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

NucPred

Fetching Q9V4C8 from www.uniprot.org...

The NucPred score for your sequence is 0.49 (see score help below)

   1  MEGSDFVDPAFSSGERISASDLNSEHIIQAENHSFANRISMDMDVPDGHQ    50
  51  LDSNLTGFRWKRVLNPTGPQPRPRHGHRAINIKELMVVFGGGNEGIVDEL   100
 101  HVYNTVTNQWYVPVLKGDVPNGCAAYGFVVEGTRMFVFGGMIEYGKYSNE   150
 151  LYELQATKWEWRKMYPESPDSGLSPCPRLGHSFTMVGEKIFLFGGLANES   200
 201  DDPKNNIPKYLNDLYILDTRGVHSHNGKWIVPKTYGDSPPPRESHTGISF   250
 251  ATKSNGNLNLLIYGGMSGCRLGDLWLLETDSMTWSKPKTSGEAPLPRSLH   300
 301  SSTMIGNKMYVFGGWVPLVINDSKSTTEREWKCTNTLAVLDLETMTWENV   350
 351  TLDTVEENVPRARAGHCAVGIQSRLYVWSGRDGYRKAWNNQVCCKDLWYL   400
 401  EVSKPLYAVKVALVRASTHALELSWTATTFAAAYVLQIQKIEQPLNTSSK   450
 451  LLSNNIVQQGTPTSAETSGINISANRSGSALGLGVEATSTVLKLEKESLQ   500
 501  LSGCQPETNVQPSVNDLLQSMSQPSSPASRADKDPLSSGGGTTFNLSTSV   550
 551  ASVHPQISVISSTAAVTGNDTASPSGAINSILQKFRPVVTAVRTSTTTAV   600
 601  SIATSTSDPLSVRVPSTMSANVVLSSSSSTLRIVPSVTASHSLRIASSQA   650
 651  SGNNCRSSSAINILKTALPNVAVQSQPTSSTTTSIGGKQYFIQKPLTLAP   700
 701  NVQLQFVKTSGGMTVQTLPKVNFTASKGTPPHGISIANPHLASGITQIQG   750
 751  STVPGSQIQKPIVSGNVLKLVSPHTMAGGKLIMKNSNILQMGKVTPNVMG   800
 801  GKPAFVITNKQGTPLGNQQIIIVTTGGNVRSVPTSTVMTSAGGSASGTNI   850
 851  VSIVNSTSTTPSPLQALSGQKTLISNQSGVKMLRNISSVQASSSMAFGQK   900
 901  QSGTPIHQKTALYIGGKAVTVMSTNTSMAASGNKVMVLPGTSSNNSPATT   950
 951  TALSARKSFVFNAGGSPRTVTLATKSINAKSIPQSQPVTETNNHSVATIK  1000
1001  DTDPMDDIIEQLDGAGDLLKLSESEGQHGSEENENNGENATSSSASALFT  1050
1051  GGDTAGPSRAQNPIVMEHPVDIIEDVSGVSSTTDVNETAIVSGDTIESLK  1100
1101  MSEKENDDVKSMGEKSILSDDCHQPTTSETEAATILTTIKSAEALVLETA  1150
1151  EIRKDHTGCTIGSLKENQDENKKFKQRQESSPSQNIHQFQNVDGSQLEAL  1200
1201  ASAALLQAATSDTTALALKELIERPESETNTRSSNIAEIQQNNVQSTLAV  1250
1251  VVPNTSQNENQKWHTVGVFKDLSHTVTSYIDSNCISDSFFDGIDVDNLPD  1300
1301  FSKFPRTNLEPGTAYRFRLSAINSCGRGEWGEISSFKTCLPGFPGAPSAI  1350
1351  KISKDVKEGAHLTWEPPPAQKTKEIIEYSVYLAVKPTAKDKALSTPQLAF  1400
1401  VRVYVGAANQCTVPNASLSNAHVDCSNKPAIIFRIAARNQKGYGPATQVR  1450
1451  WLQDPAAAKQHTPTVTPNLKRGPEKSTIGSSNIANTFCSPHKRGRNGLHD  1500

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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