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

NucPred

Fetching Q9HDV4 from www.uniprot.org...

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

   1  MICQLLWHEHNSMGSGREKKIRKLGDNFSLPYLKFDCDHNDKNYRASNRP    50
  51  FGLSTGLSVQLNASNMTDPFKFLLDNWHTIFKNGAIKLLPPEGWQIPVVL   100
 101  DQGAFEFQSKRQCLNKGCLNYEKNYDYFKKLKAFHESRGLYFYHPPIIGN   150
 151  RPVDFLRLRNAISKFTNSGSSLNNEILHKVIIYLRLEDTKEVRQVLTRCY   200
 201  DRYIKPFERDSSPSFKSKRSESSTRKIRNTRSSAQQESPIPETSAQSPVQ   250
 251  TIQVNGSTSLKRPLIERGEQCEYCGLDKNPETILLCDGCEAAYHTSCLDP   300
 301  PLTSIPKEDWYCDACKFNISDYDPRKGFKWKLSSLKERSAEIFNTLGERN   350
 351  SSSKLTNLTEDDIELFYWSSLAESNSGFAPLELEGLSQAYTSTIQSSLPS   400
 401  KEVFPLEKYSSEPWNLHNLPFENPCLFNYSFSDLSSLTITRLSIGMVFYT   450
 451  HGWTKSSLSTGLLHHHRFGDTVTWYVLPPDESDAFERYLISSYPQYTMED   500
 501  LNRSNGLPVIVSPSSLIENGFHPIAIDLRPNEFLVVSPNSYHMGFHQGFS   550
 551  SFESVNFATVNWIKDGLLNSSISVLKSMRIPSSVSYEAVIISMVLSKNPC   600
 601  FSSEWLIKCFEDMIANESASKNEIMKLVPNIQALKLESSVPLEIRCSNCK   650
 651  QPCFLSFMQCHEPKKFICLGDCVKEVSLNATSWMLFYRWDVHELSNLAER   700
 701  FVSLIRGPEEWTNRLRSVLSTSPKPQLKVLKSLLVDAEKAMLTTPETVNL   750
 751  RDFVQNANSWIDSVNECLKVASLKRKKDKKPPLFKAHDHWNNTSNLKDSA   800
 801  VLFKVLQTSRSMAFTCQEIENMKQKAFDLLEFRNRLINSFSGPLDKNTCQ   850
 851  RLLTEAELLGFTIPELGIIQKYLIQFEWLDMFYSFETTRTTDSDLERLIT   900
 901  YGVSAGIPEDNDYMIFAKAMKGRAEIWENQVYDTLSKSNISYDKLSLLRD   950
 951  EAMNLCVNKELFSKVVGILNNAEEIKNKIATLCERSQEKDFALRPSIDEV  1000
1001  KEALASAEKLPILSESTVTLQKMYDVVLEWIRRGKRLFGKANAPLEILGQ  1050
1051  HLDYVEKRNSASLSLNDRPGPPMEPASRETSPDSEGRLTIRKKKGCIFCF  1100
1101  CRLPESGVMIECEICHEWYHAKCLKMSKKKLRQDEKFTCPICDYRVEIPR  1150
1151  LSNRPKLEDLQSLYKDVKLLPFQPKETETLRKVVDLASKFRQEMQALAHN  1200
1201  PFGLTMAEVPLARFYLRKMEGAEILLVDETNLFRQKLHECVPIAPNPPPI  1250
1251  IGESKSTRKPRPTKRQRQIMKQVAEGLLPASAIAPPKSSNEKKSSNNVKA  1300
1301  VEAETKSKSEKSPKKNGTNISDANNKNESHVSLMKNWKLGSPAFVTLVKE  1350
1351  KNSSCLCGEEFSPRDSFIDCTICERRFHYDCVGLNNEIADSVSKFTCPIC  1400
1401  MEQSGGIYPWQLRPRNGMHPDHISGFSKEVETDPKLGSSGYTLNNSKFDK  1450
1451  AAVSKTLSAQDVSRLQKVSCGEHLYFGTDVFTPLGDMATSASMFSLDDSS  1500
1501  EKTDAFTENFLNV                                       1513

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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