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

NucPred

Fetching Q9WVB4 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MALGRTGAGAAVRARLALGLALASILSGPPAAACPTKCTCSAASVDCHGL    50
  51  GLRAVPRGIPRNAERLDLDRNNITRITKMDFAGLKNLRVLHLEDNQVSII   100
 101  ERGAFQDLKQLERLRLNKNKLQVLPELLFQSTPKLTRLDLSENQIQGIPR   150
 151  KAFRGVTGVKNLQLDNNHISCIEDGAFRALRDLEILTLNNNNISRILVTS   200
 201  FNHMPKIRTLRLHSNHLYCDCHLAWLSDWLRQRRTIGQFTLCMAPVHLRG   250
 251  FSVADVQKKEYVCPGPHSEAPACNANSLSCPSACSCSNNIVDCRGKGLTE   300
 301  IPANLPEGIVEIRLEQNSIKSIPAGAFTQYKKLKRIDISKNQISDIAPDA   350
 351  FQGLKSLTSLVLYGNKITEIPKGLFDGLVSLQLLLLNANKINCLRVNTFQ   400
 401  DLQNLNLLSLYDNKLQTISKGLFVPLQSIQTLHLAQNPFVCDCHLKWLAD   450
 451  YLQDNPIETSGARCSSPRRLANKRISQIKSKKFRCSGSEDYRNRFSSECF   500
 501  MDLVCPEKCRCEGTIVDCSNQKLARIPSHLPEYTTDLRLNDNDISVLEAT   550
 551  GIFKKLPNLRKINLSNNRIKEVREGAFDGAAGVQELMLTGNQLETMHGRM   600
 601  FRGLSSLKTLMLRSNLISCVSNDTFAGLSSVRLLSLYDNRITTITPGAFT   650
 651  TLVSLSTINLLSNPFNCNCHMAWLGRWLRKRRIVSGNPRCQKPFFLKEIP   700
 701  IQDVAIQDFTCDGNEESSCQLSPRCPEQCTCVETVVRCSNRGLHALPKGM   750
 751  PKDVTELYLEGNHLTAVPKELSAFRQLTLIDLSNNSISMLTNHTFSNMSH   800
 801  LSTLILSYNRLRCIPVHAFNGLRSLRVLTLHGNDISSVPEGSFNDLTSLS   850
 851  HLALGTNPLHCDCSLRWLSEWVKAGYKEPGIARCSSPESMADRLLLTTPT   900
 901  HRFQCKGPVDINIVAKCNACLSSPCKNNGTCSQDPVEQYRCTCPYSYKGK   950
 951  DCTVPINTCVQNPCEHGGTCHLSENLRDGFSCSCPLGFEGQRCEINPDDC  1000
1001  EDNDCENSATCVDGINNYACLCPPNYTGELCDEVIDYCVPEMNLCQHEAK  1050
1051  CISLDKGFRCECVPGYSGKLCETNNDDCVAHKCRHGAQCVDEVNGYTCIC  1100
1101  PQGFSGLFCEHPPPMVLLQTSPCDQYECQNGAQCIVVQQEPTCRCPPGFA  1150
1151  GPRCEKLITVNFVGKDSYVELASAKVRPQANISLQVATDKDNGILLYKGD  1200
1201  NDPLALELYQGHVRLVYDSLSSPPTTVYSVETVNDGQFHSVELVMLNQTL  1250
1251  NLVVDKGAPKSLGKLQKQPAVGSNSPLYLGGIPTSTGLSALRQGADRPLG  1300
1301  GFHGCIHEVRINNELQDFKALPPQSLGVSPGCKSCTVCRHGLCRSVEKDS  1350
1351  VVCECHPGWTGPLCDQEARDPCLGHSCRHGTCMATGDSYVCKCAEGYGGA  1400
1401  LCDQKNDSASACSAFKCHHGQCHISDRGEPYCLCQPGFSGHHCEQENPCM  1450
1451  GEIVREAIRRQKDYASCATASKVPIMECRGGCGSQCCQPIRSKRRKYVFQ  1500
1501  CTDGSSFVEEVERHLECGCRACS                             1523

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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