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

NucPred

Fetching P25653 from www.uniprot.org...

The NucPred score for your sequence is 0.46 (see score help below)

   1  MNSFASLGLIYSVVNLLTRVEAQIVFYQNSSTSLPVPTLVSTSIADFHES    50
  51  SSTGEVQYSSSYSYVQPSIDSFTSSSFLTSFEAPTETSSSYAVSSSLITS   100
 101  DTFSSYSDIFDEETSSLISTSAASSEKASSTLSSTAQPHRTSHSSSSFEL   150
 151  PVTAPSSSSLPSSTSLTFTSVNPSQSWTSFNSEKSSALSSTIDFTSSEIS   200
 201  GSTSPKSLESFDTTGTITSSYSPSPSSKNSNQTSLLSPLEPLSSSSGDLI   250
 251  LSSTIQATTNDQTSKTIPTLVDATSSLPPTLRSSSMAPTSGSDSISHNFT   300
 301  SPPSKTSGNYDVLTSNSIDPSLFTTTSEYSSTQLSSLNRASKSETVNFTA   350
 351  SIASTPFGTDSATSLIDPISSVGSTASSFVGISTANFSTQGNSNYVPEST   400
 401  ASGSSQYQDWSSSSLPLSQTTWVVINTTNTQGSVTSTTSPAYVSTATKTV   450
 451  DGVITEYVTWCPLTQTKSQAIGVSSSISSVPQASSFSGSSILSSNSSTLA   500
 501  ASNNVPESTASGSSQYQDWSSSSLPLSQTTWVVINTTNTQGSVTSTTSPA   550
 551  YVSTATKTVDGVITEYVTWCPLTQTKSQAIGISSSTISATQTSKPSSILT   600
 601  LGISTLQLSDATFKGTETINTHLMTESTSITEPTYFSGTSDSFYLCTSEV   650
 651  NLASSLSSYPNFSSSEGSTATITNSTVTFGSTSKYPSTSVSNPTEASQHV   700
 701  SSSVNSLTDFTSNSTETIAVISNIHKTSSNKDYSLTTTQLKTSGMQTLVL   750
 751  STVTTTVNGAATEYTTWCPASSIAYTTSISYKTLVLTTEVCSHSECTPTV   800
 801  ITSVTATSSTIPLLSTSSSTVLSSTVSEGAKNPAASEVTINTQVSATSEA   850
 851  TSTSTQVSATSATATASESSTTSQVSTASETISTLGTQNFTTTGSLLFPA   900
 901  LSTEMINTTVVSRKTLIISTEVCSHSKCVPTVITEVVTSKGTPSNGHSSQ   950
 951  TLQTEAVEVTLSSHQTVTMSTEVCSNSICTPTVITSVQMRSTPFPYLTSS  1000
1001  TSSSSLASTKKSSLEASSEMSTFSVSTQSLPLAFTSSEKRSTTSVSQWSN  1050
1051  TVLTNTIMSSSSNVISTNEKPSSTTSPYNFSSGYSLPSSSTPSQYSLSTA  1100
1101  TTTINGIKTVYTTWCPLAEKSTVAASSQSSRSVDRFVSSSKPSSSLSQTS  1150
1151  IQYTLSTATTTISGLKTVYTTWCPLTSKSTLGATTQTSSTAKVRITSASS  1200
1201  ATSTSISLSTSTESESSSGYLSKGVCSGTECTQDVPTQSSSPASTLAYSP  1250
1251  SVSTSSSSSFSTTTASTLTSTHTSVPLLPSSSSISASSPSSTSLLSTSLP  1300
1301  SPAFTSSTLPTATAVSSSTFIASSLPLSSKSSLSLSPVSSSILMSQFSSS  1350
1351  SSSSSSLASLPSLSISPTVDTVSVLQPTTSIATLTCTDSQCQQEVSTICN  1400
1401  GSNCDDVTSTATTPPSTVTDTMTCTGSECQKTTSSSCDGYSCKVSETYKS  1450
1451  SATISACSGEGCQASATSELNSQYVTMTSVITPSAITTTSVEVHSTESTI  1500
1501  SITTVKPVTYTSSDTNGELITITSSSQTVIPSVTTIITRTKVAITSAPKP  1550
1551  TTTTYVEQRLSSSGIATSFVAAASSTWITTPIVSTYAGSASKFLCSKFFM  1600
1601  IMVMVINFI                                           1609

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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