SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q9BXF3 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MCPEEGGAAGLGELRSWWEVPAIAHFCSLFRTAFRLPDFEIEELEAALHR    50
  51  DDVEFISDLIACLLQGCYQRRDITPQTFHSYLEDIINYRWELEEGKPNPL   100
 101  REASFQDLPLRTRVEILHRLCDYRLDADDVFDLLKGLDADSLRVEPLGED   150
 151  NSGALYWYFYGTRMYKEDPVQGKSNGELSLSRESEGQKNVSSIPGKTGKR   200
 201  RGRPPKRKKLQEEILLSEKQEENSLASEPQTRHGSQGPGQGTWWLLCQTE   250
 251  EEWRQVTESFRERTSLRERQLYKLLSEDFLPEICNMIAQKGKRPQRTKAE   300
 301  LHPRWMSDHLSIKPVKQEETPVLTRIEKQKRKEEEEERQILLAVQKKEQE   350
 351  QMLKEERKRELEEKVKAVEGMCSVRVVWRGACLSTSRPVDRAKRRKLREE   400
 401  RAWLLAQGKELPPELSHLDPNSPMREEKKTKDLFELDDDFTAMYKVLDVV   450
 451  KAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFV   500
 501  NDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMKHFPGEDGDTDEEF   550
 551  WIREDEKREKRRSRAGRSGGSHVWTRSRDPEGSSRKQQPMENGGKSLPPT   600
 601  RRAPSSGDDQSSSSTQPPREVGTSNGRGFSHPLHCGGTPSQAPFLNQMRP   650
 651  AVPGTFGPLRGSDPATLYGSSGVPEPHPGEPVQQRQPFTMQPPVGINSLR   700
 701  GPRLGTPEEKQMCGGLTHLSNMGPHPGSLQLGQISGPSQDGSMYAPAQFQ   750
 751  PGFIPPRHGGAPARPPDFPESSEIPPSHMYRSYKYLNRVHSAVWNGNHGA   800
 801  TNQGPLGPDEKPHLGPGPSHQPRTLGHVMDSRVMRPPVPPNQWTEQSGFL   850
 851  PHGVPSSGYMRPPCKSAGHRLQPPPVPAPSSLFGAPAQALRGVQGGDSMM   900
 901  DSPEMIAMQQLSSRVCPPGVPYHPHQPAHPRLPGPFPQVAHPMSVTVSAP   950
 951  KPALGNPGRAPENSEAQEPENDQAEPLPGLEEKPPGVGTSEGVYLTQLPH  1000
1001  PTPPLQTDCTRQSSPQERETVGPELKSSSSESADNCKAMKGKNPWPSDSS  1050
1051  YPGPAAQGCVRDLSTVADRGALSENGVIGEASPCGSEGKGLGSSGSEKLL  1100
1101  CPRGRTLQETMPCTGQNAATPPSTDPGLTGGTVSQFPPLYMPGLEYPNSA  1150
1151  AHYHISPGLQGVGPVMGGKSPASHPQHFPPRGFQSNHPHSGGFPRYRPPQ  1200
1201  GMRYSYHPPPQPSYHHYQRTPYYACPQSFSDWQRPLHPQGSPSGPPASQP  1250
1251  PPPRSLFSDKNAMASLQGCETLNAALTSPTRMDAVAAKVPNDGQNPGPEE  1300
1301  EKLDESMERPESPKEFLDLDNHNAATKRQSSLSASEYLYGTPPPLSSGMG  1350
1351  FGSSAFPPHSVMLQTGPPYTPQRPASHFQPRAYSSPVAALPPHHPGATQP  1400
1401  NGLSQEGPIYRCQEEGLGHFQAVMMEQIGTRSGIRGPFQEMYRPSGMQMH  1450
1451  PVQSQASFPKTPTAATSQEEVPPHKPPTLPLDQS                  1484

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

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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