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

NucPred

Fetching P08973 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MKGHQFKSWIFELREILREIKNSHYFLDSWTQFNSVGSFIHIFFYQERFL    50
  51  KLFDPRIWSILLSPNSQGSTSNRYFTIKGVVLFVVVVLIYRITNRNMVER   100
 101  KNLYLIGLFPIPMNSIGPRNDTLEKSFGSSNINRLIVSLLYLPKGKKISE   150
 151  SYFLDPKESTWFLPITKKCIMPESNRGSRWWRNWIGKRRDSSCKISNETV   200
 201  AGIEISFKEKDIQYLEFPFVYYMDDPIRKDHDWELFDCLSLFLRNVSREN   250
 251  WIWLDNVRLVNKDRFFSKVRNVSSNIQYDFTRSSFVQVTDSSQLKESSDQ   300
 301  SRDRSNSISNADSEYHTLINKREIQQLKERSILRDPSFLQTEGTEIESDR   350
 351  FPKCLSGYSSMPRLFTAREKQMIIHLLPEEIEQLLENPTRSIRSFFSGRW   400
 401  SELHLGSNPTERSTRDPQLLKKQQDVSFAPSRQSENKEMVNIFKIIKYLQ   450
 451  NTVSIHPISSDPGCDMVPKDELDMDSSDKISFLNKNSFFDLFHLFHDRNR   500
 501  GGYALHHDFESEEKFQEMADLFTLSITDPDLVYHRGFSFSIDSCGLDQKQ   550
 551  FLNEVFNSRDESKKKSLLVLSPIFYEENESFYRRIRKKGVRISRNVLNRF   600
 601  FLINRSDRSFEYGIQRDQIGNDTLNHRTIRKYMINQDFSNLKKSQKKWFD   650
 651  PLIFLSRTERFMNRDPDAYRYKWFNGSKNFQEHLEHFVSEQKSRFQVVFD   700
 701  QLRINQYSIDWSEVIDKKDLSKSLRFFLSKSLRFFLSKLLLFLSNSLPFF   750
 751  FVSFGNIPINRSEIRIYELKGPNDQLYNPLVESIGLQIVHLKKWKAFLLD   800
 801  DHDTFQKSKFLINGGTISPFLFNKIPKWMIDSFHTRNNSGKSFDNTDSYF   850
 851  SMISHDQNNWLNPVKPFHRSSLISSFYKANQLRFLNNPHHFCFYCNKRFP   900
 901  FYMEKARINNSDFTYRQFLNILFIHNKLFSLCVGKKKHAFLERDTISPIE   950
 951  SQVSNIFLPNDFPIRSDLLVRRTIYSIADISGTPLTEGQLVHFERTYCQP  1000
1001  LSDMNLSDSEKKNLHQYLNFNSNMGFIYTPCSEKYLLSEKRKKRSLCLKK  1050
1051  CVEKGQMYRTFQRDSAFSTLSKWNLFQTYMPWFLTSTGYKYLNFLFLDTF  1100
1101  SDLLPILSSSQKFLSILHDIMHGSGISWRILQKKLCLPPWNLISEISSKC  1150
1151  LHNLLLPEEMIHRNNESPLIWTHLASPNVREFFYSILFLLFVAGYLVRTH  1200
1201  LLFVFRASSELQTEFERVKSLMIPSYMIELRKLLDRYPTSEPNSFWLKNL  1250
1251  FLVALEQLGDSLEEIRGSASGDNMLLGGGPGPAYGFKSIRSKKKYLNINL  1300
1301  IDILDLISIIPNPINRITFSRNTRHLSHTSKEIYSLIRKRKRVNGDWIDD  1350
1351  KIESWVASSDSIDDEEREFLVQFSTLTTEKRIDQILLSLTHSDHLSKNDS  1400
1401  GYQLIEQPGAIYLRYLVDIHKKYLMNYEFNTSCLAERRVFLAHYQTITYS  1450
1451  QTSCGANSFHFPSHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATN  1500
1501  SYVPFITVFLNKFLDNKPKGSLIDASDDIDRDLDTELELLTMMNALTMDM  1550
1551  MPEIDQFSITLQFELAKAMSPCIIWIPNIHDLDVNESNYLSLGLFVNYLS  1600
1601  RDCERGSTRNILVIASTHIPQKVDPALIAPNQLNTCIKIRRLRIPQQRKH  1650
1651  FFTLSYTRGFHLEKKMFHTNGFGSITMGSNVRDLVAFINEALSISITQKK  1700
1701  SIIDTNTIRSALHRQTWDLRSQVRSVQDHGILFYQIGRAVAQNVLLSNCP  1750
1751  IDPISTYMKKKSCNEGDSYLYKWYFELGTSMKKLTILLYLLSCSAGSVAQ  1800
1801  DLWSLPGPDEKNGITSYGLVENDSYLVHGLLEVEGALVGSSRIEKACSQN  1850
1851  DRVTLFLRPELRNPLDMMQNGSCSILDHRFLYEKYESELEEGEGALDPQQ  1900
1901  IEEDLFNHIVWAPRIWNPWGFLFDCIERPNELGFPYWARSFRGKRSIYDK  1950
1951  EDELQENDSEFLQSGTMQYQTRDRSSKEQGFFRISQFIWDPADPLFFLFK  2000
2001  DQPFVSVFSHREFFADEEISKGLLTSQMNPPISIFQRWFIKNTQEKHFEL  2050
2051  LINRQRWLRTNSSLSNGSFRSNTLSESYQYLSNLFLSNGTLLDQMTKTLL  2100
2101  RKRWLFPDEMKIGFMQEEKDFPFLSRKDMWP                     2131

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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