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

NucPred

Fetching P08955 from www.uniprot.org...

The NucPred score for your sequence is 0.22 (see score help below)

   1  MAALVLEDGSVLQGRPFGAAVSTAGEVVFQTGMVGYPEALTDPSYKAQIL    50
  51  VLTYPLIGNYGIPSDEEDEFGLSKWFESSENHVAGLVVGECCPTPSHWSA   100
 101  TCTLHEWLQQHGIPGLQGVDTRELTKKLREQGSLLGKLVQSGTEPSTLPF   150
 151  VDPNARPLAPEVSIKTPRVFNAGGAPRICALDCGLKYNQIRCLCQLGAEV   200
 201  TVVPWNHELDSQKYDGLFLSNGPGDPASYPGVVATLNRVLSEPNPRPVFG   250
 251  ICLGHQLLALAIGAKTYKMRYGNRGHNQPCLLVGTGRCFLTSQNHGFAVD   300
 301  ADSLPAGWTPLFTNANDCSNEGIVHDSLPFFSVQFHPEHRAGPSDMELLF   350
 351  DVFLETVREAVAGNPGGQTVKERLVQRLCPPGLLIPGSGLPPPRKVLILG   400
 401  SGGLSIGQAGEFDYSGSQAIKALKEENIQTLLINPNIATVQTSQGLADKV   450
 451  YFLPITPHYVTQVIRNERPDGVLLTFGGQTALNCGVELTKAGVLARYGVR   500
 501  VLGTPVETIELTEDRRAFAARMAEIGEHVAPSEAANSLEQAQAAAERLGY   550
 551  PVLVRAAFALGGLGSGFASTKEELSALVAPAFAHTSQVLIDKSLKGWKEI   600
 601  EYEVVRDAYGNCVTVCNMENLDPLGIHTGESIVVAPSQTLNDREYQLLRR   650
 651  TAIKVTQHLGIVGECNVQYALNPESEQYYIIEVNARLSRSSALASKATGY   700
 701  PLAYVAAKLALGIPLPELRNSVTGGTAAFEPSLDYCVVKIPRWDLSKFLR   750
 751  VSTKIGSCMKSVGEVMGIGRSFEEAFQKALRMVDENCVGFDHTVKPVSDV   800
 801  ELETPTDKRIFVVAAALWAGYSVERLYELTRIDCWFLHRMKRIVTHAQLL   850
 851  EQHRGQPLSQDLLHQAKCLGFSDKQIALAVLSTELAVRKLRQELGICPAV   900
 901  KQIDTVAAEWPAQTNYLYLTYWGNTHDLDFRTPHVLVLGSGVYRIGSSVE   950
 951  FDWCAVGCIQQLRKMGYKTIMVNYNPETVSTDYDMCDRLYFDEISFEVVM  1000
1001  DIYELENPDGVILSMGGQLPNNMAMALHRQQCRVLGTSPEAIDSAENRFK  1050
1051  FSRLLDTIGISQPQWRELSDLESARQFCQTVGYPCVVRPSYVLSGAAMNV  1100
1101  AYTDGDLERFLSSAAAVSKEHPVVISKFIQEAKEIDVDAVACDGVVSAIA  1150
1151  ISEHVENAGVHSGDATLVTPPQDITPKTLERIKAIVHAVGQELQVTGPFN  1200
1201  LQLIAKDDQLKVIECNVRVSRSFPFVSKTLGVDLVALATRIIMGEKVEPI  1250
1251  GLMTGSGVVGVKVPQFSFSRLAGADVVLGVEMTSTGEVAGFGESRCEAYL  1300
1301  KAMLSTGFKIPKKNILLTIGSYKNKSELLPTVRLLESLGYSLYASLGTAD  1350
1351  FYTEHGVKVTAVDWHFEEAVDGECPPQRSILDQLAENHFELVINLSMRGA  1400
1401  GGRRLSSFVTKGYRTRRLAADFSVPLIIDIKCTKLFVEALGQIGPAPPLK  1450
1451  VHVDCMTSQKLVRLPGLIDVHVHLREPGGTHKEDFASGTAAALAGGVTMV  1500
1501  CAMPNTRPPIIDAPALALAQKLAEAGARCDFALFLGASSENAGTLGAVAG  1550
1551  SAAGLKLYLNETFSELRLDSVAQWMEHFETWPSHLPIVAHAERQSVAAVL  1600
1601  MVAQLTQRPVHICHVARKEEILLIKTAKAQGLPVTCEVAPHHLFLNREDL  1650
1651  ERLGPGRGEVRPELGSREDMEALWENMAVIDCFASDHAPHTLEEKCGPKP  1700
1701  PPGFPGLETMLPLLLTAVSEGRLSLDDLLQRLHHNPRRIFHLPLQEDTYV  1750
1751  EVDLEHEWTIPSHMPFSKARWTPFEGQKVKGTIRRVVLRGEVAYIDGQVL  1800
1801  VPPGYGQDVRKWPQGAVPQPPPSAPATTEITTTPERPRRVIPGLPDGRFH  1850
1851  LPPRIHRASDPGLPAEEPKEKPSRKVVEPELMGTPDGPCYPAPPVPRQAS  1900
1901  PQNLGSSGLLHPQTSPLLHSLVGQHILSVKQFTKDQMSHLFNVAHTLRMM  1950
1951  VQKERSLDILKGKVMASMFYEVSTRTSSSFAAAMARLGGAVLSFSEATSS  2000
2001  VQKGESLADSVQTMSCYADVVVLRHPQPGAVELAAKHCRRPVINAGDGVG  2050
2051  EHPTQALLDIFTIREELGTVNGMTITMVGDLKHGRTVHSLACLLTQYRVS  2100
2101  LRYVAPPSLRMPPSVWDFVASRGTKQEEFESIEEALPDTDVLYMTRIQKE  2150
2151  RFGSTQEYEACFGQFILTPHIMTRAKKKMVVMHPMPRVNEISVEVDSDPR  2200
2201  AAYFRQAENGMYIRMALLATVLGRF                           2225

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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