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

NucPred

Fetching P38198 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MSSFNNETNNNSNTNTHPDDSFPLYTVFKDESVPIEEKMALLTRFKGHVK    50
  51  KELVNESSIQAYFAALLFISGHYAYRSYPRLIFLSHSSLCYLIKRVAMQS   100
 101  PVQFNDTLVEQLLNHLIFELPNEKKFWLASIKAIEAIYLVNPSKIQAILA   150
 151  NFLRRPSENQNGDYLNRIKSTLLTIDELIQINEKNNSNHLQLLRFFMLSF   200
 201  TNLLNNNLNEHANDDNNNVIIELIFDIMYKYLKMDDENSQDLIDGFINDL   250
 251  EVEKFKQKFISLAKSQDQHGSQEDKSTLFDEEYEFQLLLAEAKLPQLSNN   300
 301  LSSKDPAMKKNYESLNQLQQDLENLLAPFQSVKETEQNWKLRQSNIIELD   350
 351  NIISGNIPKDNPEEFVTVIKEVQLIELISRATSSLRTTLSLTALLFLKRL   400
 401  IHILNDQLPLSILDQIFVIFKNLLSSTKKISSQTAFHCLITLIIDINHFH   450
 451  NKLFQLSFLLINEKTVTPRFCSAILLRSFLIKFNDSNLSLNNSNTTSPTS   500
 501  KLENNIIYIEEWLKKGISDSQTTVREAMRLTFWYFYKCYPTNAKRLLSSS   550
 551  FSPQLKKATELAIPAHLNINYQVSRVSSTASASSATSRLYSHSSNNSSRK   600
 601  TSLLEQKRNYPSYAQPTQSSSTSLLNAPAVTAGGSVIASKLSNKLKTNLR   650
 651  STSEYSSKENEKRARHHDSMNSVSNSNTKDNNNVTKRKVSAPPSSTAATK   700
 701  VSENYTNFDDFPSNQIDLTDELSNSYSNPLIKKYMDKNDVSMSSSPISLK   750
 751  GSNKLGEYETLYKKFNDASFPAQIKDALQYLQKELLLTSQQSSSAPKFEF   800
 801  PMIMKKLRQIMIKSPNDFKPFLSIEKFTNGVPLNYLIELYSINSFDYAEI   850
 851  LKNRMNPEKPYELTNLIITIADLFNFLNANNCPNDFKLYYMKYKTTFFNY   900
 901  NFKLLLEIFRNLNIKHDNTLRSGTNDLMPKISMILFQIYGKEFDYTCYFN   950
 951  LIFEIYKFDNNRFNKLLADFDIVSTKMKICHELEKKDANFKVEDIISRES  1000
1001  SVSFTPIDNKKSEGDEESDDAVDENDVKKCMEMTMINPFKNLETDKTLEL  1050
1051  KNNVGKRTSSTDSVVIHDDNDKDKKLSEMTKIVSVYQLDQPNPAKEEDDI  1100
1101  DMENSQKSDLNLSEIFQNSGENTERKLKDDNEPTVKFSTDPPKIINEPEK  1150
1151  LIGNGNENEKPDLETMSPIKINGDENMGQKQRITVKRERDVALTEQDINS  1200
1201  KKMKLVNNKKSEKMHLLIMDNFPRDSLTVYEISHLLMVDSNGNTLMDFDV  1250
1251  YFNHMSKAINRIKSGSFTMKHINYLIEPLITCFQNQKMTDWLTNENGFDE  1300
1301  LLDVAIMLLKSTDDTPSIPSKISSKSIILVHCLLVWKKFLNTLSENADDD  1350
1351  GVSVRMCFEEVWEQILLMLNKFSDYGNEIYKLAQEFRDSLMLSHFFKKHS  1400
1401  ATRILSMLVTEIQPDTAGVKETFLIETLWKMLQSPTICQQFKKSNISEII  1450
1451  QTMSYFIMGTDNTSWNFTSAVVLARCLRVLQTTPDYTEQETERLFDCLPK  1500
1501  NVFKMIMFIASNE                                       1513

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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