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

NucPred

Fetching Q62925 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MAAAAGDRASSSGFPGAAAASPEAGGGGGALQGSGAPAAGAGLLRETGSA    50
  51  GRERADWRRQQLRKVRSVELDQLPEQPLFLTASPPCPSTSPSPEPADAAA   100
 101  GASGFQPAAGPPPPGAASRCGSHSAELAAARDSGARSPAGAEPPSAAAPS   150
 151  GREMENKETLKGLHKMDDRPEERMIREKLKATCMPAWKHEWLERRNRRGP   200
 201  VVVKPIPIKGDGSEMSNLAAELQGEGQAGSAAPAPKGRRSPSPGSSPSGR   250
 251  SGKPESPGVRRKRVSPVPFQSGRITPPRRAPSPDGFSPYSPEETSRRVNK   300
 301  VMRARLYLLQQIGPNSFLIGGDSPDNKYRVFIGPQNCSCGRGTFCIHLLF   350
 351  VMLRVFQLEPSDPMLWRKTLKNFEVESLFQKYHSRRSSRIKAPSRNTIQK   400
 401  FVSRMSNCHTLSSSSTSTSSSENSIKDEEEQMCPICLLGMLDEESLTVCE   450
 451  DGCRNKLHHHCMSIWAEECRRNREPLICPLCRSKWRSHDFYSHELSSPVD   500
 501  SPTSLRGVQQPSSPQQPVAGSQRRNQESNFNLTHYGTQQIPPAYKDLAEP   550
 551  WIQAFGMELVGCLFSRNWNVREMALRRLSHDVSGALLLANGESTGTSGGG   600
 601  SGGSLSAGAASGSSQPSISGDVVEAFCSVLSIVCADPVYKVYVAALKTLR   650
 651  AMLVYTPCHSLAERIKLQRLLRPVVDTILVKCADANSRTSQLSISTLLEL   700
 701  CKGQAGELAVGREILKAGSIGVGGVDYVLSCILGNQAESNNWQELLGRLC   750
 751  LIDRLLLEISAEFYPHIVSTDVSQAEPVEIRYKKLLSLLAFALQSIDNSH   800
 801  SMVGKLSRRIYLSSARMVTTVPPLFSKLVTMLSASGSSHFARMRRRLMAI   850
 851  ADEVEIAEVIQLGSEDTLDGQQDSSQALAPPRYPESSSLEHTAHVEKTGK   900
 901  GLKATRLSASSEDISDRLAGVSVGLPSSATTEQPKPTVQTKGRPHSQCLN   950
 951  SSPLSPPQLMFPAISAPCSSAPSVPAGSVTDASKHRPRAFVPCKIPSASP  1000
1001  QTQRKFSLQFQRTCSENRDSEKLSPVFTQSRPPPSSNIHRAKASRPVPGS  1050
1051  TSKLGDASKNSMTLDLNSASQCDDSFGSGSNSGSAVIPSEETAFTPAEDK  1100
1101  CRLDVNPELNSSIEDLLEASMPSSDTTVTFKSEVAVLSPEKAESDDTYKD  1150
1151  DVNHNQKCKEKMEAEEEEALAIAMAMSASQDALPIVPQLQVENGEDIIII  1200
1201  QQDTPETLPGHTKANEPYREDTEWLKGQQIGLGAFSSCYQAQDVGTGTLM  1250
1251  AVKQVTYVRNTSSEQEEVVEALREEIRMMSHLNHPNIIRMLGATCEKSNY  1300
1301  NLFIEWMAGASVAHLLSKYGAFKESVVINYTEQLLRGLSYLHENQIIHRD  1350
1351  VKGANLLIDSTGQRLRIADFGAAARLASKGTGAGEFQGQLLGTIAFMAPE  1400
1401  VLRGQQYGRSCDVWSVGCAIIEMACAKPPWNAEKHSNHLALIFKIASATT  1450
1451  APSIPSHLSPGLRDVALRCLELQPQDRPPSRELLKHPVFRTTW         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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