| Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching O70576 from www.uniprot.org...
The NucPred score for your sequence is 0.99 (see score help below)
1 MPTLWSPSTQHHGSSSGSESSPLQKSVRRAQMALSPCSSSILPCDDRDSQ 50
51 GTAEWDSPSTNEDSDFEDSLRRNVKKRAAKQPPKAVPAAKHRKKQSRIVS 100
101 SGNGKNESVPSTNYLFDAVKAARSCMQSLVDEWLDNYKQDENAGFLELIN 150
151 FFIRACGCKSTVTPEMFKTMSNSEIIQHLTEEFNEDSGDYPLTAPGPSWK 200
201 KFQGSFCEFVKTLVYQCQYSLLYDGFPMDDLISLLIGLSDSQVRAFRHTS 250
251 TLAAMKLMTSLVKVALQLSLHKDNNQRQYEAERNKGPEQRAPERLESLLE 300
301 KRKEFQENQEDIEGMMNAIFRGVFVHRYRDILPEIRAICIEEIGYWMQSY 350
351 STSFLNDSYLKYIGWTLHDKHKEVRLKCVKALAGLYSNQELSLRMELFTN 400
401 RFKDRMVSMVMDRECEVAVEAIRLLTLILKNMEGVLTSADCEKIYSIVYI 450
451 SNRAMASSAGEFVYWKIFHPECGAKAVSDRERRRSPQAQKTFIYLLLAFF 500
501 MESEHHNHAAYLVDSLWDCAGSYLKDWESLTNLLLQKDQNLGDMQERMLI 550
551 EILVSSARQAAEGHPPVGRITGKKSLTAKERKLQAYDKMKLAEHLIPLLP 600
601 QLLAKFSADAENVAPLLQLLSYFDLSIYCTQRLEKHLELLLQQLQEVVVK 650
651 HVEPEVLEAAAHALYLLCKPEFTFFSRVDFARSQLVDFLTDRFQQELDDL 700
701 MQSSFLDEDEVYSLTATLKRLSAFYNAHDLTRWEISEPCSRLLRKAVDTG 750
751 EVPHQVILPALTLVYFSILWTVTHISESTSHKQLMSLKKRMVAFCELCQS 800
801 CLSDVDPEIQEQAFVLLSDLLLIFSPQMIVGGRDFLRPLVFFPEATLQSE 850
851 LASFLMDHVFLQPGELGNGQSQEDHVQIELLHQRRRLLAGFCKLLLYGVL 900
901 ELDAASDVFKHYNKFYEDYGDIIKETLTRARQIDRCQCSRILLLSLKQLY 950
951 TELIQEQGPQGLTELPAFIEMRDLARRFALSFGPQQLHNRDLVVMLHKEG 1000
1001 IKFSLSELPPAGSSHEPPNLAFLELLSEFSPRLFHQDKRLLLSYLEKCLQ 1050
1051 RVSKAPNHPWGPVTTYCHSLHPLEITAEASPRGPPHSKKRCVEGPCRPQE 1100
1101 EESSSQEESLQLNSGPTTPTLTSTAVKRKQSLRTVGKKQKGRPGPGPGPG 1150
1151 PELICSQQLLGTQRLKMSSAPCFQIRCDPSGSGLGKQLTRLSLMEEDEEE 1200
1201 ELRLLDEEWQRGDKMLHSPSSPSEHGLDLLDTTELNMEDF 1240
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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