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

NucPred

Fetching O74208 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MNTPDDSSVSSVDSHQPYMGFDDNVEKRIRELARSLTQQSLTSSNRSVNK    50
  51  EAPADGSAPLDRVSTRASSIFSADFKGVNPVFSDEEEDDYDARLDPNSDE   100
 101  FSSKAWVQNMAKITTGDPEFYKPYSIGCCWKDLSASGESADVSYQSTFLN   150
 151  LPVKLLNAVWRKARPARESDTFRILKPMDGLLKPGELLVVLGRPGSGCTT   200
 201  LLKSISSTTHGFQISKDSVISYNGLTPNEIKKHYRGEVVYNAEADIHLPH   250
 251  LTVYQTLVTVARLKTPQNRVKGVTREDFANHVTDVAMATYGLSHTRDTKV   300
 301  GNDLVRGVSGGERKRVSIAEVWICGSKFQCWDNATRGLDSATALEFVRAL   350
 351  KTQAHIAKNVATVAIYQCSQDAYNLFNKVSVLYEGYQIYFGDAQHAKVYF   400
 401  QKMGYFCPKRQTIPDFLTSITSPAERRINKEYLDKGIKVPQTPLDMVEYW   450
 451  HNSEEYKQLREEIDETLAHQSEDDKEEIKEAHIAKQSKRARPSSPYVVSY   500
 501  MMQVKYILIRNFWRIKNSASVTLFQVFGNSAMAFILGSMFYKIQKGSSAD   550
 551  TFYFRGAAMFFAILFNAFSSLLEIFSLYEARPITEKHRTYSLYHPSADAF   600
 601  ASVISEIPPKIVTAILFNIIFYFLVNFRRDAGRFFFYFLINVIAVFAMSH   650
 651  LFRCVGSLTKTLQEAMVPASMLLLALSMYTGFAIPRTKMLGWSKWIWYIN   700
 701  PLAYLFESLMVNEFHDRRFPCNTYIPRGGAYNDVTGTERVCASVGARPGN   750
 751  DYVLGDDFLKESYDYENKHKWRGFGVGMAYVIFFFFVYLILCEFNEGAKQ   800
 801  KGEMLVFPHSVVKRMKKEGKIRDKTKMHTDKNDIENNSESITSNATNEKN   850
 851  MLQDTYDENADSESITSGSRGGSPQVGLSKSEAIFHWQNLCYDVPIKTEV   900
 901  RRILNNVDGWVKPGTLTALMGASGAGKTTLLDCLAERTTMGVITGDVMVN   950
 951  GRPRDTSFSRSIGYCQQQDLHLKTATVRESLRFSAYLRQPSSVSIEEKNE  1000
1001  YVEAVIKILEMETYADAVVGVPGEGLNVEQRKRLTIGVELAAKPKLLVFL  1050
1051  DEPTSGLDSQTAWATCQLMKKLANHGQAILCTIHQPSAMLMQEFDRLLFL  1100
1101  QKGGQTVYFGDLGKGCKTMIKYFEDHGAHKCPPDANPAEWMLEVVGAAPG  1150
1151  SHANQDYHEVWRNSEQFKQVKQELEQMEKELSQKELDNDEDANKEFATSL  1200
1201  WYQFQLVCVRLFQQYWRTPDYLWSKYILTIFNQLFIGFTFFKADHTLQGL  1250
1251  QNQMLSIFMYTVIFNPLLQQYLPTFVQQRDLYEARERPSRTFSWKAFILA  1300
1301  QIVVEVPWNIVAGTLAYCIYYYSVGFYANASQAHQLHERGALFWLFSIAF  1350
1351  YVYVGSLGLFVISFNEVAETAAHIGSLMFTMALSFCGVMATPDAMPRFWI  1400
1401  FMYRVSPLTYLIDALLSTGVANVDIRCSNTELVTFTPPQGLTCGQYMTPY  1450
1451  LNVAGTGYLTDPSATDECHFCQFSYTNDFLATVSSKYYRRWRNYGIFICF  1500
1501  IVFDYVAGIFLYWLARVPKTNGKIAKNGKTAKVNFIRRLIPF          1542

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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