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

NucPred

Fetching Q17388 from www.uniprot.org...

The NucPred score for your sequence is 0.72 (see score help below)

   1  MTVKEKLLKVKQKFKRGDSSSDVDSGPERDRDEDDSDNESRNTSKTSKSS    50
  51  KKSKSGKSTGTSEMTELSDDGGSDIELLPDDGKSFGKRKLQDTDKPCTWN   100
 101  VLVRIIEAKDVSTGSARVRTIFDGNSKMTRTVTHAIPKWRQNILYTIKNQ   150
 151  PLEKLAAKVLTLRLVRPTALGESSVGEFSCYLSEVIHSPDRSVIAKWVAL   200
 201  GFPGMDDEEPDDIAYENCGFLKVTLSVYRIDESPPTLIDDDGKEQIWSGA   250
 251  HLIDYTLKIRVFSVEQLIRQMINERKIKKKQRFYVMVQCGAHKTETTMES   300
 301  AFLDEDANIASVKFEQEIYLPIQWPTVISEIIFSLFDKKGRGKTCIGKAT   350
 351  LPMKMIYEPGETGYLPTFGPAFLNVFDCERVTRFSIFSRKMRGSQQDGSR   400
 401  FVGRLFIAIDCVEYMEKANAQIMHLDHSPIMEAESICKNLEWYNCFCSMS   450
 451  GLNMINPQFASDPVCIMMSIGSFGSTSNEFRSCNSSTLPAEPNWDGCKYF   500
 501  TMPWGNLRPVAEVNAPWEVIEHRIEMSNVLMKMTNMLDTMIWEVRRIGNK   550
 551  AIDHVSSVGMEALECLEQQIDSASKYLGRINPVSSNALDRHILDYRKEKI   600
 601  LKLREHFEKEAFSIDYSDGEVDAKLLRMLLKIRSMTLELAEDVQMTIPPV   650
 651  LIKMMSHGKLIGFAKIPISEIFQSDDEAQSGEWCGRTRAINIQWPTLVDQ   700
 701  RNRKREHVAVLHAKMWFGRTDQLTKWKEHVQPADIRRFMEMYEVQTKGLA   750
 751  LKWKDEADIYDGKWEKTNEVPLENGWNAVGHWIVMNTRHMFVPKLGQHTV   800
 801  HDKAFEIQKRTEDGTWKHFKYTDCYADELKPKDLDKHAKGWEVGSWAQDK   850
 851  FRNNGDEKGWVYSTNGVFFGSGVLTDREEKVHHNFRKRCIKRPRKHEGYN   900
 901  KELEDFEHFRTTMGNENWEYSPSKKEGPYHDLEDRTDRIRRRRYVREVEN   950
 951  KDPDSEDPRFRVYEYQMQTGKWQLRCYIMWGNDLLPVVKNSSRAFVRISF  1000
1001  AQYSKQTLLVDNSQNPIWNETVMFKSVLIAGGTRDIMKYPPVVSVEVVGE  1050
1051  CSNNEEANLGHFETKPNVICGNTDVRGTPQWFPLKFSNGRTRGAVLACFE  1100
1101  LYSEEDKDLIPLEPKCKHNYKERSEIPTEFRPQFDKFHVQFLCWGVRNLK  1150
1151  KHKLLAVRRPFVGLTIGDQEFTLQPLKDVRRDPNFPEPMIVFGEVILPSA  1200
1201  LELSPPLIINLFDARAFNRQPLVGSCLVSDLHKYVSHIVPKVKSDHAERW  1250
1251  EQLDLVITEEFDQIIRMVRVPTLTTDPMVPLDWWSRYYASMSQFHRSPGY  1300
1301  PESGMEYVRIFRRPLEQMNGYNNFSDFLDTFPFVKSMKGDFDDPEEKEKA  1350
1351  GELKCRLLISKLKKGKPPAAINTVVDFVGPTRCLVRVYIIEANGLISNAR  1400
1401  KGRVDSYVKLHCGKQNVNLKKNYRSECCDPIFGERVDMTVTIPLEKDLKI  1450
1451  TVMGKRRILSDQEIGSTTIDLENRLLTKWRATGGLSGQFTVQGELQWRDQ  1500
1501  MTPMEILKSYCYKMMLSVPKIESRQTERGEEKGITIEKITFWFSEVLHVF  1550
1551  ENEEIAMLNSQRQKAGKENFSDGSDQQNEDVSDGSWDEEDLEREKEKLKW  1600
1601  EKHRSKGKPLKKVTTEKAETADGELRKKAKMRIMGSQLQTIALFILRQMN  1650
1651  LVPEHVESRPLFSDKGGRTQKGELRMFVDIFPMEYGAIPAPFNIAPRKPI  1700
1701  NYQLRIAVMDVRGAIPVKRSFAEPVSDLYVKAFINGMTKGHKTDTHFRVL  1750
1751  DGTGEFNWRFLLNFDYNPWEKKVVAYTKNRFFCKPVEELVDPILVIELWD  1800
1801  KNKFRKDRLLGDIELDLLDFIEGIGSPSDVGVYSTKKRQRGVKCPKCCTR  1850
1851  RGCLCKCCIFCFETKCLCGKRKVKKKPFPKPVLFVEPEGYDDTVNIFESR  1900
1901  NLYGWWPMLTEEYPHEEPQNAKKKNDDVGKDPKWIMGLVEMDMLLLTKQE  1950
1951  ADQEPAGKKRSEPNHSPFLEKPDRKSWANSWLVSRIKPCIKYFWHYYGLQ  2000
2001  ILLWLIIIVILILTIFVLLHTWPTILAEIIKAIF                  2034

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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