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

NucPred

Fetching P41230 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MELGSDDFLPPPECPVFEPSWAEFRDPLGYIAKIRPIAEKSGICKIRPPA    50
  51  DWQPPFAVEVDNFRFTPRIQRLNELEAQTRVKLNYLDQIAKFWEIQGSSL   100
 101  KIPNVERRILDLYSLSKIVVEEGGYETICKDRRWARVAQRLNYPPGKNIG   150
 151  SLLRSHYERIVYPYEMYQSGANLVQCNTRPFDNEEKDKEYKPHSIPLRQS   200
 201  VQPSKFNSYGRRAKRLQPDPEPTEEDIEKNPELKKLQIYGAGPKMMGLGL   250
 251  MAKDKTLRKKDKEGPECPPTVVVKEELGGDVKMESTSPKTFLEGKEELSH   300
 301  SPEPCTKMTMRLRRNHSNAQFIESYVCRMCSRGDEDDKLLLCDGCDDNYH   350
 351  IFCLLPPLPEIPKGVWRCPKCVMAECKRPPEAFGFEQATREYTLQSFGEM   400
 401  ADSFKADYFNMPVHMVPTELVEKEFWRLVNSIEEDVTVEYGADIHSKEFG   450
 451  SGFPVSDSKRHLTPEEEEYATSGWNLNVMPVLEQSVLCHINADISGMKVP   500
 501  WLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEEVMK   550
 551  KLTPELFDSQPDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRA   600
 601  YHSGFNQGYNFAEAVNFCTADWLPAGRQCIEHYRRLRRYCVFSHEELICK   650
 651  MAACPEKLDLNLAAAVHKEMFIMVQEERRLRKALLEKGITEAEREAFELL   700
 701  PDDERQCIKCKTTCFLSALACYDCPDGLVCLSHINDLCKCSSSRQYLRYR   750
 751  YTLDELPAMLHKLKVRAESFDTWANKVRVALEVEDGRKRSLEELRALESE   800
 801  ARERRFPNSELLQRLKNCLSEAEACVSRALGLVSGQEAGPDRVAGLQMTL   850
 851  AELRDFLGQMNNLPCAMHQIGDVKGILEQVEAYQTEAREALVSQPSSPGL   900
 901  LQSLLERGQQLGVEVPEAQQLQRQVEQARWLDEVKRTLAPSARRGTLAIM   950
 951  RGLLVAGASVAPSPAVDKAQAELQELLTIAERWEEKAHLCLEARQKHPPA  1000
1001  TLEAIIHEAENIPVHLPNIQSLKEALAKARAWIADVDEIQNGDHYPCLDD  1050
1051  LEGLVAVGRDLPVGLEELRQLELQVLTAHSWREKASKTFLKKNSCYTLLE  1100
1101  VLCPCADAGSDSTKRSRWMEKELGLYKSDTELLGLSAQDLRDPGSVIVAF  1150
1151  KEGEQKEKEGILQLRRTNSAKPSPLALLTTASSTASICVCGQVPAGVGAL  1200
1201  QCDLCQDWFHGRCVTVPRLLSSQRSSLPSSPLLAWWEWDTKFLCPLCMRS  1250
1251  RRPRLETILALLVALQRLPVRLPEGEALQCLTERAISWQGRARQVLASEE  1300
1301  VTALLGRLAELRQRLQAESKPEESLAYPSDGGEGTGNMPKVQGLLENGDS  1350
1351  VTSPEKVATEEGSGKRDLELLSSILPQLSGPVLELPEATRAPLEELMMEG  1400
1401  DLLEVTLDENHSIWQLLQAGQPPDLKRVQTLLELEKAERHGSRTRGRALE  1450
1451  RRRRRKVDRGGEPDDPAREELEPKRVRSSGPEAEEVQEEEELEEETGGEV  1500
1501  PPVPFPNSGSPSIQEDQDGLEPVLEAGSDTSAPFSTLTSRLLMSCPQQPS  1550
1551  LQQL                                                1554

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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