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

NucPred

Fetching Q29450 from www.uniprot.org...

The NucPred score for your sequence is 0.20 (see score help below)

   1  MPAKGRYFLNEGEEGPDQDALYEKYRLTSQHGPLLLMLLLVAIAACTTLI    50
  51  VITFSYGDPSRHRAVLGTAFFTLAMFVLLYALVYVECLDRRGLRISALLI   100
 101  WGCLVTLGYVLVFDFDSPRKDTLCLWGRCPSSSFVVFVVYTLLPFSMWGA   150
 151  VTAGLVSSISHLLVLAMHQEDFTSPVGLKLLATAVVFVCGNLTGAFHKHH   200
 201  MQDASHDLFTYTVKCIQIRRKLRIEKRQQENLLLSVLPAHISMGMKLAII   250
 251  ERLKERGDRRYLPDNNFHNLYVKRHQNVSILYADIVGFTRLASDCSPKEL   300
 301  VVVLNELFGKFDQIAKANECMRIKILGDCYYCVSGLPVSLPNHARNCVKM   350
 351  GLDMCEAIKQVREATGVDISMRVGIHSGNVLCGVIGLRKWQYDVWSHDVS   400
 401  LANRMEAAGVPGRVHITEATLKHLDKAYEVEDGHGQQRDPYLKEMNIRTY   450
 451  LVIDPRSQQPPQPSQHNSKNKGNATLKMRASVRMTRYLESWGAARPFAHL   500
 501  NQRESVSSSETLVSHGRRPKAVPLRRHRTPDRSASPKGRSEDDSYDDEML   550
 551  SAIEGLSSTRPCCSKSDDFSTFGSIFLEKGFEREYRLAPIPRVRYYFACA   600
 601  SLVFVCILLIHVLLLYSMKTLGVSFGLVACVLGLVLGLCFADVFLRCCPA   650
 651  LGKLRAIAESVETQPLLRVSLAILTIGSLLVIAVVNLPLMPFRDRGLTAG   700
 701  NETGLRAVSGWEMSPCYLLPYYTCSCILAFIACSVFLRMSLELKVVLLTV   750
 751  ALVAYLVLFNVYPSWQWDCCGHSLGNLTGTNGTLSSSSCSWHLKTMTNFY   800
 801  LVLFYTTLIMLSRQIDYYCRLDCLWKKKFKKEHEEFETMENVNRLLLENV   850
 851  LPAHVAAHFIGDKLNEDWYHQSYDCVCVMFASVPDFKVFYTECDVNKEGL   900
 901  ECLRLLNEIIADFDELLLKPKFSGVEKIKTIGSTYMAAAGLSVPSGPENQ   950
 951  DLERQHAHIGIMVEFSTALMSKLDGINRHSFNSFRLRVGINHGPVIAGVI  1000
1001  GARKPQYDIWGNTVNVASRMESTGELGKIQVTEETCTILQGLGYSCECRG  1050
1051  LIDVKGKGELRTYFVCTDTAKFQGLGLN                        1078

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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