 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q6PDI5 from www.uniprot.org...
The NucPred score for your sequence is 0.59 (see score help below)
1 MYHIDCRDQLERVFLRLGHAETDEQLQNIISKFLPPVLLKLSSTQEGVRK 50
51 KVMELLVHLNKRIKSRPKIQLPVETLLVQYQDPAAVSFVTNFTIIYVKMG 100
101 YPRLPVEKQCELAPTLLTAMEGKPQPQQDSLMHLLIPTLFHMKYPAESSK 150
151 SASPFNLAEKPKTVQLLLDFMLDVLLMPYGYVLNESQSRQNSSSSSQGSS 200
201 SNSGGGSGIPQPPPGMSFYAAKRVIGDNPWTPEQLEQCKLGIVKFIEAEQ 250
251 VPELEAVLHLVIASSDTRHSVATAADLELKSKQSLIDWNNPAIINKMYKV 300
301 YLGDIPLKTKEGAVLKPELKRDPVSTRVKLKIVPHLLRSRQAAETFPANI 350
351 QVVYDGLFGTNTNSKLRTLSLQFVHHICLTCPEIKIKPLGPMLLNGLTKL 400
401 INEYKEDPKLLSMAYSAVGKLSSRMPHLFTKDIALVQQLFEALCKEEPET 450
451 RLAIQEALSMMVGAYSTLEGAQRTLMEALVASYLIKPEVQVRQVAVKFAS 500
501 TVFPSDHIPSRYLLLLAAGDPREEVHGEAQRVLRCLPGRNKKESASKQMP 550
551 SFPEMVYYIQEKASHRMKTPVKYMTGTTVLPFNPAAFGEIVLYLRMCLAH 600
601 SAGVVPTSQSLADMQDHAPAIGRYIRALMSSSQATASSSNKSGETNPVQI 650
651 YTGLLQQLLAGVGGLPVMYCLLEAVSVYPEKLATKFVDKTEWIKSLMSSS 700
701 KEEMRELAALFYSVVVSTVSGIELKSMIEQLIKATKDNHSPEVQHGSLLA 750
751 LGFTVGRYLAKKRVRMAEQHDLETDADLLPEQEEIIRSATETIGSFLDST 800
801 SPLLAIAACTALGEIGRNGPLPIPSEGSGFTKLHLVESLLNRIPSSKETN 850
851 KMKERAIQTLGYFPVGDGVFPHQKLLLQGLMDSVEAKQIELQFTIGEAIT 900
901 SAAIGTNSVAARDAWLVTEEEYIPPAGAKVNDVVPWVLDVILNKHIISPN 950
951 PHVRQAACIWLLSLVRKLSTHREVKSHLKEIQSAFVSVLSENDELSQDVA 1000
1001 SKGLGLVYELGNEQDQQELVSTLVETLMTGKRVKHEVSGETVVFQGGGLG 1050
1051 KTPDGQGLSTYKELCSLASDLSQPDLVYKFMNLANHHAMWNSRKGAAFGF 1100
1101 NVIATRAGEQLAPFLPQLVPRLYRYQFDPNLGIRQAMTSIWNALVTDKSM 1150
1151 VDKYLKEILQDLIKNLTSNMWRVRESSCLALNDLLRGRPLDDVIDKLPEM 1200
1201 WETLFRVQDDIKESVRKAAELALKTLSKVCVKMCDPAKGAAGQRTIAVLL 1250
1251 PCLLDKGMMSPVTEVRALSINTLVKISKSAGAMLKPHAPKLIPALLESLS 1300
1301 VLEPQVLNYLSLRATEQEKDVMDSARLSAAKSSPMMETINMCLQYLDVSV 1350
1351 LGELVPRLCELIRSGVGLGTKGGCASVIVSLTTQCPQDLTPYSGKLMSAL 1400
1401 LSGLTDRNSVIQKSCAFAMGHLVRTSRDSSTEKLLQKLNGWYMEKDEPVY 1450
1451 KTSCALTIHAIGRYSPDVLKNHAKEVLPLAFLGMHEIADEEKSEKEECNM 1500
1501 WTEVWQENVPGSFGGIRLYLQELITITQKALQSQSWKMKAQGAIAMASIS 1550
1551 KQTSSLVPPYLGMILSALMQGLAGRTWAGKEELLKAIACVVTACSTELEK 1600
1601 SVPNQPTTNEILQAVLKECCKENLKYKIVAISCAADVLKATKEDRFQEFS 1650
1651 DIVIPLIKKNSLESMGVRTTKAEDENEKERELQLESLLGAFESLGKAWPR 1700
1701 NPDTQRCYRQELCKLMCERLRLSTWKVQLGVLQSMNAFFQGLMLLEEEHA 1750
1751 DPEALAEILLETCKSITYSLENKTYSSVRTEALSVVELLLKKLEEAKQWE 1800
1801 SLTAECRGLLIESLATMETDNRPELQEKASVLKKTLESLE 1840
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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