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

NucPred

Fetching Q9W1M8 from www.uniprot.org...

The NucPred score for your sequence is 0.45 (see score help below)

   1  MNFSPLPNRVIDAPKHLKTRMIQVRSSYFGYSLVIRPTSIFVGAPRAQST    50
  51  LESQGSINETGAVYRCPLASGSCSHYVLNDKLNKQFQWLGGSMDGGTKDT   100
 101  DKLLVCAPRFFVPKNKNYGQMRGICYWVRDTVADTPPLSDVRTISLIPSQ   150
 151  AEEHFMLELGLSAHVTDDNSGFLIGAPGVRSWKGSVLVHRGEDLAAQGSY   200
 201  AVKMLDSWDWVKNHFTYVGYALSSGYFSSNNRTSLLYVTTAPSSVLNTGK   250
 251  AYIFDVVGEIVRKLHVFHGEQLGEYFGYSVVAEDLNGDGLTDVVVSAPLN   300
 301  ALGDSYDVGAIYVFINKGLFKFEKKIIRLPLSSGARFGSSLSKVGDINHD   350
 351  GYNDLAVGAPFAGNGAVFIFLGSEHGLRDEPSQRLDAPSREPGPYGAHMF   400
 401  GQGLSRGSDIDGNGFNDLAIGAPGAEAVYLYRAYPVVKIHATVRSESRAI   450
 451  RPEQETITVTACYRLETTSKARQMQQQELTFRMTIDELLQRVSFAPMRTN   500
 501  EVSFQAQAGLSGSCRNFSVGVHYTGGIFTPIDLELHYELAKKIPHSHEAF   550
 551  CESCAVVDPLEPKYATGTLSFMTGCAAHVCVSDLQLSSKDVNSSFIFGSL   600
 601  EVLSFSYEITNSGEPAYVAQFNVTSSARLPFAKVPGNCRVRHEVMLCDLN   650
 651  GGRALARGDSESLTIIFDVTQLSGQSLTIEAAVSSAGMDQNPKDNTMSTT   700
 701  ISLREYAEIDASGGPIDGHIALKEYPYSAEVNNSYEFKSHGPSIIDELTV   750
 751  YVDVPIAYTVTGSAGIKSIFNISSLQMQATHGSELVPIKLYDQTNTLAKE   800
 801  YPLEDSSRRANRKRRELQQDQYAIMPDVNISDILTKENLPANRTLVLDCL   850
 851  RGNWTICVRSQMRVQLKPEQPIDLRISFKVDLNDFVNTFDYLVIFTNVEM   900
 901  FKEGDSTSIALKRNLKPNVIFNYSETPLPIWYIILSLIAGHLLLGAMTYI   950
 951  LYKLRFFKRGKKEELKRLLEEHRSETKEPATDCEGNQEEINVEMHSDLEN  1000

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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