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

NucPred

Fetching Q92547 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKI    50
  51  KENDRSLYICDPFSGVVFDHLKKLGCRIVGPQVVIFCMHHQRCVPRAEHP   100
 101  VYNMVMSDVTISCTSLEKEKREEVHKYVQMMGGRVYRDLNVSVTHLIAGE   150
 151  VGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITRYTDINMEDFKCPIF   200
 201  LGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNECTHLIVQEPKGQK   250
 251  YECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRPEAKTMPNSSTPT   300
 301  SQINTIDSRTLSDVSNISNINASCVSESICNSLNSKLEPTLENLENLDVS   350
 351  AFQAPEDLLDGCRIYLCGFSGRKLDKLRRLINSGGGVRFNQLNEDVTHVI   400
 401  VGDYDDELKQFWNKSAHRPHVVGAKWLLECFSKGYMLSEEPYIHANYQPV   450
 451  EIPVSHKPESKAALLKKKNSSFSKKDFAPSEKHEQADEDLLSQYENGSST   500
 501  VVEAKTSEARPFNDSTHAEPLNDSTHISLQEENQSSVSHCVPDVSTITEE   550
 551  GLFSQKSFLVLGFSNENESNIANIIKENAGKIMSLLSRTVADYAVVPLLG   600
 601  CEVEATVGEVVTNTWLVTCIDYQTLFDPKSNPLFTPVPVMTGMTPLEDCV   650
 651  ISFSQCAGAEKESLTFLANLLGASVQEYFVRKSNAKKGMFASTHLILKER   700
 701  GGSKYEAAKKWNLPAVTIAWLLETARTGKRADESHFLIENSTKEERSLET   750
 751  EITNGINLNSDTAEHPGTRLQTHRKTVVTPLDMNRFQSKAFRAVVSQHAR   800
 801  QVAASPAVGQPLQKEPSLHLDTPSKFLSKDKLFKPSFDVKDALAALETPG   850
 851  RPSQQKRKPSTPLSEVIVKNLQLALANSSRNAVALSASPQLKEAQSEKEE   900
 901  APKPLHKVVVCVSKKLSKKQSELNGIAASLGADYRWSFDETVTHFIYQGR   950
 951  PNDTNREYKSVKERGVHIVSEHWLLDCAQECKHLPESLYPHTYNPKMSLD  1000
1001  ISAVQDGRLCNSRLLSAVSSTKDDEPDPLILEENDVDNMATNNKESAPSN  1050
1051  GSGKNDSKGVLTQTLEMRENFQKQLQEIMSATSIVKPQGQRTSLSRSGCN  1100
1101  SASSTPDSTRSARSGRSRVLEALRQSRQTVPDVNTEPSQNEQIIWDDPTA  1150
1151  REERARLASNLQWPSCPTQYSELQVDIQNLEDSPFQKPLHDSEIAKQAVC  1200
1201  DPGNIRVTEAPKHPISEELETPIKDSHLIPTPQAPSIAFPLANPPVAPHP  1250
1251  REKIITIEETHEELKKQYIFQLSSLNPQERIDYCHLIEKLGGLVIEKQCF  1300
1301  DPTCTHIVVGHPLRNEKYLASVAAGKWVLHRSYLEACRTAGHFVQEEDYE  1350
1351  WGSSSILDVLTGINVQQRRLALAAMRWRKKIQQRQESGIVEGAFSGWKVI  1400
1401  LHVDQSREAGFKRLLQSGGAKVLPGHSVPLFKEATHLFSDLNKLKPDDSG  1450
1451  VNIAEAAAQNVYCLRTEYIADYLMQESPPHVENYCLPEAISFIQNNKELG  1500
1501  TGLSQKRKAPTEKNKIKRPRVH                              1522

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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