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

NucPred

Fetching Q9HF75 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MPLKWAARNKKPPSAPQSCASKPSSASQSSCVDERISATPRSSISSNSSP    50
  51  NSKNNMSRHSHSNGSVYSDETTLKTAQTHYTQQGQQAKPQQHTQQQQQQP   100
 101  QTPMQLQVPTGQAHKRTLTCEDMKAGARCEEQVSPCSQPAGSPVRRGGGL   150
 151  NGETYDGTVFRLGWVNKAQGAAPAREGRYSHQPTASLSSIGSERPHFTGG   200
 201  GTSGYQYVATAYRLHRAQLKGCILNLYKSGLTNVKYFDPALEPSAAALQM   250
 251  HQERQEMPLLQPPLPSEAVPAPSILEASMESGELRLEYLSEAYPHPDLQL   300
 301  DKKDGKILSGSLESLCHAVLFMPTTDAKRVTDILLLLPLLDDFTRVLNYF   350
 351  NLFGKVFSKHHPAGAAGADDLNQNYNISNETDRQLTLRLATVVQTVLDMF   400
 401  PGFLLDDKIFQSLVILLDTISFHDEDTSQELKVAIAEKQTVLVKLTGFAN   450
 451  EPIQSAKLDVLIKVQSFLKLDTEKVANQIHKINLTFNRVWSPQADYSLLY   500
 501  DSQYTQKHVELNPLVFFNDKNVQYLSRLMVSHIFCEETGFTPKKRAEVLT   550
 551  KWVQLGCKFERLGDMVSWLAIATVICSIPVLRLTRTWQYVPDSYLKIIFK   600
 601  DWVPTIVQLDRRQMSSKSMNSVFILAPPNLNDAFVRDNVIPYFGDLVIHS   650
 651  DDLPRDSKYKYLEKKIRRTKNAFYKWQQRLDQAFAQDRDSASSFTDSLHL   700
 701  DEEEHDVADFYQYWRFHMNLPPMNIETIMEMSLKMEPPSINQQTYSKTYS   750
 751  TRSALISGAYLPTLFTTLLPSYSLFPQELLIAAASTPSTKNNNSSQASNR   800
 801  ISQLSVNSTPHSNASSSSAASAVTGIDNIDVPITKEISSKLSNKQVLLKF   850
 851  IRDMFNVDINVFHISDDVIFKSIRDYEAKSRPTSVVIESPKRLSLLSSVS   900
 901  PDVSAVSSALENLDLFKNFNSSSDDIAEFTVQVVLKCASLEKIFDILVLT   950
 951  SRVFSNLVTTTDLVSYFNSEKARREKSGAQHNGQHSIGLLDFALISLIMD  1000
1001  NELFAETFFNNYKSFTTTLCVLENLAKRFIGAKSSAISISLINKLRNSES  1050
1051  SRQIPPSTTSNQFSASGIFKPSYDELKFPVWDLKVTSVEGCPLDYLAKIQ  1100
1101  IGVLESLYHLIREHYADFTDDLANNKTFLDILKIINQEVYDEWDKRLDDL  1150
1151  RNNNNSSQKRKNSCDDNSSAKITFHVNDARPENSNENKRGAATNLGDSSL  1200
1201  AALEKLQCTLQDLYVKIKSSYQRQLYRPLGVTRNCRKVHDMLCQFQPQTS  1250
1251  MSALIMNGSSDTLDKMVTEFQALKHTDYDDIINWIYKLDHFITSKLKLVS  1300
1301  NQDWIQVSQILESLSNDSLVALFNYPLHAESNNVIASGSSQLDDLQILDI  1350
1351  FTWLSTLESGSAHIIDKFPASVQLIVRLHLSLTKFFTVHIAHLHSTYEAR  1400
1401  VNTCSLILEILNFVHVKNANVNLFHSDDAGEGSMATISPHVPSFIETAIE  1450
1451  NAIISPESRFFEVSWKQAYKTISEKDEKLTFIGSVLTGLDKSTAHFLDAD  1500
1501  NRQPVRPKNFSPCPGWFISRLLEITGLVPNMSIENSKMINFDKRRFINNI  1550
1551  VINYQDLIPNTEQLPSHDDEKSAHQFGSILFHYGTESSIKAFRKASKEAA  1600
1601  SNEARKLKFQAMGLFNDILVTEVYKVQRDQKKQEQLTVQEHEAKRSVLIQ  1650
1651  HPNKVSVSSASSSVSGSSSGSTARTSNPAHAAYALNMAGSLSISAARHGR  1700
1701  SSVSSRSSVISNTATATSPASGASPNQTSTSHHGGMGKKIGGFLRRPFSI  1750
1751  SGFTSSSSQYTTTSVVLSGVQANGSISPYELPELTSEIQDTKIVTVIKTF  1800
1801  EIKSCIQINNYRQDPDMMHCFKIVMEDGTQHTLQCMDDADMHEWMKAITL  1850
1851  SKRYSFHSKRFKGKTSNKIFGVPVEDVCEREGALIPNIIVKLLDEIELRG  1900
1901  LDEVGLYRVPGSVGSINALKNAFDDEGAVHNTFTLEDDRWFEINTIAGCF  1950
1951  KLYLRELPESLFTNEKVDEFVNIMTAYKNHEVDLSQFQNGIKTLLSTLPV  2000
2001  FNYHILKRLFLHLNRVHQHVENNRMDASNLAIVFSMSFINQDDLASTMGP  2050
2051  TLGLLQMLLQHLIRNPEHYFT                               2071

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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