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

NucPred

Fetching O13776 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MGGQESKLAFQRGIARLASQPDIPLDDEVWVSLWSVPESCPEVYDFFPPG    50
  51  LIREMRDHAFVNLEKLLLVLTSRLFALKNDKKFPNPETAPASEALNCIRL   100
 101  LTRIIPFLNEKLDLEEWHQKFWWSLRKKRNLPKENSELDLSNFQDDLDFE   150
 151  NSISQKNEFSQKSPSVPLSPVSTFPASSISLDASSDVSAADVSVGGSSTI   200
 201  KEIGSIEETFTHEKTLMEELLDTVFRLLFCRGFTLPLSSPEQYAYIIWEN   250
 251  GIGTTETQEKTTKELAFNRIEVLRLLLVLISKRLYRSSEVASHTLTYLTC   300
 301  VANKQLILVFLYSLINTTLRLRPDSWKASYSTLVPYNDSSIALSKLTSQI   350
 351  LLLFLDHTPHETTVEYFRQRLNLSPGAAIENQYRLYFSRLQLQADYEFLV   400
 401  NELYRLLNAPVSAISAYISIVQKPNIAFPEIILFLWQAILYNKRFRAFLI   450
 451  TSPYATEFLTSIQFYALRYREDNEHSGLVRICLFIVHYLSCEKVLCEKLN   500
 501  RNCMNAQSLMSSLGFSVPPMSYAEFLIISSFHISAVKRSPFSSLSPVILL   550
 551  TICNIAPFVENLSFVTCAKLMQLCSSLSSPRFLFRNPRNHLLLEYLLQAI   600
 601  SSIVENKFSQNPNLSYSIIRLQQVFLNLNSMKLPAVAQTKSQPLVALNSE   650
 651  GSSDFESKSSDNTSLDGTPLQNTDFKKVATVEDDSPFDELDKFSSPFSSS   700
 701  SSRGGLSHISSRNVSISVPTVLQDVFSDSPLVLSRKLRGKIPENVSSSEL   750
 751  IKKCASNPFGKDLEIDSNLFAPSNSWFNSWHSRLELDSILAIISQFSLPV   800
 801  YKKMNEELSTTDEAVKLLANSVLNDVHPRVPNFRYFIWSVPMNNWFQSLV   850
 851  WLYTLSFDEKGLMATPSLFTTSKVYKQHGNIMKVASPENSSNSMENATKS   900
 901  ILDKLDLLYLQLPSSVNHDSSLRNK                            925

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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