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

NucPred

Fetching Q6FNY7 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MSTARFKRGNGQAGSLSNGYAVTAQQLLQAAKVDDIDAMMGFERYVPPQY    50
  51  NGRVDPDRLDQVPGRTGWLVNMHPTLISEEIASGGGSDYNPSAAGIAGVD   100
 101  FYFLDEEGGSFKSSITYDPYFFVTVTDDARLNDVEEFLKKYLETCLKDIS   150
 151  TLKKEDLKLDNHLLGLQKSLIKLSFVNSNQLFEARKLLRPILAENESNKQ   200
 201  QRNVFKHSNISNGNGMLSSNVNRFASSSVQDKKDAKQYIEDIREYDVPYH   250
 251  VRVSIDKDIRVGKWYKVTHEGFFVWPDKVAFADPVVLAFDIETTKAPLKF   300
 301  PEASVDQVMMISYMIDGDGFLITNREIISEDIEDFEYTPKPELQGHVTIF   350
 351  NEVDELAVLQRFFEHIRDVRPTVISTFNGDFFDWPFIEKRASVRGLDMFE   400
 401  EIGFAPDSEGEYKSSYCVHMDCFRWVKRDSYLPQGSQGLKAVTQAKLGYN   450
 451  PIELDPELMTPYAYERPQQLSEYSVSDAVATYYLYMKYVHPFIFSLCTII   500
 501  PLNPDEVLRKGTGTLCEMLLMVQAYQGNILLPNKHTDPLERFYDGHLLES   550
 551  ETYVGGHVESLEAGVFRSDLATEFKIDTSAIDELIEDLPHALKFAVEVEN   600
 601  KAKMEDVTNFEEIKEQIKEQLLELKENNKRHEKPLIYHVDVASMYPNIMT   650
 651  TNRLQPDSIKTEKDCASCDFNRPGKSCARRLKWAWRGEFYPAKSDEYNMI   700
 701  KRALQNETFPNKNKFSKKPYLTFDELSYSEQVAHIKKRLTEYSKKVYHRI   750
 751  KVSEIVEREAIVCQRENPFYVNTVKSFRDRRYEFKGLAKKWKGKMSSIDR   800
 801  NDKHGKDEANKMVVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGIT   850
 851  CLTGATIIQMARALVERVGRPLELDTDGIWCILPKSFPENFFLKLENGKK   900
 901  LFVSYPCSMLNYRVHQKFTNHQYQELVDPVKHKYETHSENTIFFEVDGPY   950
 951  KAMILPTSKEEGKGIKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQS  1000
1001  DIFKVFLDGKTLEECYASVAAVSNRWLDILDNKGSMLEDEDLVSLICENR  1050
1051  SMSKSLKEYEGQKSTSITTAKRLGEFLGEDMVKDKGLQCKYIISSKPHGA  1100
1101  PVTERAIPVAIFSSDINVKRSFLRRWTMDHSLDNFDIRTILDWGYYRERL  1150
1151  ASVIQKIITIPAALQNVPNPVPRVEHPDWLKRRIAVKEDKFKQSKLERFL  1200
1201  SKSSQEPQNRRIKDIEELFHEDDDIKRIKLAKVTSRNKNKRNRDVQKNDE  1250
1251  ESLVLPATMPSMEEDYVSWLSYQKIKWKIQRRDRIRRTQLFGKSGETNSR  1300
1301  SVLGSMIRKQAEMFANGSWEVLQYRDNYEAGAVDAYVIINGKVQVLKIYV  1350
1351  PRTLYINFKTDSVPLKKIKNCEVERSNAILPNDARINNDSASPLFKLTLS  1400
1401  EQVYLDELEDSGSVLNDESVLGIYESHISPAQKALMDLGTTISFKSKKVG  1450
1451  SLGKSLQDGFHLKDLTSVGNDRYLSHFDLNVCYLLHIDTNIDYEFFVIFR  1500
1501  SWENKLSIFVKKPSNNAQELLESTIIGIFKEQYHKRKDRITKFNKYINLS  1550
1551  DNVDMNSNHYTDKKKLFKAINQEFAMIKEQKGQQVLLLMQSPFPSLIKKN  1600
1601  IRYSTQIPIIELSMNILALPQLNWQNVMINKLCSYIISTSYWVSHLVSLS  1650
1651  QHSNVPICNINLEKMDFVIDVIYARRLKLDNIILWWNEQSPLPDHGGMEN  1700
1701  DFDQNTSWIMNDLDFPNINVPDVYDNVVLEVSIENLVVNTILCSTLINEA  1750
1751  EGSDLVDMNTVDVSDKPVGNNQGIVQDSFSHDALAVLKSLLKEWWDRALE  1800
1801  KNITADLLVNSLVSWVYSTDSKLFDGSLRYHIHNLTKKSLFQLMNEFNEL  1850
1851  GSFIVSADRNRLLIKTNKISPETCYAYSHYMIKSIRSNPMFTYLDLNIER  1900
1901  YWDLLIWMDKYNFSGLSCSQIEEREKQDYTAYSNWQIKYYLPRIYQSEFE  1950
1951  DWAMIILDSMVKTKRAFLESSYGTQRATQIVTGLTPQSDTEDISPLSSFS  2000
2001  KEIGKPLLQRVNKLFRNQREFILDPGFSEDYAFPILPGSHIKMDDPLLEF  2050
2051  IKSLFQILLLSKSTTLEVRQLRKEVLKFLEIREFAKEAEFQNPSDSLVIN  2100
2101  GILCEYCSYVSDLDLCRDGLDGKFQCPRCDKSINDSLLQEHMIQNLAIEY  2150
2151  QTYITQDLRCEKCHTVKRDLMSTNCNCSGNWVCTTKPEKLSNIVKIYKQV  2200
2201  AEFYNYSLVKNALESLY                                   2217

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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