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

NucPred

Fetching Q58EX2 from www.uniprot.org...

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

   1  MWGLLIWTLLALHQIRAARAQDDVSPYFKTEPVRTQVHLEGNRLVLTCMA    50
  51  EGSWPLEFKWLHNNRELTKFSLEYRYMITSLDRTHAGFYRCIVRNRMGAL   100
 101  LQRQTEVQVAYMGSFEEGEKHQSVSHGEAAVIRAPRIASFPQPQVTWFRD   150
 151  GRKIPPSSRIAITLENTLVILSTVAPDAGRYYVQAVNDKNGDNKTSQPIT   200
 201  LTVENVGGPADPIAPTIIIPPKNTSVVAGTSEVTLECVANARPLIKLHII   250
 251  WKKDGVLLSGGISDHNRRLTIPNPTGSDAGYYECEAVLRSSSVPSVVRGA   300
 301  YLSVLEPPQFVKEPERHITAEMEKVVDIPCQAKGVPPPSITWYKDAAVVE   350
 351  VEKLTRFRQRNDGGLQISGLVPDDTGMFQCFARNAAGEVQTSTYLAVTSI   400
 401  APNITRGPLDSTVIDGMSVVLACETSGAPRPAITWQKGERILASGSVQLP   450
 451  RFTPLESGSLLISPTHISDAGTYTCLATNSRGVDEASADLVVWARTRITK   500
 501  PPQDQSVIKGTQASMVCGVTHDPRVTIRYIWEKDGATLGTESHPRIRLDR   550
 551  NGSLHISQTWSGDIGTYTCRVISAGGNDSRSAHLRVRQLPHAPEHPVATL   600
 601  STVERRAINLTWTKPFDGNSPLIRYILEMSENNAPWTVLLASVDPKATSV   650
 651  TVKGLVPARSYQFRLCAVNDVGKGQFSKDTERVSLPEEPPTAPPQNVIAS   700
 701  GRTNQSIMIQWQPPPESHQNGILKGYIIRYCLAGLPVGYQFKNITDADVN   750
 751  NLLLEDLIIWTNYEIEVAAYNSAGLGVYSSKVTEWTLQGVPTVPPGNVHA   800
 801  EATNSTTIRFTWNAPSPQFINGINQGYKLIAWEPEQEEEVTMVTARPNFQ   850
 851  DSIHVGFVSGLKKFTEYFTSVLCFTTPGDGPRSTPQLVRTHEDVPGPVGH   900
 901  LSFSEILDTSLKVSWQEPGEKNGILTGYRISWEEYNRTNTRVTHYLPNVT   950
 951  LEYRVTGLTALTTYTIEVAAMTSKGQGQVSASTISSGVPPELPGPPTNLG  1000
1001  ISNIGPRSVTLQFRPGYDGKTSISRWLVEAQVGVVGEGEEWLLIHQLSNE  1050
1051  PDARSMEVPDLNPFTCYSFRMRQVNIVGTSPPSQPSRKIQTLQAPPDMAP  1100
1101  ANVSLRTASETSLWLRWMPLPEMEYNGNPESVGYKIKYSRSDGHGKTLSH  1150
1151  VVQDRVERDYTIEDLEEWTEYRVQVQAFNAIGSGPWSQTVVGRTRESVPS  1200
1201  SGPTNVSALATTSSSMLVRWSEVPEADRNGLVLGYKVMYKEKDSDTQPRF  1250
1251  WLVEGNSSRSAQLTGLGKYVLYEVQVLAFTRIGDGSPSHPPILERTLDDV  1300
1301  PGPPMGILFPEVRTTSVRLIWQPPAAPNGIILAYQITHRLNTTTANTATV  1350
1351  EVLAPSARQYTATGLKPESVYLFRITAQTRKGWGEAAEALVVTTEKRDRP  1400
1401  QPPSRPMVQQEDVRARSVLLSWEPGSDGLSPVRYYTIQTRELPSGRWALH  1450
1451  SASVSHNASSFIVDRLKPFTSYKFRVKATNDIGDSEFSEESESLTTLQAA  1500
1501  PDEAPTILSVTPHTTTSVLIRWQPPAEDKINGILLGFRIRYRELLYEGLR  1550
1551  GFTLRGINNPGATWAELTSMYSMRNLSRPSLTQYELDNLNKHRRYEIRMS  1600
1601  VYNAVGEGPSSPPQEVFVGEAVPTAAPRNVVVHGATATQLDVTWEPPPLD  1650
1651  SQNGDIQGYKIYFWEAQRGNLTERVKTLFLAENSVKLKNLTGYTAYMVSV  1700
1701  AAFNAAGDGPRSTPTQGQTQQAAPSAPSSVKFSELTTTSVNVSWEAPQFP  1750
1751  NGILEGYRLVYEPCSPVDGVSKIVTVDVKGNSPLWLKVKDLAEGVTYRFR  1800
1801  IRAKTFTYGPEIEANVTTGPGEGAPGPPGVPIIVRYSSAIAIHWSSGDPG  1850
1851  KGPITRYVIEARPSDEGLWDILIKDIPKEVSSYTFSMDILKPGVSYDFRV  1900
1901  IAVNDYGFGTPSSPSQSVPAQKANPFYEEWWFLVVIALVGLIFILLLVFV  1950
1951  LIIRGQSKKYAKKTDSGNSAKSGALGHSEMMSLDESSFPALELNNRRLSV  2000
2001  KNSFCRKNGLYTRSPPRPSPGSLHYSDEDVTKYNDLIPAESSSLTEKPSE  2050
2051  ISDSQGSDSEYEVDSNHQKAHSFVNHYISDPTYYNSWRRQQKGISRAQAY  2100
2101  SYTESDSGEPDHTTVTNSTSTQQGSLFRPKASRTPTPQNPPNPPSQQSTL  2150
2151  YRPPSSLAPGSRAPIAGFSSFV                              2172

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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