 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q920P9 from www.uniprot.org...
The NucPred score for your sequence is 0.50 (see score help below)
1 MGTRRVTPGCAAGLLVLLLRCFGLAEPSEFSGDDSFTIVNENTGKCIQPL 50
51 SDWIVAQDCSETRSMLWKWVSQHRLFHLESQKCLGLDMTKAADNLRMFRC 100
101 DSSVLLWWKCEHHSLYSAAHYRLDLKDGYATASTNSSAVWKKGGSKENLC 150
151 DQPYREIYTRDGNSYGRPCEFPFLVGETWHHDCIRDENHSGPWCATTLNY 200
201 EYDQKWGICLKPESGCEGNWEKNEQIGSCYQFNNQEVLSWKEAYVSCQNQ 250
251 GADLLSIHSAAELAYITGKEDIARIVWIGLNQLYSARGWEWSDFKPLKFL 300
301 NWDPGTPSAPMIGGSSCARMDTETGLWRSVSCEAQQPYVCKKPLNNTVEL 350
351 PDVWTYSDTHCDVGWLPQNGFCYLLANESGPWDAAHLKCKAFGGDLISIH 400
401 SLADVEVVVTKLHSGDVKEEIWTGLRNVNSPTLFQWSDGTEVTLTYWNEN 450
451 EPSVPYNKTPNCVSYLGKLGQWKVQSCEKKLRYVCKKKGEITNDTRSDKL 500
501 CPPDEGWKRHGETCYKIYENEVPFGTNCNLTITSRFEQEFLNDMMKKYDK 550
551 SFQKYFWTGLRDADARGEYSWAATGGLKQAMTFSNWNFLQPASPGGCVAM 600
601 STGKTLGRWEVKSCRSFRALSICKKMSGPQEPEEATPKPDEPCPEGWHTF 650
651 PSNLSCYKVFHIERTVRRRTWEEAERFCQALGAHLPSFSHMNEVKEFLHL 700
701 LQDQFSVQRWLWIGLNKRSPDLQGSWQWSDRTPVSTVIMHREFQQDYDVR 750
751 DCAAIKVLDNAWLRTWYYYDERKFGYLKPFSCDAKLDWVCQIPKGSTLQV 800
801 PDWYNPERTGIHGPPVIIDGSEYWFVEEPRLNYEEAVLYCASNHSFLATI 850
851 TTFTKLKAIRGKMENLSGEEQKWWVKANANPIDHYFLRTRPLWHRFSMLL 900
901 DEECLQMSAKMWHLDLNKRADCNDKLPFVCEKYNVSSLEKYSPDSAAKVQ 950
951 CTGKWIPFQNKCFLKVKSEPVTFSQASSTCHTYGGTLPSVLSKSEQDFII 1000
1001 SLLPEMETSLWIGLRWTAYDRISKWTDGRNLTYSNFHPLLVGRRLSIAAY 1050
1051 FIDEESHYHCALMLNLRKSPLTGTWNFTSCSERHSLSLCQKYSENEDGRP 1100
1101 WETNSETVKYLNNLYKIISKPLTWHGALKECLNENMRLVSITDPYQQAFL 1150
1151 SVQATLRNTSFWIGLSSQDDELNFGWSDGTYLHFSNWAVDNEKLDDCVIL 1200
1201 DTDGFWKTADCDENQPGAICYYPGNETSKEVRPLNSAKCPSPAQSTPWVP 1250
1251 FQNSCYNFMITKNRHRTITQKEVHSLCQKLHSKAQILSIRNEEENNFVVE 1300
1301 QLLYFNYIASWVMLGVTYENNSLMWFDKTALSYTHWRAGRPAVKNHKFLA 1350
1351 GLSTDGFWDIQSFNVIDETLHFYQHSILACKIEMVDYKEERNSTLPEFIP 1400
1401 YEDGVYNVIQKRVTWYQALSMCSQSGRHLASVHNPKEQLFLEDIVNRDGF 1450
1451 PLWVGLSSHDGSESSFEWSDGSAFDYIPWKSQGSPGNCVILDPKGTWKHE 1500
1501 NCLSVKDGAICYKPTKFKELASHAHSSKCPLVKRNGSQWVQYGDHCYSAE 1550
1551 QALHTFAEAKKLCQELDHSATVVTIADENENKFVSRLMRENYNITMRVWL 1600
1601 GLSQHSLDQSWSWLDGLDVTFVKWENKSKNGDGKCSILIASNETWKKVEC 1650
1651 SRGYARVVCKVPLSPDYRGIAVLFAVLSVLALISGLIWFLVQRNHFRWTG 1700
1701 LSSVRYEHGANEDEVMLPSFHD 1722
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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