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

NucPred

Fetching Q50JE5 from www.uniprot.org...

The NucPred score for your sequence is 0.44 (see score help below)

   1  MGAASGQRGQGPPSPLLLLWLSLLLLLLPPSPAPALDPGLQPGNFSADEI    50
  51  GAHLFAESYNSSAEQVIFQSTVASWAYDTNMTEENARLQEEAELIWQEFA   100
 101  EVWGKKAKELFDAIRQNFTDSKLRRVIETIRTLGPANLPLARRQQYNSLQ   150
 151  NNMNRIYSTSKVCLPNKTATCWSLEPELTNILASSRSYAKLLFAWESWHD   200
 201  VVGIPLKPLYQDFTALSNEAYKQDGFSDTGAYWRSAYDSPSFEETLEHLY   250
 251  HQLEPLYLNLHAYVRRALHRRYGDKYINLRGPIPAHLLGDMWAQSWDNIY   300
 301  DMVVPFPNKPNLDVTNTMVQKGWNVTHMFRVAEEFFTSMGLSPMPPEFWA   350
 351  ESMLEKPTDGREVVCHASAWDFFNRKDFRIKQCTRITMEQLSTVHHEMGH   400
 401  VQYYLQYKDLTVPLRRGANPGFHEAIGDVLALSVSTPAHLHKIGLLDRVA   450
 451  NDLESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGHTPPSRYNFDWWY   500
 501  FRTKYQGICPPVVRNETHFDAGAKFHIPSGTPYIRYFVSFILQFQFHQAL   550
 551  CKEAGHQGPLHQCDIYQSTQAGAKLQRVLQAGYSRPWQEVLKEMVGSDTL   600
 601  DAQALLEYFQPVIRWLQEQNQRNGEVLGWPEYQWRPPLPDNYPEGIDLVT   650
 651  DETEAERFVEEYDRTARVLWNEYAEANWQYNTNITLEASKILLQKNKKVA   700
 701  NHTLKYGTLAKKFDVSNFQNYTIKRIIKKVQNMDRAVLPPKELEEYNQIL   750
 751  MDMETTYSIANVCYLNGTCLHLEPDLTNVMATSRKYEELLWVWKSWRDKV   800
 801  GRAILPLFPKYVELSNKIAHLNGYADGGDSWRSSYESKSLEQDLEQLYQE   850
 851  LQPLYLNLHAYVRRSLHRHYGSQHINLDGPIPAHLLGNMWAQTWSNIYDL   900
 901  VAPFPSAPNLDATEAMIKQGWTPRRIFKEADDFFTSLGLLPVSEEFWNKS   950
 951  MLEKPGDGREVVCHASAWDFYNGKDFRIKQCTSVNMEDLVIAHHEMGHIQ  1000
1001  YFMQYKDLPVTFREGANPGFHEAIGDVLALSVSTPKHLHSLNLLSSEGGG  1050
1051  YEHDINFLMKMALDKIAFIPFSYLIDQWRWRVFDGSITKENYNQEWWSLR  1100
1101  LKYQGLCPPVPRSQDDFDPGSKFHVPANVPYIRYFVSFIIQFQFHEALCR  1150
1151  AAGHTGPLHKCDIYQSKEAGKLLADTMKMGYSKPWPEAMKLITGQPNMSA  1200
1201  SAMMNYFKPLTEWLVTENRRHGETLGWPEYNWTPNTARSEGPFPESGRVN  1250
1251  FLGMYLEPQQARVGQWVLLFLGVSLLVATLGLTHRLFSIRQHGHSLHRPH  1300
1301  RGPQFGSEVELRHS                                      1314

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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