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

NucPred

Fetching Q99PV0 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MAGVFPYRGPGNPVPGPLAPLPDYMSEEKLQEKARKWQQLQAKRYAEKRK    50
  51  FGFVDAQKEDMPPEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVL   100
 101  KLLENMPMPWEQIRDVPVLYHITGAISFVNEIPWVIEPVYISQWGSMWIM   150
 151  MRREKRDRRHFKRMRFPPFDDEEPPLDYADNILDVEPLEAIQLELDPEED   200
 201  APVLDWFYDHQPLRDSRKYVNGSTYQRWQFTLPMMSTLYRLANQLLTDLV   250
 251  DDNYFYLFDLKAFFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDIN   300
 301  KIIIRQPIRTEYKIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAF   350
 351  YFDPLINPISHRHSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTAN   400
 401  GIALLWAPRPFNLRSGRTRRALDIPLVKNWYREHCPAGQPVKVRVSYQKL   450
 451  LKYYVLNALKHRPPKAQKKRYLFRSFKATKFFQSTKLDWVEVGLQVCRQG   500
 501  YNMLNLLIHRKNLNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREV   550
 551  LRLTKLVVDSHVQYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMR   600
 601  QIRMCKDLKHLIYYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLER   650
 651  WLGNLLARQFEGRHSKGVAKTVTKQRVESHFDLELRAAVMHDILDMMPEG   700
 701  IKQNKARTILQHLSEAWRCWKANIPWKVPGLPTPIENMILRYVKAKADWW   750
 751  TNTAHYNRERIRRGATVDKTVCKKNLGRLTRLYLKAEQERQHNYLKDGPY   800
 801  ITAEEAVAVYTTTVHWLESRRFSPIPFPPLSYKHDTKLLILALERLKEAY   850
 851  SVKSRLNQSQREELGLIEQAYDNPHEALSRIKRHLLTQRAFKEVGIEFMD   900
 901  LYSHLVPVYDVEPLEKITDAYLDQYLWYEADKRRLFPPWIKPADTEPPPL   950
 951  LVYKWCQGINNLQDVWETSEGECNVMLESRFEKMYEKIDLTLLNRLLRLI  1000
1001  VDHNIADYMTAKNNVVINYKDMNHTNSYGIIRGLQFASFIVQYYGLVMDL  1050
1051  LVLGLHRASEMAGPPQMPNDFLSFQDIATEAAHPIRLFCRYIDRIHIFFR  1100
1101  FTADEARDLIQRYLTEHPDPNNENIVGYNNKKCWPRDARMRLMKHDVNLG  1150
1151  RAVFWDIKNRLPRSVTTVQWENSFVSVYSKDNPNLLFNMCGFECRILPKC  1200
1201  RTSYEEFTHKDGVWNLQNEVTKERTAQCFLRVDDESMQRFHNRVRQILMA  1250
1251  SGSTTFTKIVNKWNTALIGLMTYFREAVVNTQELLDLLVKCENKIQTRIK  1300
1301  IGLNSKMPSRFPPVVFYTPKELGGLGMLSMGHVLIPQSDLRWSKQTDVGI  1350
1351  THFRSGMSHEEDQLIPNLYRYIQPWESEFIDSQRVWAEYALKRQEAIAQN  1400
1401  RRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRVRTDFKQYQVLKQ  1450
1451  NPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGILEHTLFKGTYFPTWEG  1500
1501  LFWEKASGFEESMKWKKLTNAQRSGLNQIPNRRFTLWWSPTINRANVYVG  1550
1551  FQVQLDLTGIFMHGKIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQE  1600
1601  LDALEIETVQKETIHPRKSYKMNSSCADILLFASYKWNVSRPSLLADSKD  1650
1651  VMDSTTTQKYWIDIQLRWGDYDSHDIERYARAKFLDYTTDNMSIYPSPTG  1700
1701  VLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANPALYVLRERIRKG  1750
1751  LQLYSSEPTEPYLSSQNYGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTT  1800
1801  KPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIR  1850
1851  SLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVE  1900
1901  KFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRA  1950
1951  KVILKPDKTTVTEPHHIWPTLTDEEWIKVEVQLKDLILADYGKKNNVNVA  2000
2001  SLTQSEIRDIILGMEISAPSQQRQQIAEIEKQTKEQSQLTATQTRTVNKH  2050
2051  GDEIITSTTSNYETQTFSSKTEWRVRAISAANLHLRTNHIYVSSDDIKET  2100
2101  GYTYILPKNVLKKFICISDLRAQIAGYLYGVSPPDNPQVKEIRCIVMVPQ  2150
2151  WGTHQTVHLPSQLPQHEYLKEMEPLGWIHTQPNESPQLSPQDVTTHAKIM  2200
2201  ADNPSWDGEKTIIITCSFTPGSCTLTAYKLTPSGYEWGRQNTDKGNNPKG  2250
2251  YLPSHYERVQMLLSDRFLGFFMVPAQSSWNYNFMGVRHDPNMKYELQLAN  2300
2301  PKEFYHEVHRPSHFLNFALLQEGEVYSADREDLYA                 2335

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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