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

NucPred

Fetching Q62230 from www.uniprot.org...

The NucPred score for your sequence is 0.44 (see score help below)

   1  MCVLFSLLLLASVFSLGQTTWGVSSPKNVQGLSGSCLLIPCIFSYPADVP    50
  51  VSNGITAIWYYDYSGKRQVVIHSGDPKLVDKRFRGRAELMGNMDHKVCNL   100
 101  LLKDLKPEDSGTYNFRFEISDSNRWLDVKGTTVTVTTDPSPPTITIPEEL   150
 151  REGMERNFNCSTPYLCLQEKQVSLQWRGQDPTHSVTSSFQSLEPTGVYHQ   200
 201  TTLHMALSWQDHGRTLLCQFSLGAHSSRKEVYLQVPHAPKGVEILLSSSG   250
 251  RNILPGDPVTLTCRVNSSYPAVSAVQWARDGVNLGVTGHVLRLFSAAWND   300
 301  SGAYTCQATNDMGSLVSSPLSLHVFMAEVKMNPAGPVLENETVTLLCSTP   350
 351  KEAPQELRYSWYKNHILLEDAHASTLHLPAVTRADTGFYFCEVQNAQGSE   400
 401  RSSPLSVVVRYPPLTPDLTTFLETQAGLVGILHCSVVSEPLATVVLSHGG   450
 451  LTLASNSGENDFNPRFRISSAPNSLRLEIRDLQPADSGEYTCLAVNSLGN   500
 501  STSSLDFYANVARLLINPSAEVVEGQAVTLSCRSGLSPAPDTRFSWYLNG   550
 551  ALLLEGSSSSLLLPAASSTDAGSYYCRTQAGPNTSGPSLPTVLTVFYPPR   600
 601  KPTFTARLDLDTSGVGDGRRGILLCHVDSDPPAQLRLLHKGHVVATSLPS   650
 651  RCGSCSQRTKVSRTSNSLHVEIQKPVLEDEGVYLCEASNTLGNSSAAASF   700
 701  NAKATVLVITPSNTLREGTEANLTCNVNQEVAVSPANFSWFRNGVLWTQG   750
 751  SLETVRLQPVARTDAAVYACRLLTEDGAQLSAPVVLSVLYAPDPPKLSAL   800
 801  LDVGQGHMAVFICTVDSYPLAHLSLFRGDHLLATNLEPQRPSHGRIQAKA   850
 851  TANSLQLEVRELGLVDSGNYHCEATNILGSANSSLFFQVRGAWVQVSPSP   900
 901  ELREGQAVVLSCQVPTGVSEGTSYSWYQDGRPLQESTSSTLRIAAISLRQ   950
 951  AGAYHCQAQAPDTAIASLAAPVSLHVSYTPRHVTLSALLSTDPERLGHLV  1000
1001  CSVQSDPPAQLQLFHRNRLVASTLQGADELAGSNPRLHVTVLPNELRLQI  1050
1051  HFPELEDDGTYTCEASNTLGQASAAADFDAQAVRVTVWPNATVQEGQQVN  1100
1101  LTCLVWSTHQDSLSYTWYKGGQQLLGARSITLPSVKVLDATSYRCGVGLP  1150
1151  GHAPHLSRPVTLDVLHAPRNLRLTYLLETQGRQLALVLCTVDSRPPAQLT  1200
1201  LSHGDQLVASSTEASVPNTLRLELQDPRPSNEGLYSCSAHSPLGKANTSL  1250
1251  ELLLEGVRVKMNPSGSVPEGEPVTVTCEDPAALSSALYAWFHNGHWLQEG  1300
1301  PASSLQFLVTTRAHAGAYFCQVHDTQGTRSSRPASLQILYAPRDAVLSSF  1350
1351  RDSRTRLMVVIQCTVDSEPPAEMVLSHNGKVLAASHERHSSASGIGHIQV  1400
1401  ARNALRLQVQDVTLGDGNTYVCTAQNTLGSISTTQRLLTETDIRVTAEPG  1450
1451  LDVPEGTALNLSCLLPGGSGPTGNSSFTWFWNRHRLHSAPVPTLSFTPVV  1500
1501  RAQAGLYHCRADLPTGATTSAPVMLRVLYPPKTPTLIVFVEPQGGHQGIL  1550
1551  DCRVDSEPLAILTLHRGSQLVASNQLHDAPTKPHIRVTAPPNALRVDIEE  1600
1601  LGPSNQGEYVCTASNTLGSASASAYFGTRALHQLQLFQRLLWVLGFLAGF  1650
1651  LCLLLGLVAYHTWRKKSSTKLNEDENSAEMATKKNTIQEEVVAAL       1695

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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