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

NucPred

Fetching P07149 from www.uniprot.org...

The NucPred score for your sequence is 0.12 (see score help below)

   1  MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAA    50
  51  DDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND   100
 101  IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVG   150
 151  EGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIR   200
 201  TTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYV   250
 251  VTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI   300
 301  TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ   350
 351  DYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPS   400
 401  GLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSF   450
 451  NAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATH   500
 501  ILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDYGFKQEIFDV   550
 551  TSNGLKKNPNWLEEYHPKLIKNKSGKIFVETKFSKLIGRPPLLVPGMTPC   600
 601  TVSPDFVAATTNAGYTIELAGGGYFSAAGMTAAIDSVVSQIEKGSTFGIN   650
 651  LIYVNPFMLQWGIPLIKELRSKGYPIQFLTIGAGVPSLEVASEYIETLGL   700
 701  KYLGLKPGSIDAISQVINIAKAHPNFPIALQWTGGRGGGHHSFEDAHTPM   750
 751  LQMYSKIRRHPNIMLIFGSGFGSADDTYPYLTGEWSTKFDYPPMPFDGFL   800
 801  FGSRVMIAKEVKTSPDAKKCIAACTGVPDDKWEQTYKKPTGGIVTVRSEM   850
 851  GEPIHKIATRGVMLWKEFDETIFNLPKNKLVPTLEAKRDYIISRLNADFQ   900
 901  KPWFATVNGQARDLATMTYEEVAKRLVELMFIRSTNSWFDVTWRTFTGDF   950
 951  LRRVEERFTKSKTLSLIQSYSLLDKPDEAIEKVFNAYPAAREQFLNAQDI  1000
1001  DHFLSMCQNPMQKPVPFVPVLDRRFEIFFKKDSLWQSEHLEAVVDQDVQR  1050
1051  TCILHGPVAAQFTKVIDEPIKSIMDGIHDGHIKKLLHQYYGDDESKIPAV  1100
1101  EYFGGESPVDVQSQVDSSSVSEDSAVFKATSSTDEESWFKALAGSEINWR  1150
1151  HASFLCSFITQDKMFVSNPIRKVFKPSQGMVVEISNGNTSSKTVVTLSEP  1200
1201  VQGELKPTVILKLLKENIIQMEMIENRTMDGKPVSLPLLYNFNPDNGFAP  1250
1251  ISEVMEDRNQRIKEMYWKLWIDEPFNLDFDPRDVIKGKDFEITAKEVYDF  1300
1301  THAVGNNCEDFVSRPDRTMLAPMDFAIVVGWRAIIKAIFPNTVDGDLLKL  1350
1351  VHLSNGYKMIPGAKPLQVGDVVSTTAVIESVVNQPTGKIVDVVGTLSRNG  1400
1401  KPVMEVTSSFFYRGNYTDFENTFQKTVEPVYQMHIKTSKDIAVLRSKEWF  1450
1451  QLDDEDFDLLNKTLTFETETEVTFKNANIFSSVKCFGPIKVELPTKETVE  1500
1501  IGIVDYEAGASHGNPVVDFLKRNGSTLEQKVNLENPIPIAVLDSYTPSTN  1550
1551  EPYARVSGDLNPIHVSRHFASYANLPGTITHGMFSSASVRALIENWAADS  1600
1601  VSSRVRGYTCQFVDMVLPNTALKTSIQHVGMINGRKLIKFETRNEDDVVV  1650
1651  LTGEAEIEQPVTTFVFTGQGSQEQGMGMDLYKTSKAAQDVWNRADNHFKD  1700
1701  TYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEK  1750
1751  IFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPA  1800
1801  DATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRS  1850
1851  NYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVA  1900
1901  AGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEGHLFEIIDEASKK  1950
1951  SAVKPRPLKLERGFACIPLVGISVPFHSTYLMNGVKPFKSFLKKNIIKEN  2000
2001  VKVARLAGKYIPNLTAKPFQVTKEYFQDVYDLTGSEPIKEIIDNWEKYEQ  2050
2051  S                                                   2051

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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