 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q9W5D0 from www.uniprot.org...
The NucPred score for your sequence is 0.92 (see score help below)
1 MQWTAASCDQHDQHDPPAVNRNSIEQRTPANNCEVDPMDATGSTKHPHLP 50
51 KQREADRPVSGSGGGSSSLTLSGAVTTSMEVTVSTTTTTTIIESSSSTNT 100
101 TLEKNSPSPAGGSCSSGSGSLSPAYLQHHLQHHGSPLHHLQVHHHTAPPS 150
151 PLAAVRSAQMGSSVANGAGPAAACLAVCCSPGSSHHHLGHVGHLATGHPL 200
201 PHQLPHQLPHPSLYPLMAAAQLGYAGSSGPSSLVNSPALGRRKRYTSNSS 250
251 NCSSQFNNNYAGLDVDSLDDMLRKLTELEQRVIEAEERAEEAEDKVRAME 300
301 QRLSEWPKPPPQQAQHPHSHSHPHQPIPSHPQEQQAKNHCSPSHQASGGA 350
351 TAGAAGSGLPPTQETEKTITSLEIQVEEQRQLRLHDARQIEAKAAKIKEW 400
401 VNNKLRDLEEQNQLLREQNVKCNQQLELLKNHIANQSQRHSIVGPVRNSL 450
451 SLDVQDFTGSGSNPEHRRRSESLDPQEIIGRPLTSSYPHHQHRRNLSMEP 500
501 QELERNLVAAVDGLTLAPLSSISNKAPGGVPTESGVVTRPDSSDTDTAHD 550
551 YAEIYTPSCEKLPAWMKNNPALMASGGNSSTTTTTTSELGVPRPPTPPLH 600
601 RFPSWEAKIYQVANDGLAGAGTGTSTAESTASQEPDIQDGMGTNLSNGRR 650
651 HGHGHGSGTGIGTGDGHGTLGSTPGTPLPPSRQQQTASGGFCDISVPVYA 700
701 TVKGRASQIRSMPFTGDSSDDSSDGEDHAVMLTHHSHNSSSTDNTETSTS 750
751 GSASSPSKSLKTSSSLSPAKRSGSESPKNAKARVHIQSRTSTTPSSRINQ 800
801 HLQPSQHQHHTLSNQNHGHQLGAYTVTPSSGQLSLPRYHANALQPGSLPS 850
851 PLQHMRGTVISDLSFESGLSDDYALPPDAVSESTCMDASMPSLLMRQSYV 900
901 DSPSKKIESLEKMGHLAKLGGKLKTWRKRWFVLKNGSLNYWKSQHDVQRK 950
951 PQGQIQLDEVCRINRAEGASTFEIDTGKKVYYLTADSHATMDDWIRVLQN 1000
1001 VQRRNATKLLLSRDDQKPTVQGWVTKVKNGHPKKCWCVLLGKMFLYFKAP 1050
1051 AETNPLGQINMRDARVEEVEHVSDSDSEEREDAAQDQARLTVAIYPAHQG 1100
1101 PTYLILSGKPERDNWLYHLTVVSGGGPSAGTQYEQLVQKLMETDGDPNCV 1150
1151 LWRHPILLHTKDTITAPLSSMHTETMQPEAIKLFKSIQLFMSVAVNQPGI 1200
1201 DYHVVLAQNALQHALDMPELQTEMICILIKQTSRHLGQKLSVGVQVNKKL 1250
1251 GKQTRQLLLCATQSLFTCDTQQAGHAQANGSSPTSIQAPSATPIIDCKSN 1300
1301 PPVYSFVQGWQLLALAVSLFVPRSSRLLWYLKLHLSRNADTKTETGKYAA 1350
1351 YCERALERTLKNGGRETKPSRMEVLSILLKNPYHHSLPHAIPVHMMNSTY 1400
1401 QVVSFDGSTTIEEFQATLAHELGTRDATNGFCLFSDDPIEKDLEHYLEPL 1450
1451 AKLCDVISKWETALREKGSGKFENSRVIQLSYKNRLYWKHTIKCETDKER 1500
1501 LLLCYQTNSQIVQGRFPLSRELALELASLMSQIDMGDYSLEKSRDVGVGL 1550
1551 KGLDKFYPYRYRDALGAEQLKDVQELLVSKWMLLKGRSTLDCVRIYLTCC 1600
1601 RKWPYFGACLFQAKPRQSPESNTASGATPVAWLAVAEDALNVLELSTMAP 1650
1651 VARYPYSSVMTFGGCQDDFMLVVSHDDGGGGEQKLLFAMSKPKILEITLL 1700
1701 IADYMNALGHTVPGTPQMNSLTRNGSHRSLRTSQRPNLGGGSAVATGFST 1750
1751 NATTTAHNTLNSHATHTLNSNHSHTLSSSHHAGGGSQPGTLSSGHHQHHH 1800
1801 IQQHHQPDILKSTPDHQRIK 1820
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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