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

NucPred

Fetching Q9Z0T6 from www.uniprot.org...

The NucPred score for your sequence is 0.48 (see score help below)

   1  MWPGPALLLLGLGLGLGSQPPPTGPRGLPGVLRGAPGLGQGAESSVRGGD    50
  51  TGGLSPRAAPRHASPTPPRRCPSGAAARVLLKVNSSDPAAAKANVSCQTA   100
 101  PCIMQPVKINRKDQNAPLILSRDEEATLNITVRWYCPDALVIRKSWVYFS   150
 151  VASVNDTPDWNRPVLLPQVAVSKGFSLHIPKYALPYGVYVFNFTLSIFRW   200
 201  DLAWPTVTGSDIIYIWVRKRPLKAVLLGAPRVTVKFSDELILNGSMSYDP   250
 251  EADIPTWGLQFFWYCTTNPRYYSGNYVLVINQAVCHPEQDSLNWPWAVGS   300
 301  VLTIPPKTLRGNGVYYFRMVVQKQNRTAFSDKTVHVLQGLQPKAHISCIE   350
 351  NCGPTLGVSDRFSLFLNCPSCGRQDLYSWSILSLTGHEVMFDWAGQAITR   400
 401  RNGPYLSIKAFAFRNFLENRVWVSLILKSWSGMTTTLRHPVVINHGPRVG   450
 451  KCKINPASGISMVTKFAVECSDFKDENLPLKYKIIVSELDSIGAISSVEE   500
 501  NTLGSVVYSGAEPITPAFFLPVGTVTDEYNVRLYVQVYDSLGTFSQVTLQ   550
 551  ATVTAPTVRDSSKDVLQQLLNVTMKPTSLLSTLLQKQDWLQAGYLTYVVI   600
 601  SVLNNIKGEQELQDDRARLLEHLVKQSLTFAMNTADEIGQSVMVITKLTQ   650
 651  KASDLSQADLEATSFRLRQASQDLQEYQHRHKHLQQVEVVGTGILTSLSN   700
 701  LLKLINPYYTLQDPLFVVESLSDTILANKVPGSKTTALRTSNFNMYVEKV   750
 751  ENWNVFKAFRNDSLCPNCLRATLNASTVPRLPAKAPISMMFCEFADDPFP   800
 801  WLTYPENISVDVVGFRMTGVADNNKVIEITPDIAEVYLVRKDLTPSSFNL   850
 851  TVGPGIKSDGFSKVTTGGISFEVDSRWTGELLIHIVTNVTVLFEALVYEG   900
 901  CQLTPTNLMATFLVPNDIPPIVKWSGLFDPTCSVKEARVVCLSSSLLRSI   950
 951  AQRRFSFKYNISMVLQASRFVLKPTNKLVRIALFMVHCLDMYGIQSDWQQ  1000
1001  STCVLGEKTTWKTVHCVCRNGRRSRRQLTSVKLTYHHLHTHFVTAKVIVV  1050
1051  PNPVDLRLAIISNLTQNPATFLAVLFIMILYAILAFWALHRDVIDLYFRD  1100
1101  NVVILTDNDPFDTLCYLVTIFTGSRWGSGTRANVFIQLMGTEGTSDVHCL  1150
1151  SHPYFKTLYRGSINTFLLTTKNDLGDIHSIRVWHDNSGEAPSWYLSRIKV  1200
1201  ENLFNKRIWLFVCRRWLSVDTTLDATFSVTNPDEPLKRTDFFMIDVRDKL  1250
1251  RKNHMWISIFTEIVPKPFNRLQRLSCCLAMLLSSLVCNIMFFNLNQKEKI  1300
1301  ESRHMHIIRSMLIGIESVVITIPVQLLITFFFTYSQKNLKMNLDKVAPQK  1350
1351  HPLMSEEGLSWKERLHKWHEYEMKALPRRAAVSTSAPEEKEAFETSQKHE  1400
1401  KADTQMSNKNSSNNNQEASEGVPPKAFSSQPHTTESVQKKTQIILPRWCV  1450
1451  YIAWFLVFATSGISSFFIVFYGVTYGYAKSIEWLFASFCSFCQSVFLVQP  1500
1501  CNILLRSGTRSYKPKYCKNLSWSSKYHYSEIRLQGLTMTQEEMEQLHEDI  1550
1551  AYVRSLSMYQPITEDKIQILRRENRIRRRSFLFLSYLVTHFIFLTLLLLL  1600
1601  IFSLRHNDSFYYNQFIRHRFSVDLATVMKLGDIYTWLHGVFLPLLHNDPN  1650
1651  PTFLPDSSSKILGLPLVRQVRARPSNKTCLLAKKFVQSSVAGEIHCHPQY  1700
1701  GIDPEDTQHYSSVWSKAGKQSTDKASHGFTYKPPGKRWVYHSYGVLNTYG  1750
1751  SGGYVFYFFPGQQMFNSTVRLKELEGKNWLDELTWAVIVELTTLNPDTSL  1800
1801  MCSISVVFEVSPLGVVNSSLSVYSFSLADFNRKTSSEIYLYAAILIFFCA  1850
1851  YVVDEGYIIRQERASYIRSVYNLLNFSLKCMFALLIVLFFWKYFLATKMV  1900
1901  QLYLADPEAFIPFHAVSRVDHFMRIILAFLLFLTILKTLRYSRFFYNVRL  1950
1951  AQKAIQAALPGICHTALVVSIYSFMYVAFGYLVFGQHEWNYSNMIHATQT  2000
2001  IFSYCVSAFQNTEFSGNKVLGVLFLSSFMLVMICIFINLFQAVILSAYDE  2050
2051  MKQPVYEEPSDEAEAVTYLCNRLKSGFDFLTTRSRDKDQSNFFVDMLYGQ  2100
2101  PEKNTRRFLGLKARNINGKKMIYLVV                          2126

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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