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

NucPred

Fetching Q04002 from www.uniprot.org...

The NucPred score for your sequence is 0.69 (see score help below)

   1  MSYPGKDKNIPGRIIEALEDLPLSYLVPKDGLAALVNAPMRVSLPFDKTI    50
  51  FTSADDGRDVNINVLGTANSTTSSIKNEAEKERLVFKRPSNFTSSANSVD   100
 101  YVPTNFLEGLSPLAQSVLSTHKGLNDSINIEKKSEIVSRPEAKHKLESVT   150
 151  SNAGNLSFNDNSSNKKTKTSTGVTMTQANLAEQYLNDLKNILDIVGFDQN   200
 201  SAEIGNIEYWLQLPNKKFVLTTNCLTKLQMTIKNITDNPQLSNSIEITWL   250
 251  LRLLDVMVCNIKFSKSSLKMGLDDSMLRYIALLSTIVLFNIFLLGKNDSN   300
 301  LHRESYIMEPVNFLSDLIESLKILTIEYGSLKIEFDTFQEALELLPKYIR   350
 351  NGPFLDDNVTAKLVYIFSDLLMNNDIEATTNIQFQSFWDNVKRISSDILV   400
 401  SLFGSFDQQRGFIIEELLSHIEKLPTKRIQKKLRKVGNQNIYITDFTFTL   450
 451  MSMLENINCYSFCNQMKDIAPENIDLLKNEYKKQEEFLFNIVEHINDTIL   500
 501  ERFFKNPSALRYVIDNFVQDLLLLISSPQWPVTEKILSSLLKRLLSVYSP   550
 551  SMQVSANIETICLQLIGNIGSTIFDIKCSTRDHEDNNLIKMINYPETLPH   600
 601  FFKSFEECIAYNETIKCRRSATRFLWNLRLGTILILEEYTKDAKEQIITV   650
 651  DNELKKILEQIKDGGLGPELENREADFSTIKLDYFSILHAFELLNLYDPY   700
 701  LKLILSLLAKDKIKLRSTAIKCLSMLASKDKVILSNPMVKETIHRRLNDS   750
 751  SASVKDAILDLVSINSSYFEFYQQINNNYNDDSIMVRKHVLRINEKMYDE   800
 801  TNDIVTKVYVIARILMKIEDEEDNIIDMARLILLNRWILKVHEVLDQPEK   850
 851  LKEISSSVLLVMSRVAIMNEKCSQLFDLFLNFYLLNKEAHSKEAYDKITH   900
 901  VLTILTDFLVQKIVELNSDDTNEKNSIVDKQNFLNLLAKFADSTVSFLTK   950
 951  DHITALYPYMVSDEKSDFHYYILQVFRCTFEKLANFKQKFLYDLETTLLS  1000
1001  RLPKMNVREIDEAMPLIWSVATHRHDTARVAKACSSCLSHLHPYINKANN  1050
1051  EEAAIVVDGKLQRLIYLSTGFARFCFPKPSNDKIAFLQEGETLYEHITKC  1100
1101  LLVLSKDKITHVIRRVAVKNLTKLCGNHPKLFNSRHVLHLLDKEFQSDQL  1150
1151  DIKLVILESLYDLFLLEERKSVRNTGVNSTLSSNSILKKKLLKTNRVEFA  1200
1201  NDGVCSALATRFLDNILQLCLLRDLKNSLVAIRLLKLILKFGYTNPSHSI  1250
1251  PTVIALFASTSQYIRHVAYELLEDLFEKYETLVFSSLSRGVTKAIHYSIH  1300
1301  TDEKYYYKHDHFLSLLEKLCGTGKKNGPKFFKVLKRIMQSYLDDITDLTS  1350
1351  TNSSVQKSIFVLCTNISNITFVSQYDLVSLLKTIDLTTDRLKEVIMDEIG  1400
1401  DNVSSLSVSEEKLSGIILIQLSLQDLGTYLLHLYGLRDDVLLLDIVEESE  1450
1451  LKNKQLPAKKPDISKFSAQLENIEQYSSNGKLLTYFRKHVKDT         1493

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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