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

NucPred

Fetching Q61194 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MAQISNNSEFKQCSSSHPEPIRTKDVNKAEALQMEAEALAKLQKDRQMTD    50
  51  SPRGFELSSSTRQRTQGFNKQDYDLMVFPELDSQKRAVDIDVEKLTQAEL   100
 101  EKILLDDNFETRKPPALPVTPVLSPSFSTQLYLRPSGQRGQWPPGLCGPS   150
 151  TYTLPSTYPSAYSKQATFQNGFSPRMPTFPSTESVYLRLPGQSPYFSYPL   200
 201  TPATPFHPQGSLPVYRPLVSPDMAKLFEKIASTSEFLKNGKARTDLEIAN   250
 251  SKASVCNLQISPKSEDINKFDWLDLDPLSKPKVDYVEVLEHEEEKKDPVL   300
 301  LAEDPWDAVLLEERSPSCHLERKVNGKSLSGATVTRSQSLIIRTAQFTKA   350
 351  QGQVSQKDPNGTSSLPTGSSLLQEFEVQNDEVAAFCQSIMKLKTKFPYTD   400
 401  HCTNPGYLLSPVTVQRNMCGENASVKVSIEIEGLQLPVTFTCDVSSTVEI   450
 451  IIMQALCWVHDDLNQVDVGSYILKVCGQEEVLQNNHCLGSHEHIQNCRKW   500
 501  DTEIKLQLLTLSAMCQNLARTAEDDEAPVDLNKYLYQIEKPYKEVMTRHP   550
 551  VEELLDSYHYQVELALQTENQHRAVDQVIKAVRKICSALDGVETPSVTEA   600
 601  VKKLKRAVNLPRNKSADVTSLSGSDTRKNSTKGSLNPENPVQVSMDHLTT   650
 651  AIYDLLRLHANSSRCSTACPRGSRNIKEAWTATEQLQFTVYAAHGISSNW   700
 701  VSNYEKYYLICSLSHNGKDLFKPIQSKKVGTYKNFFYLIKWDELIIFPIQ   750
 751  ISQLPLESVLHLTLFGVLNQSSGSSPDSNKQRKGPEALGKVSLTLFDFKR   800
 801  FLTCGTKLLYLWTSSHTNSIPGAIPKKSYVMERIVLQVDFPSPAFDIIYT   850
 851  SPQIDRNIIQQDKLETLESDIKGKLLDIIHRDSSFGLSKEDKVFLWENRY   900
 901  YCLKHPNCLPKILASAPNWKWANLAKTYSLLHQWPPLCPLAALELLDAKF   950
 951  ADQEVRSLAVSWMEAISDDELADLLPQFVQALKYEIYLNSSLVRFLLSRA  1000
1001  LGNIQIAHSLYWLLKDALHDTHFGSRYEHVLGALLSVGGKGLREELSKQM  1050
1051  KLVQLLGGVAEKVRQASGSTRQVVLQKSMERVQSFFLRNKCRLPLKPSLV  1100
1101  AKELNIKSCSFFSSNAMPLKVTMVNADPLGEEINVMFKVGEDLRQDMLAL  1150
1151  QMIKIMDKIWLKEGLDLRMVIFRCLSTGRDRGMVELVPASDTLRKIQVEY  1200
1201  GVTGSFKDKPLAEWLRKYNPSEEEYEKASENFIYSCAGCCVATYVLGICD  1250
1251  RHNDNIMLRSTGHMFHIDFGKFLGHAQMFGSFKRDRAPFVLTSDMAYVIN  1300
1301  GGEKPTIRFQLFVDLCCQAYNLIRKQTNLFLNLLSLMIPSGLPELTSIQD  1350
1351  LKYVRDALQPQTTDAEATIFFTRLIESSLGSIATKFNFFIHNLAQLRFSG  1400
1401  LPSNDEPILSFSPKTYSFRQDGRIKEVSVFTYHKKYNPDKHYIYVVRILR  1450
1451  EGHLEPSFVFRTFDEFQELHNKLSIIFPLWKLPGFPNRMVLGRTHIKDVA  1500
1501  AKRKIELNSYLQSLMNASTDVAECDLVCTFFHPLLRDEKAEGIARSAGAV  1550
1551  PFSPTLGQIGGAVKLSVSYRNGTLFIMVMHIKDLVTEDGADPNPYVKTYL  1600
1601  LPDTHKTSKRKTKISRKTRNPTFNEMLVYSGYSKETLRQRELQLSVLSAE  1650
1651  SLRENFFLGGITLPLKDFNLSKETVKWYQLTAATYL                1686

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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