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

NucPred

Fetching P42695 from www.uniprot.org...

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

   1  MVALRGLGSGLQPWCPLDLRLEWVDTVWELDFTETEPLDPSIEAEIIETG    50
  51  LAAFTKLYESLLPFATGEHGSMESIWTFFIENNVSHSTLVALFYHFVQIV   100
 101  HKKNVSVQYREYGLHAAGLYFLLLEVPGSVANQVFHPVMFDKCIQTLKKS   150
 151  WPQESNLNRKRKKEQPKSSQANPGRHRKRGKPPRREDIEMDEIIEEQEDE   200
 201  NICFSARDLSQIRNAIFHLLKNFLRLLPKFSLKEKPQCVQNCIEVFVSLT   250
 251  NFEPVLHECHVTQARALNQAKYIPELAYYGLYLLCSPIHGEGDKVISCVF   300
 301  HQMLSVILMLEVGEGSHRAPLAVTSQVINCRNQAVQFISALVDELKESIF   350
 351  PVVRILLQHICAKVVDKSEYRTFAAQSLVQLLSKLPCGEYAMFIAWLYKY   400
 401  SRSSKIPHRVFTLDVVLALLELPEREVDNTLSLEHQKFLKHKFLVQEIMF   450
 451  DRCLDKAPTVRSKALSSFAHCLELTVTSASESILELLINSPTFSVIESHP   500
 501  GTLLRNSSAFSYQRQTSNRSEPSGEINIDSSGETVGSGERCVMAMLRRRI   550
 551  RDEKTNVRKSALQVLVSILKHCDVSGMKEDLWILQDQCRDPAVSVRKQAL   600
 601  QSLTELLMAQPRCVQIQKAWLRGVVPVVMDCESTVQEKALEFLDQLLLQN   650
 651  IRHHSHFHSGDDSQVLAWALLTLLTTESQELSRYLNKAFHIWSKKEKFSP   700
 701  TFINNVISHTGTEHSAPAWMLLSKIAGSSPRLDYSRIIQSWEKISSQQNP   750
 751  NSNTLGHILCVIGHIAKHLPKSTRDKVTDAVKCKLNGFQWSLEVISSAVD   800
 801  ALQRLCRASAETPAEEQELLTQVCGDVLSTCEHRLSNIVLKENGTGNMDE   850
 851  DLLVKYIFTLGDIAQLCPARVEKRIFLLIQSVLASSADADHSPSSQGSSE   900
 901  APASQPPPQVRGSVMPSVIRAHAIITLGKLCLQHEDLAKKSIPALVRELE   950
 951  VCEDVAVRNNVIIVMCDLCIRYTIMVDKYIPNISMCLKDSDPFIRKQTLI  1000
1001  LLTNLLQEEFVKWKGSLFFRFVSTLIDSHPDIASFGEFCLAHLLLKRNPV  1050
1051  MFFQHFIECIFHFNNYEKHEKYNKFPQSEREKRLFSLKGKSNKERRMKIY  1100
1101  KFLLEHFTDEQRFNITSKICLSILACFADGILPLDLDASELLSDTFEVLS  1150
1151  SKEIKLLAMRSKPDKDLLMEEDDMALANVVMQEAQKKLISQVQKRNFIEN  1200
1201  IIPIIISLKTVLEKNKIPALRELMHYLREVMQDYRDELKDFFAVDKQLAS  1250
1251  ELEYDMKKYQEQLVQEQELAKHADVAGTAGGAEVAPVAQVALCLETVPVP  1300
1301  AGQENPAMSPAVSQPCTPRASAGHVAVSSPTPETGPLQRLLPKARPMSLS  1350
1351  TIAILNSVKKAVESKSRHRSRSLGVLPFTLNSGSPEKTCSQVSSYSLEQE  1400
1401  SNGEIEHVTKRAISTPEKSISDVTFGAGVSYIGTPRTPSSAKEKIEGRSQ  1450
1451  GNDILCLSLPDKPPPQPQQWNVRSPARNKDTPACSRRSLRKTPLKTAN    1498

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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