 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q8VHD8 from www.uniprot.org...
The NucPred score for your sequence is 0.56 (see score help below)
1 MPKLLESIVTVIDVFYQYATEYGNCDMLSKEEMKELLVTEFHQILKNPDD 50
51 PDTVDIIMQNLDRDHNHKVDFTEYLLMILKLTKACNKIIGKDYCQASGSK 100
101 QKNHSHQHQEEQSKKETENKEQKGSISSSAGENDSYSRGSRGSNKSKSKK 150
151 LRKGKEQSSKQTTKSNSSDHENSEDYEQGQHESGFSNSSGNGRPSSRKAS 200
201 GFPQPGSEQGQSSSSSTKGSGECYSSGNGKHGSSSGGSAVSGSGHSNTYG 250
251 KQGTGSRHSSSNRRSRSTSRESSGSQEYSSGSSEEPGFTHGSGRKNSSTC 300
301 GKNGSYSGQSTGRHQQGFGSSHELESGQSITSANHGSHSNQSSCSGTREC 350
351 GSSESSMKKTHVSGSGHSSSTGKYTSTSGQNYNSTRQGCGQGKSSGSEQY 400
401 GASSGQSSGCSSGQSTRYGEQGSGSRNSSTQSRGRSTSRESSTSQQFGSG 450
451 SGRSSGFSQGGSGQGRSSRGGQQGSFSGQTEGSQQHGSCCGQSSGYGQNE 500
501 YGSGHSASSGQQGSHYSQSSSYGTHNSGGSPSSSQRGHGSRSGRSSGLGQ 550
551 YGSPSGQTSSSTRQGSGQGQASGSGRYGASSGQTSGCGSGQSTRYGEQGS 600
601 GSRNSSTQSRGRSTSRESSTSQRYGSGSGESSGFSQGGSGQGRSSRGGQQ 650
651 GSFSGQTSGRSQHQSGSRHGSGSGQFPISGQQGSHHGHSSSSGTHNSGSS 700
701 QSSSTQWSHGSGSEQSSGLGHYGSTSGQTASSTRQGSGQGQASGSGRCGA 750
751 SSGQTSGCGSGQSTRYGEQGSGSRNSSTQSRGRSTSRESSTSQRFGSGSG 800
801 GSSGFSQGRSGQGRSSRGGQQGSFSGQTEGSQQHGSCCGQSSGYGQNEYG 850
851 SGHSASSGQQGSHYSQSSSYGTHNSGGSPSSRPAGGHGSRSGRSSGLGQY 900
901 GSPSGQTSSSTRQGSGQGQASGSGRYGASSGQTSGCGSGQSTRYGEQGSG 950
951 SRNSSTQSRGRSTSRESSTSQRYGSGSGESSGFSQGGSGQGRSSRGGQQG 1000
1001 SFSGQTSGRSQHQSGSRHGSGSGQFPISGQQGSHHGHSSSSGTHNSGSSQ 1050
1051 SSSTQWSHGSGSEQSSGLGHYGSTSGQTASSTRQGSGQGQASGSGRCGAS 1100
1101 SGQTSGCGSGQSTRYGEQGSGSRNSSTQSRGRSTSRESSTSQRFGSGSGG 1150
1151 SSGFSQGRSGQGRSSRGGQQGSFSGQTEGSQQHGSCCGQSSGYGQNEYGS 1200
1201 GHSASSGQQGSHYSQSSSYGTHNSGGSPSSSQRGHGSRSGRSSGLGQYGS 1250
1251 PSGQTSSSTRQGSGQGQASGSGRYGASSGQTSGCRSGQSTRYGGQGSGSR 1300
1301 NSSTQSRGRSTSRESSTSQRYGSGSGESSGFSQGGSGQGRSSRGGQQGSF 1350
1351 SGQTSGRNQHQSGSRHGSGSGQFPISGQQGSHHGHSSSSGTHNSGSSQSS 1400
1401 STQWSHGSGSEQSSGLGHYGSTSGQTASSTRQGSGQGQASGSGRCGASSG 1450
1451 QTSGCGSGQSTRYGEQGSGSRNSSTQSRGRSTSRESSTSQRFGSGSGGSS 1500
1501 GFSQGRSGQGRSSRGGQQGSFSGQTEGSQQHGSCCGQSSGYGQNEYGSGH 1550
1551 SASSGQQGSHYSQSSSYGTHNSGGSPSSSQRGHGSRSGRSSGLGQYGSPS 1600
1601 GQTSSSTRQGSGQGQASGSGRYGASSGQTSGCGSGQPTRYGEQGSGSRNS 1650
1651 STQSRGRSTSRESSTSQRCGSGSGESSGFSQGGSGQGRSSRGGQQGSFSG 1700
1701 QTSGRSQHQSGSRHGSGSGQFPISGQQGSHHGHSSSSGTHNSGSSQSSST 1750
1751 QWSHGSGSEQSSGLGHYGSTSGQTASSTRQGSGQGQASGSGRCGASSGQT 1800
1801 SGCGSDQSTRYGEQGSGSRNSSTQSRGRSTSRESSTSQRFGSGSGGSSGF 1850
1851 SQGRSGQGRSSRGGQQGSFSGQTEGSQQHGSCCGQSSGYGQNEYGSGHSA 1900
1901 SSGQQGSHYSQSSSYGTHNSGGSPSSSQRGHGSRSGRSSGLGQYGSPSGQ 1950
1951 TSSSTRQGSGQGQASGSGRYGASSGQTSGCGSGQSTRYGEQGSGSRNSST 2000
2001 QSRGRSTSRESSTSQRYGSGSGESSGFSQGGSGQGRSSRGGQQGSFSGQT 2050
2051 SGRSQHQSGSRHGSGSGQFPISGQQGSHHGHSSSSGTHNSGSSQSSSTQW 2100
2101 SHGSGSEQSSGLGHYGSTSGQTASSTRQGSGQGQASGSGRCGASSGQTSG 2150
2151 CGSGQSTRYGEQGSGSRNSSTQSRGRSTSRESSTSQRYGSGSGESSGFSQ 2200
2201 GGSGQGRSSRGGQQGSFSGQTSGRSQHQSGSRHGSGSGQFPISGQQGSHH 2250
2251 GHSSSSGTHNSGSSQSSSTQWSHGSGSEQSSGLGQYGSPSGQTSSSTRQG 2300
2301 SGQGQASGSGRYGASSGQTSGCGSGQSTRYGEQGSGSRNSSTQSRGRSTS 2350
2351 RESSTSQRYGSGSGESSGFSQGGSGQGRSSRGGQQGSFSGQTSGRSQHQS 2400
2401 GSRHGSGSGQFPISGQQGSHHGHSSSSGTHNSGSSQSSSTQWSHGSGSEQ 2450
2451 SSGLGHYGSTSGQTASSTRQGSGQGQASGSGRCGASSGQTSGCGSG 2496
Positively and negatively influencing subsequences are coloured according to the following scale:
(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)
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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