| Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q9Y5H9 from www.uniprot.org...
The NucPred score for your sequence is 0.34 (see score help below)
1 MASSIRRGRGAWTRLLSLLLLAAWEVGSGQLRYSVPEEAKHGTFVGRIAQ 50
51 DLGLELEELVPRLFRVASKRHGDLLEVNLQNGILFVNSRIDREELCGRSA 100
101 ECSIHVEVIVDRPLQVFHVEVEVKDINDNPPIFPMTVKTIRFPESRLLDS 150
151 RFPLEGASDADIGVNALLSYKLSSSEFFFLDIQANDELSESLSLVLGKSL 200
201 DREETAEVNLLLVATDGGKPELTGTVQILIKVLDVNDNEPTFAQSVYKVK 250
251 LLENTANGTLVVKLNASDADEGPNSEIVYSLGSDVSSTIQTKFTIDPISG 300
301 EIRTKGKLDYEEAKSYEIQVTATDKGTPSMSGHCKISLKLVDINDNTPEV 350
351 SITSLSLPISENASLGTVIALITVSDRDSGTNGHVTCSLTPHVPFKLVST 400
401 FKNYYSLVLDSALDRESVSAYELVVTARDGGSPSLWATTSVSIEVADVND 450
451 NAPAFAQPEYTVFVKENNPPGCHIFTVSAWDADAQENALVSYSLVERRVG 500
501 ERALSSYVSVHAESGKVYALQPLDHEEVELLQFQVSARDAGVPPLGSNVT 550
551 LQVFVLDENDNAPALLAPRAGTAAGAVSELVPWSVGAGHVVAKVRAVDAD 600
601 SGYNAWLSYELQLGTGSARIPFRVGLYTGEISTTRALDEADSPRHRLLVL 650
651 VKDHGEPALTATATVLVSLVESGQAPKASSRAWVGAAGSEATLVDVNVYL 700
701 IIAICAVSSLLVLTVLLYTALRCSVPPTEGARAPGKPTLVCSSAVGSWSY 750
751 SQQRRQRVCSGEDPPKTDLMAFSPSLSQGPDSAEEKQLSESEYVGKPRQP 800
801 NPDWRYSASLRAGMHSSVHLEEAGILRAGPGGPDQQWPTVSSATPEPEAG 850
851 EVSPPVGAGVNSNSWTFKYGPGNPKQSGPGELPDKFIIPGSPAIISIRQE 900
901 PTNSQIDKSDFITFGKKEETKKKKKKKKGNKTQEKKEKGNSTTDNSDQ 948
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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