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

NucPred

Fetching Q9DE14 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  MATDPGLEMASMIPALRELASAGAEEYNTTVQKPRQILCQFIDRILTDVD    50
  51  VVAVELSKNTDSQPSSVMLLDFIQHIMKSTPLMFLSANNGDQSAETNQNC   100
 101  VAFSNWIISRLLRIGATPSCKALHRKIAEVIRSLLFLFKNKSSFLFGVFT   150
 151  KDLLHLFEDLIYIHEQNMEKSVVWPVTISRFLSNASENQTYLRCTQFQLL   200
 201  NMQNIEPLESTLLMVLMDNEHDISPVFFQRQNLLLWGIGCSLLDYGSTPL   250
 251  KIQALHFLRQLIKLGGPPEQGAYFFFIVFFGILTCIKDMDLEEVSLYEMP   300
 301  LLKLVKVLFPFESKSYLNIEPVYLNMLLEKLAALFDGGILSNIQSAPLKE   350
 351  ALCYMVHYFLSIVPPGYESAKEVREAHVRCICRAFVDVLGLQSKQEYLVC   400
 401  PLHEALRIENLVFMQQQRMQPLSTDSEGGGSSSSDEVQEKRPRLSLTAKP   450
 451  LRRNTPSVPAPVDMKTKSILWKAVSAKFSSILCKLEGDEVTDEEMVSLLE   500
 501  GLNTTVRVAALNTVHIFTNDSTDTDQLVSDLSNTSGIQSVEIVPHVFWLS   550
 551  PEDILKILKICRKVLDSAHQRANINDILMKIIKIFDAILYIHAGNRLNDQ   600
 601  TLKDLCSMISLPWLQNHSNHASFKVASFDPTLMTISERIGQHYSPEIQSQ   650
 651  LVFLLCLFPKMLCPEWRLAVYQWALDSPHEIVRARCIKGFPVLLCNVSQQ   700
 701  GYGPIPKILIDCLNDASELVKKELANSVGMFASGLACGFELQYSPTAPTA   750
 751  AESEFLCSSLTVTALPSSKLSRMTASALKPFLALLNRNMPSSVKMAFIEN   800
 801  MPMLFAHLSLEKDDLDSRTVIESLLNLMEDPDKDVRTAFSGNIKHLLACA   850
 851  DCEDGYLKEIVVSRMKKAYTDAKMSRDNEMKDTLILTTGDIGRAAKGELV   900
 901  PFALLHLLHCLLSKSPCVAGASYTEIRSLAAAKSTSLHIFFSQYKKPICQ   950
 951  FLIESLHSSQAALLTNTPGRSSEMQKQEATHHREAALDILSEIANVFDFP  1000
1001  DLNRFLTRTLQLLLPYLAAKASPTASTLIRTIAKQLNVNRREILINNFKY  1050
1051  IFSHLVCSCTKDELEKSLHYLKNETEIELGSLLRQDYQGLHNELLLRLGE  1100
1101  HYQQVFSGLSILATYASNDDPYQGPRNFAKPEIMADYLQPKLLGILAFFN  1150
1151  MHLLSSSIGIEDKKMALNSLVSLMKLMGPKHISSVRVKMMTTLRTGLRYK  1200
1201  EEFPGLCCSAWDLFVRCLDQAYLGPLLSHVIVALLPLLHIQPKETVAVFR  1250
1251  YLIVENRDAVQDFLHEIYFLPDHPELKEIQKVLQEYRKETTKSTDLQTAM  1300
1301  QLSIRAIQHENVDVRMHALTSLKETLYKNQAKLLQYSTDSETVEPVISQL  1350
1351  VTVLLIGCQDANPQARLFCGECLGQLGAIDPGRLDFSPSETQGKGFTFVS  1400
1401  GVEDSDFAYELLTEQTRAFLAYADNVRAQDSAAYAIQELLSIFECKEGRT  1450
1451  DCPGRRLWRRFPEHVQEILEPHLNTRYKSSRKAVNWSRVKKPIYLSKLGN  1500
1501  NFADWSATWAGYLITKVRHELARRVFSCCSIMMKHDFKVTIYLLPHILVY  1550
1551  VLLGCNKEDQQEVYAEIMAVLKHEDPLMRRLQDSASDLSQLSTQTVFSML  1600
1601  DHLTQWAREKFQALNAEKTNPKPGTRGEPKAVSNEDYGEYQNVTRFLDLI  1650
1651  PQDTLAVASFRSKAYTRALMHFESFIMEKKQEIQEHLGFLQKLYAAMHEP  1700
1701  DGVAGVSAIRKKEASLKEQILEHESIGLLRDATACYDRAIQLKPEEIIHY  1750
1751  HGVVKSMLGLGQLSTVITQVNGILNSRSEWTAELNTYRVEAAWKLSQWDL  1800
1801  VEEYLSADRKSTTWSIRLGQLLLSAKKGERDMFYETLKVVRAEQIVPLSA  1850
1851  ASFERGSYQRGYEYIVRLHMLCELEHSVKMFLQKPSVEPAVDSLNLPARL  1900
1901  EMTQNSYRAREPILAVRRALQTINKRPNHADMIGECWLQSARVARKAGHH  1950
1951  QTAYNALLNAGESRLSELNVERAKWLWSKGDVHQALIVLQKGAELFLSST  2000
2001  SAPPEQQLIHGRAMLLVGRLMEETANFESNAVMKKYKDVTALLPEWEDGH  2050
2051  FYLAKYYDKLMPMVTDNKMEKQGDLIRYIVLHFGRSLQFGNQYIYQSMPR  2100
2101  MLSLWLDFGAKVYEWEKAGRADRLQMKNELMKINKVISDHKNQLAPYQFL  2150
2151  TAFSQLISRICHSHDEVFAVLMEIVAKVFVAYPQQAMWMMTAVSKSSYPM  2200
2201  RVNRCKEILEKAIHMKPSLGKFIGDATRLTDKLLELCNKPVDGNTSTLSM  2250
2251  NIHFKMLKKLVEETTFSEILIPLQSVMIPTLPSTAGKRDHADHDPFPGHW  2300
2301  AYLSGFDDAVEILPSLQKPKKISLKGSDGKSYIMMCKPKDDLRKDCRLME  2350
2351  FNSLINKCLRKDAESRRRELHIRTYAVIPLNDECGIIEWVNNTAGFRNIL  2400
2401  IKLYKEKGIYMGGKELRQCMLPKSAPLQEKLKVFKEALLPRHPPLFHEWF  2450
2451  LRTFPDPTSWYNSRSAYCRSTAVMSMVGYILGLGDRHGENILFDSLTGEC  2500
2501  VHVDFNCLFNKGETFEVPEIVPFRLTHNMVNGMGPMGTEGLFRRACEVIM  2550
2551  RLMREQRESLMSVLKPFLHDPLVEWSKPARGSSKGQVNETGEVMNEKAKT  2600
2601  HVLDIEQRLQGVIKTRNRVKGLPLSIEGHVHYLIQEATDENLLSQMYLGW  2650
2651  APYM                                                2654

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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