SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q8TD26 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MKMKIQKKEKQLSNLKVLNHSPMSDASVNFDYKSPSPFDCSTDQEEKIED    50
  51  VASHCLPQKDLYTAEEEAATLFPRKMTSHNGMEDSGGGGTGVKKKRKKKE   100
 101  PGDQEGAAKGSKDREPKPKRKREPKEPKEPRKAKEPKKAKEHKEPKQKDG   150
 151  AKKARKPREASGTKEAKEKRSCTDSAARTKSRKASKEQGPTPVEKKKKGK   200
 201  RKSETTVESLELDQGLTNPSLRSPEESTESTDSQKRRSGRQVKRRKYNED   250
 251  LDFKVVDDDGETIAVLGAGRTSALSASTLAWQAEEPPEDDANIIEKILAS   300
 301  KTVQEVHPGEPPFDLELFYVKYRNFSYLHCKWATMEELEKDPRIAQKIKR   350
 351  FRNKQAQMKHIFTEPDEDLFNPDYVEVDRILEVAHTKDAETGEEVTHYLV   400
 401  KWCSLPYEESTWELEEDVDPAKVKEFESLQVLPEIKHVERPASDSWQKLE   450
 451  KSREYKNSNQLREYQLEGMNWLLFNWYNRKNCILADEMGLGKTIQSITFL   500
 501  SEIFLRGIHGPFLIIAPLSTITNWEREFRTWTEMNAIVYHGSQISRQMIQ   550
 551  QYEMVYRDAQGNPLSGVFKFHVVITTFEMILADCPELKKIHWSCVIIDEA   600
 601  HRLKNRNCKLLEGLKLMALEHKVLLTGTPLQNSVEELFSLLNFLEPSQFP   650
 651  SETAFLEEFGDLKTEEQVKKLQSILKPMMLRRLKDDVEKNLAPKQETIIE   700
 701  VELTNIQKKYYRAILEKNFSFLTKGANQHNMPNLINTMMELRKCCNHPYL   750
 751  INGAEEKILEDFRKTHSPDAPDFQLQAMIQAAGKLVLIDKLLPKLIAGGH   800
 801  KVLIFSQMVRCLDILEDYLIQRRYTYERIDGRVRGNLRQAAIDRFCKPDS   850
 851  DRFVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQSK   900
 901  AVKVYRLITRNSYEREMFDKASLKLGLDKAVLQDINRKGGTNGVQQLSKM   950
 951  EVEDLLRKGAYGALMDEEDEGSKFCEEDIDQILQRRTHTITIQSEGKGST  1000
1001  FAKASFVASGNRTDISLDDPNFWQKWAKIAELDTEAKNEKESLVIDRPRV  1050
1051  RKQTKHYNSFEEDELMEFSELDSDSDERPTRSRRLNDKARRYLRAECFRV  1100
1101  EKNLLIFGWGRWKDILTHGRFKWHLNEKDMEMICRALLVYCVKHYKGDEK  1150
1151  IKSFIWELITPTKDGQAQTLQNHSGLSAPVPRGRKGKKTKNQLLIPELKD  1200
1201  ADWLATCNPEVVLHDDGYKKHLKQHCNKVLLRVRMLYYLKAEILGEAAEK  1250
1251  AFEGSPARELDVPLPDIDYMEIPVDWWDAEADKSLLIGVFKHGYERYNAM  1300
1301  RADPALCFLEKVGMPDEKSLSAEQGVTDGTSDIPERGNTDKEDNAEDKVD  1350
1351  GLQKQTESSSDGGDGVFSEKKDDSRAAQDGSDPDKSPWPVSSALTARLRR  1400
1401  LVTVYQRCNRKELCRPEILGPGNQGYWVQEEMFRRTSEMDLINKEAQKRW  1450
1451  TRREQADFYRTVSSFGVVYDQEKKTFDWTQFRIISRLDKKSDESLEQYFY  1500
1501  SFVAMCRNVCRLPTWKDGGPPDTTIYVEPITEERAARTLYRIELLRKVRE  1550
1551  QVLKCPQLHERLQLCRPSLYLPVWWECGKHDRDLLIGTAKHGLNRTDCYI  1600
1601  MNDPQLSFLDAYRNYAQHKRSGTQAPGNLCCLYQTNSKLYESLTYSQMSR  1650
1651  TSESLENEPENLVRVESRDDHLSLPDVTCENFISKVQDVISINHDESLLP  1700
1701  ESLESMMYGKKVLSQEPSSFQESPSTNTESRKDVITISISKDGNCQSGGP  1750
1751  EAEIASGPTFMGSLEAGGVAQANIKNGKHLLMSISKEGELCCSEAGQRPE  1800
1801  NIGQLEAKCLASPSLNPGNESGFVDMCSLSVCDSKRNLSSDQQLIDLLEN  1850
1851  KSLESKLILSQNHSDEEEEEEENEEENLAMAVGMGERPEVLHLTEPTTNI  1900
1901  SREKNQGFQDETKKGSLEVANQTPGLQRAFPAPAACQCHCKHMERWMHGL  1950
1951  ENDEFEIEKPKAYIPDLFKSKTNTIAMEGEPTAIPSQPFKVKHELLKEPW  2000
2001  KESAEGQNVFPTYPLEGSELKSEDMDFENKDDYDRDGNCHSQDYPGKYSE  2050
2051  EESKSSTSGITGDIGDELQEARAPTIAQLLQEKTLYSFSEWPKDRVIINR  2100
2101  LDNICHVVLKGKWPSSQQYEPSGTLPTPVLTSSAGSRTSLSEPEAAEHSF  2150
2151  SNGAALAAQIHKESFLAPVFTKDEQKHRRPYEFEVERDAKARGLEQFSAT  2200
2201  HGHTPIILNGWHGESAMDLSCSSEGSPGATSPFPVSASTPKIGAISSLQG  2250
2251  ALGMDLSGILQAGLIHPVTGQIVNGSLRRDDAATRRRRGRRKHVEGGMDL  2300
2301  IFLKEQTLQAGILEVHEDPGQATLSTTHPEGPGPATSAPEPATAASSQAE  2350
2351  KSIPSKSLLDWLRQQADYSLEVPGFGANFSDKPKQRRPRCKEPGKLDVSS  2400
2401  LSGEERVPAIPKEPGLRGFLPENKFNHTLAEPILRDTGPRRRGRRPRSEL  2450
2451  LKAPSIVADSPSGMGPLFMNGLIAGMDLVGLQNMRNMPGIPLTGLVGFPA  2500
2501  GFATMPTGEEVKSTLSMLPMMLPGMAAVPQMFGVGGLLSPPMATTCTSTA  2550
2551  PASLSSTTKSGTAVTEKTAEDKPSSHDVKTDTLAEDKPGPGPFSDQSEPA  2600
2601  ITTSSPVAFNPFLIPGVSPGLIYPSMFLSPGMGMALPAMQQARHSEIVGL  2650
2651  ESQKRKKKKTKGDNPNSHPEPAPSCEREPSGDENCAEPSAPLPAEREHGA  2700
2701  QAGEGALKDSNNDTN                                     2715

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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