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

NucPred

Fetching P53114 from www.uniprot.org...

The NucPred score for your sequence is 0.59 (see score help below)

   1  MEKESVYNLALKCAERQLTSMEFSNLYKEFFNEKFPSLIQEEEEDTTTTA    50
  51  NINEVKKASDLVDTPSNNTAATADTTHLHEALDIVCSDFVKILNLEKPLI   100
 101  LADYIVEVLLVNYNSDMIKCFLPKLNSVRNSLLLAHFFSKSCSFFAKLSD   150
 151  TLIIDQVRKDLGNVIVPNILSLDMNSMNKELIAIVSKLLQTTLKLSPSPI   200
 201  LLTSAGCKNGSFTLLNQLSQTNKLLFKRVSQTFEAKLHFKDTKPFLNKDS   250
 251  TNEFVGSPSLTSPQYIPSPLSSTKPPGSVNSAAKYKDMKLLRYYKNIWLN   300
 301  NKIINWEISNPDFLSKYSAITSSIFQESFNSVQNLDQLLTDLIETSFTCF   350
 351  AQFVSNKQYHQANSNLTLLERKWVIFITKHLPLLILENSSRSPRVVTNAL   400
 401  DNIDEKVVKAIRIYFTEKDDNKTNNEDLFDDYPSTSLDIRHDFIKGLIML   450
 451  NLQPASVINNYLREDQMIDTSILPTRDDLFVRNLQGIQEVVHNTNSFIIS   500
 501  SLDTLELESITESITHDSSNGLFQVLHNFESVAPTKQREIVKAFLSIFED   550
 551  AIKELNYNRIAKICALLFFNFSHSLTTILSFSSPAALMKTLIKFVDLSRN   600
 601  GRNGSNGNDESSEYETINISLSFSWAILLIINLTQTYGISVVDVALKYPE   650
 651  LSIKNSFIINFISNLPNVSDKYYLEESNVNDSDMLTKSHNTVQSWLCDLF   700
 701  VNGSITDQLIQNIETRQLANLIPFIVKQVLLSVEIGVLTDISSLIGGFEY   750
 751  FLQPLLLVGLIKTFYWLEQFLSCVKNDTISEDILQGIFNLLNTLFNPVTL   800
 801  NEDSKAFHTAVLRLNAIPLLKVLRKFRVQSQSNYGIYSSDAQGDPNLEPL   850
 851  IAKLVAVLNVSPVYDVDPRIINSENDYSRKQLGYGKFLILNENPINKIMT   900
 901  NQINSFWSLHSSTYYNLDYLFELIELVTPKSFLFDVLKTLEYKLATYGVP   950
 951  GSENKRGSLDSEHVFDYFFYFLVLYDVKTAEEASQLIEYMENDAKKSKGD  1000
1001  VDIKGEDLHEKNDSAEVRQETQPKAEATQDDDFDMLFGENDTSTQAYEEE  1050
1051  EENEDNDGNNRTNNVPMIKAEETPSKTNKISILKRHSFAVLLHERKLLND  1100
1101  LALENGEITKTENEKFISYHDKYLCMLKTCVF                    1132

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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