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

NucPred

Fetching Q7X7E9 from www.uniprot.org...

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

   1  MAATVRFGLLVAMFQAMSRDRTAAKKRARLRALLDRAYGPGGRDDYFSAL    50
  51  RLVLPGLDRERGSYGLKEAALASVLVDALGIAKDSPDAVRLTNWRRGGGF   100
 101  RNAGNFALVAAEVLQRRQGMTSGGLTIKEVNDALDRLAATENSVCLESEK   150
 151  LLLILDRSEKASILSSLIKKTNALEMKWLLMIILKDLKLGISEKSVFHEF   200
 201  HPDAEDLFNVTCDLRLVCEKLNDRSQRHKRQDIEVGKAVRPQLSMRVNNA   250
 251  SSAWKKLHGKQVVAECKFDGDRIQIHKNGEEIHFFSRSFLDHSEYAPGMS   300
 301  KVIIENILVDRCILDGEMLVWDTVLNRFAEFGSNQEIAKAAKEGLETDRQ   350
 351  LCCILEWIASYVLALCVNILSCQDFFFSNKRESYVAFDILYAGDTSVIHQ   400
 401  SLTERHEILQKVVRPLKGHLEILVPTGGLNIHRPPDEPCWSILAHSLDDV   450
 451  EKFFKDTVDNRFFPTSPNTDELSNLSISLMIQFRFSDYSICYVLREEGII   500
 501  LKDLESKWEPGDRSGKWLKLKPDYIHAGADLDVIIIGGYYGSGRRGGEVA   550
 551  QFLVGLAVPSDDNSYPKRFLSFCRVGTGLSDEELDALVTKLKPHFRKNEY   600
 601  PKKPPRFYEVTNHSKERPDVWIESPDKQSVRFRKHLIYCITKCRSVIISI   650
 651  TSDIRTIKSEVFAAPYSLRFPRIQRLRYDKPWHECLDVQAFVDIVHSSNG   700
 701  TTHRAADDDNDLKNVKNGGSFSMNLNDSVTHCIAAEKKATRQGRIIHYSW   750
 751  ILDCCKEKRLLHLQPKFDPCLQPMHKFPEEIDSYADYFYWDIDISDLKQI   800
 801  FSNMDRAVVDSNMVHHYKKKYCADERFCFFQGCCVYFYHAPLVNADYNVI   850
 851  SDLALKRVKQDLTMHGGQVCSILAPATHLIIVSVLQAYNFDMLYKSLPPA   900
 901  ERRYLHDKRLQVVSNKWLEDSVEKQTRLPETTYSLKPDTLEEIEIERSEE   950
 951  TVQPCNDKLEENEKADTSHVKHAPRKRGRPSSSASRTAKPAPRPVRRTRA  1000
1001  RRGNQHAKIDDVEPEESDHGETGLDDQIPDTDNISKMEVDSFDKDQVSAR  1050
1051  PVRRTRARRGKQHAKIDYGQSEESDPGETGQDDQRLDADYISKMEEDSSD  1100
1101  RDQGAHPTAPRVVRRSRAQRGKWLAKIDRETGPGETGQDDKKLNADSISK  1150
1151  MEEHAHDKDQEPPPGAQLITLDEQEPKGIKSSTTETPSSPKHERNQTVLR  1200
1201  RDTAETTSSATCEKMEQMVDPLHAMLLDMIPSLGQMKTDVGNRVAEAKAE  1250
1251  TNPPWVGSSTSSYVAPVPQASASSASSSGVPAPHAGSSTQSTGVPAPDPT  1300
1301  AGAPKKKKVSYKDVAGALLKDW                              1322

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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