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

NucPred

Fetching O42690 from www.uniprot.org...

The NucPred score for your sequence is 0.56 (see score help below)

   1  MAKTSQAEGQPYKGYYNNKSQGQPYHGYYSGFNKSASAQIHHLARSLTQG    50
  51  VQSHYDDTYTTATMHPNGINPISDKTDPTLDPESPSFSSKRWVQNMWKLY   100
 101  QSDSEYYKPGKLGVAYKNLRVYGDAIESDYQTTVSNGVLKYARNIFNKFR   150
 151  KDNDDYSFDILKPMEGLIKPGEVTVVLGRPGAGCSTFLKTIACRTEGFHV   200
 201  ADGSVISYDGITQDEIRNHLRGEVVYCAETETHFPNLTVGETLEFAALMK   250
 251  TPQNRPMGVSREEYAKHVVDVVMATYGLSHTKNTKVGNDFIRGISGGERK   300
 301  RLSIAEVTLVQASIQCWDNSTRGLDAATALEFISSLKTSASILNDTPLIA   350
 351  IYQCSQNAYDLFDKVIVMYEGYQIFFGSSQRAAAYFKKMGFVCQDRQTTP   400
 401  DFLTSITSPAERIIKPGYERLVPRTPKEFYRYWRRSPERQALLEEIDEYL   450
 451  DNCENYDQKQKIFEANNAKKAKHTYNKSSYTVSLPMQVRYIMKRYWDRMR   500
 501  GDIIVPLSTVAGNIAMALILSSVFYNLQPNSSSFYYRTSVMYYALLFNAY   550
 551  SSVLEIYNMYEGRAIVQKHREYALYPPMADAIGSIISDFPLKVVCSVLFN   600
 601  LILYFMVNFKREPGAFFFYLLISFCSTLFMSHLFRTIGAFTNSLAEAMTP   650
 651  SSLLLFALSTFSGFAIPVTYMLGWCKWIRWVNPLAYAYEALISNEFHGRV   700
 701  FDCSNIVPSGFGYPKTGNSVVCASIGALPGEFKVDGDLYLKLAFDYSYSN   750
 751  VWRNFGVLMAFIIFLFGTTIFFVQTNKSSISKGETLVFRRKNIRKMRKME   800
 801  EDEEAYMDGMAPLDFSGSTEISDYSYDYMDRKLLDTSNIFHWRNLTYTVK   850
 851  IKSEERVILNNIDGWVKPGEVTALMGASGAGKTTLLNALSERLTTGVITS   900
 901  GTRMVNGGELDSSFQRSIGYVQQQDLHLETSTVREALKFSARLRQPNSVS   950
 951  IAEKDSYVEKIIDLLEMRTYVDAIVGVPGEGLNVEQRKRLTIAVELVARP  1000
1001  KLLVFLDEPTSGLDSQTAWSICKLIRKLANHGQAILCTIHQPSAILLEEF  1050
1051  DRLLLLQKGETVYFGEFGANCHTLIEYFERNGASKCPQHANPAEWMLGVI  1100
1101  GAAPGTQANQDYFETWRNSPEYRAVQNELHRLEEMPGLASGEKEPDTNQA  1150
1151  YAASFWKQYIFVVHRLFQQYWRTPSYIYSKFAMAVLCSLFNGFTYYKSQN  1200
1201  SMQGLKNQMLSIFSMFVVLTTLAQQYVPLFVTQRDLYEARERPSKTFSWL  1250
1251  AFIAAQITAEIPYQVLAATISFFSWYYPVGLYRNAVYSGAVTHRGVLMWL  1300
1301  IMTLMFIYSSTLAQFCISWNQLADYAANWISLLLTISMIFCGVIATKDSM  1350
1351  PKFWVFLYRCTPLTYLTSAMMSIGLGDSFVKCAPTEILTFPPQTPGVQKC  1400
1401  QDYMGAYISIAGGYLLNPEATDNCKFCIMDKTNQFLDFMNISIHNFGRDT  1450
1451  GIFIVFIVFNMAATVFSYWLFRVPKGNREKGSFFDKLPFLNGGGDTNHEN  1500
1501  V                                                   1501

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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