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

NucPred

Fetching O88563 from www.uniprot.org...

The NucPred score for your sequence is 0.19 (see score help below)

   1  MDRLCGSGELGSKFWDSNLTVYTNTPDLTPCFQNSLLAWVPCIYLWAALP    50
  51  CYLFYLRHHRLGYIVLSCLSRLKTALGVLLWCISWVDLFYSFHGLVHGSS   100
 101  PAPVFFITPLLVGITMLLATLLIQYERLRGVRSSGVLIIFWLLCVICAII   150
 151  PFRSKILLALAEGKILDPFRFTTFYIYFALVLCAFILSCFQEKPPLFSPE   200
 201  NLDTNPCPEASAGFFSRLSFWWFTKLAILGYRRPLEDSDLWSLSEEDCSH   250
 251  KVVQRLLEAWQKQQTQASGPQTAALEPKIAGEDEVLLKARPKTKKPSFLR   300
 301  ALVRTFTSSLLMGACFKLIQDLSPSSTHSCSASSSGLFRPHGPYWWGFLL   350
 351  AGLMFVSSTMQTLILHQHYHCIFVMALRIRTAIIGVIYRKALTITNSVKR   400
 401  EYTVGEMVNLMSVDAQRFMDVSPFINLLWSAPLQVILAIYFLWQILGPSA   450
 451  LAGVAVIVLLIPLNGAVSMKMKTYQVQQMKFKDSRIKLMSEILNGIKVLK   500
 501  LYAWEPTFLEQVEGIRQGELQLLRKGAYLQAISTFIWVCTPFMVTLITLG   550
 551  VYVCVDKNNVLDAEKAFVSLSLFNILKIPLNLLPQLISGMTQTSVSLKRI   600
 601  QDFLNQDELDPQCVERKTISPGRAITIHNGTFSWSKDLPPTLHSINIQIP   650
 651  KGALVAVVGPVGCGKSSLVSALLGEMEKLEGAVSVKGSVAYVPQQAWIQN   700
 701  CTLQENVLFGQPMNPKRYQQALETCALLADLDVLPGGDQTEIGEKGINLS   750
 751  GGQRQRVSLARAVYSDANIFLLDDPLSAVDSHVAKHIFDQVIGPEGVLAG   800
 801  KTRVLVTHGISFLPQTDFIIVLADGQITEMGHYSELLQHDGSFANFLRNY   850
 851  APDENQEANEGVLQHANEEVLLLEDTLSTHTDLTDTEPAIYEVRKQFMRE   900
 901  MSSLSSEGEGQNRPVLKRYTSSLEKEVPATQTKETGALIKEEIAETGNVK   950
 951  LSVYWDYAKSVGLCTTLFICLLYAGQNAVAIGANVWLSAWTNDVEEHGQQ  1000
1001  NNTSVRLGVYATLGILQGLLVMLSAFTMVVGAIQAARLLHTALLHNQIRA  1050
1051  PQSFFDTTPSGRILNRFSKDIYVIHEVLAPTILMLFNSFYTSISTIVVIV  1100
1101  ASTPLFCVVVLPLAVFYGFVQRFYVATSRQLKRLESVSRSPIFSHFSETV  1150
1151  TGTSVIRAYGRVQDFKVLSDAKVDSNQKTTYPYIASNRWLGVHVEFVGNC  1200
1201  VVLFSALFAVIGRNSLNPGLVGLSVSYALQVTLSLNWMIRTLSDLESNII  1250
1251  AVERVKEYSKTETEAPWVLESNRAPEGWPRSGVVEFRNYSVRYRPGLELV  1300
1301  LKNLTLHVQGGEKVGIVGRTGAGKSSMTLCLFRILEAAEGEIFIDGLNVA  1350
1351  HIGLHDLRSQLTIIPQDPILFSGTLRMNLDPFGRYSDEDIWRTLELSHLS  1400
1401  AFVSSQPTGLDFQCSEGGDNLSVGQRQLVCLARALLRKSRVLVLDEATAA  1450
1451  IDLETDDLIQGTIRTQFEDCTVLTIAHRLNTIMDYNRVLVLDKGVVAEFD  1500
1501  SPVNLIAAGGIFYGMAKDAGLA                              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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