| Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q9UJ98 from www.uniprot.org...
The NucPred score for your sequence is 0.99 (see score help below)
1 MSSPLQRAVGDTKRALSASSSSSASLPFDDRDSNHTSEGNGDSLLADEDT 50
51 DFEDSLNRNVKKRAAKRPPKTTPVAKHPKKGSRVVHRHSRKQSEPPANDL 100
101 FNAVKAAKSDMQSLVDEWLDSYKQDQDAGFLELVNFFIQSCGCKGIVTPE 150
151 MFKKMSNSEIIQHLTEQFNEDSGDYPLIAPGPSWKKFQGSFCEFVRTLVC 200
201 QCQYSLLYDGFPMDDLISLLTGLSDSQVRAFRHTSTLAAMKLMTSLVKVA 250
251 LQLSVHQDNNQRQYEAERNKGPGQRAPERLESLLEKRKELQEHQEEIEGM 300
301 MNALFRGVFVHRYRDVLPEIRAICIEEIGCWMQSYSTSFLTDSYLKYIGW 350
351 TLHDKHREVRLKCVKALKGLYGNRDLTTRLELFTSRFKDRMVSMVMDREY 400
401 DVAVEAVRLLILILKNMEGVLTDADCESVYPVVYASHRGLASAAGEFLYW 450
451 KLFYPECEIRMMGGREQRQSPGAQRTFFQLLLSFFVESELHDHAAYLVDS 500
501 LWDCAGARLKDWEGLTSLLLEKDQNLGDVQESTLIEILVSSARQASEGHP 550
551 PVGRVTGRKGLTSKERKTQADDRVKLTEHLIPLLPQLLAKFSADAEKVTP 600
601 LLQLLSCFDLHIYCTGRLEKHLELFLQQLQEVVVKHAEPAVLEAGAHALY 650
651 LLCNPEFTFFSRADFARSQLVDLLTDRFQQELEELLQSSFLDEDEVYNLA 700
701 ATLKRLSAFYNTHDLTRWELYEPCCQLLQKAVDTGEVPHQVILPALTLVY 750
751 FSILWTLTHISKSDASQKQLSSLRDRMVAFCELCQSCLSDVDTEIQEQAF 800
801 VLLSDLLLIFSPQMIVGGRDFLRPLVFFPEATLQSELASFLMDHVFIQPG 850
851 DLGSGDSQEDHLQIERLHQRRRLLAGFCKLLLYGVLEMDAASDVFKHYNK 900
901 FYNDYGDIIKETLTRARQIDRSHCSRILLLSLKQLYTELLQEHGPQGLNE 950
951 LPAFIEMRDLARRFALSFGPQQLQNRDLVVMLHKEGIQFSLSELPPAGSS 1000
1001 NQPPNLAFLELLSEFSPRLFHQDKQLLLSYLEKCLQHVSQAPGHPWGPVT 1050
1051 TYCHSLSPVENTAETSPQVLPSSKRRRVEGPAKPNREDVSSSQEESLQLN 1100
1101 SIPPTPTLTSTAVKSRQPLWGLKEMEEEDGSELDFAQGQPVAGTERSRFL 1150
1151 GPQYFQTPHNPSGPGLGNQLMRLSLMEEDEEEELEIQDESNEERQDTDMQ 1200
1201 ASSYSSTSERGLDLLDSTELDIEDF 1225
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.) |
Go back to the NucPred Home Page.