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

NucPred

Fetching Q8LGU1 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MAAFIGSLPWCDVELNLASSCFQRTAIAFVNLLFLCIFYLFLIASCVSTH    50
  51  FIVRGRKKGWIFVAVAICCAITSFIFLGVGLNSLIHGGNDVTEISWVACF   100
 101  VEGIIWVSLAVSLLVNGSKWVNILVSVWWVSFALLDLVAKSGILLQGNGI   150
 151  RILDILTLPMSLLLLLCSWMNLRSSSAAAQDCSVTGLSDPLLTKNPRKES   200
 201  ARLATAGFFSILSFSWMNPLLSLGFKKPLSPEDIPSVVPEDEAQLAYKKF   250
 251  SQAWDTLLGDESSTKERNLVFRAVVKVYFKENIFIAVFAFLRTFAVVSLP   300
 301  LMLYVFVDYANSDHRDLRNGFFNLACLVMLKLVESLTMRHWYFASRRSGM   350
 351  RIRSALMVAAYKKQLKLSSLGRKRHSSGEIVNYIAVDAYRMGEFLWWFHS   400
 401  GWSLSLQLLLSTAVLFGVVGAGAFPGLILLLLCGLLNLPFAKMLQNCQTQ   450
 451  FMIAQDKRLRSTSEILNSMKVIKLQSWEDEFKKKIESCRDDEFTWLAKAQ   500
 501  LTKAFGSFLYWMSPTIVSSVVFLGCALLKSAPLNASTIFTVLATLRVMSE   550
 551  PVKIIPDAISAIIQGNVSFQRLNNFLLDDELKMDEIERSGLDASGTAVDI   600
 601  QVGNFGWEPETKIPTLRNIHLEIKHGQKVAVCGPVGAGKSSLLHAVLGEI   650
 651  PKVSGTVKVFGSIAYVSQTSWIQSGTIRDNILYGKPMESRRYNAAIKACA   700
 701  LDKDMNGFGHGDLTEIGQRGINLSGGQKQRIQLARAVYADADVYLLDDPF   750
 751  SAVDAHTAGVLFHKCVEDSLKEKTVILVTHQVEFLSEVDQILVMEEGTIT   800
 801  QSGKYEELLMMGTAFQQLVNAHNDAVTVLPLASNESLGDLRKEGKDREIR   850
 851  NMTVVEKIEEEIEKTDIPGVQLTQEEEKESGYVGMKPFLDYIGVSRGWCL   900
 901  LWSSVLGQVGFVVFQAASTYWLAFAIGIPKITNTMLIGVYSIISTLSAGF   950
 951  VYARAITTAHLGLKASKAFFSGFTNAVFKAPMLFFDSTPVGRILTRASSD  1000
1001  LNVLDYDVPFAFIFVVAPAVELTAALLIMTYVTWQVIIIALLALAATKVV  1050
1051  QDYYLASARELIRINGTTKAPVMNYAAETSLGVVTIRAFGTAERFFKNYL  1100
1101  NLVDADAVLFFLSNAAMEWVILRIETLQNVTLFTCALLLILIPKGYIAPG  1150
1151  LVGLSLSYALTLTQTQVFLTRWYCTLSNSIISVERIKQYMNIPEEPPAII  1200
1201  DDKRPPSSWPSNGTIHLQELKIRYRPNAPLVLKGISCTFREGTRVGVVGR  1250
1251  TGSGKSTLISALFRLVEPASGCILIDGIDISKIGLKDLRMKLSIIPQEPT  1300
1301  LFRGCIRTNLDPLGVYSDDEIWKALEKCQLKTTISNLPNKLDSSVSDEGE  1350
1351  NWSVGQRQLFCLGRVLLKRNKILVLDEATASIDSATDAIIQRIIREEFAD  1400
1401  CTVITVAHRVPTVIDSDMVMVLSFGDLVEYNEPSKLMETDSYFSKLVAEY  1450
1451  WASCRGNSSQNLQL                                      1464

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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