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

NucPred

Fetching P53327 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MSTEYSADSSKSFMIAMQSMIDTSQTFNLDRSKISLPDFDDELKKVQKDE    50
  51  QNQRTELTVLSQDRNDWDDIFEEFKDISFAQLQSIIDSYKTKNAVAVYKK   100
 101  IGKLINEAETTLSSNVLLETVLQMVYKHQKQELEKELLDFLGTGNIDLVS   150
 151  LLLQHRRMIVATPIETTILLIKNAVNSTPEFLTQQDIRNQVLKSAEDAKN   200
 201  RKLNPATKIIKYPHVFRKYEAGSTTAMAFAGQKFTLPVGTTRMSYNTHEE   250
 251  IIIPAADQASNKNYLYTKLLKISDLDHFCKTVFPYETLNQIQSLVYPVAY   300
 301  KTNENMLICAPTGAGKTDIALLTIINTIKQFSVVNGENEIDIQYDDFKVI   350
 351  YVAPLKALAAEIVDKFSKKLAPFNIQVRELTGDMQLTKAEILATQVIVTT   400
 401  PEKWDVVTRKANGDNDLVSKVKLLIIDEVHLLHEDRGSVIETLVARTLRQ   450
 451  VESSQSMIRIIGLSATLPNFMDVADFLGVNRQIGMFYFDQSFRPKPLEQQ   500
 501  LLGCRGKAGSRQSKENIDKVAYDKLSEMIQRGYQVMVFVHSRKETVKSAR   550
 551  NFIKLAESNHEVDLFAPDPIEKDKYSRSLVKNRDKDMKEIFQFGFGIHHA   600
 601  GMARSDRNLTEKMFKDGAIKVLCCTATLAWGVNLPADCVIIKGTQVYDSK   650
 651  KGGFIDLGISDVIQIFGRGGRPGFGSANGTGILCTSNDRLDHYVSLITQQ   700
 701  HPIESRFGSKLVDNLNAEISLGSVTNVDEAIEWLGYTYMFVRMRKNPFTY   750
 751  GIDWEEIANDPQLYERRRKMIVVAARRLHALQMIVFDEVSMHFIAKDLGR   800
 801  VSSDFYLLNESVEIFNQMCDPRATEADVLSMISMSSEFDGIKFREEESKE   850
 851  LKRLSDESVECQIGSQLDTPQGKANVLLQAYISQTRIFDSALSSDSNYVA   900
 901  QNSVRICRALFLIGVNRRWGKFSNVMLNICKSIEKRLWAFDHPLCQFDLP   950
 951  ENIIRRIRDTKPSMEHLLELEADELGELVHNKKAGSRLYKILSRFPKINI  1000
1001  EAEIFPITTNVMRIHIALGPDFVWDSRIHGDAQFFWVFVEESDKSQILHF  1050
1051  EKFILNRRQLNNQHEMDFMIPLSDPLPPQVVVKVVSDTWIGCESTHAISF  1100
1101  QHLIRPFNETLQTKLLKLRPLPTSALQNPLIESIYPFKYFNPMQTMTFYT  1150
1151  LYNTNENAFVGSPTGSGKTIVAELAIWHAFKTFPGKKIVYIAPMKALVRE  1200
1201  RVDDWRKKITPVTGDKVVELTGDSLPDPKDVHDATIVITTPEKFDGISRN  1250
1251  WQTRKFVQDVSLIIMDEIHLLASDRGPILEMIVSRMNYISSQTKQPVRLL  1300
1301  GMSTAVSNAYDMAGWLGVKDHGLYNFPSSVRPVPLKMYIDGFPDNLAFCP  1350
1351  LMKTMNKPVFMAIKQHSPDKPALIFVASRRQTRLTALDLIHLCGMEDNPR  1400
1401  RFLNIDDEEELQYYLSQVTDDTLKLSLQFGIGLHHAGLVQKDRSISHQLF  1450
1451  QKNKIQILIATSTLAWGVNLPAHLVIIKGTQFFDAKIEGYRDMDLTDILQ  1500
1501  MMGRAGRPAYDTTGTAIVYTKESKKMFYKHFLNVGFPVESSLHKVLDDHL  1550
1551  GAEITSGSITNKQEALDFLSWTFLFRRAHHNPTYYGIEDDTSTAGVSEHL  1600
1601  SSLIDSTLENLRESQCVLLHGDDIVATPFLSISSYYYISHLTIRQLLKQI  1650
1651  HDHATFQEVLRWLSLAVEYNELPVRGGEIIMNEEMSQQSRYSVESTFTDE  1700
1701  FELPMWDPHVKTFLLLQAHLSRVDLPIADYIQDTVSVLDQSLRILQAYID  1750
1751  VASELGYFHTVLTMIKMMQCIKQGYWYEDDPVSVLPGLQLRRIKDYTFSE  1800
1801  QGFIEMTPQQKKKKLLTLEEIGRFGYKKLLNVFDQLTFGMTESEDTKKRF  1850
1851  VSVCQRLPVLEGMKFEEQENNEVLTFYSKHLSSKHNNGFEVYCDKFPKIQ  1900
1901  KELWFLIGHKGDELLMIKRCQPKQMNKEVIIHCDLFIPEEIRGEELQFSL  1950
1951  INDALGLRYDMVHKLIS                                   1967

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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