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

NucPred

Fetching P47808 from www.uniprot.org...

The NucPred score for your sequence is 0.58 (see score help below)

   1  MHFLFFFANRQFLSLKCPQAEFVWIPHPVHGYITGKFIQEDYGGTSYCQT    50
  51  EEGESLSVACAPSQLAKVAKSVLDKSVDDLVQMDDINEAMIVHNLRKRFK   100
 101  NDQIYTNIGTILISVNPFKRLPLYTPTVMDQYMHKVPKEMPPHTYNIADD   150
 151  AYRAMIDNRMNQSILISGESGAGKTECTKQCLTYFAELAGSTNGVEQNIL   200
 201  LANPILESFGNAKTLRNNSSRFGKWVEIHFDQKGSICGASTINHLLEKSR   250
 251  VVYQIKGERNFRIVATELVKAPPRSRGGGGSSPARPESFKFLSQSGCIDV   300
 301  EGVDDVKEFEERVLCHGQARVRVQFSEDDINNCMELISAILHLGNFEFVS   350
 351  GQGKNVETSTVANREEVKIVATLLKVDPATLEQNVTSKLMEIKGCDPTRI   400
 401  PLTPVQATDATNALAKAIYSKLFDWLVKKINESMEPQKGAKTTTIGVLDI   450
 451  FGFEIFDKNSFEQLCINFTNEKLQQHFNQYTFKLEEKLYQSEEVKYEHIT   500
 501  FIDNQPVLDLIEKKQPQGLMLVLDEQISIPKSSDATFFIKANQTQAARST   550
 551  QLRGGEDSRTDFIIKHYAGDVIYDSTGMLEKNKDTLQKDLLVLSESSKQK   600
 601  LMKLLFPPSEGDQKTSKVTLGGQFRKQLDSLMTALNATEPHYIRCIKPNS   650
 651  EKQADLFHGFMSLQQLRYAGVFEAVRIRQTGYPFRYSHENFLKRYGFLVK   700
 701  DIHKRYGPNLKQNCDLLLKSMKGDCXSKVQVGKTRVLYRAPEQRGLELQR   750
 751  NIAVERVTIQIQAGVRRMFARRLYKRMRAIKPVLLNAIKSRSLSVLEQAI   800
 801  DAAKDIEFDMKLIRDCKELRSVILKEMEITKKLTDYIGAPPNHKTYLQVE   850
 851  PLYAQLCAVLTEAESINYSTPLVETGQQIKYMIAQRVETREQLKQAVDGA   900
 901  VRVDLEAAIARAEQIGLEESEPTLAAGRQELQRIYREEELVAELLNALAV   950
 951  GMAMRTSETTWDHAAIDAHTLGSAIYAAESFGFRTEQGRLTLDEAKVIVE  1000
1001  VRQHLAADDYESLSMTLKKATTTLNKNSMSQSTKTEIDEAYEELSHNTAV  1050
1051  NDLIEKVVQAIQDHDQEMLDYGVQQADSLRITDRPEMMQATELLNRIVNA  1100
1101  RALLREGITNVDQAQLETALADAASFAYTREEVPTAQQLLDRIYVINHDA  1150
1151  DVGLYYMEKEPLERAWAGAQEINLKTAQIDEVRNVLANDEQKFIQEQLKT  1200
1201  ANRLGDQARAIRLNIKLKEIFFGQFGKMFVFEQFGGLRKPEDFAKAKLLG  1250
1251  REALKLGMFKWTKSPIPTSLTTLDQLAVKSATRLFKNVLGFMGDRPLPYP  1300
1301  NALAQDLLEQCLAAPELRNEVYCQIIKQLTENPSPQSVTKGWQLMRCCLQ  1350
1351  TFPPSEEFANCLEMFLAAKGKDDKYIEMLHDTQYGDKRTSAPNVEQILAA  1400
1401  KQYVTRIDLNQSTQVDTSVVPQGFVPEKLIADDTEGVIRAGSRPAQARAQ  1450
1451  PGQQAQPAGAARQQAAAPVQAAAATASYDYGQQQQQQQQGYDQQQQAYGG  1500
1501  GADYGQQQQQQDLPAEPTEEYKQVEVVYDYDGGGDAQRLVLVKGAIITVI  1550
1551  KEYEGWAYGSTDDGQVGLYPINYTRPI                         1577

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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