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

NucPred

Fetching P54697 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MTTSTIENGASSPIIVSSSTPKLYQEGAGVWIPDQELGWIGADVIEHSET    50
  51  SADQVLVRTEDDREVKIPLSKVFQKNPDILEGVDDLSFLSHLHEPAILHN   100
 101  LHHRYNLNQIYTYIGKILIAINPYTSLPLYGKEMISAYYGKQLGTLAPHV   150
 151  YAVAEDAFKDMRYDGTSQSILVSGESGAGKTETTKFLLQYFAAMGNMIKE   200
 201  STSSSSINGINTSSDGIPVTPPPSPMKKSPVDKSVEERVLESTPLLEAFG   250
 251  NAKTLRNDNSSRFGKFIEIHFNEMGSIIGAKILTYLLEKSRIVRQVYNER   300
 301  NYHIFYQLLSGASEELKEKLNLKTIEEYSYLNKSGCFEIEGVSDEEHFNK   350
 351  TCHAMQVAGITLVEQENVFRILSAILLIGNFEFENIAGSNDDSCQLIDRD   400
 401  PLEKVSVLLGCAQPDELLNSMLTRKVVTGKESYISHNTKERAENARDSLS   450
 451  MFLYGMMFDWLVVKINSSMSISTQQKSKSFIGVLDIYGFESFEVNGFEQF   500
 501  CINYANEKLQQLFNQHVFKEEQQEYIKEKIDWSYIDFNDNQDTLDLIEKK   550
 551  PICILTLLDEETMFPKATPQTLATKLYSKMTSHSKFEKPRFSSTAFTINH   600
 601  YAGKVTYETDQFLDKNKDFIIPEQISILQRSNFSFIKVLMSHSDKFTQSP   650
 651  GGHPQGNGGPTSSNTKGTSGSSSMKFLSVGSQFSTSLATLMKTISTTTPH   700
 701  YVRCIKPNPEKLPQTFNKQDVIHQLRCGGVMESVRICCAGFPTRRLLSEF   750
 751  YQRYKILYVKDINTGSGGGKKGSNNNKIKDPKILVQNLLTGIELSDDKYK   800
 801  IGLTKVFLRAGQLASLEDMRLEQLDRSATVIQKRWKGYLYRKRYKQLRDA   850
 851  SLIIQTKLRSVHAKQQLSALQRTHSAILIQKVWRAHRDRVQYQKIRDASL   900
 901  QLQTVMRRHLFSEQVHRERCENAAIILQTKIRQILSKREVDKKLRGIILI   950
 951  QARWRMKLAKRVYIQLRAEARSLRTVQEQKNKLQEKLEELQWRLTSEAKR  1000
1001  KQQLEDQKVKSDTTISELSSNNDHLELQLSEIQLKYQELDKSNQSSQLQL  1050
1051  SECLSKLEEQTQQLDHSSKLNKKLEKDLSDQHDSIEKLQSQFNETEQQLQ  1100
1101  QFKQQSEELSSKLSKTTQQLDFNKQEFDRLSQERDTDNTNNQLEIQQLKK  1150
1151  ANSTLEEDYFSLSGIRDNLERQVLELRDENQLIKERLDSLGQQSSQFQSG  1200
1201  AALEKQQLEQLVQEQSEQLIKLSSEKLGSEEEAKKQINQLELELTDHKSK  1250
1251  LQIQLQLTEQSNEKIKKLKGKLEEYQDEKKQLQQELERIKQSKQSVEDEK  1300
1301  NSLITQLTTVKFESTQVSTNVSHQKEKITTLKSTIEELNKSIGKLQAEQK  1350
1351  NKDDEIRKIQFELNDQKQQFTRQTKEFSDLQSQQSIDRQKSEITIHSLER  1400
1401  TNETLKSDFERVQQSLKQQERDCQQYKDTINRLENEVKQLTQLKERFENE  1450
1451  FFVAKEQNSNQTQESVYLKEVTTQMQQNQSRIERELEEKKQHITRIDDER  1500
1501  DELKKQLTQLQQQHEQSSTQLLLAQNELERLRKKELKYKERGHETSKQQD  1550
1551  QFNMEIQSLRITNNDQLKSLQDYEQEKKKLKDKLSSSKQEAQQQRESIIK  1600
1601  MDAELSAIKQHSQWVENSFTDMKQRNQELIESSALYKQQLLQQTSTIDST  1650
1651  IKEKENEISKLQQQLETSNQQLHQLKEELNSMKQSNQLESTEQSKQLNQL  1700
1701  IQENQQLKSVTNEISKQLDDAVFENQKINNTIKEQEIKSKRMSVELQQHI  1750
1751  DEGKQQEIQQLQSTIAQLKQQQQSETDRLEKEIQQMKRERETQMKLVEST  1800
1801  KLNYHMLEDRMELYRNVMEIIDYKETEWEKLARLAGCKELDTKLLSDFLL  1850
1851  SCKLEHTSLGSQMWFHQIDYWCPYERDSSKGIFYGIIRSIVDFTIKNFDD  1900
1901  VDLLSYLLACCSLTLFLYKKNLVKHLNGANSIMPIIPTLGDLEELNERLS  1950
1951  HQSLTTSGKFSGGGGGGGIDFIDQLQQSTGITFGLIFKATTLKLSPLVDG  2000
2001  AILNENYNKKLTSISASSFGSGSFGLGSNGVGSVLSIELITTYLSSIITI  2050
2051  FQHRMVHFTLSQRFFNQVFCWIGALIMKGFMLRQTFCTETFATFVKTKID  2100
2101  FLTRWADDIGNVWVGDVANAFQQVREVINVLNIKDKEKIIDDKIRKQYCP  2150
2151  TLNSNQLKQVLSLFSPGEFGGKRVSAKVIASICPPNKSSAGQSFVQDENK  2200
2201  LNTIPIDSLHYLEIQDIKTLSLPLSIRQTIETEIINLKQQIACKK       2245

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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