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

NucPred

Fetching Q9GLN7 from www.uniprot.org...

The NucPred score for your sequence is 0.52 (see score help below)

   1  MGAASGRRGPGLLLPLLLLLPPQPALALDPGLQPGNFSADEAGAQLFAQS    50
  51  YNSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAK   100
 101  ELYEPVWQNFTDPQLRRIIGAVRTLGSANLPLAKRQQYNALLSNMSRIYS   150
 151  TAKVCLPNKTATCWSLDPDLTNILASSRSYAMLLFAWEGWHNAAGIPLKP   200
 201  LYEDFTALSNEAYKQDGFTDTGAYWRSWYNSPTFEDDLEHLYQQLEPLYL   250
 251  NLHAFVRRALHRRYGDRYINLRGPIPAHLLGDMWAQSWENIYDMVVPFPD   300
 301  KPNLDVTSTMLQQGWNATHMFRVAEEFFTSLELSPMPPEFWEGSMLEKPA   350
 351  DGREVVCHASAWDFYNRKDFRIKQCTRVTMDQLSTVHHEMGHIQYYLQYK   400
 401  DLPVSLRGGANPGFHEAIGDVLALSVSTPAHLHKIGLLDNVTNDTESDIN   450
 451  YLLKMALEKIAFLPFGYLVDQWRWGVFSGRTPNSRYNFDWWYLRTKYQGI   500
 501  CPPVTRNETHFDAGAKFHVPNVTPYIRYFVSFVLQFQFHEALCKEAGYEG   550
 551  PLHQCDIYQSTKAGAKLRKVLQAGSSRPWQEVLKDMVGLDALDAQPLLKY   600
 601  FQPVTQWLQEQNQQNGEVLGWPEYQWHPPLPDNYPEGIDLVTDEAEASKF   650
 651  VEEYDRTSQVVWNEYAEANWNYNTNITTETSKILLQKNMQIANHTLKYGT   700
 701  QARRFDVNQLQNTTIKRIIKKVQDLERAALPAQELEEYNKILLDMETTYS   750
 751  VATVCHTNGSCLQLEPDLTNVMATSRKYEDLLWAWEGWRDKAGRAILQFY   800
 801  PKYVELINQAARLNGYVDAGDSWRSMYETPSLEQDLERLFQELQPLYLNL   850
 851  HAYVRRALHRHYGAQHINLEGPIPAHLLGNMWAQTWSNIYDLVVPFPSAP   900
 901  SMDTTEAMLKQGWTPRRMFKEADDFFTSLGLLPVPPEFWNKSMLEKPTDG   950
 951  REVVCHASAWDFYNGKDFRIKQCTTVNLEDLVVAHHEMGHIQYFMQYKDL  1000
1001  PVALREGANPGFHEAIGDVLALSVSTPKHLHSLNLLSSEGGSDEHDINFL  1050
1051  MKMALDKIAFIPFSYLVDQWRWRVFDGSITKENYNQEWWSLRLKYQGLCP  1100
1101  PVPRTQGDFDPGAKFHIPSSVPYIRYFVSFIIQFQFHEALCQAAGHTGPL  1150
1151  HKCDIYQSKEAGQRLATAMKLGFSRPWPEAMQLITGQPNMSASAMLSYFK  1200
1201  PLLDWLRTENELHGEKLGWPQYNWTPNSARSEGPLPDSGRVSFLGLDLDA  1250
1251  QQARVGQWLLLFLGIALLVATLGLSQRLFSIRHRSLHRHSHGPQFDSEVE  1300
1301  LRHS                                                1304

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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