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

NucPred

Fetching Q04656 from www.uniprot.org...

The NucPred score for your sequence is 0.18 (see score help below)

   1  MDPSMGVNSVTISVEGMTCNSCVWTIEQQIGKVNGVHHIKVSLEEKNATI    50
  51  IYDPKLQTPKTLQEAIDDMGFDAVIHNPDPLPVLTDTLFLTVTASLTLPW   100
 101  DHIQSTLLKTKGVTDIKIYPQKRTVAVTIIPSIVNANQIKELVPELSLDT   150
 151  GTLEKKSGACEDHSMAQAGEVVLKMKVEGMTCHSCTSTIEGKIGKLQGVQ   200
 201  RIKVSLDNQEATIVYQPHLISVEEMKKQIEAMGFPAFVKKQPKYLKLGAI   250
 251  DVERLKNTPVKSSEGSQQRSPSYTNDSTATFIIDGMHCKSCVSNIESTLS   300
 301  ALQYVSSIVVSLENRSAIVKYNASSVTPESLRKAIEAVSPGLYRVSITSE   350
 351  VESTSNSPSSSSLQKIPLNVVSQPLTQETVINIDGMTCNSCVQSIEGVIS   400
 401  KKPGVKSIRVSLANSNGTVEYDPLLTSPETLRGAIEDMGFDATLSDTNEP   450
 451  LVVIAQPSSEMPLLTSTNEFYTKGMTPVQDKEEGKNSSKCYIQVTGMTCA   500
 501  SCVANIERNLRREEGIYSILVALMAGKAEVRYNPAVIQPPMIAEFIRELG   550
 551  FGATVIENADEGDGVLELVVRGMTCASCVHKIESSLTKHRGILYCSVALA   600
 601  TNKAHIKYDPEIIGPRDIIHTIESLGFEASLVKKDRSASHLDHKREIRQW   650
 651  RRSFLVSLFFCIPVMGLMIYMMVMDHHFATLHHNQNMSKEEMINLHSSMF   700
 701  LERQILPGLSVMNLLSFLLCVPVQFFGGWYFYIQAYKALKHKTANMDVLI   750
 751  VLATTIAFAYSLIILLVAMYERAKVNPITFFDTPPMLFVFIALGRWLEHI   800
 801  AKGKTSEALAKLISLQATEATIVTLDSDNILLSEEQVDVELVQRGDIIKV   850
 851  VPGGKFPVDGRVIEGHSMVDESLITGEAMPVAKKPGSTVIAGSINQNGSL   900
 901  LICATHVGADTTLSQIVKLVEEAQTSKAPIQQFADKLSGYFVPFIVFVSI   950
 951  ATLLVWIVIGFLNFEIVETYFPGYNRSISRTETIIRFAFQASITVLCIAC  1000
1001  PCSLGLATPTAVMVGTGVGAQNGILIKGGEPLEMAHKVKVVVFDKTGTIT  1050
1051  HGTPVVNQVKVLTESNRISHHKILAIVGTAESNSEHPLGTAITKYCKQEL  1100
1101  DTETLGTCIDFQVVPGCGISCKVTNIEGLLHKNNWNIEDNNIKNASLVQI  1150
1151  DASNEQSSTSSSMIIDAQISNALNAQQYKVLIGNREWMIRNGLVINNDVN  1200
1201  DFMTEHERKGRTAVLVAVDDELCGLIAIADTVKPEAELAIHILKSMGLEV  1250
1251  VLMTGDNSKTARSIASQVGITKVFAEVLPSHKVAKVKQLQEEGKRVAMVG  1300
1301  DGINDSPALAMANVGIAIGTGTDVAIEAADVVLIRNDLLDVVASIDLSRK  1350
1351  TVKRIRINFVFALIYNLVGIPIAAGVFMPIGLVLQPWMGSAAMAASSVSV  1400
1401  VLSSLFLKLYRKPTYESYELPARSQIGQKSPSEISVHVGIDDTSRNSPKL  1450
1451  GLLDRIVNYSRASINSLLSDKRSLNSVVTSEPDKHSLLVGDFREDDDTAL  1500

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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