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

NucPred

Fetching Q8HXQ5 from www.uniprot.org...

The NucPred score for your sequence is 0.15 (see score help below)

   1  MALRDFCSVDGSDLFWEWNVTWNTSNPDFTKCFQNTVLVWVPCSYLWVCF    50
  51  PFYFLYLSHHDRGYIQMTHLNKAKTALGFLLWIVCWADLFYSFWERSMGK   100
 101  LLAPVFLVSPTLLGITMLLATFLIQIERRRGVQSSGIMLTFWLIALLCAL   150
 151  AILRSKIMTALKEDARVDVFRDVTFYIYFSLVLIQLVLSCFSDRSPLFSE   200
 201  TINDPNPCPESSASFLSRITFWWITGMMVQGYRQPLESTDLWSLNKEDTS   250
 251  EQVVPVLVKNWKKECAKSRKQPVKIVYSSKDPAKPKGSSKVDVNEEAEAL   300
 301  IVKCPQKERDPSLFKVLYKTFGPYFLMSFLFKAVHDLMMFAGPEILKLLI   350
 351  NFVNDKKAPEWQGYFYTALLFISACLQTLVLHQYFHICFVSGMRIKTAVI   400
 401  GAVYRKALVITNAARKSSTVGEIVNLMSVDAQRFMDLATYINMIWSAPLQ   450
 451  VILALYLLWLNLGPSVLAGVAVMVLMVPLNAVMAMKTKTYQVAHMKSKDN   500
 501  RIKLMNEILNGIKVLKLYAWELAFKDKVLAIRQEELKVLKKSAYLAAVGT   550
 551  FTWVCTPFLVALSTFAVYVTVDENNILDAQKAFVSLALFNILRFPLNILP   600
 601  MVISSIVQASVSLKRLRVFLSHEDLDPDSIQRRPIKDAGATNSITVKNAT   650
 651  FTWARNDPPTLHGITFSVPEGSLVAVVGQVGCGKSSLLSALLAEMDKVEG   700
 701  HVTVKGSVAYVPQQAWIQNISLRENILFGRQLQERYYKAVVEACALLPDL   750
 751  EILPSGDRTEIGEKGVNLSGGQKQRVSLARAVYCDSDVYLLDDPLSAVDA   800
 801  HVGKHIFENVIGPKGLLKNKTRLLVTHAISYLPQMDVIIVMSGGKISEMG   850
 851  SYQELLARDGAFAEFLRTYASAEQEQGQPEDGLAGVGGPGKEVKQMENGM   900
 901  LVTDTAGKQMQRQLSSSSSYSRDVSQHHTSTAELRKPGPTEETWKLVEAD   950
 951  KAQTGQVKLSVYWDYMKAIGLFISFLSIFLFLCNHVASLVSNYWLSLWTD  1000
1001  DPIVNGTQEHTQVRLSVYGALGISQGITVFGYSMAVSIGGIFASRRLHLD  1050
1051  LLHNVLRSPISFFERTPSGNLVNRFSKELDTVDSMIPQVIKMFMGSLFNV  1100
1101  IGACIIILLATPMAAVIIPPLGLIYFFVQRFYVASSRQLKRLESVSRSPV  1150
1151  YSHFNETLLGVSVIRAFEEQERFIRQSDLKVDENQKAYYPSIVANRWLAV  1200
1201  RLECVGNCIVLFASLFAVISRHSLSAGLVGLSVSYSLQVTTYLNWLVRMS  1250
1251  SEMETNIVAVERLKEYSETEKEAPWQIQDMAPPKDWPQVGRVEFRDYGLR  1300
1301  YREDLDLVLKHINVTIDGGEKVGIVGRTGAGKSSLTLGLFRIKESAEGEI  1350
1351  IIDDINIAKIGLHDLRFKITIIPQDPVLFSGSLRMNLDPFSQYSDEEVWT  1400
1401  SLELAHLKGFVSALPDKLNHECAEGGENLSVGQRQLVCLARALLRKTKIL  1450
1451  VLDEATAAVDLETDDLIQSTIRTQFDDCTVLTIAHRLNTIMDYTRVIVLD  1500
1501  KGEIQEWGSPSDLLQQRGLFYSMAKDSGLV                      1530

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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