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

NucPred

Fetching Q06179 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MMFPINVLLYKWLIFAVTFLWSCKILLRKLLGINITWINLFKLEICGLSL    50
  51  EDGTVRLKSVRFAVFERKLFIKGLRIDSKKSSTNDLHKELPREEERTFIE   100
 101  TPEDNGGGFISKILSLSQYWLNGVTIILEDTQLVNNDITIEKFGFFLSID   150
 151  NSKHIKSLRFDSFLRKLLWNGQTIIADAIFIVNTNLLIGEIMNPLKDGLQ   200
 201  VGLDLKLGDLNIPMNLLNLFINKENVDLMSNEKLLQRLADTTKANEELKD   250
 251  EDIAKMKDDLVYAMEKFVDRIKPLKEMNVTVDKLQIKDFPLTNHPELLGM   300
 301  NKYISYNVLVSNINFNTNRFRNEMPGYTLIFEERDSPFKFSIIMARFNIY   350
 351  LNLNRKHQSHAKQLKIIEIPNVSIFGETNLFSQKFRLSNNLHAKELENAI   400
 401  FNIKGNISSLTIDMDPVNISFIKCFLSNIKVFTSSCPKNKILKENSHVKF   450
 451  LTRRRVLFDYFKCFLPLINMKFTLDDPKFVINDKDDLIIGKFSVFMISHH   500
 501  SKRYTLGNNLMEEKEETQHIFYESHWNVELLDMKLQHIIKHQKYEHTILR   550
 551  VDSIAIEEKVQLLPDILCSANADIDTLMLDLSELPTMVMLSELVHNLDSQ   600
 601  LANVEENYFKEFYEKFASNLQNMKAECSNMAKCLRQKEILPSDFMFQQLP   650
 651  DFFDYIKINIRDISSTLGARSVFMPRDVFSSVDSQSSKDLIDGKLRKYCN   700
 701  TVEKLQIALFGDKTQWHNKIGSNHATMVRSGQLTNFSKDNKQNPNHKSSI   750
 751  ADLDDISTSDATEVNHLWNINLLVNDITTSIIGETPEVSEELSTKTVSKV   800
 801  SNLSIKLFPDTESFSSNESDSKIILQINHSRGTSVVSLMSIFLAVSGIHT   850
 851  LNQIFGHCIHQKMRQSKTKQYFLALSESKKKSCIKSIKWGQLKELLEINF   900
 901  SSEYISQIIALPNGLRTKFEPTSTFITVKNCNTISVSGQYFRMMVESPTQ   950
 951  PNFWERMICINGFKVMIHIDLLKQQMKKLNSLQNWEKLPSAITLENDSWH  1000
1001  FSIPHHFEMFKIIDSIPTIFKSIKQMLYSLKTSKDDLIIFPHKIETPLSL  1050
1051  PKIKLKSKRWLFSISDDPLEAELNTIFQIGLQEQRERLAKLQEFNKRISE  1100
1101  DLIKSQKNAKEMKDDFEAIDNAILKHRTGLWAKDGKKRLRKSATDSEIPL  1150
1151  TPAALNINGKRDDRPDRTQFISPEIENAYNTLLANFSDSWIKRVKEYKVK  1200
1201  ERREFDKNFSFLWGFIDYTKLPKDINKKVLPFSTNPFLMNLIIENIDIDI  1250
1251  IRPSCGIENIPNFIHDVGKGVPKNTEYSIMIPMHLDAKFSEVRWHLRDYP  1300
1301  LPFVSIPPLSSTQSKETIPMRIYGDFMITEDMLQSDRELRTLFVPLIPSV  1350
1351  TVENTDRYYSLFVPRTMTSAKIFTDLNFEINSNHTTRVTWGGSYQPAIQQ  1400
1401  TMQCLDNFSKPPLDPSVKLGFWDKTRYLFHGKINIVWKKRGKFEISLKGA  1450
1451  KSPYMLGGESAGFIVGFDGNVNLKCNEDNDPKKFLSCSADKVHFSIPNYF  1500
1501  AKPLLVWSRPSTNTMFIPNQDDTNMQRYASFYYLLNTTSSKNEKADKEIM  1550
1551  GKSFIEKTGIKLSGGMTLDMGILFERLGPSLNERTFESKKHYLTRLCNPI  1600
1601  YVQDLSKHDSYAGFRSDFIHMSFGLSSNSNSAYNAMQLSPNGFKAFFVWW  1650
1651  KSFSGNFPVRRGPLFGLQSISPKFGEHLYTISYHADVSPLFINYMYHNAD  1700
1701  ADQILRKNYLEVAEFAGLKAKSSHFIMDLHQRKEVLTEYQAGLNVRRRVM  1750
1751  KLKFLAGDVVCQDVDIRTVSGEFSKLNYIEEKEDAEYDIFDNDMSWLDIT  1800
1801  DFQDAFFINPDNYLPKIKIMPFAFSPQFAYQKRASYGDKYQVDPKTCKPI  1850
1851  TPFDNRVSHGCTLGHNVSLRTDLVEKRVTVLKKFREKLQEGIRKNKSAGV  1900
1901  SEENLNDLLSKANSSVENAELLLKDFQKIFKQHEAGQTEQPFHFDSLNLL  1950
1951  KNTKKTLKQFEHRFFIFNVLLKWNEDARSAIFKFFYYANLSNEFASLASG  2000
2001  KGLREFEDVIKQREMTDDTTSMEAIPEGTDKANTTKQCHSCDDTEFTTEN  2050
2051  LLNIFEKNITQLSCDIKNKIHHKFFVQFITPQIQLTSLENPEACVLVSSP  2100
2101  FFMLKTLEFDANTTSNTYMQDIFLKRHGILFGNANAFLFNKKDYQEFFEL  2150
2151  YFGSSSYGQDKKEQWPPWLGLELGFEPSALKKKAVVRNISALLHHQKLAP  2200
2201  FSAKYDSLKDKIEDNICGYVPQVNVQVNSDEYLMLTKMALKLFLYVEPED  2250
2251  EELKKYIEKLIIGYDIYDTAQTRKFVNDLHDSEQILAVVEKELLFKRSLL  2300
2301  DDIGKLDLSNIHNERMHQLLRLYILRKVFTSNGNNYINRTLVWNIKVNET  2350
2351  ILHLLDKIDKPFLDIAVAKLNFQRIQHTMGLRKNTVTVKMMQIFDLGENV  2400
2401  NYHCILGPLITSSGNDTVGLASDVPLVQITWDVDKPVGGIKVVKNVETTL  2450
2451  SSLTIKLEEDRLNKLFEWLSLKELIYDGNGDDDDGASSIFDMVSSESEEG  2500
2501  KIEFSEDISSDFNEMLKRSSDYMIVEDLKLNSFKLCISYKGKGKMRLANV  2550
2551  TNFVFNFPTLRLSNQTLRVTDLLLALKKVLIKVLIKHTGRFIGNKLKRNS  2600
2601  KENKIADDTSPLKQLTTYNSYTEPEELR                        2628

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.