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

NucPred

Fetching Q9UW20 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MSADITETPNKQLLEQIRSPSFSLFNCIYELKNHTDSIGIQHELVKKLYS    50
  51  FPYEDLQFFIPQFVQLLVTYDSESMALEEFIITYSSRYPHFSLIVFWNLQ   100
 101  AYIFELKNEPESRSFQAVRNLITKIQNIMFNADQQTVKAPEFRENFLPAL   150
 151  VLCGAVASSVLLPSFKSYCLPMIKAQGKQQKSLVFKLVNFQKSLTKNLTL   200
 201  KNQRMSADIPKGSHSDDETATSSSIKPSLSRSASVPRRNTKKTSLSFSSD   250
 251  ESEAYTTDDDDNKTSIELEKDFYKIDLDGLSKEKSANFLEPEENLNVNTA   300
 301  IKSKKRLSTLTSKVMTQPWNGIDGYNVNSQSLPDLSKAEGRDLIPFISST   350
 351  ESETSLLYHNNSISNDLQKNIPRQQKFSPGFDNVYLTKLLQVNYAKNETQ   400
 401  FIMALQNISIRLSQVPKEARLSALRAELSIINDTLLPSEIDIPQLLPITS   450
 451  NRNKKYHKILKLNVNEASVLNSAERVPFLLFIEYLSDEIDFNPTTEYNQR   500
 501  IIARKKMNGATSMTVKKINSFSEVADGNFEKENKIKSSTPETVSNIIYNE   550
 551  NTEEADLSEMPLDRKTTVSSDSFSPEMLVTPSITEQSKLSNFPSLNTKEV   600
 601  STKVLADQMRIAAVMLQQLDSSGKANSEQSFLIKNRIVESMIALQDQFDS   650
 651  FDFEKLSQLQSDEPSAGERKLENDFKLGEDWNTKKQRIKKSSAYGHLKNW   700
 701  DLCSVIAKNGDDLPQEAFACQLISMISNIWKKNNIPVWTKRMKILITSAN   750
 751  TGLVETITNAMSIHSIKKSFTEHSIKSGENSKGKIFTLLDYFHSVFGSPN   800
 801  STSFRTAQQNFAKSLAAYSIICYVLQIKDRHNGNIMVDGDGHIIHIDFGF   850
 851  LLSNSPGSVGFEAAPFKLTVEYVELLGGVDSEIYSQFVYLCKQCFKSLRD   900
 901  NSEEIIEIVELMQKDSTLPCFNNGENTSVLLKQRLQLQLNDEDTDQFVEN   950
 951  FLIGKSLGSMYTRLYDQFQMITQGIYS                          977

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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