 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q9H1A4 from www.uniprot.org...
The NucPred score for your sequence is 0.48 (see score help below)
1 MSNFYEERTTMIAARDLQEFVPFGRDHCKHHPNALNLQLRQLQPASELWS 50
51 SDGAAGLVGSLQEVTIHEKQKESWQLRKGVSEIGEDVDYDEELYVAGNMV 100
101 IWSKGSKSQALAVYKAFTVDSPVQQALWCDFIISQDKSEKAYSSNEVEKC 150
151 ICILQSSCINMHSIEGKDYIASLPFQVANVWPTKYGLLFERSASSHEVPP 200
201 GSPREPLPTMFSMLHPLDEITPLVCKSGSLFGSSRVQYVVDHAMKIVFLN 250
251 TDPSIVMTYDAVQNVHSVWTLRRVKSEEENVVLKFSEQGGTPQNVATSSS 300
301 LTAHLRSLSKGDSPVTSPFQNYSSIHSQSRSTSSPSLHSRSPSISNMAAL 350
351 SRAHSPALGVHSFSGVQRFNISSHNQSPKRHSISHSPNSNSNGSFLAPET 400
401 EPIVPELCIDHLWTETITNIREKNSQASKVFITSDLCGQKFLCFLVESQL 450
451 QLRCVKFQESNDKTQLIFGSVTNIPAKDAAPVEKIDTMLVLEGSGNLVLY 500
501 TGVVRVGKVFIPGLPAPSLTMSNTMPRPSTPLDGVSTPKPLSKLLGSLDE 550
551 VVLLSPVPELRDSSKLHDSLYNEDCTFQQLGTYIHSIRDPVHNRVTLELS 600
601 NGSMVRITIPEIATSELVQTCLQAIKFILPKEIAVQMLVKWYNVHSAPGG 650
651 PSYHSEWNLFVTCLMNMMGYNTDRLAWTRNFDFEGSLSPVIAPKKARPSE 700
701 TGSDDDWEYLLNSDYHQNVESHLLNRSLCLSPSEASQMKDEDFSQNLSLD 750
751 SSTLLFTHIPAIFFVLHLVYEELKLNTLMGEGICSLVELLVQLARDLKLG 800
801 PYVDHYYRDYPTLVRTTGQVCTIDPGQTGFMHHPSFFTSEPPSIYQWVSS 850
851 CLKGEGMPPYPYLPGICERSRLVVLSIALYILGDESLVSDESSQYLTRIT 900
901 IAPQKLQVEQEENRFSFRHSTSVSSLAERLVVWMTNVGFTLRDLETLPFG 950
951 IALPIRDAIYHCREQPASDWPEAVCLLIGRQDLSKQACEGNLPKGKSVLS 1000
1001 SDVPSGTETEEEDDGMNDMNHEVMSLIWSEDLRVQDVRRLLQSAHPVRVN 1050
1051 VVQYPELSDHEFIEEKENRLLQLCQRTMALPVGRGMFTLFSYHPVPTEPL 1100
1101 PIPKLNLTGRAPPRNTTVDLNSGNIDVPPNMTSWASFHNGVAAGLKIAPA 1150
1151 SQIDSAWIVYNKPKHAELANEYAGFLMALGLNGHLTKLATLNIHDYLTKG 1200
1201 HEMTSIGLLLGVSAAKLGTMDMSITRLLSIHIPALLPPTSTELDVPHNVQ 1250
1251 VAAVVGIGLVYQGTAHRHTAEVLLAEIGRPPGPEMEYCTDRESYSLAAGL 1300
1301 ALGMVCLGHGSNLIGMSDLNVPEQLYQYMVGGHRRFQTGMHREKHKSPSY 1350
1351 QIKEGDTINVDVTCPGATLALAMIYLKTNNRSIADWLRAPDTMYLLDFVK 1400
1401 PEFLLLRTLARCLILWDDILPNSKWVDSNVPQIIRENSISLSEIELPCSE 1450
1451 DLNLETLSQAHVYIIAGACLSLGFRFAGSENLSAFNCLHKFAKDFMTYLS 1500
1501 APNASVTGPHNLETCLSVVLLSLAMVMAGSGNLKVLQLCRFLHMKTGGEM 1550
1551 NYGFHLAHHMALGLLFLGGGRYSLSTSNSSIAALLCALYPHFPAHSTDNR 1600
1601 YHLQALRHLYVLAAEPRLLVPVDVDTNTPCYALLEVTYKGTQWYEQTKEE 1650
1651 LMAPTLLPELHLLKQIKVKGPRYWELLIDLSKGTQHLKSILSKDGVLYVK 1700
1701 LRAGQLSYKEDPMGWQSLLAQTVANRNSEARAFKPETISAFTSDPALLSF 1750
1751 AEYFCKPTVNMGQKQEILDLFSSVLYECVTQETPEMLPAYIAMDQAIRRL 1800
1801 GRREMSETSELWQIKLVLEFFSSRSHQERLQNHPKRGLFMNSEFLPVVKC 1850
1851 TIDNTLDQWLQVGGDMCVHAYLSGQPLEESQLSMLACFLVYHSVPAPQHL 1900
1901 PPIGLEGSTSFAELLFKFKQLKMPVRALLRLAPLLLGNPQPMVM 1944
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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