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

NucPred

Fetching O54898 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MDEEEDGAGAEESGQPRSFTQLNDLSGAGGRQGPGSTEKDPGSADSEAEG    50
  51  LPYPALAPVVFFYLSQDSRPRSWCLRTVCNPWFERVSMLVILLNCVTLGM   100
 101  FRPCEDIACDSQRCRILQAFDDFIFAFFAVEMVVKMVALGIFGKKCYLGD   150
 151  TWNRLDFFIVIAGMLEYSLDLQNVSFSAVRTVRVLRPLRAINRVPSMRIL   200
 201  VTLLLDTLPMLGNVLLLCFFVFFIFGIVGVQLWAGLLRNRCFLPENFSLP   250
 251  LSVDLEPYYQTENEDESPFICSQPRENGMRSCRSVPTLRGEGGGGPPCSL   300
 301  DYETYNSSSNTTCVNWNQYYTNCSAGEHNPFKGAINFDNIGYAWIAIFQV   350
 351  ITLEGWVDIMYFVMDAHSFYNFIYFILLIIVGSFFMINLCLVVIATQFSE   400
 401  TKQRESQLMREQRVRFLSNASTLASFSEPGSCYEELLKYLVYILRKAARR   450
 451  LAQVSRAIGVRAGLLSSPVARSGQEPQPSGSCTRSHRRLSVHHLVHHHHH   500
 501  HHHHYHLGNGTLRVPRASPEIQDRDANGSRRLMLPPPSTPTPSGGPPRGA   550
 551  ESVHSFYHADCHLEPVRCQAPPPRCPSEASGRTVGSGKVYPTVHTSPPPE   600
 601  ILKDKALVEVAPSPGPPTLTSFNIPPGPFSSMHKLLETQSTGACHSSCKI   650
 651  SSPCSKADSGACGPDSCPYCARTGAGEPESADHVMPDSDSEAVYEFTQDA   700
 701  QHSDLRDPHSRRRQRSLGPDAEPSSVLAFWRLICDTFRKIVDSKYFGRGI   750
 751  MIAILVNTLSMGIEYHEQPEELTNALEISNIVFTSLFALEMLLKLLVYGP   800
 801  FGYIKNPYNIFDGVIVVISVWEIVGQQGGGLSVLRTFRLMRVLKLVRFLP   850
 851  ALQRQLVVLMKTMDNVATFCMLLMLFIFIFSILGMHLFGCKFASERDGDT   900
 901  LPDRKNFDSLLWAIVTVFQILTQEDWNKVLYNGMASTSSWAALYFIALMT   950
 951  FGNYVLFNLLVAILVEGFQAEGDATKSESEPDFFSPSVDGDGDRKKRLAL  1000
1001  VALGEHAELRKSLLPPLIIHTAATPMSHPKSSSTGVGEALGSGSRRTSSS  1050
1051  GSAEPGAAHHEMKCPPSARSSPHSPWSAASSWTSRRSSRNSLGRAPSLKR  1100
1101  RSPSGERRSLLSGEGQESQDEEESSEEDRASPAGSDHRHRGSLEREAKSS  1150
1151  FDLPDTLQVPGLHRTASGRSSASEHQDCNGKSASGRLARTLRTDDPQLDG  1200
1201  DDDNDEGNLSKGERIQAWVRSRLPACCRERDSWSAYIFPPQSRFRLLCHR  1250
1251  IITHKMFDHVVLVIIFLNCITIAMERPKIDPHSAERIFLTLSNYIFTAVF  1300
1301  LAEMTVKVVALGWCFGEQAYLRSSWNVLDGLLVLISVIDILVSMVSDSGT  1350
1351  KILGMLRVLRLLRTLRPLRVISRAQGLKLVVETLMSSLKPIGNIVVICCA  1400
1401  FFIIFGILGVQLFKGKFFVCQGEDTRNITNKSDCAEASYRWVRHKYNFDN  1450
1451  LGQALMSLFVLASKDGWVDIMYDGLDAVGVDQQPIMNHNPWMLLYFISFL  1500
1501  LIVAFFVLNMFVGVVVENFHKCRQHQEEEEARRREEKRLRRLEKKRRSKE  1550
1551  KQMAEAQCKPYYSDYSRFRLLVHHLCTSHYLDLFITGVIGLNVVTMAMEH  1600
1601  YQQPQILDEALKICNYIFTVIFVFESVFKLVAFGFRRFFQDRWNQLDLAI  1650
1651  VLLSIMGITLEEIEVNLSLPINPTIIRIMRVLRIARVLKLLKMAVGMRAL  1700
1701  LHTVMQALPQVGNLGLLFMLLFFIFAALGVELFGDLECDETHPCEGLGRH  1750
1751  ATFRNFGMAFLTLFRVSTGDNWNGIMKDTLRDCDQESTCYNTVISPIYFV  1800
1801  SFVLTAQFVLVNVVIAVLMKHLEESNKEAKEEAELEAELELEMKTLSPQP  1850
1851  HSPLGSPFLWPGVEGVNSTDSPKPGAPHTTAHIGAASGFSLEHPTMVPHP  1900
1901  EEVPVPLGPDLLTVRKSGVSRTHSLPNDSYMCRNGSTAERSLGHRGWGLP  1950
1951  KAQSGSILSVHSQPADTSCILQLPKDVHYLLQPHGAPTWGAIPKLPPPGR  2000
2001  SPLAQRPLRRQAAIRTDSLDVQGLGSREDLLSEVSGPSCPLTRSSSFWGG  2050
2051  SSIQVQQRSGIQSKVSKHIRLPAPCPGLEPSWAKDPPETRSSLELDTELS  2100
2101  WISGDLLPSSQEEPLFPRDLKKCYSVETQSCRRRPGFWLDEQRRHSIAVS  2150
2151  CLDSGSQPRLCPSPSSLGGQPLGGPGSRPKKKLSPPSISIDPPESQGSRP  2200
2201  PCSPGVCLRRRAPASDSKDPSVSSPLDSTAASPSPKKDTLSLSGLSSDPT  2250
2251  DMDP                                                2254

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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