 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q8BLI0 from www.uniprot.org...
The NucPred score for your sequence is 0.70 (see score help below)
1 MECCRRAAPGTPLLVLAFLLLSSRTARSEEDREGLWDAWGPWSECSRTCG 50
51 GGASYSLRRCLSSKSCEGRNIRYRTCSNVDCPPEAGDFRAQQCSAHNDVK 100
101 YHGQLYEWLPVSNDPDNPCSLKCQAKGTSLVVELAPKVLDGTRCYTESLD 150
151 MCISGLCQIVGCDHQLGSTVKEDNCGVCNGDGSTCRLVRGQYKSQLSASK 200
201 SDDTVVAIPYGSRHIRLVLKGPDHLYLETKTLQGTKGENSLSSTGIFLVD 250
251 NSTVDFQKLPDKEILRMTGPLTADFIIKIHDLGPADSTVQFIFYQPIIHR 300
301 WRETDFFPCSATCGGGYQLTSAECYDLRSNRVVADQYCHYYPENVKPKPK 350
351 LQECNLDPCPASDGYKQIMPYDLYHPLPRWEATPWTACSSSCGGGIQSRA 400
401 VSCVEEDIQGHVTSVEEWKCMYTPKMPVVQPCNIFDCPKWLAQEWSPCTV 450
451 TCGQGLRYRVVLCIDHRGMHTGGCSAKTKPHIKEECIIPTPCYKPREKLP 500
501 IEAKLPWFKQAQELEEGAAVSEEPSFIPEAWSACTVTCGVGTQVRIIRCQ 550
551 VLLPFSQSVADLPADECEGPKPASQRACYAGPCNGETPEFNPDNGDGLLG 600
601 GLQDLDELYDWEYEGFTKCSESCGGGVQEAVVSCLNKQTRELADENLCVT 650
651 SRRPPQLLKSCNLDPCPASHLLSREMNEVVVLADELCHHPKPSTVQACNR 700
701 FNCPPAWYPAQWQLCSRTCGGGIQKRDVLCKQRMADGSFLELPETFCSAS 750
751 KPTSHQGCKKDDCPSEWLLSEWSECSVSCGEGTQTRSAICQRVLKTGVST 800
801 VVNSTLCPPLPFSSSIRPCMLATCARPGRPSTKHSPHIAAARNIYIQTRR 850
851 QRKLHFVVGGFAYLLPKTTVVLRCPTRRFRKPLITWEKDGQHSISSAHVT 900
901 VAPFGYLKIHRLKPSDAGIYTCSAGPAREQFVIKLIGGNRKLVARPLSLW 950
951 SEEEEALQVRKTNPKEALQTHKHQNGIFSNGSKAEKRGLTADPGNRYDDI 1000
1001 VSRLLEQGGWPGELLASWEVQDSAERNASSEEDPNAEQALLHLPFTMVAE 1050
1051 QKRLDDILRNLSQQPEELRDLYSKHLVAQLAQDIFRSHLENQDLLPKPSE 1100
1101 QRFPPMAVPAHKHVSGFSSSLRSSSGEAGGGSRRPHRKPAILRKISAAQQ 1150
1151 LSASEVVTHLGQTVALASGTLSVLLHCEAVGNPRPTIHWTRNGEAVQFSD 1200
1201 RILLQPDDSLQILAPVEADVGFYTCNATNALGYDSVSIAVTLAGKPLVKT 1250
1251 SRMTVLNTEKPTVTVDIGGTVRTVRGVNVTINCQVAGVPEAEVTWFRNKS 1300
1301 KLGSSHHLHEGSSHHLHEGSLLLTDVSFSDQGLYSCRAANLHGEQTESTQ 1350
1351 LLILDPPQVPTQLEDIRALLLATGPNLPSVLMSPLGTQLVLDPGNSALLG 1400
1401 CPIKGHPTPNITWFQNGQPIATAPGLTHHIWGAGQILRVANLSGGPQGEF 1450
1451 SCLAQNEAGTLLQKASLVIQDYWWSVDRLATCSASCGNRGIHQPRLRCLL 1500
1501 NTTEVDPEHCTGKPRPAVQPVACNRRDCPSRWMVTSWSACTRSCGGGVQT 1550
1551 RRVTCQKLKASGISTPVSNDMCSQLAKRPVDTQACNQQLCVEWAFSSWGQ 1600
1601 CNGPCIGPRLAVQHRQVFCQTRDGITLPSEQCSALPRPVSTQNCWSEACS 1650
1651 VHWRVSLWTLCTATCGNYGFQSRRVECVHVRTNKAVPEHLCSWGPRPANW 1700
1701 QRCNVTPCENTECRDTTRYCEKVRQLKLCQLGQFRSRCCGTCGKA 1745
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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