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

NucPred

Fetching P53349 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MAAAAGDRASSSGFPGAAAASPEAGGGGGGGGALQGSGAPAAGAAGLLRE    50
  51  PGSAGRERADWRRRQLRKVRSVELDQLPEQPLFLAAASPPCPSTSPSPEP   100
 101  ADAAAGASRFQPAAGPPPPGAASRCGSHSAELAAARDSGARSPAGAEPPS   150
 151  AAAPSGREMENKETLKGLHKMEDRPEERMIREKLKATCMPAWKHEWLERR   200
 201  NRRGPVVVKPIPIKGDGSEVNNLAAEPQGEGQAGSAAPAPKGRRSPSPGS   250
 251  SPSGRSVKPESPGVRRKRVSPVPFQSGRITPPRRAPSPDGFSPYSPEETS   300
 301  RRVNKVMRARLYLLQQIGPNSFLIGGDSPDNKYRVFIGPQNCSCGRGAFC   350
 351  IHLLFVMLRVFQLEPSDPMLWRKTLKNFEVESLFQKYHSRRSSRIKAPSR   400
 401  NTIQKFVSRMSNSHTLSSSSTSTSSSENSIKDEEEQMCPICLLGMLDEES   450
 451  LTVCEDGCRNKLHHHCMSIWAEECRRNREPLICPLCRSKWRSHDFYSHEL   500
 501  SSPVESPASLRAVQQPSSPQQPVAGSQRRNQESSFNLTHFGTQQIPSAYK   550
 551  DLAEPWIQVFGMELVGCLFSRNWNVREMALRRLSHDVSGALLLANGESTG   600
 601  NSGGGSGGSLSAGAASGSSQPSISGDVVEACCSVLSIVCADPVYKVYVAA   650
 651  LKTLRAMLVYTPCHSLAERIKLQRLLRPVVDTILVKCADANSRTSQLSIS   700
 701  TVLELCKGQAGELAVGREILKAGSIGVGGVDYVLSCILGNQAESNNWQEL   750
 751  LGRLCLIDRLLLEFPAEFYPHIVSTDVSQAEPVEIRYKKLLSLLTFALQS   800
 801  IDNSHSMVGKLSRRIYLSSARMVTAVPAVFSKLVTMLNASGSTHFTRMRR   850
 851  RLMAIADEVEIAEVIQLGVEDTVDGHQDSLQAVAPTSCLENSSLEHTVHR   900
 901  EKTGKGLSATRLSASSEDISDRLAGVSVGLPSSTTTEQPKPAVQTKGRPH   950
 951  SQCLNSSPLSHAQLMFPAPSAPCSSAPSVPDISKHRPQAFVPCKIPSASP  1000
1001  QTQRKFSLQFQRNCSEHRDSDQLSPVFTQSRPPPSSNIHRPKPSRPVPGS  1050
1051  TSKLGDATKSSMTLDLGSASRCDDSFGGGGNSGNAVIPSDETVFTPVEDK  1100
1101  CRLDVNTELNSSIEDLLEASMPSSDTTVTFKSEVAVLSPEKAENDDTYKD  1150
1151  DVNHNQKCKEKMEAEEEEALAIAMAMSASQDALPIVPQLQVENGEDIIII  1200
1201  QQDTPETLPGHTKAKQPYREDAEWLKGQQIGLGAFSSCYQAQDVGTGTLM  1250
1251  AVKQVTYVRNTSSEQEEVVEALREEIRMMGHLNHPNIIRMLGATCEKSNY  1300
1301  NLFIEWMAGGSVAHLLSKYGAFKESVVINYTEQLLRGLSYLHENQIIHRD  1350
1351  VKGANLLIDSTGQRLRIADFGAAARLASKGTGAGEFQGQLLGTIAFMAPE  1400
1401  VLRGQQYGRSCDVWSVGCAIIEMACAKPPWNAEKHSNHLALIFKIASATT  1450
1451  APSIPSHLSPGLRDVAVRCLELQPQDRPPSRELLKHPVFRTTW         1493

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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