 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q9HCF6 from www.uniprot.org...
The NucPred score for your sequence is 0.92 (see score help below)
1 MPEPWGTVYFLGIAQVFSFLFSWWNLEGVMNQADAPRPLNWTIRKLCHAA 50
51 FLPSVRLLKAQKSWIERAFYKRECVHIIPSTKDPHRCCCGRLIGQHVGLT 100
101 PSISVLQNEKNESRLSRNDIQSEKWSISKHTQLSPTDAFGTIEFQGGGHS 150
151 NKAMYVRVSFDTKPDLLLHLMTKEWQLELPKLLISVHGGLQNFELQPKLK 200
201 QVFGKGLIKAAMTTGAWIFTGGVNTGVIRHVGDALKDHASKSRGKICTIG 250
251 IAPWGIVENQEDLIGRDVVRPYQTMSNPMSKLTVLNSMHSHFILADNGTT 300
301 GKYGAEVKLRRQLEKHISLQKINTRCLPFFSLDSRLFYSFWGSCQLDSVG 350
351 IGQGVPVVALIVEGGPNVISIVLEYLRDTPPVPVVVCDGSGRASDILAFG 400
401 HKYSEEGGLINESLRDQLLVTIQKTFTYTRTQAQHLFIILMECMKKKELI 450
451 TVFRMGSEGHQDIDLAILTALLKGANASAPDQLSLALAWNRVDIARSQIF 500
501 IYGQQWPVGSLEQAMLDALVLDRVDFVKLLIENGVSMHRFLTISRLEELY 550
551 NTRHGPSNTLYHLVRDVKKGNLPPDYRISLIDIGLVIEYLMGGAYRCNYT 600
601 RKRFRTLYHNLFGPKRPKALKLLGMEDDIPLRRGRKTTKKREEEVDIDLD 650
651 DPEINHFPFPFHELMVWAVLMKRQKMALFFWQHGEEAMAKALVACKLCKA 700
701 MAHEASENDMVDDISQELNHNSRDFGQLAVELLDQSYKQDEQLAMKLLTY 750
751 ELKNWSNATCLQLAVAAKHRDFIAHTCSQMLLTDMWMGRLRMRKNSGLKV 800
801 ILGILLPPSILSLEFKNKDDMPYMSQAQEIHLQEKEAEEPEKPTKEKEEE 850
851 DMELTAMLGRNNGESSRKKDEEEVQSKHRLIPLGRKIYEFYNAPIVKFWF 900
901 YTLAYIGYLMLFNYIVLVKMERWPSTQEWIVISYIFTLGIEKMREILMSE 950
951 PGKLLQKVKVWLQEYWNVTDLIAILLFSVGMILRLQDQPFRSDGRVIYCV 1000
1001 NIIYWYIRLLDIFGVNKYLGPYVMMIGKMMIDMMYFVIIMLVVLMSFGVA 1050
1051 RQAILFPNEEPSWKLAKNIFYMPYWMIYGEVFADQIDPPCGQNETREDGK 1100
1101 IIQLPPCKTGAWIVPAIMACYLLVANILLVNLLIAVFNNTFFEVKSISNQ 1150
1151 VWKFQRYQLIMTFHERPVLPPPLIIFSHMTMIFQHLCCRWRKHESDPDER 1200
1201 DYGLKLFITDDELKKVHDFEEQCIEEYFREKDDRFNSSNDERIRVTSERV 1250
1251 ENMSMRLEEVNEREHSMKASLQTVDIRLAQLEDLIGRMATALERLTGLER 1300
1301 AESNKIRSRTSSDCTDAAYIVRQSSFNSQEGNTFKLQESIDPAGEETMSP 1350
1351 TSPTLMPRMRSHSFYSVNMKDKGGIEKLESIFKERSLSLHRATSSHSVAK 1400
1401 EPKAPAAPANTLAIVPDSRRPSSCIDIYVSAMDELHCDIDPLDNSVNILG 1450
1451 LGEPSFSTPVPSTAPSSSAYATLAPTDRPPSRSIDFEDITSMDTRSFSSD 1500
1501 YTHLPECQNPWDSEPPMYHTIERSKSSRYLATTPFLLEEAPIVKSHSFMF 1550
1551 SPSRSYYANFGVPVKTAEYTSITDCIDTRCVNAPQAIADRAAFPGGLGDK 1600
1601 VEDLTCCHPEREAELSHPSSDSEENEAKGRRATIAISSQEGDNSERTLSN 1650
1651 NITVPKIERANSYSAEEPSAPYAHTRKSFSISDKLDRQRNTASLRNPFQR 1700
1701 SKSSKPEGRGDSLSMRRLSRTSAFQSFESKHN 1732
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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