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

NucPred

Fetching Q05860 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MEGTHCTLQLHNPIAELCYISFYLPKGEVRGFSYKGTVTLDRSNNAFHNC    50
  51  YQVREGPDITSLSQQPNEHPGDIFFKQTPTKNILTELYKLTAEKERLLDS   100
 101  LLRSDNILGVSMGSQEGKLQELSVILATGDEYFQSAGNWRRELPVSSLIR   150
 151  RSTQENKKPRRSGRRRESPEELRQKRTRRKGRGCQESAFQMGKDQVCSSS   200
 201  SLSFRARPNLRLLEERGNLVPRGTLTSSLRRRESCPANILRTPDADLAFG   250
 251  NSGRTSEDTDLEGPLSPDSSPTEVGDADVGGQLKSSHQQEPPQPNVSESH   300
 301  GKHAGAERWSSRTRKSKSLERTCSKKPVSKVVAKIQEPSAPVKRIVRAHH   350
 351  DGKGRVAYGPETQTEFIPKADFLTLPGGETETHSSGRLEEEQPGIKSLRS   400
 401  SAPERASITKEPASTEAAVNKVLRKVIESEKLDEATEGKRLGFSLNTRAT   450
 451  HTFPETRSQRKAGLPQSGHKFLLLDLPHTVGPDSPQPKCDEKKPTPQVPT   500
 501  ALGMVFNNSSPQSSAHKRLSPVPSPLSPRCPSPQQHHRILLLPPLPSEGE   550
 551  VVFNEYPSRKNDVSSGFPSADTLEPSSTTKVTETKGASPTSLRASQTWLV   600
 601  SEEASEKGLGPEKITAPPQHQLPPGIASEGFPCDNFKEQTAKDLPNKDGG   650
 651  VWVPGYRAGPPCPFLLHEEKEKTSRSELYLDLNPDQSPTEQDDRTPGRLQ   700
 701  AVWPPPKTKDTEEKVGLKYTEAEYQAAILHLKREHKEEIETLQAQFELKT   750
 751  FHIRGEHALVTARLEEAIENLKQQLGKRREGCEEMRDVCISTDDDCSPKA   800
 801  FRNVCIQTDRETFLKPCDAESKATRSSQIVPKKLTISLTQLSPSKDSKDI   850
 851  HAPFQTREGTSSSSQHKISPPAPPTPPPLPPPLIPPPPPLPPGLGPLPPA   900
 901  PPIPPVCPVSPPPPPPPPPPTPVPPSDGPPPPPPPPPPLPNVLALPNSGG   950
 951  PPPPPPPPPPGLAPPPPPGLSFGLSSSSSQYPRKPAIEPSCPMKPLYWTR  1000
1001  IQINDKSQDAAPTLWDSLEEPHIRDTSEFEYLFSKDTTQQKKKPLSEAYE  1050
1051  KKNKVKKIIKLLDGKRSQTVGILISSLHLEMKDIQQAIFTVDDSVVDLET  1100
1101  LAALYENRAQEDELTKIRKYYETSKEEDLKLLDKPEQFLHELAQIPNFAE  1150
1151  RAQCIIFRAVFSEGITSLHRKVEIVTRASKGLLHMKSVKDILALILAFGN  1200
1201  YMNGGNRTRGQADGYSLEILPKLKDVKSRDNGMNLVDYVVKYYLRYYDQC  1250
1251  KHHDQEASCRGKDLFSLYFHIAVHPQRKSGLELKQEAGTDKSVFPLPEPQ  1300
1301  DFFLASQVKFEDLLKDLRKLKRQLEASEQQMKLVCKESPREYLQPFKDKL  1350
1351  EEFFKKAKKEHKMEESHLENAQKSFETTVGYFGMKPKTGEKEVTPSYVFM  1400
1401  VWFEFCSDFKTIWKRESKNISKERLKMAQASVSKLTSEKKVETKKINPTA  1450
1451  SLKERLRQKEASVATN                                    1466

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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