 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q8MSX1 from www.uniprot.org...
The NucPred score for your sequence is 0.76 (see score help below)
1 MSSTKSQVALATNIPTNLSSAASASTAAAAAAVVVVASANAAVASSANSS 50
51 GVGSGSGPGPGSGAGVSGPVAAGTATAVATGSTVTAATSVAATTSTSVAT 100
101 ISTSCSSSSINNINNNCGEECQSAAGSSNLGRQNSFGNRRGNMKGKHLTR 150
151 SHAMRESTSPPRTPTPRAASEQQQQQLQGEQHEHNNNNNINSSSKAQSAG 200
201 RGNSPLMETPAVIVTSQQPQQQQQQQQQQQQSVPPKPQQNVPLSNEAEFP 250
251 KLSPPKKSGGQHNRTNSNGSGMEFNNNNNSSNKKFVVDMKANGLDNKPHN 300
301 NSSTGVIFNSGMNYKAAERHDRHERHEMSSQNSNLSNNHDEEPYHYEPRG 350
351 GGGGKKHRANTNAKGNKPRLKNLGGSSSGSIDLGGGGGNGNCNNMSNNGQ 400
401 SNNSSNNTSGFISRENSSEQYTDYGGTDLLVFFRDTLNKNPKDRNILLKI 450
451 EKDLIDFVQENSRGCEYRFPPASSYNRMLIHRTAAFFGMEHNVDTETQQC 500
501 VIVAVAKNTRIPEIRFQSLVRDDARKSILKRDTHSFDEVRQSPYLCPLSL 550
551 DRKAKSFEEREEDYDRARSRIFSRTGGNHDGYSGGGGDEECYGGWEQQQQ 600
601 QQKQSQPPRPKRPNGKMLQMQNSTESRDGMRSGGAVPKSHNFGNYGGPPS 650
651 SGGPGNNSLPRGDSTNSIKSGRGGFVKQDSTGSTPWRLSPSSSGSIYHYD 700
701 PSNLPPNQALQHSGNQYQSQNQGNSSSGGYNNYRKSSPHQQQQSQQQQQS 750
751 QQHHQQQLQQPQQLHQQSSQQYATTELSCSSTESYAEEEAQSPGMECSEG 800
801 YESYEQQSLPVQQQLSGNGDSASTKGDDCDSLASATACLSITTSTSTKNY 850
851 DRIEVQKYKNQATSPNIPACCAVGEKLELEAGLPQEQEQEPMAGPSSSGS 900
901 ATSSVGITELPSSQTPLPMVNQVNCDLQSVSPSTTPYSQCEVKTPSQNHA 950
951 PSAAVEEPKTTTWTYTQSYQAPDGSTVFHTTTTPNGAAPYCATTYQQGPD 1000
1001 GSIYAVPQGMVYAAYPQPGVGTAGGASQPLFQLTTSSHPPAQTIFASPEA 1050
1051 GAEIPGGTYMIPVFDPAQQPREGLIPAQAIYQTGPGGPGATTVMPMATAA 1100
1101 AYPTAQFATAAPNGAPIYQAPLIYSSEPGGGAQLQQLPMAPYPIQYSYPY 1150
1151 YHPISYYVPQQAVAAAPMVASQPQVGQAPMQQQAPHTGAGTTTGPPTVVS 1200
1201 VSGQQHHQPHQQHHQQQQHSSNGSVVTSSAYGTRVKRTPGGGSIHYNPSY 1250
1251 TPSSVAHAGGAHHPSAGSAQIIAAPAASTTTYHALPTLTLAHGGPATGTD 1300
1301 LSGAGGAHVYALPAQHALIPTNIFPYAAAAAAAAGGPGGPPTTPQVVQQA 1350
1351 PPPPPQSAPHHALITAAPFYPANGGNMDQGASQSAPSTPAAPGRQAPLFS 1400
1401 TPPAPNNGSSGSSSAGGGGNSGGYHSNSSTPHYYQGQNSNEGYTSPYEKR 1450
1451 NHGGGASGAHSVGVRKPYHPGGYNPRHSVPLGGIPSGAKTPLLNSNNEPT 1500
1501 PRASPSSVSLGGASSSGGANSYPHRGPPPHTMGVKRDNKPNQLPLISGPP 1550
1551 PSYAANSSPGVSSYESKPPVRLNAGAASFRSQKSMNQDYRRSVSQRNSPS 1600
1601 ANGGGSGSHESSNNSPNSIVGSQSNSAANTPNAAAPPPPQPQPTLVSHSG 1650
1651 GFVVLDQTTGAAMNASPPSLYGGGGGPNAGISGGAGASGAAGSNGGHQPG 1700
1701 GGGGARSHIPTAQLHHSAAAAAAAAAGSQQATAAVLSGVAAAAALGGYNP 1750
1751 NGASGVYFKYGQTYFAHPSVALPNSRRSPSNDIRPQMAQVAGMYPTMMIQ 1800
1801 ARHPSRHPNPNYKGSRPR 1818
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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