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

NucPred

Fetching Q9W1I2 from www.uniprot.org...

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

   1  MNHIIQDKYIPQQLLYFLAGRRCCQQFPCTFRTSEHEAFANNARSLGLRS    50
  51  QVVHVNGNSCVKVYKQACRHYLEEPKTLVLSSGATLNMFTLLSRKSLMGK   100
 101  EDLELYADLVSMKANASDLPSLHLPLPAIRPPNLRFWTEAQLNFLTAFLG   150
 151  HSLSDEILQSLYASRVIVYNAALCWDKSVFLPLVILDDCRNKKSNVKIMC   200
 201  IERQAILATYNSQRTANFFGEQLGETVGIQLPYFSAVSSSTFIIYSTAQY   250
 251  FLRSLTSQQFRNISHLVVNDVHLHDPYTDILLSEIRMALSSHQNLRVVLL   300
 301  SQMGNPKKFTDFFGEGLQLNMIKQPEVAPRVSYLNELHSCIALAGIHKGP   350
 351  DIYKEIPEAFRANNPRNEQMDKCLQAYGELGTDAALRPFLYAVNYDLAPV   400
 401  NYRHSLTGKTAVHFASELNKANHLRLLLFMGADPYIVDLFQQNAISLAAM   450
 451  NGNHECIDVLNSYSLHGYVVKSAKPDFVDYDLIIDIMYLLRTKPEYSPGE   500
 501  YSPGNILIILPTYYHIVKLNYMILSHCLTGSLQECSIFLLYDNMRNDYLQ   550
 551  ALVNASDETVKVVLATDIIESLCLKVPFKYQIDTACRLNNVYDTTSCSGD   600
 601  DRFEWVAKDALLRRELILQPNKGDVQCFRLISKEAYEELSETSQPSLQTM   650
 651  QLDKICLAVKLLSPNTIISEYLGITISPPPLINVHHAVQFLKKIDVLDDA   700
 701  EDVTWLGCRLMDIPVSCQLGRMLIFGILLRCLDPILTIVSSLSTADPLGI   750
 751  PFTEDIDNLWDRFTIYIQNSIKKERTYLSDNQFSDHFIFVRLYKEWQNRM   800
 801  HNRTPPLYLKDEYEFMLNGLMEQLTSIRSEIVSSLRAANLIHSRGKLSMN   850
 851  NLNQMSCNWHMVKAALTGGMYPNIYAVDTRKSSLKSAFSGNVSMHPNTVL   900
 901  RDFLEPLNISAQSFRTPWIVCNRQKSHIVYATLVVPLAVAMFSGHPRIRL   950
 951  SPICDSEMSLTDRNVNVFIDEWIWMVMSKATAEMVMRTRYYFFKMYHDLL  1000
1001  KHCSELDMWRRDCEPVSQYTVLTDTLSKIFESEDGFVGFFKPPPITFLPT  1050
1051  PQLPSLYLLSVNAHFSWAREVEENMLSKPHHFNSHFIERQFFVLYAGGDC  1100
1101  EEFHSRNTPAFIESVLGKFVRPIDTPNRHIFVILYRKDPDMMLSISRAKF  1150
1151  VNGVFMLQEYFRNNIPVFEILDACVSLNVQTPVFDGRLMSALIDKRVGNL  1200
1201  IMELFAFRHHWIHKR                                     1215

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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