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

NucPred

Fetching P32334 from www.uniprot.org...

The NucPred score for your sequence is 0.53 (see score help below)

   1  MQFPFACLLSTLVISGSLARASPFDFIFGNGTQQAQSQSESQGQVSFTNE    50
  51  ASQDSSTTSLVTAYSQGVHSHQSATIVSATISSLPSTWYDASSTSQTSVS   100
 101  YASQESDYAVNQNSWSASTNQLPSTSTTSYYAPTFSTSADFAASSVNAAS   150
 151  DVSTASVPIDTSANSIPFTTTSNIETTTSAPLTSDTPLISTSTMSAADNV   200
 201  FSSANPISASLTTTDSSESFDQTSTAGAIPVQSSADFSSSSEILVQSSAD   250
 251  FSSPSSPTTTDISLSAAPLQTSESSSFTTASAALPVSSTDVDGSSASPVV   300
 301  SMSAAGQIASSSSTDNPTMSETFSLTSTEVDGSDVSSTVSALLSAPFLQT   350
 351  STSNSFSIVSPSVSFVPSQSSSDVASSSTANVVSSSFSDIPPQTSTSGSV   400
 401  VSVAQSASALAFQSSTEVYGASASSTMSSLLSTTSLQSTTLDSSSLASSS   450
 451  ASSSDLTDYGVSSTASIPLLSASEQASTSSSFSVVSPSVSFVPSQSSSDV   500
 501  ASTSAPSVVSSSFSYTSLQAGGSSMTNPSSSTIVYSSSTGSSEESAASTA   550
 551  SATLSGSSSTYMAGNLQSQPPSTSSLLSESQATSTSAVLASSSVSTTSPY   600
 601  TTAGGASTEASSLISSTSAETSQVSYSQSTTALQTSSFASSSTTEGSETS   650
 651  SQGFSTSSVLVQMPSSISSEFSPSQTTTQMNSASSSSQYTISSTGILSQV   700
 701  SDTSVSYTTSSSSVSQVSDTPVSYTTSSSSVSQVSDTPVSYTTSSSSVSQ   750
 751  VSDTPVSYTTSSSSVSQVSDTPVSYTTSSSSVSQVSDTSVPSTSSRSSVS   800
 801  QVSDTPVPSTSSRSSVSQTSSSLQPTTTSSQRFTISTHGALSESSSVSQQ   850
 851  ASEITSSINATASEYHSIQTTAATQSTTLSFTDANSSSASAPLEVATSTP   900
 901  TPSSKASSLLLTPSTSSLSQVATNTNVQTSLTTESTTVLEPSTTNSSSTF   950
 951  SLVTSSDNNWWIPTELITQAPEAASTASSTVGGTQTMTLPHAIAAATQVP  1000
1001  EPEGYTLITIGFKKALNYEFVVSEPKSSAQIFGYLPEALNTPFKNVFTNI  1050
1051  TVLQIVPLQDDSLNYLVSVAEVYFPTAEIEELSNLITNSSSAFYTDGMGT  1100
1101  AKSMAAMVDSSIPLTGLLHDSNSNSGGSSDGSSSSNSNSGSSGSGSNSNS  1150
1151  GVSSSSGNSYQDAGTLEYSSKSNSNVSTSSKSKKKIIGLVIGVVVGGCLY  1200
1201  ILFMIFAFKYIIRRRIQSQEIIKNPEISSISSSEFGGEKNYNNEKRMSVQ  1250
1251  ESITQSMRIQNWMDDSYYGHGLTNNDSTPTRHNTSSSIPKISRPIASQNS  1300
1301  LGWNEV                                              1306

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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