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

NucPred

Fetching Q06706 from www.uniprot.org...

The NucPred score for your sequence is 0.58 (see score help below)

   1  MVEHDKSGSKRQELRSNMRNLITLNKGKFKPTASTAEGDEDDLSFTLLDS    50
  51  VFDTLSDSITCVLGSTDIGAIEVQQFMKDGSRNVLASFNIQTFDDKLLSF   100
 101  VHFADINQLVFVFEQGDIITATYDPVSLDPAETLIEIMGTIDNGIAAAQW   150
 151  SYDEETLAMVTKDRNVVVLSKLFEPISEYHLEVDDLKISKHVTVGWGKKE   200
 201  TQFRGKGARAMEREALASLKASGLVGNQLRDPTMPYMVDTGDVTALDSHE   250
 251  ITISWRGDCDYFAVSSVEEVPDEDDETKSIKRRAFRVFSREGQLDSASEP   300
 301  VTGMEHQLSWKPQGSLIASIQRKTDLGEEDSVDVIFFERNGLRHGEFDTR   350
 351  LPLDEKVESVCWNSNSEALAVVLANRIQLWTSKNYHWYLKQELYASDISY   400
 401  VKWHPEKDFTLMFSDAGFINIVDFAYKMAQGPTLEPFDNGTSLVVDGRTV   450
 451  NITPLALANVPPPMYYRDFETPGNVLDVACSFSNEIYAAINKDVLIFAAV   500
 501  PSIEEMKKGKHPSIVCEFPKSEFTSEVDSLRQVAFINDSIVGVLLDTDNL   550
 551  SRIALLDIQDITQPTLITIVEVYDKIVLLRSDFDYNHLVYETRDGTVCQL   600
 601  DAEGQLMEITKFPQLVRDFRVKRVHNTSAEDDDNWSAESSELVAFGITNN   650
 651  GKLFANQVLLASAVTSLEITDSFLLFTTAQHNLQFVHLNSTDFKPLPLVE   700
 701  EGVEDERVRAIERGSILVSVIPSKSSVVLQATRGNLETIYPRIMVLAEVR   750
 751  KNIMAKRYKEAFIVCRTHRINLDILHDYAPELFIENLEVFINQIGRVDYL   800
 801  NLFISCLSEDDVTKTKYKETLYSGISKSFGMEPAPLTEMQIYMKKKMFDP   850
 851  KTSKVNKICDAVLNVLLSNPEYKKKYLQTIITAYASQNPQNLSAALKLIS   900
 901  ELENSEEKDSCVTYLCFLQDVNVVYKSALSLYDVSLALLVAQKSQMDPRE   950
 951  YLPFLQELQDNEPLRRKFLIDDYLGNYEKALEHLSEIDKDGNVSEEVIDY  1000
1001  VESHDLYKHGLALYRYDSEKQNVIYNIYAKHLSSNQMYTDAAVAYEMLGK  1050
1051  LKEAMGAYQSAKRWREAMSIAVQKFPEEVESVAEELISSLTFEHRYVDAA  1100
1101  DIQLEYLDNVKEAVALYCKAYRYDIASLVAIKAKKDELLEEVVDPGLGEG  1150
1151  FGIIAELLADCKGQINSQLRRLRELRAKKEENPYAFYGQETEQADDVSVA  1200
1201  PSETSTQESFFTRYTGKTGGTAKTGASRRTAKNKRREERKRARGKKGTIY  1250
1251  EEEYLVQSVGRLIERLNQTKPDAVRVVEGLCRRNMREQAHQIQKNFVEVL  1300
1301  DLLKANVKEIYSISEKDRERVNENGEVYYIPEIPVPEIHDFPKSHIVDF   1349

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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