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

NucPred

Fetching P97608 from www.uniprot.org...

The NucPred score for your sequence is 0.11 (see score help below)

   1  MGSPEGRFHFAIDRGGTFTDVFAQCPGGHVRVLKLLSEDPANYADAPTEG    50
  51  IRRILEQEEGVLLPRGRPLDTSRIASIRMGTTVATNALLERQGERVALLV   100
 101  TRGFRDLLHIGTQARPDLFDLAVPMPEVLYEEVLEVDERVVLYRGEPGAG   150
 151  SPVKGRTGDLLEIQQPVDLEALRGKLEGLLSRGIHSLAVVLMHSYTWAQH   200
 201  EQQVGTLARELGFTHVSLSSEVMPMVRIVPRGHTACADAYLTPTIQRYVQ   250
 251  GFRRGFQGQLKNVQVLFMRSDGGLAPMDAFSGSRAVLSGPAGGVVGYSAT   300
 301  TYHLEGGQPVIGFDMGGTSTDVSRYAGEFEHVFEASTAGVTLQAPQLDIN   350
 351  TVAAGGGSRLFFRSGLFVVGPESAGAHPGPACYRKGGPVTVTDANLVLGR   400
 401  LLPASFPCIFGPGEDQPLSPEASRKALEAVAMEVNSFLTNGPCPASQLSL   450
 451  EEVAMGFVRVANEAMCRPIRALTQARGHDPSAHVLACFGGAGGQHACAIA   500
 501  RALGMDTVHIHRHSGLLSALGLALADVVHEAQEPCSLSYTPETFAQLDQR   550
 551  LSRLEEQCVDALQVQGFPRSQISTESFLHLRYQGTDCALMVSAHQHPATA   600
 601  CSPRAGDFGAAFVERYMREFGFIIPERPVVVDDVRVRGTGRSGLQLEDTP   650
 651  KIQTGPPHVEKVTQCYFEGGYQETPVYLLGELGYGHQLQGPCLIIDNNST   700
 701  ILVEPGCQAEVTDTGDIRISVGAEGPSMADTRLDPIQLSIFSHRFMSIAE   750
 751  QMGRILQRTAISTNIKERLDFSCALFGPDGGLVSNAPHIPVHLGAMQETV   800
 801  QFQIQHLGADLHPGDVLLSNHPSAGGSHLPDLTVITPVFWPGQTRPVFYV   850
 851  ASRGHHADIGGITPGSMPPHSTTLQQEGAVFLSFKLVQGGVFQEEAVTEA   900
 901  LRAPGKISGCSGTRNLHDNLSDLRAQVAANQKGIQLVGELIGQYGLDVVQ   950
 951  AYMGHIQANAELAVRDMLRAFGTSRQARGLPLEVSAEDHMDDGSPICLRV  1000
1001  QINLSQGSAVFDFTGSGSEVFGNLNAPRAITLSALIYCLRCLVGRDIPLN  1050
1051  QGCLAPVRVIIPKGSILDPSPEAAVVGGNVLTSQRVVDVILGAFGACSAS  1100
1101  QGCMNNVTLGNARMGYYETVAGGAGAGPGWHGRSGVHSHMTNTRITDPEI  1150
1151  LESRYPVILRRFELRPGSGGRGRFRGGDGVVRELVFREEALLSVLTERRA  1200
1201  FQPYGLHGGEPGARGLNLLIRKDGRTVNLGGKTSVTVYPGDVFCLHTPGG  1250
1251  GGYGDPEDPAPPPGSPPLFPAFPERGSVFEYRRAQEAV              1288

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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