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

NucPred

Fetching P29993 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MGDNIIGSASFLHLGDIVSLYAEGSVCGFLSTLGLVDDRTVVCPEAGDLS    50
  51  CPPKKFRDCLIKICPMNRYSAQKQFWKAAKQSASSNTDPNLLKRLHHAAE   100
 101  IEKKQNETENKKLLGTSIQYGRAVVQLLHLKSNKYLTVNKRLPSLLEKNA   150
 151  MRVYLDANGNEGSWFYIKPFYKLRSIGDYVVVGDKVILSPVNADQQNLHV   200
 201  AANYELPDNPGCKEVNVLNSSTSWKISLFMEHKENQEHILKGGDVVRLFH   250
 251  AEQEKFLTMDEYKKQYHVFLRTTGRTSATAATSSKALWEIEVVQHDSCRG   300
 301  GAGDWNSLYRFKHLATGHYLAAEAEIDVSAGAMSATSASGHDLHLGDCSK   350
 351  DSGLSCSTMNSTINDKPKGKQYRLVSVPYSADIASVFVLDATTMARPDSL   400
 401  VPQSSYVRLQHICSNTWVHATSIPIDADDDKPVMSMVCCSPIKEDKEAFA   450
 451  LIPVSPVEVRDLDFANDACKVLATVTSKLDNGSISINERRALISLLQDIV   500
 501  YFIAGMENEQNKTKALEFTIKNPIRDRQKLLREQYILKQLFKILQGPFQQ   550
 551  HTAGDGPFLRLDELSDPKNSPYKNIFRLCYRILRLSQQDYRKNQEYIAKH   600
 601  FGLMQKQIGYDILAEDTITALLHNNRKLLEKHITAAEIETFVGLVRKNMH   650
 651  NWDSRFLDYLSDLCVSNRKAIAVTQELICKSVLSDKNKDILIETQVKALR   700
 701  TGSGPVRCYKGNSEDVCLATLAEDAGDDEDRSDVQSTSTTTTWDSASLNE   750
 751  DDGTPSTGDKYEIHLKWTGQPTSRSMADLASCDGGELEAAILNYYRHQLN   800
 801  LFSNMCLNRQYLALNELSPRLDIDLILKCMSDETMPYELRASFCRLMLHL   850
 851  HVDRDPQEPVTPVKYARLWSEIPSKMSIQDYDGKNQQPDQNKQACRAKFN   900
 901  TTIAFVENYLCNVATKVWLFTDQEQNKLTFEVVKLARDLIYFGFYSFSDL   950
 951  LRLTKTLLSILDCVSDTSSGEFASTDIDSVEEETNAEAEGGVLRSIGDIN  1000
1001  TVMTSLALGSVGQAIAAPTISLQQRKSVSQLMKEYPLVMDTKLKIIEILQ  1050
1051  FILDVRLDYRISCLLSIFKREFDESEVAASAASNEASQQQSQQQEPQTPG  1100
1101  SSNETDPLDSAESVAAGAAAAAATTARQKNIDLESIGVQAEGIFDCERSD  1150
1151  AANLDLDGQGGRTFLRVLLHLIMHDYAPLVSGALHLLFRHFSQRQEVLQA  1200
1201  FRQVQLLVSDSDVESYKQIKSDLDILRQSVEKSELWVYKAKATDELGATD  1250
1251  AGGDAVSLEYNAALSQEQRNEYRKVKEILIRMNKFCVTASGPGSVVKPRK  1300
1301  HEQRLLRNVGVHTVVLDLLQNPYDEKDDELMKELMCLAHEFLQNFCLGNQ  1350
1351  QNQVLLHNHLDLFLNPGILEAKTVCAIFKDNLALCNEVTDKVVQHFVHCI  1400
1401  EIHGRHVAYLQFLQTVVRAENQFIRRCQDMVMQELINSGEDVLVFYNDKG  1450
1451  SFNHFVQMMQQQMLRMEKLSDDSPLKYHVELVKLLACCTMGKNVYTEIKC  1500
1501  NNLLSLDDIVTIICHPLCMPEVKEAYVDFLNHCYIDTEVEMKEIYASGHM  1550
1551  WSLFEKSFLVDINQLITNPAAASNKTLQAYVLNGVTNLLGSFFASPFSDQ  1600
1601  SAIVQSRQLIFVQLLQAAHRITQCRWLSLGDRFNVENCIRTLTESAKMRS  1650
1651  IALPPELEQQVATMSSKTAMLTRQTTKWLLASKQPKYEAQQAASLMRWDR  1700
1701  SIIEGLQDIVSLLEDQLKPVVEAELSLLVDILYRSELLFPAGTEARKRCE  1750
1751  SGGFIRKLIKHTEKLLEEKEERMCVKVLRTLREMMAIDVNYGEKGDALRQ  1800
1801  TLLLRYFQTKSTPRLPEDEVPLLAAPLMDPAKQNHLVTHGPGAKYLQRAG  1850
1851  KTLHEMQNHLDREGASDLVVELVIKSVHSPNIFVEAVELGIALLEGGNPI  1900
1901  IQKGMFQKFLSDDLNQAFFKVFFEKMKDAQQEIKSTVTVNTTDIAAKAHE  1950
1951  HKQDTNLELDKIARKHGLKSNGVVITEELKRELHNAGLATARAYGNARNI  2000
2001  HSGEESSAISVNSPLEDILAEKLEKHKDSRDQRNQLSNKVLVMQPILRFL  2050
2051  QLLCENHNPDMQNLLRNQNNKTNNNLVSETLMFLDCICGSTTGGLGLLGL  2100
2101  YINEHNVALINQTLEALTEYCQGPCHENQNCIATHESNGLDIITALILNN  2150
2151  INPLGENRMDLVLELKNNASKLLLAIMESRGDSENAERILYNMNPKQLVE  2200
2201  VACKAYHQEELIDEQDDGDEPDAGSDDDDATVSPREVGHNIYILCHQLAQ  2250
2251  HNKELAGLLKASEDPQSASFDAKTSQALMYYATHTAQIEIVRNDRTLEQI  2300
2301  VFPIPEICEYLTTDTKIKILNTAERDDQGSKVADFFDKAEEMFNEMKWQK  2350
2351  KLRSQPLLFWISSYMSLWSNILFNCVVVINMIVAFFYPFDNTVPELSSHI  2400
2401  SLLFWIITIFSLVIVLALPRESGIRTFIGSVILRFIFLLGPESTLCLLGV  2450
2451  VTVTLKSVHIVSIMGNKGTLEKQLIKIITDFQLLYHCIYIAFCFCGLIFH  2500
2501  PFFYSLLLFDVVYREETLVNVIRSVTRNGRSIVLTAVLALILVYLFSIIG  2550
2551  YMFFKDDFLVSVDFEEQDNAPPPSVPLTLSVPVSGDSCSAPDDLGNCQAA  2600
2601  KEVAPPSAGGGEVKERSCDSLVMCIVTTLNQGLRNGGGIGDILRAPSSKE  2650
2651  GLFVARVIYDLLFFFIVIIIVLNLIFGVIIDTFADLRSEKQQKEAILKTT  2700
2701  CFICSLNRSAFDNKTVSFEEHIKSEHNMWHYLYFIVLVKVKDPTEFTGPE  2750
2751  SYVYAMVKAGILEWFPRLRAMSLAAVDADGEQIELRSMQAQLLDTQLLIK  2800
2801  NLSTQLHELKDHMTEQRKQKQRLGLLNTTANSLLPFQ               2837

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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