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

NucPred

Fetching P21359 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MAAHRPVEWVQAVVSRFDEQLPIKTGQQNTHTKVSTEHNKECLINISKYK    50
  51  FSLVISGLTTILKNVNNMRIFGEAAEKNLYLSQLIILDTLEKCLAGQPKD   100
 101  TMRLDETMLVKQLLPEICHFLHTCREGNQHAAELRNSASGVLFSLSCNNF   150
 151  NAVFSRISTRLQELTVCSEDNVDVHDIELLQYINVDCAKLKRLLKETAFK   200
 201  FKALKKVAQLAVINSLEKAFWNWVENYPDEFTKLYQIPQTDMAECAEKLF   250
 251  DLVDGFAESTKRKAAVWPLQIILLILCPEIIQDISKDVVDENNMNKKLFL   300
 301  DSLRKALAGHGGSRQLTESAAIACVKLCKASTYINWEDNSVIFLLVQSMV   350
 351  VDLKNLLFNPSKPFSRGSQPADVDLMIDCLVSCFRISPHNNQHFKICLAQ   400
 401  NSPSTFHYVLVNSLHRIITNSALDWWPKIDAVYCHSVELRNMFGETLHKA   450
 451  VQGCGAHPAIRMAPSLTFKEKVTSLKFKEKPTDLETRSYKYLLLSMVKLI   500
 501  HADPKLLLCNPRKQGPETQGSTAELITGLVQLVPQSHMPEIAQEAMEALL   550
 551  VLHQLDSIDLWNPDAPVETFWEISSQMLFYICKKLTSHQMLSSTEILKWL   600
 601  REILICRNKFLLKNKQADRSSCHFLLFYGVGCDIPSSGNTSQMSMDHEEL   650
 651  LRTPGASLRKGKGNSSMDSAAGCSGTPPICRQAQTKLEVALYMFLWNPDT   700
 701  EAVLVAMSCFRHLCEEADIRCGVDEVSVHNLLPNYNTFMEFASVSNMMST   750
 751  GRAALQKRVMALLRRIEHPTAGNTEAWEDTHAKWEQATKLILNYPKAKME   800
 801  DGQAAESLHKTIVKRRMSHVSGGGSIDLSDTDSLQEWINMTGFLCALGGV   850
 851  CLQQRSNSGLATYSPPMGPVSERKGSMISVMSSEGNADTPVSKFMDRLLS   900
 901  LMVCNHEKVGLQIRTNVKDLVGLELSPALYPMLFNKLKNTISKFFDSQGQ   950
 951  VLLTDTNTQFVEQTIAIMKNLLDNHTEGSSEHLGQASIETMMLNLVRYVR  1000
1001  VLGNMVHAIQIKTKLCQLVEVMMARRDDLSFCQEMKFRNKMVEYLTDWVM  1050
1051  GTSNQAADDDVKCLTRDLDQASMEAVVSLLAGLPLQPEEGDGVELMEAKS  1100
1101  QLFLKYFTLFMNLLNDCSEVEDESAQTGGRKRGMSRRLASLRHCTVLAMS  1150
1151  NLLNANVDSGLMHSIGLGYHKDLQTRATFMEVLTKILQQGTEFDTLAETV  1200
1201  LADRFERLVELVTMMGDQGELPIAMALANVVPCSQWDELARVLVTLFDSR  1250
1251  HLLYQLLWNMFSKEVELADSMQTLFRGNSLASKIMTFCFKVYGATYLQKL  1300
1301  LDPLLRIVITSSDWQHVSFEVDPTRLEPSESLEENQRNLLQMTEKFFHAI  1350
1351  ISSSSEFPPQLRSVCHCLYQATCHSLLNKATVKEKKENKKSVVSQRFPQN  1400
1401  SIGAVGSAMFLRFINPAIVSPYEAGILDKKPPPRIERGLKLMSKILQSIA  1450
1451  NHVLFTKEEHMRPFNDFVKSNFDAARRFFLDIASDCPTSDAVNHSLSFIS  1500
1501  DGNVLALHRLLWNNQEKIGQYLSSNRDHKAVGRRPFDKMATLLAYLGPPE  1550
1551  HKPVADTHWSSLNLTSSKFEEFMTRHQVHEKEEFKALKTLSIFYQAGTSK  1600
1601  AGNPIFYYVARRFKTGQINGDLLIYHVLLTLKPYYAKPYEIVVDLTHTGP  1650
1651  SNRFKTDFLSKWFVVFPGFAYDNVSAVYIYNCNSWVREYTKYHERLLTGL  1700
1701  KGSKRLVFIDCPGKLAEHIEHEQQKLPAATLALEEDLKVFHNALKLAHKD  1750
1751  TKVSIKVGSTAVQVTSAERTKVLGQSVFLNDIYYASEIEEICLVDENQFT  1800
1801  LTIANQGTPLTFMHQECEAIVQSIIHIRTRWELSQPDSIPQHTKIRPKDV  1850
1851  PGTLLNIALLNLGSSDPSLRSAAYNLLCALTCTFNLKIEGQLLETSGLCI  1900
1901  PANNTLFIVSISKTLAANEPHLTLEFLEECISGFSKSSIELKHLCLEYMT  1950
1951  PWLSNLVRFCKHNDDAKRQRVTAILDKLITMTINEKQMYPSIQAKIWGSL  2000
2001  GQITDLLDVVLDSFIKTSATGGLGSIKAEVMADTAVALASGNVKLVSSKV  2050
2051  IGRMCKIIDKTCLSPTPTLEQHLMWDDIAILARYMLMLSFNNSLDVAAHL  2100
2101  PYLFHVVTFLVATGPLSLRASTHGLVINIIHSLCTCSQLHFSEETKQVLR  2150
2151  LSLTEFSLPKFYLLFGISKVKSAAVIAFRSSYRDRSFSPGSYERETFALT  2200
2201  SLETVTEALLEIMEACMRDIPTCKWLDQWTELAQRFAFQYNPSLQPRALV  2250
2251  VFGCISKRVSHGQIKQIIRILSKALESCLKGPDTYNSQVLIEATVIALTK  2300
2301  LQPLLNKDSPLHKALFWVAVAVLQLDEVNLYSAGTALLEQNLHTLDSLRI  2350
2351  FNDKSPEEVFMAIRNPLEWHCKQMDHFVGLNFNSNFNFALVGHLLKGYRH  2400
2401  PSPAIVARTVRILHTLLTLVNKHRNCDKFEVNTQSVAYLAALLTVSEEVR  2450
2451  SRCSLKHRKSLLLTDISMENVPMDTYPIHHGDPSYRTLKETQPWSSPKGS  2500
2501  EGYLAATYPTVGQTSPRARKSMSLDMGQPSQANTKKLLGTRKSFDHLISD  2550
2551  TKAPKRQEMESGITTPPKMRRVAETDYEMETQRISSSQQHPHLRKVSVSE  2600
2601  SNVLLDEEVLTDPKIQALLLTVLATLVKYTTDEFDQRILYEYLAEASVVF  2650
2651  PKVFPVVHNLLDSKINTLLSLCQDPNLLNPIHGIVQSVVYHEESPPQYQT  2700
2701  SYLQSFGFNGLWRFAGPFSKQTQIPDYAELIVKFLDALIDTYLPGIDEET  2750
2751  SEESLLTPTSPYPPALQSQLSITANLNLSNSMTSLATSQHSPGIDKENVE  2800
2801  LSPTTGHCNSGRTRHGSASQVQKQRSAGSFKRNSIKKIV             2839

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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