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

NucPred

Fetching Q63120 from www.uniprot.org...

The NucPred score for your sequence is 0.42 (see score help below)

   1  MDKFCNSTFWDLSLLESPEADLPLCFEQTVLVWIPLGFLWLLAPWQLYSV    50
  51  YRSRTKRSSITKFYLAKQVFVVFLLILAAIDLSLALTEDTGQATVPPVRY   100
 101  TNPILYLCTWLLVLAVQHSRQWCVRKNSWFLSLFWILSVLCGVFQFQTLI   150
 151  RALLKDSKSNMAYSYLFFVSYGFQIVLLILTAFSGPSDSTQTPSVTASFL   200
 201  SSITFSWYDRTVLKGYKHPLTLEDVWDIDEGFKTRSVTSKFEAAMTKDLQ   250
 251  KARQAFQRRLQKSQRKPEATLHGLNKKQSQSQDVLVLEEAKKKSEKTTKD   300
 301  YPKSWLIKSLFKTFHVVILKSFILKLIHDLLVFLNPQLLKLLIGFVKSSN   350
 351  SYVWFGYICAILMFAVTLIQSFCLQSYFQHCFVLGMCVRTTVMSSIYKKA   400
 401  LTLSNLARKQYTIGETVNLMSVDSQKLMDATNYMQLVWSSVIQITLSIFF   450
 451  LWRELGPSILAGVGVMVLLIPVNGVLATKIRNIQVQNMKNKDKRLKIMNE   500
 501  ILSGIKILKYFAWEPSFQEQVQGIRKKELKNLLRFGQLQSLLIFILQITP   550
 551  ILVSVVTFSVYVLVDSANVLNAEKAFTSITLFNILRFPLSMLPMVTSSIL   600
 601  QASVSVDRLERYLGGDDLDTSAIRRVSNFDKAVKFSEASFTWDPDLEATI   650
 651  QDVNLDIKPGQLVAVVGTVGSGKSSLVSAMLGEMENVHGHITIQGSTAYV   700
 701  PQQSWIQNGTIKDNILFGSEYNEKKYQQVLKACALLPDLEILPGGDMAEI   750
 751  GEKGINLSGGQKQRVSLARAAYQDADIYILDDPLSAVDAHVGKHIFNKVV   800
 801  GPNGLLAGKTRIFVTHGIHFLPQVDEIVVLGKGTILEKGSYRDLLDKKGV   850
 851  FARNWKTFMKHSGPEGEATVNNDSEAEDDDDGLIPTMEEIPEDAASLAMR   900
 901  RENSLRRTLSRSSRSSSRRGKSLKNSLKIKNVNVLKEKEKEVEGQKLIKK   950
 951  EFVETGKVKFSIYLKYLQAVGWWSILFIILFYGLNNVAFIGSNLWLSAWT  1000
1001  SDSDNLNGTNNSSSHRDMRIGVFGALGLAQGICLLISTLWSIYACRNASK  1050
1051  ALHGQLLTNILRAPMRFFDTTPTGRIVNRFSGDISTVDDLLPQTLRSWMM  1100
1101  CFFGIAGTLVMICMATPVFAIIIIPLSILYISVQVFYVATSRQLRRLDSV  1150
1151  TKSPIYSHFSETVTGLPIIRAFEHQQRFLAWNEKQIDINQKCVFSWITSN  1200
1201  RWLAIRLELVGNLVVFCSALLLVIYRKTLTGDVVGFVLSNALNITQTLNW  1250
1251  LVRMTSEAETNIVAVERISEYINVENEAPWVTDKRPPADWPRHGEIQFNN  1300
1301  YQVRYRPELDLVLKGITCNIKSGEKVGVVGRTGAGKSSLTNCLFRILESA  1350
1351  GGQIIIDGIDVASIGLHDLRERLTIIPQDPILFSGSLRMNLDPFNKYSDE  1400
1401  EVWRALELAHLRSFVSGLQLGLLSEVTEGGDNLSIGQRQLLCLGRAVLRK  1450
1451  SKILVLDEATAAVDLETDSLIQTTIRKEFSQCTVITIAHRLHTIMDSDKI  1500
1501  MVLDNGKIVEYGSPEELLSNRGSFYLMAKEAGIENVNHTEL           1541

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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