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

NucPred

Fetching P12465 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MVKKKKFKTKNIQNPPFSSQNSSHLFFSLKKKEEKESTPEVFVIDDHFNT    50
  51  FKTPKALKFRTPIFFNVSFDKNTLKTVIAWFLDQYGGKATVDLVETLKQV   100
 101  GFHQATRAGVSLGLEDLQIPPQKASFLSAASVSGVEAAQALETGNLTSVE   150
 151  KSQRLIDTWNKTSESLRQAAVHNFRATNPVNPVYMMAFSGARGNISQVRQ   200
 201  LVAMRGLMADPQGAILEFPIQSNFREGLTITEYLLSCYGARKGLVDTALR   250
 251  TASAGYLTRRLVDAVQHVVIYTKNCKTEKGITFKGLHIEQNLLGRVLLKD   300
 301  VILNTTTVIPKDTLVSSSLAKKLAAINQKIFVRSPLTCQTEKTVCQLCYG   350
 351  LDLAQGKLVCFGEAVGIIAAQSIGEPGTQLTMRTFHTGGVGVFSEQAMKS   400
 401  FPAPFDGKIEFQEALPGRFVRTPYGKIVYLLKHTGTNPKQVLLRVVSSSL   450
 451  TMRPLVYEILHQDVPAGSLLWVKQGEDVRTGQLLVQGSRLQKSKQKMPES   500
 501  THIVRTPFSGELFFEHMPIVSLEKIITRGPRTNPKEEFSPIKVFLKDLGR   550
 551  FWVFSSFIQKQTFSFLDQKKGKANSFFFKGDLVSAETPLSQYNLQIPVRG   600
 601  HLKKLGSSVVLAQTVFKFCFSKIYYFSKFYFLVENQNLIASTTTLNFTSL   650
 651  TWYPFFNQFETSGYYVDLSFSSDSEVLKTTELTKVKSETYDFTKNGGFFT   700
 701  SHQSFVGSTTRVFLLKTFEFFSAASKQTQKTALERLPFVDSMSFSLEKIQ   750
 751  LKKQNQKRKENPLFSLEVGKVKRNTQQRLPQFGFMVTCEENSLSRKGIFQ   800
 801  IKKAQEKNWSHKKTFQLSFLLNPKKRKKPLKKHFMCSSLFLEKAVKRAQT   850
 851  TFGIQTETKLIEKKCSWFSVSKNFTDFSSQLTGIVLEPGKHMESFSFQHS   900
 901  YVSVNLISRENVFLVKSKTKRSQFSYVLKDLLSSSRFCHKVFEKNFSEQK   950
 951  MESVEKISQIFSSQTESFFSRNNQLLSFFSQKKRIKNKLFFHSQLNFPSK  1000
1001  MPRRSDVLNSSKLLFFTREFLSDFSFYKRKELIQKRERKPHTLQNIKVKN  1050
1051  KKFLQVIQPCFQLKKKRCLSNLFFLQKLSYQIFPERKFFYETWLNQSSFD  1100
1101  FSLPSPFSTKQFKTTGFFSKNELQKASFDFQPSFLSQKISSSSQLTLRGS  1150
1151  WVSMTNSFKIHFEVKTPKFFGKIEEFQQKKFFDKKLKFGIQSPSKSLSKA  1200
1201  LSFGIPIPEFSLAVSRKIIFEKAHTYIFQSFQCRQVLPKVPITQVFLKSK  1250
1251  TVGEFQRIQLKNQKGSSSFLRAEDTVTFLLPSLVPKKQSFLKKEEKVLVS  1300
1301  CGQRIRWGQEIFPGFASSLSGRILDITATQITVRKALPFLGSRRGLVHVA  1350
1351  QNDLLQKNHILMTLRSKQLQTEDIVQGIPKIEQLFEARETKDGEIIRYNM  1400
1401  HFRLNSFFSLAKRVKPFLEAFDLSLLYIQRFLVKTLLEAYSNQGVNIAEK  1450
1451  HVEVVVRQMTARVRITFGKDTSLLPGEFIQLRLLEEINRSLVEAKKEPAL  1500
1501  YEPVILGLTKSVLQSESFLLAASFQQVSKVLVRSALATKTDFLRGLMKPL  1550
1551  YVASLSQREQEL                                        1562

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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