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

NucPred

Fetching P56645 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MPRGEAPGPGRRGAKDEALGEESGERWSPEFHLQRKLADSSHSEQQDRNR    50
  51  VSEELIMVVQEMKKYFPSERRNKPSTLDALNYALRCVHSVQANSEFFQIL   100
 101  SQNGAPQADVSMYSLEELATIASEHTSKNTDTFVAVFSFLSGRLVHISEQ   150
 151  AALILNRKKDVLASSHFVDLLAPQDMRVFYAHTARAQLPFWNNWTQRAAR   200
 201  YECAPVKPFFCRIRGGEDRKQEKCHSPFRIIPYLIHVHHPAQPELESEPC   250
 251  CLTVVEKIHSGYEAPRIPVNKRIFTTTHTPGCVFLEVDEKAVPLLGYLPQ   300
 301  DLIGTSILSYLHPEDRSLMVAIHQKVLKYAGHPPFEHSPIRFCTQNGDYI   350
 351  ILDSSWSSFVNPWSRKISFIIGRHKVRTSPLNEDVFATKIKKMNDNDKDI   400
 401  TELQEQIYKLLLQPVHVSVSSGYGSLGSSGSQEQLVSIASSSEASGHRVE   450
 451  ETKAEQMTLQQVYASVNKIKNLGQQLYIESMTKSSFKPVTGTRTEPNGGG   500
 501  ECKTFTSFHQTLKNNSVYTEPCEDLRNDEHSPSYQQINCIDSVIRYLKSY   550
 551  NIPALKRKCISCTNTTSSSSEEDKQNHKADDVQALQAGLQIPAIPKSEMP   600
 601  TNGRSIDTGGGAPQILSTAMLSLGSGISQCGYSSTIVHVPPPETARDATL   650
 651  FCEPWTLNMQPAPLTSEEFKHVGLTAAVLSAHTQKEEQNYVDKFREKILS   700
 701  SPYSSYLQQESRSKAKYSYFQGDSTSKQTRSAGCRKGKHKRKKLPEPPDS   750
 751  SSSNTGSGPRRGAHQNAQPCCPSAASSPHTSSPTFPPAAMVPSQAPYLVP   800
 801  AFPLPAATSPGREYAAPGTAPEGLHGLPLSEGLQPYPAFPFPYLDTFMTV   850
 851  FLPDPPVCPLLSPSFLPCPFLGATASSAISPSMSSAMSPTLDPPPSVTSQ   900
 901  RREEEKWEAQSEGHPFITSRSSSPLQLNLLQEEMPRPSESPDQMRRNTCP   950
 951  QTEYCVTGNNGSESSPATTGALSTGSPPRENPSHPTASALSTGSPPMKNP  1000
1001  SHPTASALSTGSPPMKNPSHPTASTLSMGLPPSRTPSHPTATVLSTGSPP  1050
1051  SESPSRTGSAASGSSDSSIYLTSSVYSSKISQNGQQSQDVQKKETFPNVA  1100
1101  EEPIWRMIRQTPERILMTYQVPERVKEVVLKEDLEKLESMRQQQPQFSHG  1150
1151  QKEELAKVYNWIQSQTVTQEIDIQACVTCENEDSADGAATSCGQVLVEDS  1200
1201  C                                                   1201

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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