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

NucPred

Fetching Q6DT37 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MERRLRALEQLARGEAGGCPGLDGLLDLLLALHHELSSGPLRRERSVAQF    50
  51  LSWASPFVSKVKELRLQRDDFEILKVIGRGAFGEVTVVRQRDTGQIFAMK   100
 101  MLHKWEMLKRAETACFREERDVLVKGDSRWVTTLHYAFQDEEYLYLVMDY   150
 151  YAGGDLLTLLSRFEDRLPPELAQFYLAEMVLAIHSLHQLGYVHRDVKPDN   200
 201  VLLDVNGHIRLADFGSCLRLNTNGMVDSSVAVGTPDYISPEILQAMEEGK   250
 251  GHYGPQCDWWSLGVCAYELLFGETPFYAESLVETYGKIMNHEDHLQFPPD   300
 301  VPDVPASAQDLIRQLLCRQEERLGRGGLDDFRNHPFFEGVDWERLASSTA   350
 351  PYIPELRGPMDTSNFDVDDDTLNHPGTLPPPSHGAFSGHHLPFVGFTYTS   400
 401  GSHSPESSSEAWAALERKLQCLEQEKVELSRKHQEALHAPTDHRELEQLR   450
 451  KEVQTLRDRLPEMLRDKASLSQTDGPPAGSPGQDSDLRQELDRLHRELAE   500
 501  GRAGLQAQEQELCRAQGQQEELLQRLQEAQEREAATASQTRALSSQLEEA   550
 551  RAAQRELEAQVSSLSRQVTQLQGQWEQRLEESSQAKTIHTASETNGMGPP   600
 601  EGGPQEAQLRKEVAALREQLEQAHSHRPSGKEEALCQLQEENRRLSREQE   650
 651  RLEAELAQEQESKQRLEGERRETESNWEAQLADILSWVNDEKVSRGYLQA   700
 701  LATKMAEELESLRNVGTQTLPARPLDHQWKARRLQKMEASARLELQSALE   750
 751  AEIRAKQGLQERLTQVQEAQLQAERRLQEAEKQSQALQQELAMLREELRA   800
 801  RGPVDTKPSNSLIPFLSFRSSEKDSAKDPGISGEATRHGGEPDLRPEGRR   850
 851  SLRMGAVFPRAPTANTASTEGLPAKPGSHTLRPRSFPSPTKCLRCTSLML   900
 901  GLGRQGLGCDACGYFCHTTCAPQAPPCPVPPDLLRTALGVHPETGTGTAY   950
 951  EGFLSVPRPSGVRRGWQRVFAALSDSRLLLFDAPDLRLSPPSGALLQVLD  1000
1001  LRDPQFSATPVLASDVIHAQSRDLPRIFRVTTSQLAVPPTTCTVLLLAES  1050
1051  EGERERWLQVLGELQRLLLDARPRPRPVYTLKEAYDNGLPLLPHTLCAAI  1100
1101  LDQDRLALGTEEGLFVIHLRSNDIFQVGECRRVQQLTLSPSAGLLVVLCG  1150
1151  RGPSVRLFALAELENIEVAGAKIPESRGCQVLAAGSILQARTPVLCVAVK  1200
1201  RQVLCYQLGPGPGPWQRRIRELQAPATVQSLGLLGDRLCVGAAGGFALYP  1250
1251  LLNEAAPLALGAGLVPEELPPSRGGLGEALGAVELSLSEFLLLFTTAGIY  1300
1301  VDGAGRKSRGHELLWPAAPMGWGYAAPYLTVFSENSIDVFDVRRAEWVQT  1350
1351  VPLKKVRPLNPEGSLFLYGTEKVRLTYLRNQLAEKDEFDIPDLTDNSRRQ  1400
1401  LFRTKSKRRFFFRVSEEQQKQQRREMLKDPFVRSKLISPPTNFNHLVHVG  1450
1451  PANGRPGARDKSPAPEEKGRVARGSGPQRPHSFSEALRRPASMGSEGLGG  1500
1501  DADPMKRKPWTSLSSESVSCPQGSLSPATSLMQVSERPRSLPLSPELESS  1550
1551  P                                                   1551

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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