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

NucPred

Fetching P33527 from www.uniprot.org...

The NucPred score for your sequence is 0.19 (see score help below)

   1  MALRGFCSADGSDPLWDWNVTWNTSNPDFTKCFQNTVLVWVPCFYLWACF    50
  51  PFYFLYLSRHDRGYIQMTPLNKTKTALGFLLWIVCWADLFYSFWERSRGI   100
 101  FLAPVFLVSPTLLGITMLLATFLIQLERRKGVQSSGIMLTFWLVALVCAL   150
 151  AILRSKIMTALKEDAQVDLFRDITFYVYFSLLLIQLVLSCFSDRSPLFSE   200
 201  TIHDPNPCPESSASFLSRITFWWITGLIVRGYRQPLEGSDLWSLNKEDTS   250
 251  EQVVPVLVKNWKKECAKTRKQPVKVVYSSKDPAQPKESSKVDANEEVEAL   300
 301  IVKSPQKEWNPSLFKVLYKTFGPYFLMSFFFKAIHDLMMFSGPQILKLLI   350
 351  KFVNDTKAPDWQGYFYTVLLFVTACLQTLVLHQYFHICFVSGMRIKTAVI   400
 401  GAVYRKALVITNSARKSSTVGEIVNLMSVDAQRFMDLATYINMIWSAPLQ   450
 451  VILALYLLWLNLGPSVLAGVAVMVLMVPVNAVMAMKTKTYQVAHMKSKDN   500
 501  RIKLMNEILNGIKVLKLYAWELAFKDKVLAIRQEELKVLKKSAYLSAVGT   550
 551  FTWVCTPFLVALCTFAVYVTIDENNILDAQTAFVSLALFNILRFPLNILP   600
 601  MVISSIVQASVSLKRLRIFLSHEELEPDSIERRPVKDGGGTNSITVRNAT   650
 651  FTWARSDPPTLNGITFSIPEGALVAVVGQVGCGKSSLLSALLAEMDKVEG   700
 701  HVAIKGSVAYVPQQAWIQNDSLRENILFGCQLEEPYYRSVIQACALLPDL   750
 751  EILPSGDRTEIGEKGVNLSGGQKQRVSLARAVYSNADIYLFDDPLSAVDA   800
 801  HVGKHIFENVIGPKGMLKNKTRILVTHSMSYLPQVDVIIVMSGGKISEMG   850
 851  SYQELLARDGAFAEFLRTYASTEQEQDAEENGVTGVSGPGKEAKQMENGM   900
 901  LVTDSAGKQLQRQLSSSSSYSGDISRHHNSTAELQKAEAKKEETWKLMEA   950
 951  DKAQTGQVKLSVYWDYMKAIGLFISFLSIFLFMCNHVSALASNYWLSLWT  1000
1001  DDPIVNGTQEHTKVRLSVYGALGISQGIAVFGYSMAVSIGGILASRCLHV  1050
1051  DLLHSILRSPMSFFERTPSGNLVNRFSKELDTVDSMIPEVIKMFMGSLFN  1100
1101  VIGACIVILLATPIAAIIIPPLGLIYFFVQRFYVASSRQLKRLESVSRSP  1150
1151  VYSHFNETLLGVSVIRAFEEQERFIHQSDLKVDENQKAYYPSIVANRWLA  1200
1201  VRLECVGNCIVLFAALFAVISRHSLSAGLVGLSVSYSLQVTTYLNWLVRM  1250
1251  SSEMETNIVAVERLKEYSETEKEAPWQIQETAPPSSWPQVGRVEFRNYCL  1300
1301  RYREDLDFVLRHINVTINGGEKVGIVGRTGAGKSSLTLGLFRINESAEGE  1350
1351  IIIDGINIAKIGLHDLRFKITIIPQDPVLFSGSLRMNLDPFSQYSDEEVW  1400
1401  TSLELAHLKDFVSALPDKLDHECAEGGENLSVGQRQLVCLARALLRKTKI  1450
1451  LVLDEATAAVDLETDDLIQSTIRTQFEDCTVLTIAHRLNTIMDYTRVIVL  1500
1501  DKGEIQEYGAPSDLLQQRGLFYSMAKDAGLV                     1531

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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