 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching P25202 from www.uniprot.org...
The NucPred score for your sequence is 0.69 (see score help below)
1 MEPNRRLRYFRSEIPQPVTEHRFPKRVEKLVFSVLSSNALMKLSEVQITT 50
51 PILYEHYPSPATNGVLDKRLGLSDKVGKCATCGKDTKMCIGHFGTISLAL 100
101 PVFHPGLINDARTMLSIVCPFCSRVKISEADRLKYKVLNHKFSLAIVKEA 150
151 QEQAKKQVNCPFCHAPSTICKKSQGFRVLREMHYEERATKILADVIKHQK 200
201 DIEKIQELDQRLRNHVVDPIQALHILQKVPECDYPYLGIPWQSRNVYASQ 250
251 QTPDSIASNDASQLFSRGSSKLLARTASRFIAQHQGISDRATRLTSHAFL 300
301 TRPQDVILTHIPVPPSCLRPSVQSGSGAGTTEDNLTSHLVRILTINDKLK 350
351 EAMVSGAVATSKVYAKWDQLNMDVSLLYIGKIPGGVQPVKNKTDSGTKEG 400
401 TGIIDRLKGKAGRFRSNLSGKRVNFSGRTVISPNPYLSMQQVAIPRLIAQ 450
451 NLTFPEIVTSRNIRFLRELILNGKTYPGANEVLLLNDTIRYNPALKRLGI 500
501 DVKQSRDMEAKAMELVSRCVDTFNLNSLCADLPELQAAIQHLVSESSNAI 550
551 NSELKAEDLPQNQPLFAKEVYDPAQKGESNNIDNNVCEIDELKLEDTADY 600
601 QVGESAGQASTVAVEQPPESRTVLKLNSIASLQLTNASSQHLSTFKLNTV 650
651 SLLQKDRRGRQAIANSLRPNDIVYRHLLPNDTLLFNRQPSLHRMSIMQFN 700
701 AVIHENRTFSFNPVVCSPFNADFDGDEMNIFYMQGQEARAEAGILMGSHE 750
751 NIISPRHGECMIGLTQDFLTGIYLLSGKGIFMTRQEYCQHVSYGCDGFGD 800
801 ATYGVSLYNYGREFIKSIHDRRGTEEDTVGFVKVPCLSQPCIVYPRQLYS 850
851 GKQVLSVLMKGNDFDSVNINLEHGDKTYKKDSDRRALSVNDDYIIIQNSE 900
901 HLVGRLTKTFLASSKNCIFYFLVQNYGPVSAARIMLRFAKVAARFLMNYG 950
951 FTIGIDDVMPSQRVLGKKEVIVQEGYEKAQEKIRDYESGKLEAIPGSTVQ 1000
1001 ETLEATLNQILSNVRESCAQIALKELHFTNKPLIMSLCGSKGSPINIAQM 1050
1051 IIILGQQSFGGSRAPDDFYTRSTPYFYHYSKEPNAKGFILNSFYTGLLPF 1100
1101 EFLAHARAGRDGVIDSACKTADTGYLQRRLVKCLEDLSVSYDFTVRNSKK 1150
1151 SVVQFRFGHDGFDPIKLEVGTGQCFDLDTLLRHIILLNRSQDLAEGAFPV 1200
1201 LLDRYKAEAELDVLLNKDFYGQEACLIERSNVTSYFQQSILPKLTTNTHI 1250
1251 ATTVAPALAASFLQTTLTKKDIDDFLRQVRRKYIRLNLEPGSPCGAVAAQ 1300
1301 SVGEPSTQMTLKSFHHAGLASMNITQGVPRLKEIVDGVVKISTPITTVEL 1350
1351 HVDVDKEELAATVTEKYLEKARMMKNIIECTYLGQISASIIECYSQSVCH 1400
1401 IEVNLDMKIIADMGLAGIITVETVVASILHNDKAKKLVGQDQSSGSVSIH 1450
1451 SATRFSVRPLTQSRDDLLFDIQSLKLLLPMIPVSGISTCSRAVINEYKEF 1500
1501 CQGATSSAPLTKYNLLVEGIGLQNILNVSGIDFTRTLSNNIVEVANTLGI 1550
1551 EAAVATISNEIKACMDSHGMAVDMRHIRLLADIMCFRGRVLGFTRFGLTK 1600
1601 MKADSVIMLASFEKTGEHLFNAALGNKVDEANGVTESIILGKPMSMGTGS 1650
1651 FSLLQAPYFDEKTGKTIEYQPKQTTRFLGEVLNKQYDEEVDAIVNAFWYD 1700
1701 EKLYLTGAEAKAKLLRGRRHANKRSWSRGKERHASLKPKNR 1741
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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