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

NucPred

Fetching P40890 from www.uniprot.org...

The NucPred score for your sequence is 0.57 (see score help below)

   1  MALFRALYIIWVFLLIPLSNAEEFTPKVTRTLSRYVFDIVNFDDSNTLIR    50
  51  AEEDSVEISFDAGENWKTIDEIEEPIESFVVDPFRGHDRAFAFVKTAPKF   100
 101  YVTDDQGKSWRPLTIPISEKASNYFCDVTTHPIKKKHLIIRCDLLTIKNS   150
 151  GLMYVGREIYTTNDGVSFSQVKPSFGKIDGHISTARCDFIKSSEDSDLGG   200
 201  NDASILCLFRNTEYIESTGSTIDKSELILSADGGETFKELVQFKDKVVSR   250
 251  YEILKHHVIVLTQDDMYNEMSSTNIWISNDVSTFQVARTPTKIRHVNMGQ   300
 301  IHEDSIGRIVLPVSRERDDEDSNQPGAAEVLISDSEGLKFLPINWIPNNQ   350
 351  FGYINVAYPGFLKGTFFGSFHPFIEYSDRKRKYSRQKVREETKVSVDNGL   400
 401  TWTNLKVVDRENVDLFGCDVTKPERCSLQTHFYDLRNLNPSAGIMMISGI   450
 451  VGDGSAYNWKEEKTFISRDSGLTWRLVHNSTGLYTTGDLGNIIMYIPYRS   500
 501  NENGDVPSKFYYSLDQGKTWGEYDLIMPIYPYRLVSTISDGSGSKFILTG   550
 551  TSITEDPIFITYSIDFSAVFDYKSCEEGDFEDWNLADGKCVNGAKYKYRR   600
 601  RKQDAQCLVKKAFKDLSLDETPCNSCTGSDYECSFEFVRDAKGDCIPDYN   650
 651  LIALSDICDKSKGKSVLVKPLQLIKGDKCKTPMKIESVDIPCDEIPKEGS   700
 701  SDKEIVTTENKFDFEIKFYQYFDTVADESLVMLNSIGDAYISHDGGQTIK   750
 751  RFDTDGEKIVEIVFNPYFNSSAYLFGSKGNIFLTHDRGYSFMIAKLPEAR   800
 801  QLGMPLDFSAKAQDTFIYYGGKNCESILSPECHAVAYLTKDGGETFTEML   850
 851  DNAIHCEFAGTLFKYPSNDDMVMCQVKEKFSQTRSLVSSTDFFQDDRKTV   900
 901  FENIIGYLSTGGYIIVAVPHEDNELRAYVTNDGAEFTEAKFPYDEDIGKQ   950
 951  DAFTILGSEEGSIFLHLATNLESGHDFGNLLKSNSNGTSFVTLEHAVNRN  1000
1001  TFGYVDFEKVQGLEGIIITNIVSNSEKVGENKEDEQLKTKITFNDGSDWN  1050
1051  FLKPPKKDSEGKKFPCDSVSLDKCSLHLHGYTERKDIRDTYSSGSALGMM  1100
1101  FGVGNVGDRLLPYEECSTFLTTDGGETWTEVKKGPHQWEYGDHGGVLVLV  1150
1151  PENAETDSISYSTDFGKTWKDYKFCGDKVLVKDIITVPRDSALRFLLFGE  1200
1201  AKNMGSGSFRTYTIDFRNIFERQCEFDITGRKRADFKYSPLGSRTGCLFG  1250
1251  HKTEFLRKTDEKCFIGNIPLSEFSRNVKNCPCTRQDFECDYNFYKASDGT  1300
1301  CKLVKGLSSANGADICKKEPDLIEYYDSSGYRKIPLSTCKGGLKLDAHLA  1350
1351  PHPCPGKEKAFREKYSINTGAYALVFVTILLVIFFVAWFVYDRGIRRNGG  1400
1401  FSRFEEIRLGDDGLIENNRTDRVVNIIVRLGLCISLITKSAFQRAKAGTA  1450
1451  QLSSKFRARFGNKKGATYSSLLHDQLSDEPDGFHEDSNDLSSFRGQGSNS  1500
1501  EIEQEDVDTSQQEHTSRTDLLGASNIPDALPARSASHESDLAAARSEDK   1549

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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