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

NucPred

Fetching Q9HDV6 from www.uniprot.org...

The NucPred score for your sequence is 0.73 (see score help below)

   1  MSLNEIAHDQPVENGPLYSEKQDHTAVDYALHILFTQFVRLSEQKISFLS    50
  51  RYHANEGKNAEPVRFNVGEQEAILLLKKGEDNEFDRCIQALVALASSKPV   100
 101  AVIESLLCWRKVRVDITSSSGTPRVVNERRSSISIYILCRVLTEIAETIP   150
 151  SNALEESTVSCLLECVFHQLLSAKNLPVSSSYFSLANWESFAFLVGSMSR   200
 201  FNFVMVSDRFIEEIEHLEKSGCDSRQKETVLVHLLRAMRYLRLQLYPTTL   250
 251  LEESIAFLQSLTSFFMKANTALKIEYAYLMEQLLRPLISRATFEVNIPAW   300
 301  SRTIETIYPVVLKMCTKTKYWNVFFPFCCTLLCLSPKQFFLKHWISSLDA   350
 351  AFFRVKDRRLRNTGLPHLSRVVWTYSNQYKEEPSIMNSNISNILKSGFSI   400
 401  GKKFSVVPFATLEELDGYAQIVRVVGAHFPELVIKEILTPLSTDAFTENI   450
 451  GPEKLMIVVRSVYYILHDMKYKKSDSTIFEYIEFEFVDLHEVAVGTPLQQ   500
 501  FVHNLSQKLLFLVFQLSTNTNCYLDSKNATSLLALYINALKVFPCLMGKL   550
 551  EQRVIDAYVKCLNCSNKIIHTVCHNSLIYFSSGLKMSKSVISCLSRKLVK   600
 601  GSEYLLRTYHEVIRIWISQQEAVIEKRNSVLSNKSCASSESNTPASVKQD   650
 651  YDDIQSWTIIEEIQSLGVLHLSSPSVGIRKFAVALLNDVKQLNTEYLMLS   700
 701  SDKVEVGDIYSEPTIVDVLKDCDSSILSVESHLPTAAERSRLRKFINDGT   750
 751  KDMLLKLATSNSGVDISIWYNVFPRFIKVCFERFPTTMALLRNTVCEKLP   800
 801  SITMQLLSRIESSELNFNLKSAVKNDNFPEFLLVQWKLYLIVACCTITYT   850
 851  SNVDYSHTDLRRTLTAVQSGNHLRGLQETIKITSAESLFSMVLPLIFTEF   900
 901  SPIREAVVFAIGCINVNAFPQLVRSLKPYISVLKQDHQEFIFAGLNFPSV   950
 951  KRRNKPDLLLRSEIAHIFAMTSHLLLHELLNEDREALSVISEFLKDLKGF  1000
1001  LSTPNVQADEKYLKLRCYFSQLLEKVLLVQNLHPSSEVLPFSGRASCWKL  1050
1051  LDEWTGFGPARAITKNREELMRAHIRGNNKDIRERDKLLASFEAGKQNLE  1100
1101  YLAIKAMIALCTAKLQQELTEGVFLFDIEILLNWFTAVFGSPSKAIVGLA  1150
1151  RKGLTALLLENSSNEVLLQKVINRCFSKEISQTISNYYFLSLSEMLIQIN  1200
1201  PNNLSKPKLLPLCLVNLSTNNLSVRLKAFELLGNFHLNNFTMTALMEFKT  1250
1251  FLESSNPALYLKPQYLFSVQLASDFTEDSFTLTSECLRYFNYGHQHRRGL  1300
1301  VTVLLPWLQNLELKMDVENKTFDSFTAVILIDLIEVTAKFTNDLPNEIEA  1350
1351  LWTSLALSRHKSNWTVILFFLMQQCYQRKTFSFVDCTRQITIYLAKTELL  1400
1401  SDLYSTLLSFVCPANVSNENQEVYKFSLEDLSSTYVANLEDLFPSEKNHI  1450
1451  SYSPCQLSLLLLMDILPNPSIITVTDDVATILHAAFIQFDHYSRIVQEQC  1500
1501  QQIFQYVVRKVLAMEGRLDYDDAYFDFNVESSLITGLRGKTKKEDDLVKY  1550
1551  HNMILKTIELLSSSYPELKQIWGEVALSWATTCPSRRLACNSFQLFRSLL  1600
1601  PDFDARMLLEIISRLVGTISDETSYLRDYSVEILRTFNSYVLVMNSDDLL  1650
1651  SYSQILWTAIACLTTIHEDEFIESVKIAYAYFLRVEETDSATQQIMETFP  1700
1701  QNWVGDYQGLQILILKGFRSTNSFEITMNFFLLLMDFKDNDLVGVGYLRI  1750
1751  LSCLLVSLPAMVYTYEHSDPITFDLSVFCHKLATLASQFNDDALIELLDT  1800
1801  YLKRKFRSIKDFLKHTVSYLYSYYFEDYELEIVSTLTMFLSNNLTWFRKS  1850
1851  TLDVLKELFPLIDFQKPIYSEHGLGIVSPLLRLLPTGYAMEALSLLTDSV  1900
1901  LHVSAPTDMQTLKLLMVDPKLKNSDDRLAGFFEIPDEDGWYEPNSEYAAA  1950
1951  ITKSNVHAVFYSCSTTEASVSTPEVRFHADEVSNYPRHVPTDSHGSLDEN  2000
2001  SLGELVTTLHSLDVFFAEDRDEELIQPDVAVDPKLDITSEDYDDRIATIL  2050
2051  SGSLRRQKQGLMAYETESFRDYSPNEEIDASAKLPMDMPPVRVRKSSFIS  2100
2101  KLKPHYFMDAESYYPSLKALGNSAEHRLSLDEIRGAAELKQNKNWNSMLD  2150
2151  QSVSMINEDSVEDHETHENYYHLRTMFQGSESNESFTDTTRSRGWH      2196

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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