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

NucPred

Fetching P47820 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MGAASGQRGRWPLSPPLLMLSLLLLLLLPPSPAPALDPGLQPGNFSADEA    50
  51  GAQLFADSYNSSAEVVMFQSTAASWAHDTNITEENARLQEEAALINQEFA   100
 101  EVWGKKAKELYESIWQNFTDQKLRRIIGSVQTLGPANLPLTQRLQYNSLL   150
 151  SNMSRIYSTGKVCFPNKTATCWSLDPELTNILASSRNYAKVLFAWEGWHD   200
 201  AVGIPLRPLYQDFTALSNEAYRQDGFSDTGAYWRSWYESPSFEESLEHLY   250
 251  HQVEPLYLNLHAFVRRALHRRYGDKYINLRGPIPAHLLGDMWAQSWENIY   300
 301  DMVVPFPDKPNLDVTSTMVQKGWNATHMFRVAEEFFTSLGLSPMPPEFWA   350
 351  ESMLEKPADGREVVCHASAWDFYNRKDFRIKQCTRVTMDQLSTVHHEMGH   400
 401  VQYYLQYKDLHVSLRRGANPGFHEAIGDVLALSVSTPAHLHKIGLLDRVA   450
 451  NDIESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGRTPPSRYNYDWWY   500
 501  LRTKYQGICPPVARNETHFDAGAKFHIPSVTPYIRYFVSFVLQFQFHQAL   550
 551  CKEAGHQGPLHQCDIYQSTKAGAKLQQVLQAGCSRPWQEVLKDLVGSDAL   600
 601  DASALMEYFQPVSQWLQEQNQRNGEVLGWPEYQWRPPLPDNYPEGIDLET   650
 651  DEAKANRFVEEYDRTAKVLWNEYAEANWHYNTNITIEGSKILLQKNKEVS   700
 701  NHTLKYGTWAKTFDVSNFQNSTIKRIIKKVQNVDRAVLPPNELEEYNQIL   750
 751  LDMETTYSVANVCYTNGTCLSLEPDLTNIMATSRKYEELLWVWKSWRDKV   800
 801  GRAILPFFPKYVDFSNKIAKLNGYSDAGDSWRSSYESDDLEQDLEKLYQE   850
 851  LQPLYLNLHAYVRRSLHRHYGSEYINLDGPIPAHLLGNMWAQTWSNIYDL   900
 901  VAPFPSAPSIDATEAMIKQGWTPRRIFKEADNFFTSLGLLPVPPEFWNKS   950
 951  MLEKPTDGREVVCHASAWDFYNGKDFRIKQCTSVNMEELVIAHHEMGHIQ  1000
1001  YFMQYKDLPVTFREGANPGFHEAIGDVLALSVSTPKHLHSLNLLSSEGSG  1050
1051  YEHDINFLMKMALDKIAFIPFSYLIDQWRWRVFDGSITKENYNQEWWSLR  1100
1101  LKYQGLCPPVPRSQGDFDPGSKFHVPANVPYIRYFISFIIQFQFHEALCR  1150
1151  AAGHTGPLYKCDIYQSKEAGKLLADAMKLGYSKQWPEAMKIITGQPNMSA  1200
1201  SAIMNYFKPLTEWLVTENRRHGETLGWPEYTWTPNTARAEGSLPESSRVN  1250
1251  FLGMYLEPQQARVGQWVLLFLGVALLVATVGLAHRLYNIHNHHSLRRPHR  1300
1301  GPQFGSEVELRHS                                       1313

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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