 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching P21675 from www.uniprot.org...
The NucPred score for your sequence is 0.98 (see score help below)
1 MGPGCDLLLRTAATITAAAIMSDTDSDEDSAGGGPFSLAGFLFGNINGAG 50
51 QLEGESVLDDECKKHLAGLGALGLGSLITELTANEELTGTDGALVNDEGW 100
101 VRSTEDAVDYSDINEVAEDESRRYQQTMGSLQPLCHSDYDEDDYDADCED 150
151 IDCKLMPPPPPPPGPMKKDKDQDSITGVSENGEGIILPSIIAPSSLASEK 200
201 VDFSSSSDSESEMGPQEATQAESEDGKLTLPLAGIMQHDATKLLPSVTEL 250
251 FPEFRPGKVLRFLRLFGPGKNVPSVWRSARRKRKKKHRELIQEEQIQEVE 300
301 CSVESEVSQKSLWNYDYAPPPPPEQCLSDDEITMMAPVESKFSQSTGDID 350
351 KVTDTKPRVAEWRYGPARLWYDMLGVPEDGSGFDYGFKLRKTEHEPVIKS 400
401 RMIEEFRKLEENNGTDLLADENFLMVTQLHWEDDIIWDGEDVKHKGTKPQ 450
451 RASLAGWLPSSMTRNAMAYNVQQGFAATLDDDKPWYSIFPIDNEDLVYGR 500
501 WEDNIIWDAQAMPRLLEPPVLTLDPNDENLILEIPDEKEEATSNSPSKES 550
551 KKESSLKKSRILLGKTGVIKEEPQQNMSQPEVKDPWNLSNDEYYYPKQQG 600
601 LRGTFGGNIIQHSIPAVELRQPFFPTHMGPIKLRQFHRPPLKKYSFGALS 650
651 QPGPHSVQPLLKHIKKKAKMREQERQASGGGEMFFMRTPQDLTGKDGDLI 700
701 LAEYSEENGPLMMQVGMATKIKNYYKRKPGKDPGAPDCKYGETVYCHTSP 750
751 FLGSLHPGQLLQAFENNLFRAPIYLHKMPETDFLIIRTRQGYYIRELVDI 800
801 FVVGQQCPLFEVPGPNSKRANTHIRDFLQVFIYRLFWKSKDRPRRIRMED 850
851 IKKAFPSHSESSIRKRLKLCADFKRTGMDSNWWVLKSDFRLPTEEEIRAM 900
901 VSPEQCCAYYSMIAAEQRLKDAGYGEKSFFAPEEENEEDFQMKIDDEVRT 950
951 APWNTTRAFIAAMKGKCLLEVTGVADPTGCGEGFSYVKIPNKPTQQKDDK 1000
1001 EPQPVKKTVTGTDADLRRLSLKNAKQLLRKFGVPEEEIKKLSRWEVIDVV 1050
1051 RTMSTEQARSGEGPMSKFARGSRFSVAEHQERYKEECQRIFDLQNKVLSS 1100
1101 TEVLSTDTDSSSAEDSDFEEMGKNIENMLQNKKTSSQLSREREEQERKEL 1150
1151 QRMLLAAGSAASGNNHRDDDTASVTSLNSSATGRCLKIYRTFRDEEGKEY 1200
1201 VRCETVRKPAVIDAYVRIRTTKDEEFIRKFALFDEQHREEMRKERRRIQE 1250
1251 QLRRLKRNQEKEKLKGPPEKKPKKMKERPDLKLKCGACGAIGHMRTNKFC 1300
1301 PLYYQTNAPPSNPVAMTEEQEEELEKTVIHNDNEELIKVEGTKIVLGKQL 1350
1351 IESADEVRRKSLVLKFPKQQLPPKKKRRVGTTVHCDYLNRPHKSIHRRRT 1400
1401 DPMVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQT 1450
1451 LRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDE 1500
1501 KLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFH 1550
1551 HPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANS 1600
1601 VKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEA 1650
1651 ELESLDPMTPGPYTPQPPDLYDTNTSLSMSRDASVFQDESNMSVLDIPSA 1700
1701 TPEKQVTQEGEDGDGDLADEEEGTVQQPQASVLYEDLLMSEGEDDEEDAG 1750
1751 SDEEGDNPFSAIQLSESGSDSDVGSGGIRPKQPRMLQENTRMDMENEESM 1800
1801 MSYEGDGGEASHGLEDSNISYGSYEEPDPKSNTQDTSFSSIGGYEVSEEE 1850
1851 EDEEEEEQRSGPSVLSQVHLSEDEEDSEDFHSIAGDSDLDSDE 1893
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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