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

NucPred

Fetching P06238 from www.uniprot.org...

The NucPred score for your sequence is 0.28 (see score help below)

   1  MGKHRLRSLALLPLLLRLLLLLLPTDASAPQKPIYMVMVPSLLHAGTPEK    50
  51  ACFLFSHLNETVAVRVSLESVRGNQSLFTDLVVDKDLFHCTSFTVPQSSS   100
 101  DEVMFFTVQVKGATHEFRRRSTVLVKKKESLVFAQTDKPIYKPGQTVRFR   150
 151  VVSLDESFHPLNELIPLLYIQDPKNNRIAQWQNFNLEGGLKQLSFPLSSE   200
 201  PTQGSYKVVIRTESGRTVEHPFSVEEFVLPKFEVRVTVPETITILEEEMN   250
 251  VSVCGIYTYGKPVPGRVTVNICRKYSNPSNCFGEESVAFCEKLSQQLDGR   300
 301  GCFSQLVKTKSFQLKRQEYEMQLDVHAKIQEEGTGVEETGKGLTKITRTI   350
 351  TKLSFVNVDSHFRQGIPFVGQVLLVDGRGTPIPYETIFIGADEANLYINT   400
 401  TTDKHGLARFSINTDDIMGTSLTVRAKYKDSNACYGFRWLTEENVEAWHT   450
 451  AYAVFSPSRSFLHLESLPDKLRCDQTLEVQAHYILNGEAMQELKELVFYY   500
 501  LMMAKGGIVRAGTHVLPLKQGQMRGHFSILISMETDLAPVARLVLYAILP   550
 551  NGEVVGDTAKYEIENCLANKVDLVFRPNSGLPATRALLSVMASPQSLCGL   600
 601  RAVDQSVLLMKPETELSASLIYDLLPVKDLTGFPQGADQREEDTNGCVKQ   650
 651  NDTYINGILYSPVQNTNEEDMYGFLKDMGLKVFTNSNIRKPKVCERLRDN   700
 701  KGIPAAYHLVSQSHMDAFLESSESPTETRRSYFPETWIWDLVVVDSAGVA   750
 751  EVEVTVPDTITEWKAGAFCLSNDTGLGLSPVVQFQAFQPFFVELTMPYSV   800
 801  IRGEAFTLKATVLNYLPTCIRVAVQLEASPDFLAAPEEKEQRSHCICMNQ   850
 851  RHTASWAVIPKSLGNVNFTVSAEALNSKELCGNEVPVVPEQGKKDTIIKS   900
 901  LLVEPEGLENEVTFNSLLCPMGAEVSELIALKLPSDVVEESARASVTVLG   950
 951  DILGSAMQNTQDLLKMPYGCGEQNMVLFAPNIYVLDYLNETQQLTQEIKT  1000
1001  KAIAYLNTGYQRQLNYKHRDGSYSTFGDKPGRNHANTWLTAFVLKSFAQA  1050
1051  RKYIFIDEVHITQALLWLSQQQKDNGCFRSSGSLLNNAMKGGVEDEVTLS  1100
1101  AYITIALLEMSLPVTHPVVRNALFCLDTAWKSARGGAGGSHVYTKALLAY  1150
1151  AFALAGNQDTKKEILKSLDEEAVKEEDSVHWTRPQKPSVSVALWYQPQAP  1200
1201  SAEVEMTAYVLLAYLTTEPAPTQEDLTAAMLIVKWLTKQQNSHGGFSSTQ  1250
1251  DTVVALHALSKYGSATFTRAKKAAQVTIHSSGTFSTKFQVNNNNQLLLQR  1300
1301  VTLPTVPGDYTVKVTGEGCVYLQTSLKYSVLPREEEFPFTVVVQTLPGTC  1350
1351  EDPKAHTSFQISLNISYTGSRSESNMAIADVKMVSGFIPLKPTVKMLERS  1400
1401  VHVSRTEVSNNHVLIYLDKVSNQTVNLSFTVQQDIPIRDLKPAVVKVYDY  1450
1451  YEKDEFAVAKYSAPCSTDYGNA                              1472

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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