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

NucPred

Fetching Q9B1K6 from www.uniprot.org...

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

   1  MKGHQFKSWIFELREILKEIKNSRYFLYSWTQFNSTGSFIHIFFHQESFI    50
  51  KLLDSRIWSILLSGNSQGSTSNRYFTIKDVVLFVVAILLYRINNRKMVER   100
 101  KNLYLTGLLPIPMNSIGPRNDTLEESFESSNINRLIVPLLYLPKEKKISE   150
 151  SSFLDPKESTQVLPITKKCIMPESNWGSRWWRDWIRKKRDSSCKISNETV   200
 201  AGIEISFKEKDIKYLEFPFVYYMDDPIRKDHDWELFDRLSPRKRRNIINL   250
 251  NSGQLFEILVKDWISYLMFAFREKKPIEVEGFFKQQGAGSTIQSNDIEHV   300
 301  SHLFLRNKRAISLQNCAQFHMWQFRQDLFVSWGKKQPHESDFLRNISREN   350
 351  WIWLDNVWLVNKDRFFSKIRNVSSNIQYDSTRSSFIQVTDSSQLKGSSDQ   400
 401  SRDHFDSIRNEDSKYDTLINQREIQQLKERSILCWDPSFLQTERTDIESE   450
 451  RFRFPKSLSGYSSMCRLFMQREKQMNNHLLPEEIEEFLGNPTRADRFFFS   500
 501  DRWSELHLGSNPTERSTRDQKLLKKEQDVSFVLSKRSEKKEIVNIFKIIL   550
 551  YLQNTVSIHPISSDPVCDMVPKDEPDSSNKMSFLNKNGLFHLFHDRNRGV   600
 601  YTLHHDFESEEIFQEMADLFNLSITEPDLVYHKGFAFSIDSSGLDQKQFL   650
 651  NEVFNSRDESKKKSLLVLPTLFYEENESFYRRIIKKWVQTSCGNDLEDPK   700
 701  PKIVVFTSNNIMEAVNQYRLIRNLIPIQYITYGYGYIRNVLNRFIQKNRF   750
 751  DRNFEYRIQRYQIENDTLNHRTRMKYTINQHFSNLKKKSQKKWFDSLILI   800
 801  SRTERSMNRDPNAYRYKWSNGNKNFQEHLDHFISEQNSRFQVVFDRLRIN   850
 851  QYSIDWSEVIDKKDLSKSLCFFLYKFLLFFSKFLLFLSKSLPFFFVSFGS   900
 901  IPIHRSEIHIYELKSPNHPLCNQLFESIGLQIVHLKKWKPFLLDDHDTSQ   950
 951  KSRFLINGGTISPFLFNKIPKWMIDSFDTIKNRRKFFDNTDSYFSMISHD  1000
1001  EDNWLNPVKPFHRSSLISSFYKANRLRFLNNRYHFCFYCNKRLPFYVEKA  1050
1051  CINNYDFTYGQFLNILFIRNKRFSLCGGKKKHAFLERDTISPIESRVFNI  1100
1101  LILNDFPQSGDEGYNLYKSFHFPIRSDPFVHRAIYSIADISVTPLTEGQI  1150
1151  VNFERTYCQPLSDMNLPDSEGKNLHQYLKFNSNMGLIHIPCSEKYLPSEN  1200
1201  RKKGIPCLKKCLEKGQMYRTFQRDSVFSTLSKWNLFQTYIPWFLTSTGYK  1250
1251  YLNFIFLDTFSDLLPILSSSQKFVSIFHDIMHRSDISWRILQKKWCLSQW  1300
1301  NLISEISSKCFHNLLLSEEIIHRNNESPLISTHLRSLNVREFLYSILFLL  1350
1351  LVAGYLVRTHLLFVSRVYSELQTEFEKVKSLMIPSYMIELRKLLDRYPTS  1400
1401  EQNSFWLKNLFLVTLEQLGNSLEEIRSSASGGNMLWGGGSAYGVKSIRSK  1450
1451  KKYLNLIDLISIIPNPINRIAFSRNMRHLSHTSKAIYSLIRKIKNVNGDW  1500
1501  IDDKIESWVSNSDSIDDKEREFLVQFSTLTTEKRIDQILLSLTHSDHLSK  1550
1551  NNSGYQMIEQPGTIYLRYLVDIQKKYLMNYEFNTSCLVEKRIFLAHYQTI  1600
1601  TYSQTLCGTNSFHFSSHGKPFSLRLALSPPRGLLVIGSIGTGRSYLVKYL  1650
1651  AANSYVPFIRVFLNKFLDNKPKGFLIDDSDDIDDIDDSHDIDDIDDSNDS  1700
1701  DDIDRDLDTELELLTMMNALTMDMMPEIDRFYITLQFELAKAMSPCIIWI  1750
1751  PNIHDLDVNESNSLSLGLLANHLSRDCERCSTRNILVIASTHIPQKVDPA  1800
1801  LIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRRFHFEKKMFHTNGFGSIT  1850
1851  LGSNVQDLVALTNEALSISIIQKKSIIDTNLIRSALHKQTWDLRSQVRSV  1900
1901  QDHGILFYQIGRAVSQNVLLSNCSIDPISIYMKKKSCNEGDSYLYKWYFE  1950
1951  LGTSMKNLTILLYLLSCSAGAVAQDLWSLPGPDEKNGITSYGLVENDSDL  2000
2001  VHGLLEVEGALVGSSRTEKDCSQFDNDRVTLLLRPEPSNPLNMIQNGSCS  2050
2051  IVDQRFLYEKYESEFEEGEGVLDLQQIEEDLFNHIVWAPRIWCPWGFLFD  2100
2101  CIERPNELGFPYWARSFRGKRIIYDEEDELQENDSEFLQGGTMQYQTQDR  2150
2151  SSKEQGFFRISQFIWDPTDPLFFLFKDQPFVSVFSHREFFADEEISRGLL  2200
2201  TFQTDLPTSIYKRWFIKNTQEKHFELLIHRQRWLRTNNSLSNGFFRSNTL  2250
2251  SESYQYLSNMFLSNGTLLDQMTKTLLRKRWLFPDEMVVAICSNNESLV    2298

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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