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

NucPred

Fetching Q9N281 from www.uniprot.org...

The NucPred score for your sequence is 0.43 (see score help below)

   1  MDVTKKNKRDGSEVTERIITETVSTRLTSLPPKGGTSNGYAKTGSLSGGS    50
  51  RLEKHSLTHGSSGYINSSGSTRGNASTSSYRRAHSPASTLPNSPGSTFER   100
 101  KIHITRHGTYEGSSSGNSSPEYPRKEFASSSTRGRSQTRESEIRVRLQSA   150
 151  SPSTRWTELDDVKRLLKGSRSASVSPTRNSSNTLPIPKKGTVETKMVTAS   200
 201  SQSVSGTYDATILDANLPSHMWSSTLPAGSSMGTYHNNVTTQSSSLLNTN   250
 251  AYSAGSVFGVPNNMTSGSSTLHPGVSTCSSVFGMQNNLAPSSSTLSHSTA   300
 301  TASTAYGMKKNLPQSPAVVSTGVSTSAACTTNVQNEDLLHKDCKFLILEK   350
 351  DNTPAKKEMELLIMTKDSGKVFTASPASIAATSFSDDTLKKEKQAAYTAD   400
 401  TCLVSDANGDVKTVSTKGKAASAEMHNYNHRGGGSGGGGGGGGGGGGGPW   450
 451  GAAPAWCPCGSCCSWWKWLLGLLLTWLLLLGLLFGLIALAEEVRALKARV   500
 501  AELEQSRSNVLLFKEEMQRANKDWLQGEAPSVEAGGKLGLDGHQQEELWL   550
 551  FVRNRLMAEQENGNLRGSPGPKGDMGSQGPKGDRGLPGTPGIPGVLGHPG   600
 601  PQGPKGQKGSVGEPGMEGPMGQRGREGPMGPRGEPGPPGFGEKGDRGAAG   650
 651  EPGVQGPPGVPGSVGPKGSGGSPGPRGPPGPMGPQGLRGEVGLPGIKGDK   700
 701  GPLGSPGPKGDQGEKGPRGLTGEPGLRGLPGAVGEPGAKGAVGPAGPDGH   750
 751  QGPRGEQGLTGMPGTRGPPGPSGDPGKPGFTGPQGPQGLPGTPGRPGAKG   800
 801  EPGAPGRIMTSEGSSTITVPGPPGPPGAMGPPGPPGAPGPRGERGLAGES   850
 851  FMGSSSSISELLSTRSFKEPMQTCHRASFLEARVAKTTPALSGRHCVLDT   900
 901  CRKGVDLRGPPGPPGPPGPPDLPFRVRQDPEAPQVKAELPGKRYESIGTQ   950
 951  SLGLALGKSLPATSPQHRVLETYFSGPPGPPGPPGPKGDQGSSSLGLNLQ  1000
1001  GPPGPRGPKGDKGGSSSSTMFMPGPPGPPGPPGPPGSISSSGREIQQYIS  1050
1051  EYLQSDSIRSYLSGVQGPPGPPGPPGPVTTIAGETFDYSELASRVSSYLQ  1100
1101  TSGYSIGSSVSISTEDIVAALQREYLRRAGGWEPWGLGLPLPELLRASEE  1150
1151  ALVLVPSGQGRPGCGRAVAREPCGLGGPTPALPVLAGDDVRQYLRQYVIG  1200
1201  DWSLQSLDYAELSSRILSYMSSSGISIGLPGPPGPPGLPGTSYEELLSLL  1250
1251  QGSEYRGIIGPPGPPGPPGIPGNAWSSISVEDLSSYLHTAGVSSIPGPPG  1300
1301  PPGPPGPRGPPGVSGALATYAAENSDSFRSELISYLTSPDVRSFIVGPPG  1350
1351  PPGPQGPPGDSRLVSMDGSYSRDSRSSSHSASVSRGSSYSSSMGIGGASG  1400
1401  GSLGEAGAFGLDMGLGRGYGGAAEGGMYGGEGGPLGAGFAGGLDYNELAV  1450
1451  RVSESLQRQGLLQGMAYTVQGPPGQPGPQGPPGISKVFSAYSNVTEDLMD  1500
1501  FFRSKSTSVIVFLTPCCPVRGALQDHQVGLGHPALEGTREKKETKVTKSM  1550
1551  RGGEREASPSSHELPLEEQPLASVLAMAYGVHVKISPKGGSWRLTSY     1597

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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