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

NucPred

Fetching Q13017 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MMAKNKEPRPPSYTISIVGLSGTEKDKGNCGVGKSCLCNRFVRSKADEYY    50
  51  PEHTSVLSTIDFGGRVVNNDHFLYWGDIIQNSEDGVECKIHVIEQTEFID   100
 101  DQTFLPHRSTNLQPYIKRAAASKLQSAEKLMYICTDQLGLEQDFEQKQMP   150
 151  EGKLNVDGFLLCIDVSQGCNRKFDDQLKFVNNLFVQLSKSKKPVIIAATK   200
 201  CDECVDHYLREVQAFASNKKNLLVVETSARFNVNIETCFTALVQMLDKTR   250
 251  SKPKIIPYLDAYKTQRQLVVTATDKFEKLVQTVRDYHATWKTVSNKLKNH   300
 301  PDYEEYINLEGTRKARNTFSKHIEQLKQEHIRKRREEYINTLPRAFNTLL   350
 351  PNLEEIEHLNWSEALKLMEKRADFQLCFVVLEKTPWDETDHIDKINDRRI   400
 401  PFDLLSTLEAEKVYQNHVQHLISEKRRVEMKEKFKKTLEKIQFISPGQPW   450
 451  EEVMCFVMEDEAYKYITEADSKEVYGRHQREIVEKAKEEFQEMLFEHSEL   500
 501  FYDLDLNATPSSDKMSEIHTVLSEEPRYKALQKLAPDRESLLLKHIGFVY   550
 551  HPTKETCLSGQNCTDIKVEQLLASSLLQLDHGRLRLYHDSTNIDKVNLFI   600
 601  LGKDGLAQELANEIRTQSTDDEYALDGKIYELDLRPVDAKSPYFLSQLWT   650
 651  AAFKPHGCFCVFNSIESLSFIGEFIGKIRTEASQIRKDKYMANLPFTLIL   700
 701  ANQRDSISKNLPILRHQGQQLANKLQCPFVDVPAGTYPRKFNETQIKQAL   750
 751  RGVLESVKHNLDVVSPIPANKDLSEADLRIVMCAMCGDPFSVDLILSPFL   800
 801  DSHSCSAAQAGQNNSLMLDKIIGEKRRRIQITILSYHSSIGVRKDELVHG   850
 851  YILVYSAKRKASMGMLRAFLSEVQDTIPVQLVAVTDSQADFFENEAIKEL   900
 901  MTEGEHIATEITAKFTALYSLSQYHRQTEVFTLFFSDVLEKKNMIENSYL   950
 951  SDNTRESTHQSEDVFLPSPRDCFPYNNYPDSDDDTEAPPPYSPIGDDVQL  1000
1001  LPTPSDRSRYRLDLEGNEYPIHSTPNCHDHERNHKVPPPIKPKPVVPKTN  1050
1051  VKKLDPNLLKTIEAGIGKNPRKQTSRVPLAHPEDMDPSDNYAEPIDTIFK  1100
1101  QKGYSDEIYVVPDDSQNRIKIRNSFVNNTQGDEENGFSDRTSKSHGERRP  1150
1151  SKYKYKSKTLFSKAKSYYRRTHSDASDDEAFTTSKTKRKGRHRGSEEDPL  1200
1201  LSPVETWKGGIDNPAITSDQELDDKKMKKKTHKVKEDKKQKKKTKNFNPP  1250
1251  TRRNWESNYFGMPLQDLVTAEKPIPLFVEKCVEFIEDTGLCTEGLYRVSG  1300
1301  NKTDQDNIQKQFDQDHNINLVSMEVTVNAVAGALKAFFADLPDPLIPYSL  1350
1351  HPELLEAAKIPDKTERLHALKEIVKKFHPVNYDVFRYVITHLNRVSQQHK  1400
1401  INLMTADNLSICFWPTLMRPDFENREFLSTTKIHQSVVETFIQQCQFFFY  1450
1451  NGEIVETTNIVAPPPPSNPGQLVEPMVPLQLPPPLQPQLIQPQLQTDPLG  1500
1501  II                                                  1502

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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