPLKLPDQCYYRPSWALLPKMEHYSSLPPSHHTPFIRDGYVNIPSVGDQEYTQLSASALSVGTTGGILPSPSPATPRFSVPTPRTPRTPRGVGTASGQGSVKQEGTGTELSSPTSTPSTSLPMSSVAEPHTSSPPIPEAHSLYAALLLSDSVLNVFKDRNFDSCCICACNMNVKGADVGVYIPDSTLEDQYRCMCGFSAIVNRRLAHGTGLFLEDELDIFGRGSEVGQAAERRLALCRRDPPMGDPRAKRPQDSSPAPSSVMVLLQQQCSQPISSLASMHLPPSCSCNGRQGALLQSWMADKQWADGSDACVECYNALVQGQQYVDNPAGGKVDPAVVRSSALHSWPHTNMLDISMLSSQDVVRMLLSLQPYLQDAIQKKRMGRTWENIQHVQGPLTWQQFHKMAGRGSYGSEESPEPLPIPTLLLGYYDYYDRNFLALSPLALPFWEKLLLEPYGGQRDVAFLVLCPNSDTLLAGAQVFFQELSAVYETCRLGKHRPLAKVSRDGLVRVGAEKEKERQEEEQIDQWFTGPWAGQQHIDNLRKLKLYARACRRQLGPQLSALSLDSSLFIPPKHQPPLAPTPSSAQPAPSSSQLPSGPGAPAEGDPAAAPSSGSTPTPTAAASDQPGPAEITQGGAAEAKTTPNATPPPPPPSQPAETPESLAERERIGIPTLADSADSHAHPPAIVIYVVDPFLCSGGARDGGGEEVEVGSVWLLGLMRCYTEMLKTLPESMRPALVLQVVPCQYLLQPASGESPLYLQHLRSLAFSAYSQCRRLLPTKTHIKSLTGFGPASTLESVLKSPEHPSPLQGYSPPYILGPTRAKMPEPGEVWAEIPPRYNVLFVGYCLSHDQRWILVSCTDQQGELLETCIINIDVPNRVRRPKVSARKMGLQKLWDWCVGIIQMTSLPWRIVIGRLGRLGHGELKDWSVLLGEHSLHSISRQLKEACRMCGISSADSPSVLSACLVAMEPQGSIVVMPDAVTMGSVFGRSTALNLQTSQLNTPQDASCTHILVFPTSATTQLAASSYPTEDNADDMFDLPFPDELENDIGHDILNLHPSPNTSPVPSPGSPSGMGGSSHFQHNRSQGERLLSRENPPEELKQQPLALGYYVSTAQADSLPHWFWASCPQAQNQCPLFLKASLHHHISIATAQSDEPTQTSSDKTAKRTPHPLDSKTTSDVLRFVLEQYNALSWLTCNPATQDRRSCLPVHLAVLTQMYNAILNML
Length1838
PositionMiddle
OrganismOncorhynchus mykiss (Rainbow trout) (Salmo gairdneri)
KingdomMetazoa
LineageEukaryota> Metazoa> Chordata> Craniata> Vertebrata> Euteleostomi> Actinopterygii> Neopterygii> Teleostei> Protacanthopterygii> Salmoniformes> Salmonidae> Salmoninae> Oncorhynchus.
Aromaticity0.06
Grand average of hydropathy-0.448
Instability index61.02
Isoelectric point5.91
Molecular weight199605.37
Publications
PubMed=24755649

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	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

>MDP00457
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             6|     385.63|      74|     120|     247|     320|       2
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  136-  180 (50.14/12.34)	........................ANPPSGANP....TPssgPALPP.....PSL.PKHKATD......KP.EKADKQPKRAAAMT
  249-  320 (126.74/42.03)	PHPRGGQDPEVLNTSLGMAPFPDGASGMGGMEP....SE...TALYA.....APLGPREREAGAGWWRGFRTPRADKAGFRPPE..
  525-  556 (41.12/ 8.84)	QHPAFS.............PIMTYRDTPSQEPP....AP...SVGSD.....HPLGP.............................
  676-  715 (34.69/ 6.34)	..........................TTGGILP....SP...SPATPrfsvpTPRTPRT.PRGVGTASGQG............SVK
  716-  753 (34.45/ 6.25)	Q........EGTGTELS.SP....TSTPSTSLPmssvAE...PHTSS.....PPIPEAH...........................
 1200- 1262 (98.48/31.08)	PAPSSSQLPSGPGAPAEGDP...AAAPSSGSTP....TP...TAAAS.....DQPGPAEITQG.GAAEAKTTPNATP....PP...
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             4|     131.43|      22|      22|    1395|    1416|       3
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 1177- 1195 (28.87/ 9.52)	LDSSL..FIPPKHQPPL.APTP.
 1374- 1394 (31.57/11.14)	HLRSL.AFSAYSQCRRL.LPTKT
 1395- 1416 (34.28/12.77)	HIKSLTGFGPASTLESV.LKSPE
 1417- 1439 (36.71/14.23)	HPSPLQGYSPPYILGPTrAKMPE
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     130.15|      37|     262|    1441|    1477|       5
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 1441- 1477 (72.95/40.40)	GE..VWAEIPP...RYNVLFVGYCLSHDQ.....RWILVSCTDQQGE
 1700- 1746 (57.20/30.08)	GErlLSRENPPeelKQQPLALGYYVSTAQadslpHWFWASCPQAQNQ
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      56.65|      15|      22|     472|     486|       6
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  472-  486 (28.70/17.12)	EDEEELRTACPNQHT
  495-  509 (27.95/16.46)	EDRREGRVAVPYPST
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.71|      17|      22|    1334|    1353|       7
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 1334- 1353 (22.41/21.87)	CyTEMLKtlPESMRPALVLQ
 1357- 1373 (32.30/17.73)	C.QYLLQ..PASGESPLYLQ
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.81|      16|      22|     900|     919|       8
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  900-  919 (24.98/32.77)	CNGRQGALLQSwmadKQWAD
  924-  939 (30.83/22.96)	CVECYNALVQG....QQYVD
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      86.42|      24|      26|    1029|    1054|       9
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 1031- 1054 (46.36/32.77)	PLPI..PTLLLGYYDYYDRNFLALSP
 1056- 1081 (40.06/20.20)	ALPFweKLLLEPYGGQRDVAFLVLCP
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      66.86|      19|      26|     608|     632|      10
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  611-  632 (33.65/25.16)	QCLPP.LKLPdqcYYRPSWALLP
  638-  657 (33.22/10.12)	SSLPPsHHTP...FIRDGYVNIP
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      49.33|      12|      27|    1501|    1512|      11
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 1501- 1512 (26.05/16.92)	KMGLQKLWDWCV
 1531- 1542 (23.28/14.28)	RLGHGELKDWSV
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      55.54|      15|      15|     869|     883|      12
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  869-  883 (27.27/11.63)	PAPSSVMVLLQQQCS
  885-  899 (28.28/12.32)	PISSLASMHLPPSCS
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      65.03|      22|      26|     795|     819|      13
---------------------------------------------------------------------------
  798-  819 (40.34/26.31)	ST...LEDQ...YRCMCGFSAIVNRRLA
  821-  848 (24.69/ 6.99)	GTglfLEDEldiFGRGSEVGQAAERRLA
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      45.52|      14|      15|    1268|    1281|      14
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 1268- 1281 (24.04/13.65)	P..AETPESLAERERI
 1284- 1299 (21.48/11.16)	PtlADSADSHAHPPAI
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      54.65|      16|      16|     577|     592|      15
---------------------------------------------------------------------------
  577-  592 (28.61/16.15)	KPE.DIKDFSFVYRVPS
  594-  610 (26.04/13.97)	QPQmGCSMFAPLRTLPS
---------------------------------------------------------------------------
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      33.31|      10|      26|     372|     384|      16
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  372-  384 (12.21/15.77)	GDpGDDPYdfKEG
  398-  407 (21.10/ 9.56)	GQ.GRDPN..KRG
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|     119.66|      40|    1132|     422|     470|      19
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  422-  470 (57.01/52.14)	KDA..MSIFSSApkaddDSPQEDDAAAKAQNP..SLTRETDLVVLISdlenIF
 1557- 1600 (62.65/36.05)	KEAcrMCGISSA.....DSPSVLSACLVAMEPqgSIVVMPDAVTMGS....VF
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No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.49|      12|    1132|     511|     524|      20
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  511-  524 (20.73/20.51)	ADlqRMF..PTPPSLE
 1646- 1659 (20.76/11.77)	AD..DMFdlPFPDELE
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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 MDP00457 with Med13 domain of Kingdom Metazoa
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