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

NucPred

Fetching Q2PQA9 from www.uniprot.org...

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

   1  MADPAECNIKVMCRFRPLNESEVNRGDKYVAKFQGEDTVMIASKPYAFDR    50
  51  VFQSSTSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLH   100
 101  DPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSK   150
 151  TNLSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEH   200
 201  SSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDE   250
 251  AKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVI   300
 301  CCSPSSYNESETKSTLLFGQRAKTIKNTVCVNVELTAEQWKKKYEKEKEK   350
 351  NKTLRNTIQWLENELNRWRNGETVPIDEQFDKEKANLEAFTADKDVAITN   400
 401  DKPAAAIGMAGSFTDAERRKCEEEIAKLYKQLDDKDEEINQQSQLVEKLK   450
 451  TQMLDQEELLASTRRDQDNMQAELNRLQAENDASKEEVKEVLQALEELAV   500
 501  NYDQKSQEVEDKTKEYELLSDELNQKSATLASIDAELQKLKEMTNHQKKR   550
 551  AAEMMASLLKDLAEIGIAVGNNDVKQPEGTGMIDEEFTVARLYISKMKSE   600
 601  VKTMVKRCKQLESTQTESNKKMEENEKELAACQLRISQHEAKIKSLTEYL   650
 651  QNVEQKKRQLEESVDSLGEELVQLRAQEKVHEMEKEHLNKVQTANEVKQA   700
 701  VEQQIQSHRETHQKQISSLRDEVEAKEKLITDLQDQNQKMVLEQERLRVE   750
 751  HERLKAVDQEKSRKLHELTVMQDRREQARQDLKGLEETVAKELQTLHNLR   800
 801  KLFVQDLATRVKKSAEVDSDDTGGSAAQKQKISFLENNLEQLTKVHKQLV   850
 851  RDNADLRCELPKLEKRLRATAERVKALESALKEAKENASRDRKRYQQEVD   900
 901  RIKEAVRSKNMARRGHSAQIAKPIRPGQHPAASPTHPGAVRGGGSFVQNN   950
 951  QPVGLRGGGGKQA                                        963

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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