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

NucPred

Fetching P97393 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MMAKNKEPRPPSYTVSVVGLSGTEKDKGNCGVGKSCLCNRFVRSKADEYY    50
  51  PEHTSVLSTIDFGGRVVNNDHFLYWGDITQNGEDGVECKIHVIEQTEFID   100
 101  DQTFLPHRSTNLQPYIKRAAASKLQSAEKLMYICTDQLGLEQDFEQKQMP   150
 151  EGKLNVDGFLLCIDVSQGCNRKFDDQLKFVNNLFVQLSKSKKPVIIAATK   200
 201  CDECVDHYLREVQAFASNKKNLLVVETSARFNVNIETCFTALVQMLDKTR   250
 251  GKPKIIPYLDAYKTQRQLVVTATDKFEKLVQTVRDYHATWKTVSNKLKNH   300
 301  PDYEEYINLEGTRKARNTFSKHIEQLKQEHIRKRREEYISTLPRAFNTLL   350
 351  PDLEEIEHLNWLEALKLMEKRADFQLCFVVLEKTPWDETDHIDKINDRRI   400
 401  PFDLLSTLEAEKVYQNHVQHLISEKRRIEMKEKFKKTLEKIQFISPGQPW   450
 451  EEVMCFVMEDEAFKYITEADSKEVYGRHQREIVEKAKEEFQEMLFEHSEL   500
 501  FYDLDLNATPSSDKMSEIHTVLSEEPRYKALQKLAPDRESLLLKHIGFVY   550
 551  HPTKETCLSGQYCTDIKVENLLATSLLEMDHNRVRLYHDSTNIDKVNLFI   600
 601  LGKDGLAQELANEIRTQSTDDEYALDGKIYELDLRPVDAKSPYILSQLWT   650
 651  AAFKPHGCFCVFNSIESLSFIGEFIGKIRTEASQIRKDKYMTNLPFTLIL   700
 701  ANQRDSISKNLPILRHQGQQLANKLQCPFVDVPTGTYPRKFNESQIKQAL   750
 751  RGVLESVKHNLDVVSPVPINKDVSEADLRIVMCAMCGDPFSVDLILSPFL   800
 801  DSHSCSAAQAGQNNSLMLDKIIGEKRRRIQITILSYHSSIGVRKDELVHG   850
 851  YILVYSAKRKASMGMLRAFLSEVQDTIPVQLVAVTDSQADFFENEAIKEL   900
 901  MTEGEHIATEITAKFTALYSLSQYHRQTEVFTLFFSDVLEKKNMIENSYL   950
 951  SDNTRESTHQSEDVFLPSPRDCFPYNNYPDSDDDTEAPPPYSPIGDDVQL  1000
1001  LPTPSDRSRYRLDLEGNEYPVHSTPNCHDHERNHKVPPPIKPKPVVPKTN  1050
1051  VKKLDPNLLKTIEAGIGKNPRKQTSRVPLAHPEDMDSSDNYVEPLDTIFK  1100
1101  QKGYSDEIYVVPDDSQNRIIKIRNSFVNNTQGDEENGFSDRTSKGHGERR  1150
1151  PSKYKYKSKTLFSKAKSYYRRTHSDASDDEAFTTSKTKRKGRHRGSEEDP  1200
1201  LLSPVETWKGGIDNPAITSDQEVDDKKIKKKTHKVKEDKKQKKKTKTFNP  1250
1251  PTRRNWESNYFGMPLQDLVTAEKPIPLFVEKCVEFIEDTGLCTEGLYRVS  1300
1301  GNKTDQDNIQKQFDQDHNINLASMEVTVNAVAGALKAFFADLPDPLIPYS  1350
1351  LHPELLEAAKIPDKTERFHALKEIVKKFHPVNYDVFRYVITHLNRVSQQN  1400
1401  KINLMTADNLSICFWPTLMRPDFENREFLSTTKIHQSVVETFIQQCQFFF  1450
1451  YNGEIVETANTVAPPPTSNPGQLVESMVPLQLPPPLQPQLIQPQLQTDPL  1500
1501  GII                                                 1503

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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