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

NucPred

Fetching P20241 from www.uniprot.org...

The NucPred score for your sequence is 0.20 (see score help below)

   1  MWRQSTILAALLVALLCAGSAESKGNRPPRITKQPAPGELLFKVAQQNKE    50
  51  SDNPFIIECEADGQPEPEYSWIKNGKKFDWQAYDNRMLRQPGRGTLVITI   100
 101  PKDEDRGHYQCFASNEFGTATSNSVYVRKAELNAFKDEAAKTLEAVEGEP   150
 151  FMLKCAAPDGFPSPTVNWMIQESIDGSIKSINNSRMTLDPEGNLWFSNVT   200
 201  REDASSDFYYACSATSVFRSEYKIGNKVLLDVKQMGVSASQNKHPPVRQY   250
 251  VSRRQSLALRGKRMELFCIYGGTPLPQTVWSKDGQRIQWSDRITQGHYGK   300
 301  SLVIRQTNFDDAGTYTCDVSNGVGNAQSFSIILNVNSVPYFTKEPEIATA   350
 351  AEDEEVVFECRAAGVPEPKISWIHNGKPIEQSTPNPRRTVTDNTIRIINL   400
 401  VKGDTGNYGCNATNSLGYVYKDVYLNVQAEPPTISEAPAAVSTVDGRNVT   450
 451  IKCRVNGSPKPLVKWLRASNWLTGGRYNVQANGDLEIQDVTFSDAGKYTC   500
 501  YAQNKFGEIQADGSLVVKEHTRITQEPQNYEVAAGQSATFRCNEAHDDTL   550
 551  EIEIDWWKDGQSIDFEAQPRFVKTNDNSLTIAKTMELDSGEYTCVARTRL   600
 601  DEATARANLIVQDVPNAPKLTGITCQADKAEIHWEQQGDNRSPILHYTIQ   650
 651  FNTSFTPASWDAAYEKVPNTDSSFVVQMSPWANYTFRVIAFNKIGASPPS   700
 701  AHSDSCTTQPDVPFKNPDNVVGQGTEPNNLVISWTPMPEIEHNAPNFHYY   750
 751  VSWKRDIPAAAWENNNIFDWRQNNIVIADQPTFVKYLIKVVAINDRGESN   800
 801  VAAEEVVGYSGEDRPLDAPTNFTMRQITSSTSGYMAWTPVSEESVRGHFK   850
 851  GYKIQTWTENEGEEGLREIHVKGDTHNALVTQFKPDSKNYARILAYNGRF   900
 901  NGPPSAVIDFDTPEGVPSPVQGLDAYPLGSSAFMLHWKKPLYPNGKLTGY   950
 951  KIYYEEVKESYVGERREYDPHITDPRVTRMKMAGLKPNSKYRISITATTK  1000
1001  MGEGSEHYIEKTTLKDAVNVAPATPSFSWEQLPSDNGLAKFRINWLPSTE  1050
1051  GHPGTHFFTMHRIKGETQWIRENEEKNSDYQEVGGLDPETAYEFRVVSVD  1100
1101  GHFNTESATQEIDTNTVEGPIMVANETVANAGWFIGMMLALAFIIILFII  1150
1151  ICIIRRNRGGKYDVHDRELANGRRDYPEEGGFHEYSQPLDNKSAGRQSVS  1200
1201  SANKPGVESDTDSMAEYGDGDTGQFTEDGSFIGQYVPGKLQPPVSPQPLN  1250
1251  NSAAAHQAAPTAGGSGAAGSAAAAGASGGASSAGGAAASNGGAAAGAVAT  1300
1301  YV                                                  1302

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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