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  MRVYLDANGNEGSWFYIKPFYKLRSIGDYVVVVGDKVILSPVNADQQNLH   200
 201  VAANYELPDNPGCKEVNVLNSSTSWKISLFMEHKENQEHILKGGDVVRLF   250
 251  HAEQEKFLTMDEYKKQYHVFLRTTGRTSATAATSSKALWEIEVVQHDSCR   300
 301  GGAGDWNSLYRFKHLATGHYLAAEAEIDVSAGAMSATSASGHDLHLGDCS   350
 351  KDSGLSCSTMNSTINDKPKGKQYRLVSVPYSADIASVFVLDATTMARPDS   400
 401  LVPQSSYVRLQHICSNTWVHATSIPIDADDDKPVMSMVCCSPIKEDKEAF   450
 451  ALIPVSPVEVRDLDFANDACKVLATVTSKLDNGSISINERRALISLLQDI   500
 501  VYFIAGMENEQNKTKALEFTIKNPIRDRQKLLREQYILKQLFKILQGPFQ   550
 551  EHTAGDGPFLRLDELSDPKNSPYKNIFRLCYRILRLSQQDYRKNQEYIAK   600
 601  HFGLMQKQIGYDILAEDTITALLHNNRKLLEKHITAAEIETFVGLVRKNM   650
 651  HNWDSRFLDYLSDLCVSNRKAIAVTQELICKSVLSDKNKDILIETQVKAL   700
 701  RTGSGPVRCYKGNSEDVCLATLAEDPGDDEDRSDVQSTSTTTTWDSASLN   750
 751  EDDGTPSTGDKYEIHLKWTGQPTSRSMADLASCDGGELEAAILNYYRHQL   800
 801  NLFSNMCLNRQYLALNELSPRLDIDLILKCMSDETMPYELRASFCRLMLH   850
 851  LHVDRDPQEPVTPVKYARLWSEIPSKMSIQDYDGKNQQPDQNKQACRAKF   900
 901  NTTIAFVENYLCNVATKVWLFTDQEQNKLTFEVVKLARDLIYFGFYSFSD   950
 951  LLRLTKTLLSILDCVSDTSSGEFASTDIDSVEEETNAEAEGGVLRSIGDI  1000
1001  NTVMTSLALGSVGQAIAAPTISLQQRKSVSQLMKEYPLVMDTKLKIIEIL  1050
1051  QFILDVRLDYRISCLLSIFKREFDESEVAASAASNEASQQQSQQQEPQTP  1100
1101  GSSNETDPLDSAESVAAGAAAAAATTARQKNIDLESIGVQAEGIFDCERS  1150
1151  DAANLDLDGQGGRTFLRVLLHLIMHDYAPLVSGALHLLFRHFSQRQEVLQ  1200
1201  AFRQVQLLVSDSDVESYKQIKSDLDILRQSVEKSELWVYKAKATDELGAT  1250
1251  DAGGDAVSLEYNAALSQEQRNEYRKVKEILIRMNKFCVTASGPGSVVKPR  1300
1301  KHEQRLLRNVGVHTVVLDLLQNPYDEKDDELMKELMCLAHEFLQNFCLGN  1350
1351  QQNQVLLHNHLDLFLNPGILEAKTVCAIFKDNLALCNEVTDKVVQHFVHC  1400
1401  IEIHGRHVAYLQFLQTVVAAENQFIRRCQDMVMQELINSGEDVLVFYNDK  1450
1451  GSFNHFVQMMQQQMLGMEKLSDDSPLKYHVELVKLLACCTMGKNVYTEIK  1500
1501  CNNLLSLDDIVTIICHPLCMPEVKEAYVDFLNHCYIDTEVEMKEIYASGH  1550
1551  MWSLFEKSFLVDINQLITNPAAASNKTLQAYVLNGVTNLLGSFFASPFSD  1600
1601  QSAIVQSRQLIFVQLLQAAHRITQCRWLSLGDRFNVENCIRTLTESAKMR  1650
1651  SIALPPELEQQVATMSSKTAMLTRQTTKWLLASKQPKYEAQQAASLMRWD  1700
1701  RSIIEGLQDIVSLLEDQLKPVVEAELSLLVDILYRSELLFPAGTEARKRC  1750
1751  ESGGFIRKLIKHTEKLLEEKEERMCVKVLRTLREMMAIDVNYGEKGDALR  1800
1801  QTLLLRYFQTKSTPRLPEDEVPLLAAPLMDPAKQNHLVTHGPGAKYLQRA  1850
1851  GKTLHEMQNHLDREGASDLVVELVIKSVHSPNIFVEAVELGIALLEGGNP  1900
1901  IIQKGMFQKFLSDDLNQAFFKVFFEKMKDAQQEIKSTVTVNTTDIAAKAH  1950
1951  EHKQDTNLELDKIARKHGLKSNGVVITEELKRELHNAGLATARAYGNARN  2000
2001  IHSGEESSAISVNSPLEDILAEKLEKHKDSRDQRNQLSNKVLVMQPILRF  2050
2051  LQLLCENHNPDMQNLLRNQNNKTNNNLVSETLMFLDCICGSTTGGLGLLG  2100
2101  LYINEHNLALINQTLEALTEYCQGPCHENQNCIATHESNGLDIITALILN  2150
2151  NINPLGENRMDLVLELKNNASKLLLAIMESRGDSENAERILYNMNPKQLV  2200
2201  EVACKAYHQEELIDEQDDGDEPDAGSDDDDATVSPREVGHNIYILCHQLA  2250
2251  QHNKELAGLLKASEDPQSASFDAKTSQALMYYATHTAQIEIVRNDRTLEQ  2300
2301  IVFPIPEICEYLTTDTKIKILNTAERDDQGSKLADFFDKAEEMFNEMKWQ  2350
2351  KKLRSQPLLFWISSYMSLWSNILFNCVVVINMIVAFFYPFDNTVPELSSH  2400
2401  ISLLFWIITIFSLVIVLALPRESGIRTFIGSVILRFIFLLGPESTLCLLG  2450
2451  VVTVTLKSVHIVSIMGNKGTLEKQLIKIITDFQLLYHCIYIAFCFCGLIF  2500
2501  HPFFYSLLLFDVVYREETLVNVIRSVTRNGRSIVLTAVLALILVYLFSII  2550
2551  GYMFFKDDFLVSVDFEEQDNAPPPSVPLTLSVPVSGDSCSAPDDLGNCQA  2600
2601  AKEVAPPSAGGGEVKERSCDSLVMCIVTTLNQGLRNGGGIGDILRAPSSK  2650
2651  EGLFVARVIYDLLFFFIVIIIVLNLIFGVIIDTFADLRSEKQQKEAILKT  2700
2701  TCFICSLNRSAFDNKTVSFEEHIKSEHNMWHYLYFIVLVKVKDPTEFTGP  2750
2751  ESYVYAMVKAGILEWFPRLRAMSLAAVDADGEQIELRSMQAQLLDTQLLI  2800
2801  KNLSTQLHELKDHMTEQRKQKQRLGLLNTTANSLLPFQ              2838

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.)

Go back to the NucPred Home Page.