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

NucPred

Fetching Q05471 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MTTSRKSHAKDKKAGGEQDLADLKFRYDLLTNELFHLREFVSLVDYDPTH    50
  51  FNDSESFQKFLRETHLSLEERGEKFTDDVAKKGTNGDLTRRRRNLRTSTV   100
 101  VSSETTNEKKGDIELKLESIAPLVRNKCEELKYKLSDHSNRKSIVPQKRP   150
 151  IQHLKKREAAKSLKFKSERKENPLPLHEHIAEERYDHIAKVEEPSEAFTI   200
 201  KCPSDDSSFENTSEHYSDNFYFTTSSEEEDIKKKRGRKKKKPRIKLVVHP   250
 251  PKQTITNPLHVVKPGYESLHEYIASFKSLEDDLTLEEYNKYIDEQRRLLS   300
 301  RLKKGIENGALKYDKETDSLQPITSKEIKTIITYKPDPISYFYKQQDLQI   350
 351  HTDHLINQGIHMSKLFRSSTKARIARAKKVSQMIEQHFKHVAGAEERKAK   400
 401  EEERHKKSLARFAVQAVKKRWNMAEKAYRILRKDEEEQLKRIEGKQHLSK   450
 451  MLEKSTQLLEAQLNQVNDDGRSSTPSSDSNDVLSESDDDMDDELSTSSDE   500
 501  DEEVDADVGLENSPASTEATPTDESLNLIQLKEKYGHFNGSSTVYDSRNK   550
 551  DEKFPTLDKHESSSSESSVMTGEESSIYSSSENESQNENDRESDDKTPSV   600
 601  GLSALFGKGEESDGDLDLDDSEDFTVNSSSVEGEELEKDQVDNSAATFER   650
 651  AGDFVHTQNENRDDIKDVEEDAETKVQEEQLSVVDVPVPSLLRGNLRTYQ   700
 701  KQGLNWLASLYNNHTNGILADEMGLGKTIQTISLLAYLACEKENWGPHLI   750
 751  VVPTSVLLNWEMEFKRFAPGFKVLTYYGSPQQRKEKRKGWNKPDAFHVCI   800
 801  VSYQLVVQDQHSFKRKRWQYMVLDEAHNIKNFRSTRWQALLNFNTQRRLL   850
 851  LTGTPLQNNLAELWSLLYFLMPQTVIDGKKVSGFADLDAFQQWFGRPVDK   900
 901  IIETGQNFGQDKETKKTVAKLHQVLRPYLLRRLKADVEKQMPAKYEHIVY   950
 951  CKLSKRQRFLYDDFMSRAQTKATLASGNFMSIVNCLMQLRKVCNHPNLFE  1000
1001  VRPILTSFVLEHCVASDYKDVERTLLKLFKKNNQVNRVDLDFLNLVFTLN  1050
1051  DKDLTSYHAEEISKLTCVKNFVEEVNKLRETNKQLQEEFGEASFLNFQDA  1100
1101  NQYFKYSNKQKLEGTVDMLNFLKMVNKLRCDRRPIFGKNLIDLLTKDRRV  1150
1151  KYDKSSIIDNELIKPLQTRVLDNRKIIDTFAVLTPSAVSLDMRKLALGLN  1200
1201  DDSSVGENTRLKVMQNCFEVSNPLHQLQTKLTIAFPDKSLLQYDCGKLQK  1250
1251  LAILLQQLKDNGHRALIFTQMTKVLDVLEQFLNYHGYLYMRLDGATKIED  1300
1301  RQILTERFNTDSRITVFILSSRSGGLGINLTGADTVIFYDSDWNPAMDKQ  1350
1351  CQDRCHRIGQTRDVHIYRFVSEHTIESNILKKANQKRQLDNVVIQEGDFT  1400
1401  TDYFSKLSVRDLLGSELPENASGGDKPLIADADVAAKDPRQLERLLAQAE  1450
1451  DEDDVKAANLAMREVEIDNDDFDESTEKKAANEEEENHAELDEYEGTAHV  1500
1501  DEYMIRFIANGYYY                                      1514

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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