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

NucPred

Fetching P12822 from www.uniprot.org...

The NucPred score for your sequence is 0.44 (see score help below)

   1  MGAAPGRRGPRLLRPPPPLLLLLLLLRPPPAALTLDPGLLPGDFAADEAG    50
  51  ARLFASSYNSSAEQVLFRSTAASWAHDTNITAENARRQEEEALLSQEFAE   100
 101  AWGKKAKELYDPVWQNFTDPELRRIIGAVRTLGPANLPLAKRQQYNSLLS   150
 151  NMSQIYSTGKVCFPNKTASCWSLDPDLNNILASSRSYAMLLFAWEGWHNA   200
 201  VGIPLKPLYQEFTALSNEAYRQDGFSDTGAYWRSWYDSPTFEEDLERIYH   250
 251  QLEPLYLNLHAYVRRVLHRRYGDRYINLRGPIPAHLLGNMWAQSWESIYD   300
 301  MVVPFPDKPNLDVTSTMVQKGWNATHMFRVAEEFFTSLGLLPMPPEFWAE   350
 351  SMLEKPEDGREVVCHASAWDFYNRKDFRIKQCTQVTMDQLSTVHHEMGHV   400
 401  QYYLQYKDQPVSLRRANPGFHEAIGDVLALSVSTPAHLHKIGLLDHVTND   450
 451  TESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGRTPSSRYNFDWWYLR   500
 501  TKYQGICPPVVRNETHFDAGAKFHIPSVTPYIRYFVSFVLQFQFHQALCM   550
 551  EAGHQGPLHQCDIYQSTRAGAKLRAVLQAGCSRPWQEVLKDMVASDALDA   600
 601  QPLLDYFQPVTQWLQEQNERNGEVLGWPEYQWRPPLPNNYPEGIDLVTDE   650
 651  AEASRFVEEYDRSFQAVWNEYAEANWNYNTNITTEASKILLQKNMQIANH   700
 701  TLTYGNWARRFDVSNFQNATSKRIIKKVQDLQRAVLPVKELEEYNQILLD   750
 751  METIYSVANVCRVDGSCLQLEPDLTNLMATSRKYDELLWVWTSWRDKVGR   800
 801  AILPYFPKYVEFTNKAARLNGYVDAGDSWRSMYETPTLEQDLERLFQELQ   850
 851  PLYLNLHAYVGRALHRHYGAQHINLEGPIPAHLLGNMWAQTWSNIYDLVA   900
 901  PFPSASTMDATEAMIKQGWTPRRMFEEADKFFISLGLLPVPPEFWNKSML   950
 951  EKPTDGREVVCHASAWDFYNGKDFRIKQCTTVNMEDLVVVHHEMGHIQYF  1000
1001  MQYKDLPVALREGANPGFHEAIGDVLALSVSTPKHLHSINLLSSEGGGYE  1050
1051  HDINFLMKMALDKIAFIPFSYLVDEWRWRVFDGSITKENYNQEWWSLRLK  1100
1101  YQGLCPPAPRSQGDFDPGAKFHIPSSVPYIRYFVSFIIQFQFHEALCKAA  1150
1151  GHTGPLHTCDIYQSKEAGKRLADAMKLGYSKPWPEAMKVITGQPNMSASA  1200
1201  MMNYFKPLMDWLLTENGRHGEKLGWPQYTWTPNSARSEGSLPDSGRVNFL  1250
1251  GMNLDAQQARVGQWVLLFLGVALLLASLGLTQRLFSIRYQSLRQPHHGPQ  1300
1301  FGSEVELRHS                                          1310

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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