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

NucPred

Fetching O95487 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MSAPAGSSHPAASARIPPKFGGAAVSGAAAPAGPGAGPAPHQQNGPAQNQ    50
  51  MQVPSGYGLHHQNYIAPSGHYSQGPGKMTSLPLDTQCGDYYSALYTVPTQ   100
 101  NVTPNTVNQQPGAQQLYSRGPPAPHIVGSTLGSFQGAASSASHLHTSASQ   150
 151  PYSSFVNHYNSPAMYSASSSVASQGFPSTCGHYAMSTVSNAAYPSVSYPS   200
 201  LPAGDTYGQMFTSQNAPTVRPVKDNSFSGQNTAISHPSPLPPLPSQQHHQ   250
 251  QQSLSGYSTLTWSSPGLPSTQDNLIRNHTGSLAVANNNPTITVADSLSCP   300
 301  VMQNVQPPKSSPVVSTVLSGSSGSSSTRTPPTANHPVEPVTSVTQPSELL   350
 351  QQKGVQYGEYVNNQASSAPTPLSSTSDDEEEEEEDEEAGVDSSSTTSSAS   400
 401  PMPNSYDALEGGSYPDMLSSSASSPAPDPAPEPDPASAPAPASAPAPVVP   450
 451  QPSKMAKPFGYGYPTLQPGYQNATAPLISGVQPSNPVYSGFQQYPQQYPG   500
 501  VNQLSSSIGGLSLQSSPQPESLRPVNLTQERNILPMTPVWAPVPNLNADL   550
 551  KKLNCSPDSFRCTLTNIPQTQALLNKAKLPLGLLLHPFRDLTQLPVITSN   600
 601  TIVRCRSCRTYINPFVSFIDQRRWKCNLCYRVNDVPEEFMYNPLTRSYGE   650
 651  PHKRPEVQNSTVEFIASSDYMLRPPQPAVYLFVLDVSHNAVEAGYLTILC   700
 701  QSLLENLDKLPGDSRTRIGFMTFDSTIHFYNLQEGLSQPQMLIVSDIDDV   750
 751  FLPTPDSLLVNLYESKELIKDLLNALPNMFTNTRETHSALGPALQAAFKL   800
 801  MSPTGGRVSVFQTQLPSLGAGLLQSREDPNQRSSTKVVQHLGPATDFYKK   850
 851  LALDCSGQQTAVDLFLLSSQYSDLASLACMSKYSAGCIYYYPSFHYTHNP   900
 901  SQAEKLQKDLKRYLTRKIGFEAVMRIRCTKGLSMHTFHGNFFVRSTDLLS   950
 951  LANINPDAGFAVQLSIEESLTDTSLVCFQTALLYTSSKGERRIRVHTLCL  1000
1001  PVVSSLADVYAGVDVQAAICLLANMAVDRSVSSSLSDARDALVNAVVDSL  1050
1051  SAYGSTVSNLQHSALMAPSSLKLFPLYVLALLKQKAFRTGTSTRLDDRVY  1100
1101  AMCQIKSQPLVHLMKMIHPNLYRIDRLTDEGAVHVNDRIVPQPPLQKLSA  1150
1151  EKLTREGAFLMDCGSVFYIWVGKGCDNNFIEDVLGYTNFASIPQKMTHLP  1200
1201  ELDTLSSERARSFITWLRDSRPLSPILHIVKDESPAKAEFFQHLIEDRTE  1250
1251  AAFSYYEFLLHVQQQICK                                  1268

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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