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

NucPred

Fetching Q16927 from www.uniprot.org...

The NucPred score for your sequence is 0.62 (see score help below)

   1  MATDGITSRFGFNERRRTHNRNSCRILEDKMLAKLLLLALAGLTAAYQYE    50
  51  NSFKGYNPGYKGYDAGYKGYGYDAGYKYNNQGYSYKNGFEYGYQNAYQAA   100
 101  FYKHRPNVTEFEFSSWMPNYEYVYNVTSKTMTALAELDDQWTGVFTRAYL   150
 151  VIRPKSRDYVVAYVKQPEYAVFNERLPYGYATKFYHDMFKFQPMPMSSKP   200
 201  FGIRYHKGAIKGLYVEKTIPNNEVNILKAWISQLQVDTRGANLMHSSKPI   250
 251  HPSKNEWNGHYKVMEPLVTGECETHYDVNLIPAYMIQAHKQWVPQGQLRG   300
 301  EDGQFIQVTKTQNFDRCDQRMGYHFGFTGYSDFRPNTNQMGNVASKSLVS   350
 351  YMYLTGNWYNFTIQSSSMINKVAIAPSLVNKEPALVYAQVNMTLNDVHPY   400
 401  DKVPMGPAEDLKVFVDLVYSYNMPSDKKNYVRPGNETSSSSSSSSSSSSS   450
 451  SSESSSSSSESVENPKISPVEQYKPLLDKVEKRGNRYRRDLNAIKEKKYY   500
 501  EAYKMDQYRLHRLNDTSSDSSSSDSSSSSSSESKEHRNGTSSYSSSSSSS   550
 551  SSSSSSESSSYSSSSSSSSESYSISSEEYYYQPTPANFSYAPEAPFLPFF   600
 601  TGYKGYNIFYARNVDAIRSVGKLVEEIASDLENPSDLPKSNTMSKFNILT   650
 651  RAIRAMGYEDIYELAQKYFVSQKERQVAQFSDKKFSKRVDAWVTLRDAVA   700
 701  EAGTPSAFKLIFDFIKEKKLRGYEAATVIASLAQSIRYPTEHLLHEFFLL   750
 751  VTSDVVLHQEYLNATALFAYSNFVNQAHVSNRSAYNYYPVFSFGRLADAD   800
 801  YKIIEHKIVPWFAHQLREAVNEGDSVKIQVYIRSLGNLGHPQILSVFEPY   850
 851  LEGTIQITDFQRLAIMVALDNLVIYYPSLARSVLYRAYQNTADVHEVRCA   900
 901  AVHLLMRTDPPADMLQRMAEFTHHDPSLYVRAAVKSAIETAALADDYDED   950
 951  SKLAINAKAAINFLNPEDVSIQYSFNHIRDYALENLELSYRLHYGEIASN  1000
1001  DHRYPSGLFYHLRQNFGGFKKYTSFYYLVSSMEAFFDIFKKQYNTKYFAD  1050
1051  YYKSADYSTNYYNFDKYSKYYKQYYYSKDSEYYQKFYGQKKDYYNDKEPF  1100
1101  KFTAPRIAKLLNIDAEEAEQLEGQLLFKLFNGYFFTAFDNQTIENLPHKM  1150
1151  RHLFENLEDGYAFDVTKFYQQQDVVLAWPLATGFPFIYTLKAPTVFKFEV  1200
1201  DASAKTHPQVYKMPAGHPETENDDFFYMPQSINGSVDVNLLYHRMVDAKV  1250
1251  GFVTPFDHQRYIAGYQKKLHGYLPFNVELGLDFVKDEYEFEFKFLEPKDD  1300
1301  HLLFHMSSWPYTGYKDITDMRPIAENPNAKIVHDDNQSTKTMEHTFGQDM  1350
1351  TGVALRFHAKYDFDLINFQQFWSLVQKNDFVSAVNYPFAYQPYEYHQFNL  1400
1401  FYDSQRTHAKSFKFYAYQKFGAPSFEETGPKHPANRHSYSGNYYESNYAQ  1450
1451  PFVYSPGSQRRYEQFFRNAASGIRNSFVRYYDFGFEFYAPQYKSEFTFTT  1500
1501  AFADSPVDKTSRQLYYFYASPMFPSQSYFKDIPFSGKQFQFCATATSEFP  1550
1551  RVPYLKFSDFDKYYGDASQYFDFLYGESCQGGAHIAVKGKQKQTGKYREY  1600
1601  LRFSDVAKACKEQMANGYYQFEECQQAIDQAYYYDFYDYAIEYKDVGSVA  1650
1651  KNLTNKFYNYFQYAFYPYFESNFFYHGKSNYIKAEFEFAPYGDYYNASFF  1700
1701  GPSYAFQVQNYPVFNDYSTYFPYFFKYTFFPRYQPYYMHRLPAHKPRNRP  1750
1751  YYELSNYEQFAVFDRKPQYPSCSFSNDYFYTFDNKKYFYDMGECWHAVMY  1800
1801  TVKPDYDFYAQQSHFYNSDFEYKYKNGFEEYEQFAALARRGSDNQLYFKF  1850
1851  LFGDNYIEVFPNNGGIPFVKYNGRPYDISKSNIAHFEYKEGYPSFPFFYA  1900
1901  FAYPNKDLEVSFFGGKLKFATDGYRARFFSDYSFYNNFVGLCGTNNGEYF  1950
1951  DEFVTPDQCYMRKPEFFAASYAITGQNCTGPAKAFNYAYQQKAKQECVKR  2000
2001  EVYYGDIIYNQEYYHPRYRYYNHNVEESSSSSSSSSSDSSSSSSSSESSS  2050
2051  RSRSGSSSSSSSSEEQKEFHPHKQEHSMKECPVQHQHQFFEQGDRTCFSL  2100
2101  RPLPVCHSKCVATEKISKYFDVHCFEKDSTQAKKYKSDIGRGYTPDFKSF  2150
2151  APHKTYKFNYPKSCVYKAY                                 2169

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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