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

NucPred

Fetching Q9BMN8 from www.uniprot.org...

The NucPred score for your sequence is 0.44 (see score help below)

   1  MIQFRNKNNSMNRIARHLRNVARRKGSSLLLFLMLSTVLVAAKEDDPARL    50
  51  VVRPDSSTVVDESKISFFCRADGNPLPSVIWRVNGKSITDHNRISIKSLA   100
 101  TGLSTLRFERVSLDDNATVVSCSADNGVANPVVAEASLTVVPRDKVPIGF   150
 151  PQIELHPSLKSVEQGKTAYVSCRVRGDPRAKVLWLRDLIPLDIRADGRYS   200
 201  VSTIGNPGALMIQHAREEDQGKYECIARNTLGVAHSKAANLYVKVRRVPP   250
 251  YFSYKLERQYVVGVGGNINLTCVAVGYPMPRVFWKKTDLMVLDDPSTAPI   300
 301  GKNVLTLTHVESTENFTCVAVSALGNIEATTTVIAKELPPPPVNIVVSSV   350
 351  TSESVVITWKPPKYNEAINKYVVNYRLKYSEGRSSRGKTMETLENSLVID   400
 401  GLVAFQTYEFTVRSAGPVGVGLESLPVEAQTKPSKPATAPVSPQARSLNR   450
 451  DSILVKWGPCEQPNGLITGYKVYYTNDLVTTPIREWKQHDAKSDEFMTTI   500
 501  NGLEPDSRYFVRVIAQNSEGDSPLSTLVTVATRQGIPGQPPMLTVKALDS   550
 551  RRMQLTWDKPLYSSPVVGYTVRYNTSDGEKELTLTSPHEKHVVTGLHPDK   600
 601  YYYFRVAAYSDRGQGEFTEPMISKTIASIPLSSPTIVSAAATSSKSVEIR   650
 651  WKGPEQKKLNGVLTAYRINYFRLEDSKTANLESVEYDEDMDDSSSFLDRM   700
 701  SVVVPSDATSYVLSDLLPYSSYEITVAASTMDGYGPESSIRVVKTLEDVP   750
 751  SAPRNFNAELTSATSVKLTWDAPAAANGALLGYYVYLDRMVNGEPVVEKG   800
 801  SKKRIVMIRDSSKRYFELDSLDPNTEYSFRLNAFNRNGDGEFSERKSIIT   850
 851  QGIPPEAPEIVSVSLDRDEPPVVARIEWKMPKMKPNETPIEKYNLWLRAQ   900
 901  GYPDSYVKAKTVDGTDLSTTISGLWMGVVYDVLLAAENREGRSQNATETI   950
 951  ATPVGSPDGEPIDVQYEVMKGKIVVSWRPPSEEKRNGNITSYKAILSAMD  1000
1001  ATADRYEQPVPAPSTSSTFEVNVRRAYLFKVAAATMKGIGPYSPVLTINP  1050
1051  DPAALVGPPTNVRVEATSNSTAVVQWDFESQKADSFVVKYMHEPGNRMDT  1100
1101  EKWKQLPVVSIDKENPKRFAVVSDLNAHKPYAFCVLAVKNNLTLNEQFNK  1150
1151  VRVTNYMTNFQRQGPCSDPPTVLESVTPTYMVQNLRVLWKTSNSVQLTWE  1200
1201  YNGPRNVGFYVNHTGRKDYVNHELQEKTMSTPGFGQDVDEKHREYLWTNL  1250
1251  RPHMMYTIHVGVRTLPPGARKYWPQEVVTITDPTGPPFVDVPKLVDSSGT  1300
1301  QPGQQMIRLTPATEEYGPISHYWIILVPANYSTEDVVNLDPIELEKATAE  1350
1351  KRAQLARSLSVSPSKKLKRKASEVGDDSQSASYHPKEKRARRATVPGAYV  1400
1401  TARLSADRVKQQYRNNQPFIVGDSQLYDGFTNYPLEHNLHYRLMMRAFAK  1450
1451  NDVRTKDSFEQRAPMSEKLSRMYSDSVLTEPFTIKSALRGASQKSSPWVG  1500
1501  ACIAFLVLFSIVGMLICWWLRCNKKSAGRHPRHGSITKVALTGNIMNGGG  1550
1551  GIPGETSKLLSTSNEYGRQIMNPYEQMNGNHHMESSMDLYPLPTSHSRSN  1600
1601  GYAPVPVAIPSLPNNGNNMTTVSHPAVPIAELANHIERLRMNNNAGFQSE  1650
1651  FESIETGQHFTWEHSSADMNKHKNRYANVAAYDHSRVVLSNVEGYPGMDY  1700
1701  INANYVDGYDKPRSYIATQGPLPETFSDFWRMVWEEQSVTIVMLTNLEER  1750
1751  SRVKCDQYWPSRGTATYGDIEVTLLESVHLAHYTMRTMRLKMVGEPEVRE  1800
1801  IKHLQYTAWPDHGVPDHPTPFLIFLKRVKTLNPNDAGPIISHCSAGIGRT  1850
1851  GAFIVIDCMLERLRYDNTVDIYGCVTALRAQRSYMVQTEEQYIFIHDAVL  1900
1901  DAVNSGSTEVPASRLHQHLHILSQPSADQLSGIDMEFRHLTTLKWTSNRC  1950
1951  TVANLPVNRPKNRMLSAVPYDSNRVIMRLLPGADGSDYINASWIDGYKER  2000
2001  GAYIATQAPTNETAADFWRAIWEHNSPIIAMLVRTNERGQEQCSDYWPLE  2050
2051  TGVQVGMLVVEPMAEYDMKHYHLREFRISDINTREVRTVRQFHFMEWPDV  2100
2101  GKPHTADHFLDFVTQVHNTYAQFGCTGPITVHCCSGAGRTAVFIALSIIL  2150
2151  DRMRAEHVVDVFTTVKLLRTERQNMIQEPEQYHFLYLAAYEYLAAYDNFS  2200

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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