 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching P17545 from www.uniprot.org...
The NucPred score for your sequence is 0.61 (see score help below)
1 MSGGAALPVSQMELHKVNEVQFEIFKERQIKSYAVCLVEHAKSYANAADQ 50
51 SGEASMICVWVPLTSNSACETCHRKHPECPGHFGYIELAEPVFNIGVFDL 100
101 VLLVLKCVCKTCGALLLNTREQDVHKKLQHMTGLNRLRQVAKMAEAKCRV 150
151 STSTEDDMGIDGFDSAPFNGGSGMGPGATRGCGASQPRVSRFYGIYPTLV 200
201 IKAVHEEQDAEWHADKVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLP 250
251 VPPPQVRPAISFGGLRSDDELTHQIMSIVKRNNQLRRDKESDVQAAIDRS 300
301 RALLQEHVATYFNNASTYYKPTKVNDTKKLKSLTERLKGKYGRLRGNLMG 350
351 KRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTINKKRLTEFA 400
401 RRTVYPSANYIHHPNGTITKLALLRDRSKVTLNIGDVVERHVINGDVVLF 450
451 NRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQS 500
501 LLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDKY 550
551 FVQSVALWLDLWQLPIPAILKPRPLWTGKQVFSLILPEVNHPATPQDRPP 600
601 FPHNDSVVMIRRGQLLCGPITKSIVGAAPGSLIHVIFNEHGSDEVARFIN 650
651 GVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNDVLVKTRRNVEKIGAAA 700
701 NNRTLNRKAGMTLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMI 750
751 EAGSKGTDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSR 800
801 GMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALED 850
851 VHAAYDGTVRNANDELIQFMYGEDGLDGARIEGGQLFPLPFRDDKEMEDT 900
901 YKYEYDVDGTFSGKVGGNYMDPHVRKMLRADPQNVRKLQEEYEQLTADRE 950
951 WSRKMLDLEDRDKLKLNLPVNPGRLIQNARSTMGKRSQVSNLSPITIIDH 1000
1001 VRKLQEDLMKLFPSYHRGGDGYIRNTLSRERIESALTLFNVHLRQLLASK 1050
1051 RVLKEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQM 1100
1101 TLNTFHNAGISSKNVTLGVPRLLELLNVSRNQKHASMTVSLFPPYDEKRN 1150
1151 AQKAQHLIEYCTLESITRRIQFIYDPDPRHTVVEADRDILELEWNVMDES 1200
1201 DAELRIQEVVAGSPWVVRLELDVDMVTDKALDMKDVKQAILRVDESYIIE 1250
1251 TGMANNVRQRTIRMRSRYNEGADSIPKLKREIPALLARVHLRGIPGVRRA 1300
1301 LLKDTTEFTVDQATGKMSGNKIWAIDTDGTALRRAFIGVVGEDGKNIINA 1350
1351 VKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDT 1400
1401 ICQHGYLMAVSRSGINRSDTSGPLMRCSFEETVKVLMAAASFGECDPVRG 1450
1451 VSANLVLGNQARVGTGLFDLVLNMAALQQAVPQAEAVAPGKDVNVYHSLG 1500
1501 STLQQNIQSSIAYRPRDHDATPFVNNASLFLRQGFGGGSSSAPVTASAPY 1550
1551 NPSTTYHGGRLEASAVHRSQAYSTSPALEYGGREASASQMYSVMSSASAF 1600
1601 NPVSTRMSSVAHSYSEYSEASSYHLQHSVAPTSMQASLPRTDNSMTMQGI 1650
1651 GSVSVPYTPHAMSSAAPPSQVYASTEVGRSHSEDSRSQSALYVPTLSPTH 1700
1701 AGYAIRGDEPSTHRSDSNVMWREAGGGREQDEEDDLSTNYMPTAKTPQQA 1750
1751 APPTAAEFGDEEEEEQ 1766
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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