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

NucPred

Fetching Q9JL19 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MVLDDLPNFEDIYTSLCSSTMGDSEVEFDSGLEDDDTKGDSILEDSTIFV    50
  51  AFKGNIDDKDFKWKLDAILKNVPNLLHMESSKLKVQKVEPWNSVRVTFNI   100
 101  PREAAERLWILAQSNNQQLRDLGILSVQIEGEGAINLALGQNRSQDVRMN   150
 151  GPVASGNSVRMEAGFPMASGPGLIRMTSPAAVMTPQGGNMSSSMMAPGPN   200
 201  PELQPRTPRPASQSDAMDPLLSGLHIQQQSHPSGSLPPAHHSMQPVPVNR   250
 251  QMNPANFPQLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLQTRPLQQHQ   300
 301  QQPQGIRPQFTAPTQVPVPPGWNQLPSGALQPPPAQGSLGTMTTNQGWKK   350
 351  APLPSPMQAQLQARPSLATVQTPSHPPPPYPFGSQQASQAHTNFPQMSNP   400
 401  GQFTAPQMKGLQGGPSRVPTPLQQPHLTNKSPASSPSSFQQGSPASSPTV   450
 451  NQTQQQMGPRPPQNNPLSQGFQQPVSSPGRNPMVQQGNVPPNFMVMQQQP   500
 501  PNQGPQSLHPGLGGMPKRLPPGFSAGQANPNFMQGQVPSTTAATPGNSGA   550
 551  LQLQANQNVQHAGGQGAGPPQNQMQVSHGPPNMMQPSLMGIHGNINNQQA   600
 601  GSSGVPQVTLGNMQGQPQQGPPSQLMGMHQQIVPSQGQMAQQQGTLNPQN   650
 651  PMILSRAQLMPQGQMMVNAQNQNLGPSPQRMTPPKQMLPQQGPQMMAPHN   700
 701  QMMGPQGQVLLQQNPMIEQIMTNQMQGNKAQFNSQNQSNVMPGPAQIMRG   750
 751  PTPNMQGNMVQFTGQMSGQMLPQQGPVNNSPSQVMGIQGQVLRPPGPSPH   800
 801  MAQQHTDPVTTANNDVNLSQMMPDVSMQQASMVPPHVQSMQGNSASGSHF   850
 851  SGHGVSFNAPFGGAPNGSQMSCGQNPGFPVNKDVTLTSPLLVNLLQSDIS   900
 901  AGHFGVNNKQNNTNANKPKKKKPPRKKKNCHQDLNTPDNRPTGLEEVDQQ   950
 951  SLPGEQGINLDTTGPKLPDFSNRPPGYPTQPVEQRPLPQMPPQLMQHVAP  1000
1001  PPQPPQQQPQPQLPQQQQPPPPSQPQSQQQQQQQQMMMMLMMQQDPKSIR  1050
1051  LPVSQNVHPPRGPLNPDSQRMPVQQSGNVPVMVGLQGPASVPPSPDKQRM  1100
1101  PMSVNTPMGSNSRKMVYQENPQNSSSSPLGEMSSLPEASGSEVPSVAGGP  1150
1151  NNMPSHLVVSQNQLMMTGPKPGPSPLSATQGATPQQPPVNSLPSSHGHHF  1200
1201  PNVAAPTQTSRPKTPNRASPRPYYPQTPNNRPPSTEPSEISLSPERLNAS  1250
1251  IAGLFPPQINIPLPPRPNLNRGFDQQGLNPTTLKAIGQAPSNLTITNPPN  1300
1301  FAAPQAHKLDSVVVNSGKQSNPGTTKRASPSNSRRSSPGSSRKTTPSPGR  1350
1351  QNSKAPKLTLASQTSTTMLQNMELPRNVLVGPTPLANPPLPGSFPNNTGL  1400
1401  NPQNPTVPVPAMGTVLEDNKESVNIPQDSDCQNAQGRKEQVNTELKVVPT  1450
1451  QEAKMAVPEDQSKKDGQPLDPNKLPSVEENKNLMSPAMREAPTSLSQLLD  1500
1501  NSGAPNVTIKPPGLTDLEVTPPVVSGEDLRKASVIPTLQDPPSKEPSTSL  1550
1551  SSPHSSEPCSTLARSELSEVSSNAAPSIPPVMSRPVSSSSISTPLPPNQI  1600
1601  TVFVTSNPITTSSNTSAALPTHLQSALMSTVVTMPNVGNKVMVSEGQSAA  1650
1651  QSNARPQFITPVFINSSSIIQVMKGSQPSTIPATPLTTNSGLMPPSVAVV  1700
1701  GPLHIPQNIKFSSAPVTPNVPSSSPAPNIQTGRPLVLSSRATPVQLPSPP  1750
1751  CTSSPVVAPNPSVQQVKELNPDEASPQTNTSADQSTLPPSQPTTVVSSLL  1800
1801  TNSPGSSANRRSPVSSSKGKGKVDKIGQILLTKACKKVTGSLEKGEEQYG  1850
1851  ADGETEGPGLEITTPGLMGTEQCSTELDSKTPTPSAPTLLKMTSSPMAPS  1900
1901  STSTGPILPGGALPTSVRSIVTTLVPSELISTAPTTKGNHGGVTSEPLAG  1950
1951  GLVEEKVGSHPELLPSIAPSQNLAPKETPATALQGSVARPELEANAAIAS  2000
2001  GQSCEPKEIVEKSKTLTSRRNSRTEEPTMASESVENGHRKRSSRPASASS  2050
2051  STKDITGAVQSKRRKSK                                   2067

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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