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

NucPred

Fetching O14022 from www.uniprot.org...

The NucPred score for your sequence is 0.43 (see score help below)

   1  MDSIELKQLVPENDSEPGTPRQLLFQHYDISNEETIGIKPFKSIPAKVYI    50
  51  LRVTEILTLGLLHLILTWLPEFRLKWIEAPCSNEDVEFVAISDPSGTSSI   100
 101  EKVSSICLKNDIQTSSFVLPSGKTRYFEYKKLRFYLEPLNLQWVLMPLET   150
 151  SAYSLVTSTPAYIQNGLDTFTIAKLRQVYGSNSLVSTKKSIVTILLNEVL   200
 201  HPFYLFQAVSVLIWLCDSFVFYSCCIVFISSYSIFLSVKESKESENRIHS   250
 251  IIGAPQPVTVIRNQVKQTVLADDLVIGDLLYFSNLDLKTCPVDGILFSSS   300
 301  CLLDESMVTGESVPARKFPLEDNSLDSWMIASCNIFSPHLIHAGTKFLKI   350
 351  DSTPSTPCLISVVRTGFRSNKGQLIRNLLYPNLRPSQLYLDSMSFLKTMA   400
 401  ILSFVSIVFIAIYLNLYNASFGHVVLRSLDVLTILVPPALPATLSVGIAN   450
 451  SIARLSRALIYTTSPESIHNAGCLSTFVFDKTGTLTENSVQLSCVYVKSG   500
 501  SNGLLKQVDADSLSLDSTKLNAHAYRVATCSQSLELVGNELVGDPLEVTL   550
 551  FTQFNGTFCATIRASNTPHPPLFSVSNSFDGPSQIFSIYKALEFDPVLRR   600
 601  MSVICSTSTERSLMLFTKGAPESILAISSQQSIPSNVQEVIHTLSSKGFR   650
 651  IIAFASKNLITPLQELIHLSRSTLESNVTFQGLFVLESPLRESSKDVISS   700
 701  LLRSKMEVSICSGDSLFTSVFVAKHCGALDSCNFIYTAELADSGDDCPQI   750
 751  HFEKIDLQTQNFQPIPDGFSLKDVILEKDSSLCMDGKLLQRLLTMLSFNE   800
 801  IKILLSKLRVLARMSPFDKATYVELCQKYGCKVGFCGDGANDCIALKQAD   850
 851  VGVSLSDSEACAAASFVSKKKSIKDVFNVLLEGRCSLILSHRCFQYMVLC   900
 901  AIVQFSGVFFLYLKNYNFNDNQFLFMDLLIIFPLSAAMSYFDPAQNLTSN   950
 951  RPNSTLFGKGRVKDLGIQSVLIWLSHGLLTLILHELNWVELPEWQLEKSN  1000
1001  TKNVLVTSIFLLSSLQYLGICIGINQSSEFLSPIWKKKTYVCLCTTIGLC  1050
1051  NIYLCFANENHIISRCLQITRLPTLYRFIILFMGVISCCLTSILNM      1096

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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