 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching P21271 from www.uniprot.org...
The NucPred score for your sequence is 0.92 (see score help below)
1 MSYSELYTRYTRVWIPDPDEVWRSAELTKDYKEGDKSLQLRLEDDTILEY 50
51 PVDVQNNQVPFLRNPDILVGENDLTALSHLHEPAVLHNLKVRFLESNHIY 100
101 TYCGIVLVAINPYEQLPIYGQDVIYAYSGQNMGDMDPHIFAVAEEAYKQM 150
151 ARDEKNQSIIVSGESGAGKTVSAKYAMRYFATVGGSASDTNIEEKVLASS 200
201 PIMEAIGNAKTTRNDNSSRFGKFIEIGFDKKYHIIGANMRTYLLEKSRVV 250
251 FQADDERNYHIFYQLCAAASLPEFKELALTCAEDFFYTAHGGNTTIEGVN 300
301 DADDFEKTRQALTLLGVRDSHQISIFKIIASILHLGSVEIQSERDGDSCS 350
351 ISPQDEHLSNFCSLLGIEHSQMEHWLCHRKLVTTSETYVKTMSLQQVVNA 400
401 RDALAKHIYAQLFSWIVEHINKALHTSHKQHSFIGVLDIYGFETFEINSF 450
451 EQFCINYANEKLQQQFNSHVFKLEQEEYMKEQIPWTLIDFYDNQPCIDLI 500
501 EAKLGILDLLDEECKVPKGTDQNWAQKLYERHSNSQHFQKPRMSNTAFIV 550
551 NHFADKVEYLSDGFLEKNRDTVYEEQINILKASKFPLVADLFHDDKDSAP 600
601 ATNTAKNRSSSKINVRSSRPLIKVPNKEHKKSVGYQFRTSLNLLMETLNA 650
651 TTPHYVRCIKPNDEKLPFHFDPKRAVQQLRACGVLETIRISAAGYPSRWT 700
701 YHDFFNRYRVLMKKRELTNTDKKNICKSVLESLIKDPDKFQFGRTKIFFR 750
751 AGQVAYLEKLRADKFREATIMIQKSVRGWLQRVKYRRLRAATLSLQRFCR 800
801 GYLARRLAEHLRRTRAAIVFQKQYRMLKARRAYRRVCRATVIIQSFTRAM 850
851 FVRRNYRQVLMEHKATIIQKYARGWMARKRFLRERDAAIVIQCAFRRLKA 900
901 RQELKALKIEARSAEHLKRLNVGMENKVVQLQRKIDDQNKEFKTLSEQLS 950
951 AVTSSHAVEVEKLKKELAHYQQNQEADTSLQLQEEVQSLRTELQKAHSER 1000
1001 RVLEDAHNKENGELRKRVADLEHENALLKDEKEYLNNQILCQSKAESSQS 1050
1051 SVEENLLMKKELEEERSRYQNLVKEYSQLEQRYENLRDEQTPGHRKNPSN 1100
1101 QSSLESDSNYPSISTSEIGDTEDALQQVEEIGIEKAAMDMTVFLKLQKRV 1150
1151 RELEQERKKLQAQLEKGQQDSKKGQVEQQNNGLDVDQDADIAYNSLKRQE 1200
1201 LESENKKLKNDLNELRKAVADQAMQDNSTHSSPDSYSLLLNQLKLANEEL 1250
1251 EVRKEEVLILRTQIMNADQRRLSGKNMEPNINARTSWPNSEKHVDQEDAI 1300
1301 EAYHGVCQTNRLLEAQLQAQSLEHEEEVEHLKAQVEALKEEMDKQQQTFC 1350
1351 QTLLLSPEAQVEFGVQQEISRLTNENLDFKELVEKLEKNERKLKKQLKIY 1400
1401 MKKVQDLEAAQALAQSDRRHHELTRQVTVQRKEKDFQGMLEYHKEDEALL 1450
1451 IRNLVTDLKPQMLSGTVPCLPAYILYMCIRHADYTNDDLKVHSLLSSTIN 1500
1501 GIKKVLKKHNDDFEMTSFWLSNTCRFLHCLKQYSGDEGFMTQNTAKQNEH 1550
1551 CLKNFDLTEYRQVLSDLSIQIYQQLIKIAEGLLQPMIVSAMLENESIQGL 1600
1601 SGVRPTGYRKRSSSMVDGENSYCLEAIVRQMNSFHTVLCDQGLDPEIILQ 1650
1651 VFKQLFYMINAVTLNNLLLRKDACSWSTGMQLRYNISQLEEWLRGKNLHQ 1700
1701 SGAVQTMEPLIQAAQLLQLKKKTHEDAEAICSLCTSLSTQQIVKILNLYT 1750
1751 PLNEFEERVTVSFIRTIQAQLQERNDPQQLLLDSKHVFPVLFPYNPSALT 1800
1801 MDSIHIPACLNLEFLNEV 1818
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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