 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q8TEM1 from www.uniprot.org...
The NucPred score for your sequence is 0.21 (see score help below)
1 MAARGRGLLLLTLSVLLAAGPSAAAAKLNIPKVLLPFTRATRVNFTLEAS 50
51 EGCYRWLSTRPEVASIEPLGLDEQQCSQKAVVQARLTQPARLTSIIFAED 100
101 ITTGQVLRCDAIVDLIHDIQIVSTTRELYLEDSPLELKIQALDSEGNTFS 150
151 TLAGLVFEWTIVKDSEADRFSDSHNALRILTFLESTYIPPSYISEMEKAA 200
201 KQGDTILVSGMKTGSSKLKARIQEAVYKNVRPAEVRLLILENILLNPAYD 250
251 VYLMVGTSIHYKVQKIRQGKITELSMPSDQYELQLQNSIPGPEGDPARPV 300
301 AVLAQDTSMVTALQLGQSSLVLGHRSIRMQGASRLPNSTIYVVEPGYLGF 350
351 TVHPGDRWVLETGRLYEITIEVFDKFSNKVYVSDNIRIETVLPAEFFEVL 400
401 SSSQNGSYHRIRALKRGQTAIDAALTSVVDQDGGVHILQVPVWNQQEVEI 450
451 HIPITLYPSILTFPWQPKTGAYQYTIRAHGGSGNFSWSSSSHLVATVTVK 500
501 GVMTTGSDIGFSVIQAHDVQNPLHFGEMKVYVIEPHSMEFAPCQVEARVG 550
551 QALELPLRISGLMPGGASEVVTLSDCSHFDLAVEVENQGVFQPLPGRLPP 600
601 GSEHCSGIRVKAEAQGSTTLLVSYRHGHVHLSAKITIAAYLPLKAVDPSS 650
651 VALVTLGSSKEMLFEGGPRPWILEPSKFFQNVTAEDTDSIGLALFAPHSS 700
701 RNYQQHWILVTCQALGEQVIALSVGNKPSLTNPFPAVEPAVVKFVCAPPS 750
751 RLTLAPVYTSPQLDMSCPLLQQNKQVVPVSSHRNPRLDLAAYDQEGRRFD 800
801 NFSSLSIQWESTRPVLASIEPELPMQLVSQDDESGQKKLHGLQAILVHEA 850
851 SGTTAITATATGYQESHLSSARTKQPHDPLVPLSASIELILVEDVRVSPE 900
901 EVTIYNHPGIQAELRIREGSGYFFLNTSTADVVKVAYQEARGVAMVHPLL 950
951 PGSSTIMIHDLCLVFPAPAKAVVYVSDIQELYIRVVDKVEIGKTVKAYVR 1000
1001 VLDLHKKPFLAKYFPFMDLKLRAASPIITLVALDEALDNYTITFLIRGVA 1050
1051 IGQTSLTASVTNKAGQRINSAPQQIEVFPPFRLMPRKVTLLIGATMQVTS 1100
1101 EGGPQPQSNILFSISNESVALVSAAGLVQGLAIGNGTVSGLVQAVDAETG 1150
1151 KVVIISQDLVQVEVLLLRAVRIRAPIMRMRTGTQMPIYVTGITNHQNPFS 1200
1201 FGNAVPGLTFHWSVTKRDVLDLRGRHHEASIRLPSQYNFAMNVLGRVKGR 1250
1251 TGLRVVVKAVDPTSGQLYGLARELSDEIQVQVFEKLQLLNPEIEAEQILM 1300
1301 SPNSYIKLQTNRDGAASLSYRVLDGPEKVPVVHVDEKGFLASGSMIGTST 1350
1351 IEVIAQEPFGANQTIIVAVKVSPVSYLRVSMSPVLHTQNKEALVAVPLGM 1400
1401 TVTFTVHFHDNSGDVFHAHSSVLNFATNRDDFVQIGKGPTNNTCVVRTVS 1450
1451 VGLTLLRVWDAEHPGLSDFMPLPVLQAISPELSGAMVVGDVLCLATVLTS 1500
1501 LEGLSGTWSSSANSILHIDPKTGVAVARAVGSVTVYYEVAGHLRTYKEVV 1550
1551 VSVPQRIMARHLHPIQTSFQEATASKVIVAVGDRSSNLRGECTPTQREVI 1600
1601 QALHPETLISCQSQFKPAVFDFPSQDVFTVEPQFDTALGQYFCSITMHRL 1650
1651 TDKQRKHLSMKKTALVVSASLSSSHFSTEQVGAEVPFSPGLFADQAEILL 1700
1701 SNHYTSSEIRVFGAPEVLENLEVKSGSPAVLAFAKEKSFGWPSFITYTVG 1750
1751 VLDPAAGSQGPLSTTLTFSSPVTNQAIAIPVTVAFVVDRRGPGPYGASLF 1800
1801 QHFLDSYQVMFFTLFALLAGTAVMIIAYHTVCTPRDLAVPAALTPRASPG 1850
1851 HSPHYFAASSPTSPNALPPARKASPPSGLWSPAYASH 1887
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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