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

NucPred

Fetching O43497 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MDEEEDGAGAEESGQPRSFMRLNDLSGAGGRPGPGSAEKDPGSADSEAEG    50
  51  LPYPALAPVVFFYLSQDSRPRSWCLRTVCNPWFERISMLVILLNCVTLGM   100
 101  FRPCEDIACDSQRCRILQAFDDFIFAFFAVEMVVKMVALGIFGKKCYLGD   150
 151  TWNRLDFFIVIAGMLEYSLDLQNVSFSAVRTVRVLRPLRAINRVPSMRIL   200
 201  VTLLLDTLPMLGNVLLLCFFVFFIFGIVGVQLWAGLLRNRCFLPENFSLP   250
 251  LSVDLERYYQTENEDESPFICSQPRENGMRSCRSVPTLRGDGGGGPPCGL   300
 301  DYEAYNSSSNTTCVNWNQYYTNCSAGEHNPFKGAINFDNIGYAWIAIFQV   350
 351  ITLEGWVDIMYFVMDAHSFYNFIYFILLIIVGSFFMINLCLVVIATQFSE   400
 401  TKQRESQLMREQRVRFLSNASTLASFSEPGSCYEELLKYLVYILRKAARR   450
 451  LAQVSRAAGVRVGLLSSPAPLGGQETQPSSSCSRSHRRLSVHHLVHHHHH   500
 501  HHHHYHLGNGTLRAPRASPEIQDRDANGSRRLMLPPPSTPALSGAPPGGA   550
 551  ESVHSFYHADCHLEPVRCQAPPPRSPSEASGRTVGSGKVYPTVHTSPPPE   600
 601  TLKEKALVEVAASSGPPTLTSLNIPPGPYSSMHKLLETQSTGACQSSCKI   650
 651  SSPCLKADSGACGPDSCPYCARAGAGEVELADREMPDSDSEAVYEFTQDA   700
 701  QHSDLRDPHSRRQRSLGPDAEPSSVLAFWRLICDTFRKIVDSKYFGRGIM   750
 751  IAILVNTLSMGIEYHEQPEELTNALEISNIVFTSLFALEMLLKLLVYGPF   800
 801  GYIKNPYNIFDGVIVVISVWEIVGQQGGGLSVLRTFRLMRVLKLVRFLPA   850
 851  LQRQLVVLMKTMDNVATFCMLLMLFIFIFSILGMHLFGCKFASERDGDTL   900
 901  PDRKNFDSLLWAIVTVFQILTQEDWNKVLYNGMASTSSWAALYFIALMTF   950
 951  GNYVLFNLLVAILVEGFQAEEISKREDASGQLSCIQLPVDSQGGDANKSE  1000
1001  SEPDFFSPSLDGDGDRKKCLALVSLGEHPELRKSLLPPLIIHTAATPMSL  1050
1051  PKSTSTGLGEALGPASRRTSSSGSAEPGAAHEMKSPPSARSSPHSPWSAA  1100
1101  SSWTSRRSSRNSLGRAPSLKRRSPSGERRSLLSGEGQESQDEEESSEEER  1150
1151  ASPAGSDHRHRGSLEREAKSSFDLPDTLQVPGLHRTASGRGSASEHQDCN  1200
1201  GKSASGRLARALRPDDPPLDGDDADDEGNLSKGERVRAWIRARLPACCLE  1250
1251  RDSWSAYIFPPQSRFRLLCHRIITHKMFDHVVLVIIFLNCITIAMERPKI  1300
1301  DPHSAERIFLTLSNYIFTAVFLAEMTVKVVALGWCFGEQAYLRSSWNVLD  1350
1351  GLLVLISVIDILVSMVSDSGTKILGMLRVLRLLRTLRPLRVISRAQGLKL  1400
1401  VVETLMSSLKPIGNIVVICCAFFIIFGILGVQLFKGKFFVCQGEDTRNIT  1450
1451  NKSDCAEASYRWVRHKYNFDNLGQALMSLFVLASKDGWVDIMYDGLDAVG  1500
1501  VDQQPIMNHNPWMLLYFISFLLIVAFFVLNMFVGVVVENFHKCRQHQEEE  1550
1551  EARRREEKRLRRLEKKRRNLMLDDVIASGSSASAASEAQCKPYYSDYSRF  1600
1601  RLLVHHLCTSHYLDLFITGVIGLNVVTMAMEHYQQPQILDEALKICNYIF  1650
1651  TVIFVLESVFKLVAFGFRRFFQDRWNQLDLAIVLLSIMGITLEEIEVNAS  1700
1701  LPINPTIIRIMRVLRIARVLKLLKMAVGMRALLDTVMQALPQVGNLGLLF  1750
1751  MLLFFIFAALGVELFGDLECDETHPCEGLGRHATFRNFGMAFLTLFRVST  1800
1801  GDNWNGIMKDTLRDCDQESTCYNTVISPIYFVSFVLTAQFVLVNVVIAVL  1850
1851  MKHLEESNKEAKEEAELEAELELEMKTLSPQPHSPLGSPFLWPGVEGPDS  1900
1901  PDSPKPGALHPAAHARSASHFSLEHPTDRQLFDTISLLIQGSLEWELKLM  1950
1951  DELAGPGGQPSAFPSAPSLGGSDPQIPLAEMEALSLTSEIVSEPSCSLAL  2000
2001  TDDSLPDDMHTLLLSALESNMQPHPTELPGPDLLTVRKSGVSRTHSLPND  2050
2051  SYMCRHGSTAEGPLGHRGWGLPKAQSGSVLSVHSQPADTSYILQLPKDAP  2100
2101  HLLQPHSAPTWGTIPKLPPPGRSPLAQRPLRRQAAIRTDSLDVQGLGSRE  2150
2151  DLLAEVSGPSPPLARAYSFWGQSSTQAQQHSRSHSKISKHMTPPAPCPGP  2200
2201  EPNWGKGPPETRSSLELDTELSWISGDLLPPGGQEEPPSPRDLKKCYSVE  2250
2251  AQSCQRRPTSWLDEQRRHSIAVSCLDSGSQPHLGTDPSNLGGQPLGGPGS  2300
2301  RPKKKLSPPSITIDPPESQGPRTPPSPGICLRRRAPSSDSKDPLASGPPD  2350
2351  SMAASPSPKKDVLSLSGLSSDPADLDP                         2377

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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