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

NucPred

Fetching P13709 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MSSSEPPPRYEPPVEPVNGIVQPPVIPPAERPGRNTNQLQYLIKTVMKVI    50
  51  WKHHFSWPFQQPVDAKKLNLPDYHKIIKQPMDMGTIKKRLENNYYWSAKE   100
 101  TIQDFNTMFNNCYVYNKPGEDVVVMAQTLEKVFLQKIESMPKEELELEPV   150
 151  TAKGGKKKQRAPATPKSSSGGAGASTGSGTSSAAVTSGPGSGSTKVSVAA   200
 201  SSAQQSGLQGATGAGGGSSSTPGTQPGSGAGGAIAARPVSAMGGTVSSTA   250
 251  GGAPSIPPISTMPPHTVPGSTNTTTTAMAGGVGGPGAAGANPNAAALMAS   300
 301  LLNAGQTGAYPGAPGQTAVNSSSLLDGSTAAVAAAAAAAAAAAAAAGGAA   350
 351  GAAGGAGTIPAVAVNAANAVQAYVNAGVSVGVDAVIPPQQPAKIKKGVKR   400
 401  KADTTTPTANAFESPYTQMDSKSAKIATRRESNRQDLTFQGSGYNMSPLG   450
 451  VSGVPGLGGLVAGGVAGVAVAKNKEKLSDALKSCNEILKELFSKKHSGYA   500
 501  WPFYKPVDAEMLGLHDYHDIIKKPMDLGTVKRKMDNREYKSAPEFAADVR   550
 551  LIFTNCYKYNPPDHDVVAMGRKLQDVFEMRYANIPDEPVANAAHHHGHGH   600
 601  GHGHGHGHGHGHGHGHGHGHGYGGSSSLKHDASDSSSEDSSDTENESNSD   650
 651  EERSARLKMLESKLLGLQEEIRKLSEEASAKKKAKKKLKEKKKSIGGGSG   700
 701  SGSASHHCHATGGGANAGGAGGPGSGGHGSVSVPGGVGSLGPGGAGGANL   750
 751  NALLGGSLVGHGGAAVAGGVPNVGALHSQVHDVAMAFSQMAGGGAAAGAG   800
 801  FGAGVTAAGASSGGKAGTLAGALAAGAAAGAGGTTAGSGSSKGAKSKGGR   850
 851  GAKGSGAGGVGASNNAAAGNAAGGAAGAAAGAGSVGGVGGAGAAGGGNAS   900
 901  KRAKGSSSAGAGGGVGGANASAGGAGARGSSKKKPSQVMNFDSEEEDTAK   950
 951  PMSYDEKRQLSLDINKLPGDKLGRVVHIIQNREPSLRDSNPDEIEIDFET  1000
1001  LKPSTLRELESYVASCLRKKTHKKPSGKSKDEQMAEKKQELEKRLQDVTG  1050
1051  QLGASKKTAKKDESASSKVEAVQPANPVSSSSSSSDSSSSSSSDSSSSDS  1100
1101  SDSEAGDGDERPPRKKKSRDSNGSNVNNPSINVVMGGNLPSGALSPTTML  1150
1151  MGLDHVVNSNTPTSQMSNMLGNANPLTAAAMLNNNNKTSLPGSNFGGAPA  1200
1201  PGNMMHAGAGVPVAGAAVSASTGQQHNKNGPNDLSKVQPGGPINAALPPH  1250
1251  SFAGGTATVATSQSSGGIRIASNLHKPSGLGGGDLGEHHAALAAALTSGI  1300
1301  NSTGTAGGGINNNGGSNNNANPLGGSHGDAMVNASLASLASGLKQIPQFD  1350
1351  DPVEQSLASLEFSAGSTGKSGLTDNFLMQQHLMQPAGPQQQQQQQQQQPF  1400
1401  GHQQQQQQQQQQQQQQQQHMDYVTELLSKGAENVGGMNGNHLLNFNLDMA  1450
1451  AAYQQKHPQQQQQQAHNNGFNVADFGMAGFDGLNMTAASFLDLEPSLQQQ  1500
1501  QMQQMQLQQQHHQQQQQQTHQQQQQHQQQHHQQQQQQQLTQQQLQQQQQQ  1550
1551  QQQQQHLQQQQHQQQHHQAANKLLIIPKPIESMMPSPPDKQQLQQHQKVL  1600
1601  PPQQSPSDMKLHPNAAAAAAVASAQAKLVQTFKANEQNLKNASSWSSLAS  1650
1651  ANSPQSHTSSSSSSSKAKPAMDSFQQFRNKAKERDRLKLLEAAEKEKKNQ  1700
1701  KEAAEKEQQRKHHKSSSSSLTSAAVAQAAAIAAATAAAAVTLGAAAAAAL  1750
1751  ASSASNPSGGSSSGGAGSTSQQAITGDRDRDRDRERERERSGSGGGQSGN  1800
1801  GNNSSNSANSNGPGSAGSGGSGGGGGSGPASAGGPNSGGGGTANSNSGGG  1850
1851  GGGGGPALLNAGSNSNSGVGSGGAASSNSNSSVGGIVGSGGPGSNSQGSS  1900
1901  GGGGGGPASGGGMGSGAIDYGQQVAVLTQVAANAQAQHVAAAVAAQAILA  1950
1951  ASPLGAMESGRKSVHDAQPQISRVEDIKASPGGQGQSSPAQQSPQDRAAA  2000
2001  KRAEQRRAEQERRRREALAGQIDMNMQSDLMAAFEETL              2038

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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