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

NucPred

Fetching Q14146 from www.uniprot.org...

The NucPred score for your sequence is 0.63 (see score help below)

   1  MAAVYSGISLKLKSKTTSWEDKLKLAHFAWISHQCFLPNKEQVLLDWARQ    50
  51  SLVAFYKKKLELKEDIVERLWIYIDNILHSRKLQNLLKNGKTINLQISLV   100
 101  KIINERVAEFSLSGSQRNICAVLRCCQGILSTPALAVIYTAKQELMVALL   150
 151  SQLCWSACRQPEGAVVAQLFEVIHLALGHYLLILQQQVNPRRAFGDVTAH   200
 201  LLQPCLVLRHLLSGGTWTQAGQGQLRQVLSRDIRSQIEAMFRGGIFQPEL   250
 251  LSSYKEGLLDQQQGDVKTGAMKNLLAPMDTVLNRLVDAGYCAASLHTSVV   300
 301  ANSVALLYKLFLDSYFKEGNQLLCFQVLPRLFGCLKISHLQEEQSKALST   350
 351  SDWTTELLVVEQLLNSVANNNIYNIAADRIRHEEAQFRFYRHVAELLINH   400
 401  AQAPIPAWFRCLKTLISLNHLILEPDLDDLLASAWIDAEVTEFRTKKAQE   450
 451  ALIRTVFQTYAKLRQVPRLFEEVLGVICRPAAEALRQPVLASGPSTVLSA   500
 501  CLLELPPSQILDTWSLVLEKFQSLVLPYLQSDADMALKSLSLSLLLHCIM   550
 551  FNMRSLDSSTPLPIVRRTQCMMERMMRELVQPLLALLPDTPGPEPELWLQ   600
 601  KVSDSVLLLSYTWAQVDAMFSLNCSQYHSMSGPLIGVALEISNLPSLLPG   650
 651  VKTQHWKKIEKFTAQFSSLGTYCLEQLYLQKMKRTLMQTSFRSEGAIQSL   700
 701  RCDAAFIIGSGRKSLNQRTTASWDGQVGMVSGLTYPVAHWHLIVSNLTIL   750
 751  ISYLCPDDVGYLASVLLRTLPMGKAQEVSIDEEAYITLEKISKAFLHSPL   800
 801  FPEMQSLHSAFLTCVTTSCSSILCSGAQRDSGLVSQQLPWLFEKDHMVVG   850
 851  HWENRFAKAGPEGIEPRGEIAQNLLSLVKSDFPIQLEGEQLESILGLLEV   900
 901  ISALQLDSLLPPYHVHYFLVLLSMAVTKLGCSCSSSLALKFLTTCYQLLG   950
 951  YLQKGKSARSVFKIMYGSDIFEVVLTSLFRASSRFLIEMDDPAWLEFLQV  1000
1001  IGTFLEELMQMLIQMKLSLVLNFRKITAFLSSSKPYTEAASSKQLENQNP  1050
1051  QGRQLLLVSLTRLCHVLGPFLKEQKLGQEAPAALSELLQQVVLQTGAVLQ  1100
1101  LCSVPGARGWRLPSVLISSVSTLLEADLGQHCRDGGADISQGSDRTLLSH  1150
1151  VALYQGVYSQILLELPALAGHDQSFQAALQFLTLFFLAPELHPKKDSVFT  1200
1201  SMFHSVRRVLADPEIPVQVTQDIEPHLGALFTQMLEVGTTEDLRLVMQCI  1250
1251  LQGLDVSNMWKADVQAVVSAVTLLRLLLNCPLSGEKASLLWRACPQIVTA  1300
1301  LTLLNREASQEQPVSLTVVGPVLDVLAALLRQGEEAIGNPHHVSLAFSIL  1350
1351  LTVPLDHLKPLEYGSVFPRLHNVLFSILQCHPKVMLKAIPSFLNSFNRLV  1400
1401  FSVMREGRQKDKGSIDDLPTVLKCARLVERMYSHIAARAEEFAVFSPFMV  1450
1451  AQYVLEVQKVTLYPAVKSLLQEGIYLILDLCIEPDVQFLRASLQPGMRDI  1500
1501  FKELYNDYLKYHKAKHEGEKRYTA                            1524

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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