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

NucPred

Fetching O60840 from www.uniprot.org...

The NucPred score for your sequence is 0.47 (see score help below)

   1  MSESEGGKDTTPEPSPANGAGPGPEWGLCPGPPAVEGESSGASGLGTPKR    50
  51  RNQHSKHKTVAVASAQRSPRALFCLTLANPLRRSCISIVEWKPFDILILL   100
 101  TIFANCVALGVYIPFPEDDSNTANHNLEQVEYVFLVIFTVETVLKIVAYG   150
 151  LVLHPSAYIRNGWNLLDFIIVVVGLFSVLLEQGPGRPGDAPHTGGKPGGF   200
 201  DVKALRAFRVLRPLRLVSGVPSLHIVLNSIMKALVPLLHIALLVLFVIII   250
 251  YAIIGLELFLGRMHKTCYFLGSDMEAEEDPSPCASSGSGRACTLNQTECR   300
 301  GRWPGPNGGITNFDNFFFAMLTVFQCVTMEGWTDVLYWMQDAMGYELPWV   350
 351  YFVSLVIFGSFFVLNLVLGVLSGEFSKEREKAKARGDFQKQREKQQMEED   400
 401  LRGYLDWITQAEELDMEDPSADDNLGSMAEEGRAGHRPQLAELTNRRRGR   450
 451  LRWFSHSTRSTHSTSSHASLPASDTGSMTETQGDEDEEEGALASCTRCLN   500
 501  KIMKTRVCRRLRRANRVLRARCRRAVKSNACYWAVLLLVFLNTLTIASEH   550
 551  HGQPVWLTQIQEYANKVLLCLFTVEMLLKLYGLGPSAYVSSFFNRFDCFV   600
 601  VCGGILETTLVEVGAMQPLGISVLRCVRLLRIFKVTRHWASLSNLVASLL   650
 651  NSMKSIASLLLLLFLFIIIFSLLGMQLFGGKFNFDQTHTKRSTFDTFPQA   700
 701  LLTVFQILTGEDWNVVMYDGIMAYGGPFFPGMLVCIYFIILFICGNYILL   750
 751  NVFLAIAVDNLASGDAGTAKDKGGEKSNEKDLPQENEGLVPGVEKEEEEG   800
 801  ARREGADMEEEEEEEEEEEEEEEEEGAGGVELLQEVVPKEKVVPIPEGSA   850
 851  FFCLSQTNPLRKGCHTLIHHHVFTNLILVFIILSSVSLAAEDPIRAHSFR   900
 901  NHILGYFDYAFTSIFTVEILLKMTVFGAFLHRGSFCRSWFNMLDLLVVSV   950
 951  SLISFGIHSSAISVVKILRVLRVLRPLRAINRAKGLKHVVQCVFVAIRTI  1000
1001  GNIMIVTTLLQFMFACIGVQLFKGKFYTCTDEAKHTPQECKGSFLVYPDG  1050
1051  DVSRPLVRERLWVNSDFNFDNVLSAMMALFTVSTFEGWPALLYKAIDAYA  1100
1101  EDHGPIYNYRVEISVFFIVYIIIIAFFMMNIFVGFVIITFRAQGEQEYQN  1150
1151  CELDKNQRQCVEYALKAQPLRRYIPKNPHQYRVWATVNSAAFEYLMFLLI  1200
1201  LLNTVALAMQHYEQTAPFNYAMDILNMVFTGLFTIEMVLKIIAFKPKHYF  1250
1251  TDAWNTFDALIVVGSIVDIAVTEVNNGGHLGESSEDSSRISITFFRLFRV  1300
1301  MRLVKLLSKGEGIRTLLWTFIKSFQALPYVALLIAMIFFIYAVIGMQMFG  1350
1351  KVALQDGTQINRNNNFQTFPQAVLLLFRCATGEAWQEIMLASLPGNRCDP  1400
1401  ESDFGPGEEFTCGSNFAIAYFISFFMLCAFLIINLFVAVIMDNFDYLTRD  1450
1451  WSILGPHHLDEFKRIWSEYDPGAKGRIKHLDVVALLRRIQPPLGFGKLCP  1500
1501  HRVACKRLVAMNMPLNSDGTVTFNATLFALVRTSLKIKTEGNLEQANQEL  1550
1551  RIVIKKIWKRMKQKLLDEVIPPPDEEEVTVGKFYATFLIQDYFRKFRRRK  1600
1601  EKGLLGNDAAPSTSSALQAGLRSLQDLGPEMRQALTCDTEEEEEEGQEGV  1650
1651  EEEDEKDLETNKATMVSQPSARRGSGISVSLPVGDRLPDSLSFGPSDDDR  1700
1701  GTPTSSQPSVPQAGSNTHRRGSGALIFTIPEEGNSQPKGTKGQNKQDEDE  1750
1751  EVPDRLSYLDEQAGTPPCSVLLPPHRAQRYMDGHLVPRRRLLPPTPAGRK  1800
1801  PSFTIQCLQRQGSCEDLPIPGTYHRGRNSGPNRAQGSWATPPQRGRLLYA  1850
1851  PLLLVEEGAAGEGYLGRSSGPLRTFTCLHVPGTHSDPSHGKRGSADSLVE  1900
1901  AVLISEGLGLFARDPRFVALAKQEIADACRLTLDEMDNAASDLLAQGTSS  1950
1951  LYSDEESILSRFDEEDLGDEMACVHAL                         1977

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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