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

NucPred

Fetching Q8CIZ5 from www.uniprot.org...

The NucPred score for your sequence is 0.43 (see score help below)

   1  MGISIVIFEICLLWGQILSTASQSRSSTPDWWNHGGTINDVIYDTQETPE    50
  51  VTTTQVPDSTSIGTDSGLAVRLVNGGDRCRGRVEILYQGSWGTMCDDGTD   100
 101  SGLAVRLVNGGDRCRGRVEILYQGSWGTMCDDSWDINDANVVCRQLGCGW   150
 151  ALSAPGSAQFGQGLGPIVLDDVACRGHEAYLWSCSHRGWLSHNCGHQEDA   200
 201  GVICSDSQTSSPTPGWWNPGGTNNDVIYDTQETTETSQTSSPTPDWWNHG   250
 251  GTINDVIYDTQETTEGTDSGLAVRLVNGGDRCRGRVEILYQGSWGTVCDD   300
 301  SWDINDANVVCRQLGCGWALSAPGSAQFGQGSGSIVLDDVACRGHEAYLW   350
 351  SCSHRGWLSHNCGHQEDAGVICSYSQTSSPTPDSQTSSPTPGWWNPGGTN   400
 401  NDVSYGPEQTTDATDSGLAVRLVNGGDRCQGRVEILYQGSWGTVCDDSWD   450
 451  TKDANVVCRQLVCGWALSAPGSAHFGQGSGSIVLDDVACTGHEAYLWSCS   500
 501  HRGWLSHNCGHHEDAGVICSDAQTQSTTWPDMWPTTTPETTTDWWTTKYS   550
 551  SSVPTTQFPTIADWWTTPSPEYTCGGLLTLPYGQFSSPYYPGSYPNNARC   600
 601  LWKIFVSSMNRVTVVFTDVQLEGGCNYDYILVFDGPENNSSLIARVCDGF   650
 651  NGSFTSTQNFMSVVFITDGSVTRRGFQADYYSTPISTSTTSPTTFPIVTD   700
 701  WWTTPSPEYTCGGLLTLPYGQFSSPYYPGSYPNNARCLWKIFVPSMNRVT   750
 751  VVFTDVQLEGGCNYDYILGFDGPEYNSSLIARVCDGSNGSFTSTQNFMSV   800
 801  VFITDGSVTRRGFQADYYSTPIRTSTTPPTTFPIITGNDSSLVLRLVNGT   850
 851  NRCEGRVEILYRGSWVPCADDSWDINDANVVCRQLGCGSALSAPGNAWFG   900
 901  QGSGLIVLDDVSCSGYESHLWNCRHPGWLVHNCRHVEDAGVICSLPDPTP   950
 951  SPGPVWTSPPFVNYTCGGFLTGLSGQFSSPYYPGSYPNNARCLWNIEVPN  1000
1001  NYRVTVVFRDVQLEGGCNYDYIEIFDGPHHSSPLIARVCDGAMGSFTSTS  1050
1051  NFMSVRFTTDHSVTRRGFRADYYSDFDNNTTNLLCLSNHMRASVSRSYLQ  1100
1101  SMGYSSRDLVIPGWNVSYQCQPQITQREVIFTIPYTGCGTTKQADNETIN  1150
1151  YSNFLKAAVSNGIIKRRKDLHIHVSCKMLQNTWVNTMYITNNTVEIQEVQ  1200
1201  YGNFDVNISFYTSSSFLYPVTSSPYYVDLDQNLYLQAEVLHSDTSLALFV  1250
1251  DTCVASPHPNDFSSLTYDLIRSGCIRDETYQSYSSPSPRITRFKFSSFHF  1300
1301  LNRFPSVYLQCKLVVCRANDVSSRCYRGCVVRSKRDVGSYQEKVDVVLGP  1350
1351  IQLQSPSKEKRSLDLAVADVEKPASSQEVYPTAAIFGGVFLALVVAVAAF  1400
1401  TLGRKTRTARGQPPSTKM                                  1418

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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