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

NucPred

Fetching P70670 from www.uniprot.org...

The NucPred score for your sequence is 0.64 (see score help below)

   1  MPGEATETVPATEQELPQPQAETAVLPMSSALKVAAVGQPGPTPPSSLGP    50
  51  QQSPIVTAHQPSPLPSSVSSTPFEVPFAQPITAETALPSGTAPPTPTFLP   100
 101  HLIGPPISPAALALASPMIGLAQKGARSSSAPLSLVALAPHSVQKSSVCP   150
 151  PHPLTSPPSAAGAELGALTASIPPLEPKTSTSQVPSQGTLNLKGTAPCPP   200
 201  DVVRAFPSHLENPLASVQPGLMSCPQTLSNTSPVKGVPISSALTQSRLSL   250
 251  NLKGPVSPPARNTAAPSIPLAPSTSLGCHLPLLHHSSVDSPIQPPGQSGL   300
 301  AVSNPTSVGHSGIAASCPPERCVVPALPSRLLAVDSGAAPSDDKGSSAVT   350
 351  NELCSPPGSSNVAGTSLSPKASLVPKGSNVALQPLVTQVPASQKTGLKEI   400
 401  PVSCIGATHHALDNPSAISVAPATHVPPPTSSGLVSSKDPASPVTSLVVP   450
 451  AAHKQFPAPPASATLGVPVSPLPATEGLKNLPISALVNVGAPVSPAQAGL   500
 501  PTRKDTTLQPLAPIALKESPSSQSASSLEVLSEDTVTKKTTGGPAPVVRP   550
 551  AIAGVATTTSLRADSPPAVIRADSCVSPNTVSQPLKRSVTDPAMAPRTAK   600
 601  NTAPSTTSPLVPLASEGCPVASSMALSPQNASVSETALALSPEIPKSVPF   650
 651  PDPPLAEISFSNARKVDAVSHMESSGSSRQGHPDASVTAKGTVVCLADSS   700
 701  LDTSVSASKGSALSGASSPLYPLEVSFLPEAGLAVQGPKGSLNKLSPTPP   750
 751  SSKGAPVPSTGAPPSPKGAPIVPTESSISSKQVPAEILPSPQKTPEVTAS   800
 801  RLISAVQSPKVDPIMSDVTPTSPKKTSATAVPKDTSATLSLKSVPAVTSL   850
 851  SPPKAPVAPSNEATIVPTEIPTSLKNALAAATPKETLATSIPKVTSPSPQ   900
 901  KTPKSVSLKGAPAMTSKKATEIAASKDVSPSQFPKEVPLLPHVPPTSPPK   950
 951  SPVSDTLSGALTSPPPKGPPATLAETPTYPKKSPKPAASKKTPATPSPEG  1000
1001  VTAVPLEIPPCSKKAPKTAAPKESSATSSSKRAPKTAVSKEIPSKGVTAV  1050
1051  PLEISLPLKETSKSATPGEKSASSPKRSPKTAGPKETPPGGVTAVPPEIS  1100
1101  LPPKETPQNATPNESLAASSQKRSPKTSVPKETPPGGVTAMPLEIPSAPQ  1150
1151  KAPKTAVPKQIPTPEDAVTILAGSPLSPKKASKTAAPKEAPATPSVGVIA  1200
1201  VSGEISPSPKKTSKTAAPKENSATLPPKRSPKTAAPKETPATSSEGVTAV  1250
1251  PSEISPSPPTPASKGVPVTLTPKGAPNALAESPASPKKVPKTAAPEETST  1300
1301  TPSPQKIPKVAGPKEASATPPSKKTPKTAVPKETSAPSEGVTAVPLEIPP  1350
1351  SPRKAPKTAAPKETPAPSPEGATTAPVQIPPSPRKGSKKAGSKETPTTPS  1400
1401  PEGVTAAPLEIPISSKKTSKMASPKETLVTPSSKKLSQTVGPKETSLEGA  1450
1451  TAVPLEIPPSHKKAPKTVDPKQVPLTPSPKDAPTTLAESPSSPKKAPKTA  1500
1501  APPSERVTTVPPEKPATPQKASATTASKVPVPAETQEVAVSSRETPVTPA  1550
1551  VPPVKNPSSHKKTSKTIELKEAPATLPPSPTKSPKIPSSKKAPRTSAPKE  1600
1601  FPASPSIKPVTTSLAQTAPPSLQKAPSTTIPKENLAAPAVLPVSSKSPAA  1650
1651  PAAASASLSPATAAPQTAPKEATTIPSCKKAAATETPIETSTAPSLEGAP  1700
1701  KETSETSVSKVLMSSPPKKASSSKRASTLPATTLPSLKEASVLSPTATSS  1750
1751  GKDSHISPVSDACSTGTTTPQASEKLPSKKGPTAFTEMLAAPAPESALAI  1800
1801  TAPIQKSPGANSNSASSPKCPDPSSKKDTKGLPSAVALAPQTVPVEKDTS  1850
1851  KAIETLLVSPAKGSDCLHSPKGPVGSQVATPLAAFTSDKVPPEAVSASVA  1900
1901  PKPAPAASLTLAPSPVAPLPPKQPLLESAPGSVLESPSKLPVPAEEDELP  1950
1951  PLIPPEAVSGGEPFQPILVNMPAPKPAGTPAPAPSAKQPVLKNNKGSGTE  2000
2001  SDSDESVPELEEQDSTQTATQQAQLAAAAEIDEEPVSKAKQSRSEKKARK  2050
2051  AMSKLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKI  2100
2101  EDLSQQAQLAAAEKFKVQGEAVSNIQENTQTPTVQEESEEEEVDETGVEV  2150
2151  KDIELVMSQANVSRAKAVRALKNNSNDIVNAIMELTM               2187

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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