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

NucPred

Fetching P26675 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MFSGPSGHAHTISYGGGIGLGTGGGGGSGGSGSGSQGGGGGIGIGGGGVA    50
  51  GLQDCDGYDFTKCENAARWRGLFTPSLKKVLEQVHPRVTAKEDALLYVEK   100
 101  LCLRLLAMLCAKPLPHSVQDVEEKVNKSFPAPIDQWALNEAKEVINSKKR   150
 151  KSVLPTEKVHTLLQKDVLQYKIDSSVSAFLVAVLEYISADILKMAGDYVI   200
 201  KIAHCEITKEDIEVVMNADRVLMDMLNQSEAHILPSPLSLPAQRASATYE   250
 251  ETVKELIHDEKQYQRDLHMIIRVFREELVKIVSDPRELEPIFSNIMDIYE   300
 301  VTVTLLGSLEDVIEMSQEQSAPCVGSCFEELAEAEEFDVYKKYAYDVTSQ   350
 351  ASRDALNNLLSKPGASSLTTAGHGFRDAVKYYLPKLLLVPICHAFVYFDY   400
 401  IKHLKDLSSSQDDIESFEQVQGLLHPLHCDLEKVMASLSKERQVPVSGRV   450
 451  RRQLAIERTRELQMKVEHWEDKDVGQNCNEFIREDSLSKLGSGKRIWSER   500
 501  KVFLFDGLMVLCKANTKKQTPSAGATAYDYRLKEKYFMRRVDINDRPDSD   550
 551  DLKNSFELAPRMQPPIVLTAKNAQHKHDWMADLLMVITKSMLDRHLDSIL   600
 601  QDIERKHPLRMPSPEIYKFAVPDSGDNIVLEERESAGVPMIKGATLCKLI   650
 651  ERLTYHIYADPTFVRTFLTTYRYFCSPQQLLQLLVERFNIPDPSLVYQDT   700
 701  GTAGAGGMGGVGGDKEHKNSHREDWKRYRKEYVQPVQFRVLNVLRHWVDH   750
 751  HFYDFEKDPMLLEKLLNFLEHVNGKSMRKWVDSVLKIVQRKNEQEKSNKK   800
 801  IVYAYGHDPPPIEHHLSVPNDEITLLTLHPLELARQLTLLEFEMYKNVKP   850
 851  SELVGSPWTKKDKEVKSPNLLKIMKHTTNVTRWIEKSITEAENYEERLAI   900
 901  MQRAIEVMMVMLELNNFNGILSIVAAMGTASVYRLRWTFQGLPERYRKFL   950
 951  EECRELSDDHLKKYQERLRSINPPCVPFFGRYLTNILHLEEGNPDLLANT  1000
1001  ELINFSKRRKVAEIIGEIQQYQNQPYCLNEESTIRQFFEQLDPFNGLSDK  1050
1051  QMSDYLYNESLRIEPRGCKTVPKFPRKWPHIPLKSPGIKPRRQNQTNSSS  1100
1101  KLSNSTSSVAAAAAASSTATSIATASAPSLHASSIMDAPTAAAANAGSGT  1150
1151  LAGEQSPQHNPHAFSVFAPVIIPERNTSSWSGTPQHTRTDQNNGEVSVPA  1200
1201  PHLPKKPGAHVWANNNSTLASASAMDVVFSPALPEHLPPQSLPDSNPFAS  1250
1251  DTEAPPSPLPKLVVSPRHETGNRSPFHGRMQNSPTHSTASTVTLTGMSTS  1300
1301  GGEEFCAGGFYFNSAHQGQPGAVPISPHVNVPMATNMEYRAVPPPLPPRR  1350
1351  KERTESCADMAQKRQAPDAPTLPPRDGELSPPPIPPRLNHSTGISYLRQS  1400
1401  HGKSKEFVGNSSLLLPNTSSIMIRRNSAIEKRAAATSQPNQAAAGPISTT  1450
1451  LVTVSQAVATDEPLPLPISPAASSSTTTSPLTPAMSPMSPNIPSHPVEST  1500
1501  SSSYAHQLRMRQQQQQQTHPAIYSQHHQHHATHLPHHPHQHHSNPTQSRS  1550
1551  SPKEFFPIATSLEGTPKLPPKPSLSANFYNNPDKGTMFLYPSTNEE      1596

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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