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

NucPred

Fetching Q8SSC4 from www.uniprot.org...

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

   1  MFEAKVKKQIKSIQFGLFSPDEVRNGSVALIVHPEVMEGGVPKTGGLIDL    50
  51  RMGTTDRMYLCQSCGGDNFSCPGHFGHIELTKPMFHVGYISKIKKVLECV   100
 101  CFYCSKIKIPRKGIKSTLSNVWGMSKGRSVCEGEVLDNGRSGCGNKQPVI   150
 151  KREGLTLVAFMKGEESNEGKVMLNGERVYSIFKKISDEDSVYMGFDLKYS   200
 201  RPEWMILTVLLVPPPAVRPSIVMEGSLRGEDDLTHKLADIIKSNGYLKKY   250
 251  EQEGAPGHIVRDYEQLLQFHVATFIDNDIGGLPQALQKSGRPLKSLSARL   300
 301  KGKEGRIRGNLMGKRVDFSARTVITPDPNISLEEVGVPLEIAKIHTFPEK   350
 351  VTSFNIDRLEKLVRAGPNEHPGANYVLRSDGQKIDLNFNRSDIRLEEGYV   400
 401  VERHMQSGDVVLFNRQPSLHKMSMMAHYARVMGNKTFRLNLSVTSPYNAD   450
 451  FDGDEMNLHMPQSYTSKAELEELALVSRQIISPQSNKPVMGIVQDTLTGL   500
 501  RLFTLRDTFLNEREVMSLLYAVNLEFCDIPLGDAVQTGLRKGKDYDIMKI   550
 551  LRKPAIAKPMRLWTGKQVLSFVLPNLNYIGLSSEHDDDDKENIGDTRVII   600
 601  QDGYIHSGVIDKKAAGATQGGLVHIIFNDFGPKRAAQFFDGVQRMINAFM   650
 651  TGIHTFSMGIGDTIADPKTVKVVESAIRKAKEEVSALIENARQNRLERLP   700
 701  GMTMKESFESHLNLVLNRARDVSGTSAQRSLSENNNMKTMVLAGSKGSFI   750
 751  NISQVTACVGQQNVEGKRIPFGFSHRTLPHFVKDDYTGKSRGFVENSYLT   800
 801  GLDPEEFFFHAMGGREGLIDTAIKTAETGYIQRRLVKALEDAIVRQDESV   850
 851  RSGNGLVYQIKYGEDGFDATFLESQKVDVKNFTKRYYIDMFGTEELEIKH   900
 901  GQVSEEVYGMLSSDVDLQKLLDQEYEWLVGEIFEGPPILSVGEVDIERDY   950
 951  KVRDIYQSAVMSPCNFTRILATAKRTFHLSTGDVSPYYILEAHKHLTTSN  1000
1001  RILNVLIRTNLSVKRVLLEHRLNTEAFNWVVEVIDAKILKAKITPNEMVG  1050
1051  TLAAQSVGEPATQMTLNTFHLAGVASTVTMGVPRLKEIFNVTKNLKTPSM  1100
1101  KIYLDREHGKSIEAAKTIQNEIECLTVKDLCLFSEIYYDPEITGTEISDD  1150
1151  KDFVEAYFEFPDEDVDFSCLSPFLMRLVVDRAKLVGRGINLEYVAMFIRK  1200
1201  ELGGGAHVICSDENAVNMVVRVRTTKSEDESLNFYTTALNSLLRLQLGGY  1250
1251  KNVKKVYISEDKDRKEWYLQTDGICLSQILGNPAVNSRLTISNDLVEIAE  1300
1301  TLGIEAARESILRELTIVIDGNGSYVNYRHMSLLADVMTMRGYLCGITRH  1350
1351  GVNKVGAGALKRSSFEETVEILLDAALVSEKNICRGITENIMMGQLAPMG  1400
1401  TGNIEIMLDMKKLDKAIPLSNPVFKPNEPATPVISTPSSDSFSISSGNWS  1450
1451  PTHLEMAYSRDLGERLSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS  1500
1501  YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY  1550
1551  SPTSPSYSPTSPSYSPTSPSYSVSMSSFSNKNKSKNQDGDKKRRNDGSF   1599

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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