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

NucPred

Fetching Q9VHH9 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MSTAVETGSSPAKSNSNNSSSGGNNNNGNGNLSPNAKGVQRRQLRERKQR    50
  51  KLYLEEWSLGDEDGEGTRGFSVAEKLESSKFAQAGMVREMRGCDLTVAFL   100
 101  QQHGFNIPLLFRDKAGLGLRMPDPQEFTVNDVRLCVGSRRLLDVMDVNTQ   150
 151  KNLQMTMKEWQQYYDSPQKDRLLNVISLEFSHTRLDRFVQSPEIVRQIDW   200
 201  VDVVWPKQLKDAQREGTNLLGGMMYPKVQKYCLMSVKNCYTDFHIDFGGT   250
 251  SVWYHILRGSKVFWLIPPTDRNLQLYEKWVLSGKQADIFFGDTVEKCARV   300
 301  YLTAGNTFFIPTGWIHAVYTPTQSLVFGGNFLHSFGIVKQLKTASVEDST   350
 351  KVPQKFRYPFFTEMLWYVLARYVHTLLGHSHLEGEASLSEDEMAARPHTH   400
 401  LTHHELFGLKEIVMYLYDLPPQKKNVPSLVLDPVALIKDVRSLVERHCKD   450
 451  QQDLAITGVSVLKSPPGSQPPFLLYDRTRVKQEIKQEIARKNAEVIREQQ   500
 501  QLEAGRAREAESDTSQSTGVGSVIGMGAGVEYSNGVMKKEQLENGSGVTV   550
 551  GGHGSQPEATFALPTDTLKYRPPKKMHLATALVAAAASSSSGGGGPVAGV   600
 601  GGSAVVGSSHSPTGGGVGPVTGAGGAISVIATSSSYIEGGQVGGILNMDN   650
 651  CHSPEGGGAKLSPNLTGTGQPRRRRTRCKNCAACQRSDCGTCPFCMDMVK   700
 701  FGGPGRAKQTCMMRQCLSPMLPVTAQCVYCHLDGWRQTPVSPQTKQLASA   750
 751  DGPSALMECSVCYEIAHPDCALSQLDGTEDAADAKGIVNEDLPNSWECPS   800
 801  CCRSGKNYDYKPRHFRARQKSSEVRRVSVSHGQGGAEGHADGNTLLPPPV   850
 851  GQYNDFVFTSESEMESGTVSGHMTHWKHGMKRHHQLEVKTERNNSCDTPS   900
 901  PGISPNAIGGDSKVGKRRKSDDGTSVSSSMHESNDAPCGSSAEGAGGAGN   950
 951  ANVSTNQWSGSGGGGGSRKKNSIRSQLAQQMLNSSTRVLKKPQYVVRPAS  1000
1001  GTGSSSSSGNGGSASATNGISNGSNQSGANSCGAGNGERGTNNGGLSGSN  1050
1051  GLGNQHYSSSQNLALDPTVLKIIFRYLPQDTLVTCCSVCKVWSNAAVDPD  1100
1101  LWKKMNCSEHKMSASLLTAIVRRQPEHLILDWTQIAKRQLAWLVARLPAL  1150
1151  KNLSLQNCPIQAVLALHTCLCPPLQTLDLSFVRGLNDAAIRDILSPPKDS  1200
1201  RPGLSDSKTRLRDLKVMKLAGTDISDVAVRYITQSLPYLRHLDLSSCQRI  1250
1251  TDAGVAQIGTSTTATARLTELNLSACRLVSENALEHLAKCEGLIWLDLRH  1300
1301  VPQVSTQSVIRFASNSKHDLCVRDIKLVERRRRNSTTANRSWHHD       1345

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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