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

NucPred

Fetching Q8IN94 from www.uniprot.org...

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

   1  MNEKIKSPQTQQQQQGGAPAPAATPPSAGAAPGAATPPTSGPPTPNNNSN    50
  51  NGSDPSIQQQQQNVAPHPYGAPPPPGSGPGGPPGPDPAAVMHYHHLHQQQ   100
 101  QQHPPPPHMQQQQHHGGPAPPPPGGAPEHAPGVKEEYTHLPPPHPHPAYG   150
 151  RYHADPNMDPYRYGQPLPGGKPPQQQQPHPQQQPPQQPGPGGSPNRPPQQ   200
 201  RYIPGQPPQGPTPTLNSLLQSSNPPPPPQHRYANTYDPQQAAASAAAAAA   250
 251  AQQQQAGGPPPPGHGPPPPQHQPSPYGGQQGGWAPPPRPYSPQLGPSQQY   300
 301  RTPPPTNTSRGQSPYPPAHGQNSGSYPSSPQQQQQQQQQQQQQAGQQPGG   350
 351  PVPGGPPPGTGQQPPQQNTPPTSQYSPYPQRYPTPPGLPAGGSNHRTAYS   400
 401  THQYPEPNRPWPGGSSPSPGSGHPLPPASPHHVPPLQQQPPPPPHVSAGG   450
 451  PPPSSSPGHAPSPSPQPSQASPSPHQELIGQNSNDSSSGGAHSGMGSGPP   500
 501  GTPNPQQVMRPTPSPTGSSGSRSMSPAVAQNHPISRPASNQSSSGGPMQQ   550
 551  PPVGAGGPPPMPPHPGMPGGPPQQQQSQQQQASNSASSASNSPQQTPPPA   600
 601  PPPNQGMNNMATPPPPPQGAAGGGYPMPPHMHGGYKMGGPGQSPGAQGYP   650
 651  PQQPQQYPPGNYPPRPQYPPGAYATGPPPPPTSQAGAGGANSMPSGAQAG   700
 701  GYPGRGMPNHTGQYPPYQWVPPSPQQTVPGGAPGGAMVGNHVQGKGTPPP   750
 751  PVVGGPPPPQGSGSPRPLNYLKQHLQHKGGYGGSPTPPQGPQGYGNGPTG   800
 801  MHPGMPMGPPHHMGPPHGPTNMGPPTSTPPQSQMLQGGQPQGQGASGGPE   850
 851  SGGPEHISQDNGISSSGPTGAAGMHAVTSVVTTGPDGTSMDEVSQQSTLS   900
 901  NASAASGEDPQCTTPKSRKNDPYSQSHLAPPSTSPHPVVMHPGGGPGEEY   950
 951  DMSSPPNWPRPAGSPQVFNHVPVPQEPFRSTITTTKKSDSLCKLYEMDDN  1000
1001  PDRRGWLDKLRAFMEERRTPITACPTISKQPLDLYRLYIYVKERGGFVEV  1050
1051  TKSKTWKDIAGLLGIGASSSAAYTLRKHYTKNLLTFECHFDRGDIDPLPI  1100
1101  IQQVEAGSKKKTAKAASVPSPGGGHLDAGTTNSTGSSNSQDSFPAPPGSA  1150
1151  PNAAIDGYPGYPGGSPYPVASGPQPDYATAGQMQRPPSQNNPQTPHPGAA  1200
1201  AAVAAGDNISVSNPFEDPIAAGGGPGSGTGPGPGQGPGPGAASGGAGAVG  1250
1251  AVGGGPQPHPPPPHSPHTAAQQAAGQHQQQHPQHQHPGLPGPPPPQQQQG  1300
1301  QQGQQPPPSVGGGPPPAPQQHGPGQVPPSPQQHVRPAAGAPYPPGGSGYP  1350
1351  TPVSRTPGSPYPSQPGAYGQYGSSDQYNATGPPGQPFGQGPGQYPPQNRN  1400
1401  MYPPYGPEGEAPPTGANQYGPYGSRPYSQPPPGGPQPPTQTVAGGPPAGG  1450
1451  APGAPPSSAYPTGRPSQQDYYQPPPDQSPQPRRHPDFIKDSQPYPGYNAR  1500
1501  PQIYGAWQSGTQQYRPQYPSSPAPQNWGGAPPRGAAPPPGAPHGPPIQQP  1550
1551  AGVAQWDQHRYPPQQGPPPPPQQQQQPQQQQQQPPYQQVAGPPGQQPPQA  1600
1601  PPQWAQMNPGQTAQSGIAPPGSPLRPPSGPGQQNRMPGMPAQQQQSQQQG  1650
1651  GVPQPPPQQASHGGVPSPGLPQVGPGGMVKPPYAMPPPPSQGVGQQVGQG  1700
1701  PPGGMMSQKPPPMPGQAMQQQPLQQQPPSHQHPHPHQHPQHQHPHQMPPN  1750
1751  QTAPGGYGPPGMPGGGAQLVKKELIFPHDSVESTTPVLYRRKRLMKADVC  1800
1801  PVDPWRIFMAMRSGLLTECTWALDVLNVLLFDDSTVQFFGISNLPGLLTL  1850
1851  LLEHFQKNLAEMFDERENEEQSALLAEDADDDADSGTVMCEKLRTSGRQP  1900
1901  RCVRSISSYNRRRHYENMDRSGKDGAGNGSDSEDADEGIDLGQVRVQPNP  1950
1951  EERSLLLSFTPNYTMVTRKGVPVRIQPAENDIFVDERQKAWDIDTNRLYE  2000
2001  QLEPVGSDAWTYGFTEPDPLDGIIDVFKSEIVNIPFARYIRSDKKGRKRT  2050
2051  ELASSSRKPEIKTEENSTEEQTFNKKRRLVSGGSSSSGAHAEGKKSKLTS  2100
2101  EEFAQPNAEVKKEPGTADSDCRPVDMDIEAPQQRLTNGVAPCSSTPAIFD  2150
2151  PRTTAKDEARVLQRRRDSSFEDECYTRDEASLHLVSESQDSLARRCIALS  2200
2201  NIFRNLTFVPGNETVLAKSTRFLAVLGRLLLLNHEHLRRTPKTRNYDREE  2250
2251  DTDFSDSCSSLQGEREWWWDYLITIRENMLVAMANIAGHLELSRYDELIA  2300
2301  RPLIDGLLHWAVCPSAHGQDPFPSCGPNSVLSPQRLALEALCKLCVTDAN  2350
2351  VDLVIATPPFSRLEKLCAVLTRHLCRNEDQVLREFSVNLLHYLAAADSAM  2400
2401  ARTVALQSPCISYLVAFIEQAEQTALGVANQHGINYLRENPDSMGTSLDM  2450
2451  LRRAAGTLLHLAKHPDNRSLFMQQEQRLLGLVMSHILDQQVALIISRVLY  2500
2501  QVSRGTGPIHSVEFRLLQQRQQQQLRPGPAGKQAASAGGSATVKAETAST  2550
2551  ETSSTEAKPAPAATTAVVNDENSNSSQQLPPAATFNDVSNSSTNSNSCGT  2600
2601  ASSNQTNNSTTNSSHSSSAISSQSAITVAAPSAAATGAGSATAAAIASDQ  2650
2651  QQVSKVAAAAAAAAALSNASAAAAAAAAAAAASVGPPTSSSVSAGAAVAQ  2700
2701  PAAPPPTNAGTTTAVA                                    2716

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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