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

NucPred

Fetching Q2PMM5 from www.uniprot.org...

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

   1  MKGHQFKSWIFELREILREIKNSRYFLDSWTQFNSAGFFIHIFFHQESFI    50
  51  KLLDSRIWSILLSRNSQGSTSNRYFTIKYVVLFVVAVLIYRINNRKMVER   100
 101  KNPYLTRLLTIPMNSIGPKNDTLEESSESSNINRLIVPLLYLPKGKKISE   150
 151  SYFLDPKESTRVLPITKKYIMPESNWGSRWWRNWIGKKSDSSCKISNETI   200
 201  AGIEISFKEKDIKYLEFLFVYYMDDPIRKDHDWEFFDRLSPRKRRNIINL   250
 251  NSGQLFEILVKDWIYYLMFAFREKIPKEVEGFFKQQGTGSIIQSNDIEHV   300
 301  SHLFLRNKRAISLQNCAQFHMWQFRQDLFVSWGKSPHESDFLRNNMSREN   350
 351  WIWLDNVWLVNKDRFFSKVRNVSSNIQYDSTRSSFIQVTGSSQLKGSSDQ   400
 401  SKDYFDSIRNEDSKYHTLINQREIQQLKERSILCWDPSFLQTERTEIESE   450
 451  RFPKILSGYSSMCRLFMEREKQMNNHLLPQEIEEFLGNPARATRSFFSDR   500
 501  WSELHLSSNPTERSTRDQKLLKKEQKKHLVLSRRSENKEIVNLFKIIMYL   550
 551  QNTVSIHPISSYPGCDMVPKGELDSSNKISFLNKNPFWGLFHLFHDRNSG   600
 601  RYTLHHDFESEEIFQEMADLFTLSITEPDLVYHKGFAFSIDSSGLGQKHF   650
 651  LNELFNSRDESKNHSLLVLPPLFYEENESFYRRIIKKWVQTSCGNNLEDP   700
 701  KPKIVVFTSNNIMEAVNQYRLIRNLIQIQYSTHGYIRNVLNRFNCNFEYG   750
 751  IQRYQIGNDTLNHRTIMKYTINQHLSNLKKSQKKWFDPLIFISRTERSMN   800
 801  RDPNAYRYKWSNGSKNFQEHLDYFISEQNSRFQVVFDRFHINQYSIDWSE   850
 851  VIDKKDLSKSLCFFLSKLLLFLPKFLLFLSNSLPSFFFVSFGGIPIHRSE   900
 901  IHIYELKGPNNPLCNQLLESIGLQIFHLKKWKPLLLDDQDTSQKSKFLIN   950
 951  GGTISPFLFNKIPKWMIDSFHTRKNRRKSFDNTDSYFSMISHDPDNWLNP  1000
1001  VKPFHRSSLIYSFYKANRLRFLNNQYHFCFYCNKRFPFYVEKACINNYDF  1050
1051  TYGQFLNILFIRNKIFSFCDGQKKHAFLKRDTISPIESQVSNILIPNDFP  1100
1101  QSGDEGYNLYKSFHFPIRYDLFVRGAIYSIADISGTPLTEGQIVHFEKTY  1150
1151  CQPLSDMNIPDSEGKNLHQYLNFNSNMGLIHTPCSEKYLPSEKRKKRSPC  1200
1201  LKKCLEKGQMYRTFQQDSVFSTLSKWNLFQTYIPWFLTSTGYKYLNFIFL  1250
1251  DTFSDLLPILSSSQKFVSIFHDIMHGSDILWRIRQIPLCLPQWNLISEIW  1300
1301  NLISEIPGNCLHNLLLSEEIIHRNNELLLISTHLRSLNVQEFFYSILFLL  1350
1351  LVAGYLVRTHLLFVSRVYSELQTEFEKVKSLMIPSYMIELRKLLDRYPTS  1400
1401  ELNSFWLKNLFLVALEQLGDSLEEIRSFAFGGNMLWGGGPTYGVKSIRSK  1450
1451  KKYLNLIDLISIIPNPINRIAFSRNTRHLSHPSKTIYSLIRKIKNVNGDW  1500
1501  IDDKIESWVLNSNSIDDKEREFLVQFSTLTTEKRIDQILLSLTHSHHLSK  1550
1551  NNSGYQMIEQPGAIYLRYLVDIHKKYLMIYEFNTSCLAERRIFLANYQTI  1600
1601  TYSQTLRGANSFHFPSHGKPFSLRLALPPPSRGILVIGSIGTGRSYLVKY  1650
1651  LATNSYVPFITVFLNKFLDNKPKGFLIDDSDDIDDSYDSDDIDRDLDMEL  1700
1701  ELLTMMNTLTMDMMPEIDRFYITFQFELAKAMSPCIIWIPNIHDLDVNES  1750
1751  NYLSLGLLVNYLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCI  1800
1801  KIRRLLISQQRKHFFTLSYTRGFHLEKKMSHTNGFGSTTMGSNVRDLVAL  1850
1851  TNEALSISIIQKKSIIDTNIIRSVLHRQTWDFRSQVRSVQDHGILFYQIG  1900
1901  RAVSQNVLLSNCSIDPISIYMKKKSCDGGDSYLYKWYFELGTSMKKLTIL  1950
1951  LYLLSCSAGSVAQDLWSLPGPDEKNGITSYGLVENNSDLVHGLLEVEGAL  2000
2001  VGSSRTEKDCSQFDKDRVTLLLRSEPRNPLNMIQNGSYSIVDQRFLYEKY  2050
2051  ESEFEEGGGVLDPQQIEEDFFNHIVWAPRIWSPWGFLFYCIERPNELGFP  2100
2101  YWARSFRDKRIIYDEEDELQENDSEFLQGGTMQYQTRDRSSKEQGFFRIS  2150
2151  QFIWDPADPLFFLFKDQPFVSVFSHRQFFTDEEMSRELLTSQTDLPTSIY  2200
2201  KHWFIKNTQEKHFELLIHCQRWLRINSSLSNGFFRSNTLSESYQYLSNLF  2250
2251  LSNEALLDQMTKTLLRKRWLFPDEMVVAICSNNESLV               2287

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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