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

NucPred

Fetching P70399 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MPGEQMDPTGSQLDSDFSQQDTPCLIIEDSQPESQVLEEDAGSHFSVLSR    50
  51  HLPNLQMHKENPVLDIVSNPEQSAVEQGDSNSSFNEHLKEKKASDPVESS   100
 101  HLGTSGSISQVIERLPQPNRTSSALAVTVEAASLPEEEKEEEELEEEKEG   150
 151  VGANAPGADSLAAEDSASSQLGFGVLELSQSQDVEEHTVPYDVNQEHLQL   200
 201  VTTNSGSSPLSDVDASTAIKCEEQPTEDIAMIEQPSKDIPVTVQPGKGIH   250
 251  VVEEQNLPLVRSEDRPSSPQVSVAAVETKEQVPARELLEEGPQVQPSSEP   300
 301  EVSSTQEDLFDQSSKTASDGCSTPSREEGGCSPVSTPATTLQLLQLSGQK   350
 351  PLVQESLSTNSSDLVAPSPDAFRSTPFIVPSSPTEQGGRKDEPMDMSVIP   400
 401  VGGEPFQKLHDDEAMETEKPLLPSQPAVSPQASTPVSRSTPVFTPGSLPI   450
 451  PSQPEFSHDIFIPSPSLEEPSDDVKKGGGLHSSSLTVECSKTSESEPKNF   500
 501  TDDLGLSMTGDSCKLMLSTSEYSQSSKMESLGSPRTEEDRENTQIDDTEP   550
 551  LSPVSNSKLPADSENVLVTPSQDDQVEMSQNVDKAKEDETEDRGDCKGRE   600
 601  DAVAEDVCIDLTCDSGSQAVPSPATRSEALSSVLDQEEAMDTKEHHPEEG   650
 651  FSGSEVEEVPETPCGSHREEPKEEPMESIPLHLSLTETQSEALCLQKEAP   700
 701  KEECPEAMEVETSVISIDSPQKLQVLDQELEHKDPDTWEEATSEDSSVVI   750
 751  VDVKEPSPRADVSCEPLEEVEKCSDSQSWEGVAPEEEPCAENRLDTPEEK   800
 801  RIECDGDSKAETTEKDAVTEDSPQPPLPSVRDEPVRPDQETQQPQVQEKE   850
 851  SPVTVDAEVADDKQLGPEGACQQLEKAPACASQSFCESSSETPFHFTLPK   900
 901  EGDIIPPLTGATPPLIGHLKLEPKRHSTPIGISNYPESTIATSDVTSESM   950
 951  VEINDPLLGNEKGDSESAPEMDGKLSLKMKLVSPETEASEESLQFSLEKP  1000
1001  TTAERKNGSTAIAEPVASLQKPVPVFGCIYEAQQEKEAQSEAPPSAPDRA  1050
1051  NLLHFPSAQEEDKERPDVTPKLRQSEQPVKPVGPVMDDAAPEDSASPVSQ  1100
1101  QRASQEQRASQEPFSPAEDVMETDLLEGLAANQDRPSKMLMDRPTQSNIG  1150
1151  IQTVDHSLCAPETVSAATQTVKSVCEQGTSTAEQNSGKQDATVQTERGSG  1200
1201  EKPASAPVDDTESLHSQGEEEFEMPQPPHGHVLHRHMRTIREVRTLVTRV  1250
1251  ITDVYYVDGTEVERKVTEETEEPIVECQECETEVSPSQTGGSSGDLGDIS  1300
1301  SFSSKASSSHHTSSGTSLSAIHSSGSSGRGAGPLKGKASGTEAADFALPS  1350
1351  SRGGPGKLSPRKGISQTGAPVCEEDGDAGLGIRQGGKAPVTPRGRGRRGR  1400
1401  PPSRTTGTRETVVSGPLGVEDISPSMSPDDKSFTRIMPRVPDSTKRTDAS  1450
1451  SSTLRRSDSPEIPFQAATGSSDGLDSSSSGNSFVGLRVVAKWSSNGYFYS  1500
1501  GKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYF  1550
1551  SAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYGLG  1600
1601  PYEAVTPLTKAADISLDNLVEGKRKRRSNISSPVTPTAASSSSTTPTRKA  1650
1651  TESPRASTGVPSGKRKLPTSEEERSPAKRGRKSATVKPGTVGAAEFVSPC  1700
1701  ETGDNIGEPSVLEEPRGPLPLNKTLFLGYAFLLTMATTSDKLASRSKLLD  1750
1751  GPTGSSEEEEEFLEIPPFNKQYTECQLRAGAGYILEDFNEAQCNTAYQCL  1800
1801  LIADQHCRTRKYFLCLASGIPCVSHVWVHDSCHANQLQNYRNYLLPAGYS  1850
1851  LEEQRILDWQPRENPFQNLKVLLVSDQQQNFLELWSEILMTGGAASVKQH  1900
1901  HSSAHNKDIALGVFDVVVTDPSCPASVLKCAEALQLPVVSQEWVIQCLIV  1950
1951  GERIGFKQHPKYKHDYVSH                                 1969

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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