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

NucPred

Fetching P70705 from www.uniprot.org...

The NucPred score for your sequence is 0.16 (see score help below)

   1  MEPNMDANSITITVEGMTCISCVRTIEQQIGKVNGVHHIKVSLEEKSATV    50
  51  IYNPKLQTPKTLQEAIDDMGFDALLHNANPLPVLTNTVFLTVTAPLALPW   100
 101  DHIQSTLLKTKGVTGVKISPQQRSAVVTIIPSVVSANQIVELVPDLSLDM   150
 151  GTQEKKSGTSEEHSTPQAGEVLLKMRVEGMTCHSCTSTIEGKVGKLQGVQ   200
 201  RIKVSLDNQEATIVYQPHLITAEEIKKQIEAVGFPAFIKKQPKYLKLGAI   250
 251  DVERLKSTPVKSSEGSQQKSPAYPSDSAITFTIDGMHCKSCVSNIESALS   300
 301  TLQYVSSIVVSLENRSAIVKYNASLVTPEILRKAIEAVSPGQYRVSISSE   350
 351  VESPTSSPSSSSLQKMPLNLVSQPLTQEVVININGMTCNSCVQSIEGVIS   400
 401  KKPGVKSIHVSLTNSTGTIEYDPLLTSPEPLREAIEDMGFDAVLPADMKE   450
 451  PLVVIAQPSLETPLLPSTTEPENVMTPVQNKCYIQVSGMTCASCVANIER   500
 501  NLRREEGIYSVLVALMAGKAEVRYNPAVIQPRVIAELIRELGFGAVVMEN   550
 551  AGEGNGILELVVRGMTCASCVHKIESTLTKHKGIFYCSVALATNKAHIKY   600
 601  DPEIIGPRDIIHTIGNLGFEASLVKKDRSANHLDHKREIKQWRGSFLVSL   650
 651  FFCIPVMGLMIYMMVMDHHLATLNHNQNMSNEEMINMHSSMFLERQILPG   700
 701  LSIMNLLSLLLCLPVQFCGGWYFYIQAYKALRHKTANMDVLIVLATTIAF   750
 751  AYSLVILLVAMYERAKVNPITFFDTPPMLFVFIALGRWLEHIAKGKTSEA   800
 801  LAKLISLQATEATIVTLNSENLLLSEEQVDVELVQRGDIIKVVPGGKFPV   850
 851  DGRVIEGHSMVDESLITGEAMPVAKKPGSTVIAGSINQNGSLLIRATHVG   900
 901  ADTTLSQIVKLVEEAQTSKAPIQQFADKLSGYFVPFIVLVSIVTLLVWII   950
 951  IGFQNFEIVEAYFPGYNRSISRTETIIRFAFQASITVLCIACPCSLGLAT  1000
1001  PTAVMVGTGVGAQNGILIKGGEPLEMAHKVKVVVFDKTGTITHGTPVVNQ  1050
1051  VKVLVESNKISRNKILAIVGTAESNSEHPLGAAVTKYCKQELDTETLGTC  1100
1101  TDFQVVPGCGISCKVTNIEGLLHKSNLKIEENNIKNASLVQIDAINEQSS  1150
1151  PSSSMIIDAHLSNAVNTQQYKVLIGNREWMIRNGLVISNDVDESMIEHER  1200
1201  RGRTAVLVTIDDELCGLIAIADTVKPEAELAVHILKSMGLEVVLMTGDNS  1250
1251  KTARSIASQVGITKVFAEVLPSHKVAKVKQLQEEGKRVAMVGDGINDSPA  1300
1301  LAMASVGIAIGTGTDVAIEAADVVLIRNDLLDVVASIDLSRKTVKRIRIN  1350
1351  FVFALIYNLIGIPIAAGVFLPIGLVLQPWMGSAAMAASSVSVVLSSLFLK  1400
1401  LYRKPTYDNYELRPRSHTGQRSPSEISVHVGIDDTSRNSPRLGLLDRIVN  1450
1451  YSRASINSLLSDKRSLNSVVTSEPDKHSLLVGDFREDDDTTL          1492

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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