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

NucPred

Fetching O75643 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MADVTARSLQYEYKANSNLVLQADRSLIDRTRRDEPTGEVLSLVGKLEGT    50
  51  RMGDKAQRTKPQMQEERRAKRRKRDEDRHDINKMKGYTLLSEGIDEMVGI   100
 101  IYKPKTKETRETYEVLLSFIQAALGDQPRDILCGAADEVLAVLKNEKLRD   150
 151  KERRKEIDLLLGQTDDTRYHVLVNLGKKITDYGGDKEIQNMDDNIDETYG   200
 201  VNVQFESDEEEGDEDVYGEVREEASDDDMEGDEAVVRCTLSANLVASGEL   250
 251  MSSKKKDLHPRDIDAFWLQRQLSRFYDDAIVSQKKADEVLEILKTASDDR   300
 301  ECENQLVLLLGFNTFDFIKVLRQHRMMILYCTLLASAQSEAEKERIMGKM   350
 351  EADPELSKFLYQLHETEKEDLIREERSRRERVRQSRMDTDLETMDLDQGG   400
 401  EALAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPAL   450
 451  KPKPFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLL   500
 501  LCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQE   550
 551  MVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKG   600
 601  GERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIG   650
 651  LSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKR   700
 701  FQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGL   750
 751  FLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDL   800
 801  FADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDIL   850
 851  QMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDM   900
 901  LNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLD   950
 951  QRRLDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQT  1000
1001  YNQLLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKE  1050
1051  SIEEPSAKINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVL  1100
1101  NRGWAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPF  1150
1151  ERLYDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKV  1200
1201  ELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEH  1250
1251  LITFFVPVFEPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTE  1300
1301  LLDLQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGA  1350
1351  PTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDR  1400
1401  LNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINL  1450
1451  FVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDV  1500
1501  AHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAI  1550
1551  TKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPY  1600
1601  LEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSL  1650
1651  CWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEG  1700
1701  RCVIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQD  1750
1751  AVDYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSK  1800
1801  CISIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIIS  1850
1851  NAAEYENIPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLS  1900
1901  RMQLSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVT  1950
1951  QAMWSKDSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLT  2000
2001  DSQIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGP  2050
2051  VIAPLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATG  2100
2101  AHNYTLYFMSDAYMGCDQEYKFSVDVKEAETDSDSD                2136

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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