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

NucPred

Fetching Q22366 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MDDPSMMPDLSHLSAEEREIIENVFKRQKDEEAKETQISQKASEELSELD    50
  51  KQITERKETSKKLVGTQDDAICQICQKTKFADGIGHKCFYCQLRSCARCG   100
 101  GRAQSKNKAIWACSLCQKRQQILAKTGKWFQPEEQPQPKISGSEPSPSPQ   150
 151  PLTDDNVPEPQQRRAEPPDKMNTPNYQNNQQPRGMGMQPNHNQTQQNFMN   200
 201  QNQNSNQHPNQNHNQNQMQNPHQNQNHVQNNHQGANNHQQNNRRAMQQQP   250
 251  MSQNQANQINQMNQNQNQQQSHNQNMTQNQRNQTGPQNQQRTNDSRTMKQ   300
 301  TPQQQPSQYQNNVGAAHQHHNQHGQQEQHHQQMNEQRTDNNRMRENTNGQ   350
 351  GGMFNRQPSLEQTTPMNKYNHVEDDGMNQRPTFYTGNSENDQRQFDGQMQ   400
 401  QGSQQNNQNQNQNNRNLRKNTVSRVTEEDYASSSNFESKKQRNNSSQSQS   450
 451  NTQGVRACPSTDDHLNRVKNRLHRQLRSMSSSEEDIIAGGGGNTLKMSTS   500
 501  AVVASGGKTAFHDDMGASNVQRLSEECNSEKDLLRYIYGDHKNSDSSSLG   550
 551  AGVGGSGGGGVLSGNSVLKSKSHALLKGSYQGGLDMQANRRRDKSLSLSP   600
 601  SRNDHFGTGSISGGDLLASRIRTFLSHPVTWQPSADQKKLIGHMILHRTE   650
 651  NSAANGDLGLKIVGGRRTDTGKLGAFITQVKPGSVADTIGRLRPGDEVVE   700
 701  WNGQSLQNATYEQVYDSIAASRYDTSVELIVSRSAIIPGGDDFLNLTPSQ   750
 751  MSSSAYSRVPSAYPSQFQRQLPNPDLFLDIHPALQQLSLPHSQSAVFPHN   800
 801  NTLTSRNRSTSSYYYSDVPDLGVPSNREMQESQAFGTGHIFGRIEVSFVY   850
 851  SHHDRQLSVALVRGFDLPPRSDGTPRNPYVKIFLLPDRSEKSRRQSAVIA   900
 901  ETLMPVWDEVFYYNGLTEPMLLQRVLELTVWDYDKFGTNSFLGETLIDLA   950
 951  SVPLDGEHSLMCILVDMDDDNPLRTVISIFKFHVIILTFLQRLKLRKASY  1000
1001  NAPTRRPQSELNYYDHSSNYYDHISQNIDKQPHHHHLAPNDEENDEYIDD  1050
1051  DELENDIDLATGGGARKSRTYRREKGMHGGHGYADWTQNHQRQSGYTSDH  1100
1101  GYGRQNMIGRAYNRRQQRRPRSATALSQMEREDMYDPTRKHRDDNEYSMR  1150
1151  ESVRHGSQYYLGDQPLYEDGRYKISQGQMTPKQHNQQHQPHPLSQAHQQQ  1200
1201  QTAGVQPQHHQGFQQQQHPQQPNQQMQQMQPPMPNQGYYSDGSETLSVHS  1250
1251  TNSMPTTMTTVNRRNMNANNTSNDNTSFAETPTANTNRVPIKETKQNSLA  1300
1301  SSSSVAGGGSAANNVMKERKKSLMTRFIPGRGAEGKRTGFARSEEVGIPG  1350
1351  NLSSDRLTEPTPPFLKQASKESTDSAHSDKFARQCWLPVLADGPLGTFVD  1400
1401  NLGPGQVVGRQVLASPVLGEIQIALMAGRSGIDVEIIKAKNLVVKPGVKV  1450
1451  CPAPYVKVYLMEGKQCIAKAKTNAATKTTSPLFQQHLIFNDSPKKKTLQV  1500
1501  TVLGDYGRMERKVFMGISQIRLEDLELGSQPLIGWYKLFHSSSLAGTGPV  1550
1551  RKDSDVSVGGAQQ                                       1563

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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