 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q5DUY0 from www.uniprot.org...
The NucPred score for your sequence is 0.02 (see score help below)
1 MTKIVMLDYIPMLNNGGHRHPADIKPSMINSLLDSMSIILTSLCTFCEQL 50
51 SLNEAIIVNLGINTLDQLLMSQAGRYLLLYYCIYALELYTVCYSTLSLIL 100
101 LYLIQLNYILLTNIVGYLQYSCSEIANLVYTYILLEGLLDVSELDALVVE 150
151 TLLDYLWVPCDLIIRYYRAYWYFEGVYFNLNIPYVQRSAYWLCVVIWNNI 200
201 GWWTYQLMIIGWYSLSCLCIRLVPTILAIINLILTYIDLIIYLYDIYSNY 250
251 SNMTWLGILYSTINSIIRYDISRIHAYQHLLTVIIPNYCLAIYNSGLILS 300
301 SLLLDIYHYQIGLTILALQYLVAPLYISCSLLIYILCYIMTELLYSRSFY 350
351 IDLLLRLLEIIYLDILVNSLISIIILILSVDVAYLIQLQVIILSQYINII 400
401 SGYVAMPTTILITWYLYNIAVYIYYLVDYIATISTLIIWLLERILWVYGI 450
451 CANNIEPVVIDLPQLTLTSLDALLNQLLSEWCLLDAIMNVVTSVILLITV 500
501 SCLGVLRIILFIAVYPVYCIGVLLLNTLLQVVVGLISYIIGTFMNAIILI 550
551 CDIYVYSIHRPFLPLIMYVYFVAAIILEPIIDIIHTIILAEHALFNTYCY 600
601 IIFDILQPLHLQAFEFYRDLIWLIADLILAYIDLIRSTLVEGIISFIKWR 650
651 LEQDFQLVYDICEFYLDEVKPRIIRYWNIYSRWVRFLIYCAGNNINLLVL 700
701 LYVQFKGYTLPMIILFDLTRIQLYATIPVIISSYIYQGILQTMLIISYYN 750
751 TLLVATLEFIQIWLTILSVSPEMLYTSTLGILLRSYYLLYEILLLEPTWV 800
801 LFECLSTCVGLVELYLVTVETTVSNILIIDLILMEVLLEDIRQVATILTC 850
851 ILDWYILETCLDMQYADILLLMSSGLQSTVLNTIFDLLSLLGLLDETSIR 900
901 FILELTVQVCTIPAALYSTIIYPYIVLVTRCLLYLPDVVQLYLTIGEYLL 950
951 RETLYQLLIDWASCKLYSYNLYLLELYNIYYFWLSLLEKYWTFTYHIYNY 1000
1001 TTLVELSPDLLISLISYIIDICILSLELLLEDIRWGSTIFVNLLDWYLLD 1050
1051 TQLNIQYIDILLITSYSVQNTLLTVVFYILNLCGILNEISIQILFEITVQ 1100
1101 ICTILATIYCTVVLPYILIILEILSYLPEIVQLYLDIGEHLLLEILWQLL 1150
1151 IDLLYYRAYDYILIAQLLCKVTYLLYIVLEQLLLVIIDLYIYIIGDLLII 1200
1201 GSCHVGNHIIDILCSAENVYFLYFMIFIGYLLCGIFAFFYHGYLGTRGIF 1250
1251 YLSEMIIMGILIFSIVTLYYNLKYHLALDIILGELALSNEVIFTNIITFD 1300
1301 ILSILGVLLVATLTAIILTFGVEYMLREAFAYNVLATLVLFSASIICFIV 1350
1351 SYSFGLMIIFWEISGTLSLFLIDMYYARIRTTQAVTRTFALNRFGDLWMF 1400
1401 TASIEIYSLCHNDALPTLFALLPYAQFNLSILGNLIFDFTIPTVIVFSIF 1450
1451 SAAACKCAQFLLFVWLPDAMEAPTPASALIHSSTLVVMGIFMILRFAPIL 1500
1501 HLSVYTLYIMSILGSLTVAYGAILATQTSDLKKAVAYSTISQIGYLFTGC 1550
1551 AFLAFRATLIYLILHAICKALLFVLVGYIVHMFGGTTSLRRMGGIYYIVP 1600
1601 DIAIYMFILCMVLAGAPYTVGFFAKELIVTTLTNTSSPVATFIICCWIIS 1650
1651 FACTPFYLYRICVLPLFGRPRCSRRVFRNIVSPQSTYNFIDSDSSLNSLL 1700
1701 HKFTNLITRWSVQGRFTNLLHLLLLLIVLFCGEFLVFLVTGLFGTSTTLF 1750
1751 SDTAIDDSVYQLTDYYLLSYYRVRNIQLLIIVLFALVTLYITAINNQLTF 1800
1801 NIIYLSVVLPILAIIFICLGHYFLVDFTVYIYNISNSLIFELLCDLAIC 1849
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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