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

NucPred

Fetching P90761 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MSWRDRDFDPHGGRNAFRLTDESKQSSSERAASMRAMRSFTQSIEDEGPP    50
  51  ELPASLDIDMIEGVSMKTSDTNDTIIEVKPGKVDPQLGETQKYKMAVPGP   100
 101  GHSEQEQELHKSLIRDEEEDAEVEQVFAASAEPVVTPPKSLNFAETAEEL   150
 151  RHAYDQKIRKRPTTPTSACVLDGIAFFAGSVDGSNDTIPTDAEKKIKVSI   200
 201  PSGRRRKTENMSYSEFYESMANQIPGGGGRRMSQSGRTTPLHDYEGDILD   250
 251  ENPQYKDKAPPAPVVHRRSSIEWENFADMEDKMEQAEEKARKEEKKEKEE   300
 301  TAEVAQNDDVTTEKHQNEVEKSKKMLNFLAKPPTVEITSPDAPHQGAFHD   350
 351  NTPKEPKVVEEEEDDDLPTFSEDMDEARQQVMKEMTESVVKTENVENEKQ   400
 401  EDTHISEGHVEYGTEESPAVTDGSYQQDGTENAYDPNAYPGYIWNYETQE   450
 451  WEYDPSYVAPEEPIDQSAYEAQAAAYAEVDQRAAEVVYQREHAGYDQGDF   500
 501  YTHQDTSYSSEAYAHDQAKGYQDPNAYGAEAAADNSQEYDYSAYGGYEGY   550
 551  LAACRAYDEESQQPQYGETVATEAYSQDYGYEQQGDYHHEGVGATDENST   600
 601  SAISGYEQNGASTSLGYGDAQGYDGYDHNASYYQGQEYQQEYYQNHKYEN   650
 651  SQYQVDQHPAESAAPPRPVAPMEPLFKQAPPQPDPFGWDSSGHTGDAPTA   700
 701  SEPVQELSPTPEASSSTGTSAPARPPPARPEAPKKDETAVDAAAPPRPPP   750
 751  AARPPPPRPAPANKEKPKEPEPEEDAWAQFKRMTEKVSTAVKSTESTLKN   800
 801  LEETSAANDIKDESYLANVGGSQGFVNESTQKEIQRLTEEKKMEKLQKKK   850
 851  LKQQGKKAATPTLEPDEEDAMDRAAQELAMKMASMRSDMADWKAPEMIPV   900
 901  KEIKKAPEIRRVDSASAIPPRKRSSIKDVQQDSGGSLELPPHLAAPQDSI   950
 951  APNPKGDHAPDDPILSAPAWADFETSEPMLPPSESGFFSNKDASNEGGVS  1000
1001  RDATDDPFVTTVASSEKRSSFVADPFAPQQAALIDESYDPFAVVAVEEVV  1050
1051  AMAKAKAEQAAANAENEDDFYNGRQSPTLSTPTPEGGSPISQQRPNAFED  1100
1101  DFKCAELTGLDTPTPLYDEDDSQPLTDFIPKFDGDGWDLMVRHPIKKKSF  1150
1151  MAERCWKPCYVRLHGLTLYLYNDKKDAQPIQELLLQATYSLSDTTLQAYD  1200
1201  VYGKIHTVKLQFVVYKEKVGIRPGQISRLVDGHITKYGLPLEHSAQCTVL  1250
1251  LKFGSLNASHLQTFVTTVEDLLFKCKITRTAKPVYKQDEVQIHCYDEYSA  1300
1301  FVDKEGILSDQKARVRLFCLAFLTGSPVLEVGLNDRRRQGKEIVRRKDIL  1350
1351  PMYTERWIRFEALEFHSIVNKPEFDKEQVIAFSPPDGCFFEIMRFRVRPP  1400
1401  RNREKAMTVKSIMKIAGSKVEIRIEAMAAAQIQRTRGSDERRNIPCEDIA  1450
1451  IRFPIPEAWIYLFREERHWGVGSIHSKKLRPGKVKNLKDRLLGAVQASEP  1500
1501  NLIECAIGEAKYEHVYRSLVWRIPRLPEKHHAAYKSHLLKCRFELSSFDL  1550
1551  MPEEFLPRCDVDFTMPLATVSNTVVRSVSVEQHEDSDRVEKFVRYVAKYQ  1600
1601  YKVEIDYVQCADLDLDMADPSVNPEAAAAPVPELHQPTFNPSTQESDTQQ  1650
1651  GYRIDFNEAEMGGSNRRDDSSSDEEPDSHKMPIIQIDMKNYGY         1693

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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