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

NucPred

Fetching Q11001 from www.uniprot.org...

The NucPred score for your sequence is 0.22 (see score help below)

   1  FTIFLGVALLQGVLTLSPIPVPEEEWAEFSRMLRDPSYRLPTTTRPRHYA    50
  51  VTLTPYFDVVPAGVSGLTTFSFDGEVTIYISPTQANVNEIVLHCNDLTIQ   100
 101  SLRVTYVSGNSEVDITATGQTFTCEMPYSFLRIRTSTPLVMNQEYIIRST   150
 151  FRGNLQTNMRGFYRSWYVDRTGKRWMATTQFQPGHARQAFPCYDEPGFKA   200
 201  TFDITMNREADFSPTISNMPIRATTTLTNGRISETFFTTPLTSTYLLAFI   250
 251  VSHYQVISNNNNAARPFRIYARNNVGSQGDWSLEMGEKLLLAMENYTAIP   300
 301  YYTMAQNLDMKQAAIPDFSAGAMENWGLLTYREALILYDPLNSNHHYRQR   350
 351  VANIVSHEIAHMWFGNLVTCAWWDNLWLNEGFARFSQYYLTATVDPELGY   400
 401  EIRFIPEQLQVAMFSDSVDSAHALTDTSVNDPVAVSAHFSTITYARGAAI   450
 451  LRMTQHLLSYDTFVKGLRQYLRARQFDVAEPYHLFSALDAAAAEDNALAA   500
 501  YRGITIDAYFRTWSEKAGHPLLSVTVDHESGRMTLVQARWERNTGVSRFP   550
 551  GLWHIPITWTRAGAPDFENLKPSQVMTGQSLVIDRGTRGQEWVIFNKQVS   600
 601  GFYRVNYDNTTWGLITRALRSANRTVIHELSRSQIVDDVFQLARSGVMSY   650
 651  QRALNILSYLRFEDAYAPWLSAISGFNWVIRRFAHDAANLQTLQNQIIGL   700
 701  SEAVVARLGFTEVSGGTYMTDLQRLHVMQFLCNVGHQQCIDAGRQNFLNW   750
 751  RNGSFIPANMRPWVYCTGLRYGSAEDFNYFWNRYIVEDLSNEKVVMLEAA   800
 801  GCTRDQASLEKFLNAIVSGNDDVRPQDHSSALSSAITSNDVNTMRAFDWL   850
 851  TKNVDQITRTLGSITSPLNTITSRLLTEAQMTQVQTWLDANRNTIGAAYN   900
 901  TGVNGIATSRANLQWSANRMSEFLRFFETGFVDDVPSEATTVAPPAETTV   950
 951  TPSTFPPTVAPATTPAPGSGNIAALSVVSLLVTLAINMVA             990

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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