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

NucPred

Fetching Q5RDC1 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MNRTTPDQELAPASEPVWERPWSVEEIRRSSQSWSLAADAGLLQFLQEFS    50
  51  QQTISRTHEIKKQVDGLIRETKATDCRLHNVFNDFLMLSNTQFIENRVYD   100
 101  EEVEEPVLKAEAEKTEQEKTREQKEVDLIPKVQEAVNYGLQVLDSAFEQL   150
 151  DIKAGNSDSEEDDANGRVELILEPKDLYIDRPLPYLIGSKLFMEQEDVGL   200
 201  GELSSEEGSVGSDRGSIVDTEEEKEEEESDEDFAHHSDNDQNRNTTQMSD   250
 251  EEEDDDGCDLFADSEKEEEDIEDIEEITRPKRNGPTSFADELAARIKGDA   300
 301  VGRVDEEPTTLSSGEAKPRKTLKEKKERRTPSDDEEDNLFAPPKLTDEDF   350
 351  SPFGSGGGLFSGGKGLFDDEDEESDLFTEAPQDRQAGASVKEESSSSKPG   400
 401  KKIPAGAVSVFLGDTDVFGAASVPSLKEPQKPEQPTPRKSPYFPPPTGLF   450
 451  DDDDGDDDDDFFSTPHSKPSKTGKVQSTADIFGDDEGDLFKEKAVTLPEA   500
 501  TVSQTDENKARAEKKVSLPSSKNLKPSSETKTQKGLFSDEEDSEDLFSSQ   550
 551  SASKLKGAPLLPGKLPTSVSLFEDEDEEDNLFGGTAAKRQTLSLQAQGEE   600
 601  KAKASELSKKKASALLFSSDEEDQWNIPASQTHSASDSRSKGESRDSGTL   650
 651  QSQEAKAVKKASLFEEDEEDDLFAIAKDSQKKTQRVSLLFEDDVDSGGSL   700
 701  FGSPPTSVPPATTKKETVSEAPPLLFSDEEEKEAQLGVKPVDKKVESAKE   750
 751  SLKFGRTDVAESEKEGLLTRSAQEAVKHSDLFSSSSPLDKGTKPRTKTVL   800
 801  SLFDEEEDKMEDQNTIQAPQKEVGKGRDPDARPKSTGVFQDEELLFSHKL   850
 851  QKDNDPDVDLFAGTKKTKLLEPSVGSLFGDDEDDDLFSSAKSQPLVQEKK   900
 901  RVVKKDYSVDSVKNQKHPETIQGIKEKGIWKPETPQDSSGLAPFKTKEPS   950
 951  TRIGKIQANLAINPAALLPTAASQISEVKPVLPELAFPSSEHRRSHGLES  1000
1001  VPVLPGSGEAGVSFDLPAQADTLHSANKSRVKMRGKRRPQTRAARRLAAQ  1050
1051  ESSEAEDMSVPRGPIAQWADGTISPNGHRPQLRAASGEDSTEEALAAAAA  1100
1101  PWEGGPVPGVDRSPFAKSLGHSRGEADLFDSGDIFSTGTGSQSEERTKPK  1150
1151  AKIAENLANPPVGGKAKSPMFPALGEASSDDDLFQSAKPKPAKKTNPFPL  1200
1201  LEDEDDLFTDQKVKKNETKSDSQQDVISTTQDIFEDDIFATEAIKPSQKT  1250
1251  REKEKTLESNLFDDNIDIFADLTVKPKEKSKKKVEAKSIFDDDMDDIFSS  1300
1301  GIQAKTAKPKSRSAQAAPEPRFEHKVSNIFDDPLNAFGGQ            1340

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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