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

NucPred

Fetching P97499 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MEKLCGHVPGHSDILSLKNRCLTMLPDLQPLEKIHGHRSVHSDILSLENQ    50
  51  CLTMLSDLQPTERIDGHISVHPDILSLENRCLTMLPDLQPLEKLCGHMSS   100
 101  HPDVLSLENQCLATLPTVKSTALTSPLLQGLHISHTAQADLHSLKTSNCL   150
 151  LPELPTKKTPCFSEELDLPPGPRALKSMSATAQVQEVALGQWCVSKEKEF   200
 201  QEEESTEVPMPLYSLSLEEEEVEAPVLKLTSGDSGFHPETTDQVLQEKKM   250
 251  ALLTLLCSALASNVNVKDASDLTRASILEVCSALASLEPEFILKASLYAR   300
 301  QQLNLRDIANTVLAVAALLPACRPHVRRYYSAIVHLPSDWIQVAEFYQSL   350
 351  AEGDEKKLVSLPACLRAAMTDKFAEFDEYQLAKYNPRKHRSKRRSRQPPR   400
 401  PQKTERPFSERGKCFPKSLWPLKNEQITFEAAYNAMPEKNRLPRFTLKKL   450
 451  VEYLHIHKPAQHVQALLGYRYPATLELFSRSHLPGPWESSRAGQRMKLRR   500
 501  PETWERELSLRGNKASVWEELIDNGKLPFMAMLRNLCNLLRTGISARHHE   550
 551  LVLQRLQHEKSVVHSRQFPFRFLNAHDSIDKLEAQLRSKASPFPSNTTLM   600
 601  KRIMIRNSKKNRRPASRKHLCTLTRRQLRAAMTIPVMYEQLKREKLRLHK   650
 651  ARQWNCDVELLERYRQALETAVNLSVKHNLSPMPGRTLLVYLTDANADRL   700
 701  CPKSHSQGPPLNYVLLLIGMMVARAEQVTVCLCGGGFVKTPVLTADEGIL   750
 751  KTAIKLQAQVQELEGNDEWPLDTFGKYLLSLAVQRTPIDRVILFGQRMDT   800
 801  ELLKVAKQIIWQHVNSKCLFVGVLLQKTQYISPNLNPNDVTLSGCTDGIL   850
 851  KFIAEHGASRLLEHVGQLDKLFKIPPPPGKTQAPSLRPLEENIPGPLGPI   900
 901  SQHGWRNIRLFISSTFRDMHGERDLLMRSVLPALQARVFPHRISLHAIDL   950
 951  RWGITEEETRRNRQLEVCLGEVENSQLFVGILGSRYGYIPPSYDLPDHPH  1000
1001  FHWTHEYPSGRSVTEMEVMQFLNRGQRSQPSAQALIYFRDPDFLSSVPDA  1050
1051  WKPDFISESEEAAHRVSELKRYLHEQKEVTCRSYSCEWGGVAAGRPYTGG  1100
1101  LEEFGQLVLQDVWSMIQKQHLQPGAQLEQPTSISEDDLIQTSFQQLKTPT  1150
1151  SPARPRLLQDTVQQLLLPHGRLSLVTGQAGQGKTAFLASLVSALKVPDQP  1200
1201  NEPPFVFFHFAAARPDQCLALNLLRRLCTHLRQKLGELSALPSTYRGLVW  1250
1251  ELQQKLLLKFAQSLQPAQTLVLIIDGADKLVDRNGQLISDWIPKSLPRRV  1300
1301  HLVLSVSSDSGLGETLQQSQGAYVVALGSLVPSSRAQLVREELALYGKRL  1350
1351  EESPFNNQMRLLLAKQGSSLPLYLHLVTDYLRLFTLYEQVSERLRTLPAT  1400
1401  LPLLLQHILSTLEQEHGHDVLPQALTALEVTRSGLTVDQLHAILSTWLIL  1450
1451  PKETKSWEEVLAASHSGNPFPLCPFAYLVQSLRSLLGEGPVERPGARLCL  1500
1501  SDGPLRTTIKRRYGKRLGLEKTAHVLIAAHLWKTCDPDASGTFRSCPPEA  1550
1551  LKDLPYHLLQSGNHGLLAEFLTNLHVVAAYLEVGLVPDLLEAHVLYASSK  1600
1601  PEANQKLPAADVAVFHTFLRQQASLLTQYPLLLLQQAASQPEESPVCCQA  1650
1651  PLLTQRWHDQFTLKWINKPQTLKGQQSLSLTMSSSPTAVAFSPNGQRAAV  1700
1701  GTASGTIYLLNLKTWQEEKAVVSGCDGISSFAFLSDTALFLTTFDGHLEL  1750
1751  WDLQHGCWVFQTKAHQYQITGCCLSPDRRLLATVCLGGYLKLWDTVRGQL  1800
1801  AFQYTHPKSLNCVAFHPEGQVVATGSWAGSITFFQADGLKVTKELGAPGP  1850
1851  SVCSLAFNKPGKIVAVGRIDGTVELWAWQEGARLAAFPAQCGCVSAVLFL  1900
1901  HAGDRFLTAGEDGKAQLWSGFLGRPRGCLGSLPLSPALSVALNPDGDQVA  1950
1951  VGYREDGINIYKISSGSQGPQHQELNVAVSALVWLSPSVLVSGAEDGSLH  2000
2001  GWMFKGDSLHSLWLLSRYQKPVLGLAASRELMAAASEDFTVRLWPRQLLT  2050
2051  QPHVHAVELPCCAELRGHEGPVCCCSFSPDGGILATAGRDRNLLCWDMKI  2100
2101  AQAPLLIHTFSSCHRDWITGCAWTKDNILVSCSSDGSVGLWNPEAGQQLG  2150
2151  QFSGHQSAVSAVVAVEEHIVSVSRDGTLKVWDHQGVELTSIPAHSGPISQ  2200
2201  CAAALEPRPGGQPGSELLVVTVGLDGATKLWHPLLVCQIRTLQGHSGPVT  2250
2251  AAAASEASGLLLTSDDSSVQLWQIPKEADDSYKPRSSVAITAVAWAPDGS  2300
2301  MVVSGNEAGELTLWQQAKAVATAQAPGRVSHLIWYSANSFFVLSANENVS  2350
2351  EWQVGLRKGSTSTSSSLHLKRVLQEDWGVLTGLGLAPDGQSLILMKEDVE  2400
2401  LLEMKPGSIPSSICRRYGVHSSILCTSKEYGLFYLQQGDSGLLSILEQKE  2450
2451  SGEFEEILDFNLNLNNPNGSPVSITQAKPESESSLLCATSDGMLWNLSEC  2500
2501  TSEGEWIVDNIWQKKAKKPKTQTLETELSPHSELDFSIDCWIDPTNLKAQ  2550
2551  QCKKIHLGSVTALHVLPGLLVTASKDRDVKLWERPSMQLLGLFRCEGPVS  2600
2601  CLEPWMEPSSPLQLAVGDTQGNLYFLSWE                       2629

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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