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

NucPred

Fetching Q41406 from www.uniprot.org...

The NucPred score for your sequence is 0.11 (see score help below)

   1  LDQSSRYADLSLDEDTLIRNGKHVLVAYIMKPKAGYDYLATAAHFAAESS    50
  51  TGTNVNVCTTDDFTKSVDALVYYIDPDNEEMKIAYPTLLFDRNITDGRGM   100
 101  MCSFLTLAIGNNQGMGDVEYGKIYDFYLPPAFLRLYDGPSVNVEDMWRIL   150
 151  GRGTTNGGLVVGTIIKPKLGLQPKPFGEACYSFWQGGDFIKNDEPQGNQV   200
 201  FCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQ   250
 251  FGPLSENCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQ   300
 301  RGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADG   350
 351  PYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHK   400
 401  DGPKIGAISCRQGEEAWKQWKAGQFGNISLSDGVIEYAKTHEEIKGAFLT   450
 451  FQKDADQIYPGWKEKLGYTGESSVQAASFDWAKRASAAAFVGASVAPAKK   500
 501  ENVVARQALDQSSRYADLSLDEDTLIRNGKHVLVAYIMKPKAGYDYLATA   550
 551  AHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDNEEMKIAYPTLLFDR   600
 601  NITDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPAFLRLYDGPSVN   650
 651  VEDMWRILGRGTTNGGLVVGTIIKPKLGLQPKPFGEACYSFWQGGDFIKN   700
 701  DEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIA   750
 751  RGKYIMSQFGPLSENCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHG   800
 801  SVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYM   850
 851  LQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTA   900
 901  GGGSFGHKDGPKIGAISCRQGEEAWKQWKAGQFGNISLSDGVIEYAKTHE   950
 951  EIKGAFLTFQKDADQIYPGWKEKLGYTGESSVQAASFDWAKRASAAAFVG  1000
1001  ASVAPAKKENVVARQALDQSSRYADLSLDEDTLIRNGKHVLVAYIMKPKA  1050
1051  GYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDNEEMKIA  1100
1101  YPTLLFDRNITDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPAFLR  1150
1151  LYDGPSVNVEDMWRILGRGTTNGGLVVGTIIKPKLGLQPKPFGEACYSFW  1200
1201  QGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITA  1250
1251  DDPEEMIARGKYIMSQFGPLSENCAFLVDGYVAGGTAVTCCRRNFPKQFL  1300
1301  HYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDA  1350
1351  SDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLG  1400
1401  HSKVILTAGGGSFGHKDGPKIGAISCRQGEEAWKQWKAGQFGNISLSDGV  1450
1451  IEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLGYTGESSVQAASFDWAKR  1500
1501  A                                                   1501

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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