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

NucPred

Fetching Q26255 from www.uniprot.org...

The NucPred score for your sequence is 0.08 (see score help below)

   1  MTGKKLLLIGSGGREHALAWKLQQSKNVTEIFAFPGSIGISQLEKVQLVN    50
  51  NNEMNLKDFKGIASWCKINHIDLVIVGPEDPLAEGIADQLKAANIHCFGP   100
 101  SKAGARIESDKSWSKDFMIRHHIPTAQYGSFIDALKAKDFIRNTPNALVV   150
 151  KASGLAAGKGVIVAENIEEACAAVDEILGDHKFGTAGDVVVVEEKLSGQE   200
 201  VSVLGFVDSNSVRILPPAQDHKRLKDNDEGLNTGGMGAYCPCPLISQQEL   250
 251  DIVKSQVLQRAVDGLRKENILYNGILYAGIMLTHDGPKTLEFNCRFGDPE   300
 301  TQIILPLLDEDLYDLMMASCTNHLCNVPELKFKSNINAVGVVMASKGYPE   350
 351  TSTKGCVISGIESVETMDNHIVFHSGTSKNNKDEWITNGGRVLINIALAD   400
 401  NLKKAADLATKACDVVKFDGSQYRRDIGKKAFQIHSLTYKESGVNIEAGN   450
 451  SLVGRIKSLSYGTHRSGVVGQIGSFGGLMRLNDIKYINSNGEESNYKDIV   500
 501  LVQGTDGVGTKLKIAESMNVWDTIGIDLVAMCVNDVLCNGAEPIGFLDYI   550
 551  ACGHLEVPTVATIVKGIADGCRKANCALIGGETAEMPSMYGKGKYDLAGY   600
 601  CVGITEYDEILPKINDVHVGDVVIGLPSSGIHSNGFSLVNKIFQQTGFKL   650
 651  TDIAEFSDSHKSYGMEFLTPTRLYVSETLPFLRNGYVKALAHITGGGLLE   700
 701  NIPRILPNHLSVQIDALTWKLPKVFSWLAAHGNVNANEMLRTFNCGIGMI   750
 751  IIMPRNDIEWETIPEARMIGSITQRDHNGPQVIVKNFKEVLHKEVTHWKK   800
 801  GDAETTSISYKDSGVDITAGNELVDNIKPHAKSTNRKGVIGGLGSFGGLF   850
 851  RINECGTKFEDPMLVLATDGVGTKLKIAQQLGKHDTVGIDLVAMCNNDIL   900
 901  CNGAEPLTFLDYFACGKLDVNVATNVVSGIAEGCRQSDSTLLGGETAEMP   950
 951  GMYNPNVYDLAGFSLGVAEHEDILPKKNCLEVGDIIIGFPSNGVHSNGFS  1000
1001  LIHKLFELTGYKWTDIAPFSAYGKTFGEEFLEPTKVYVKEISPALKTGYV  1050
1051  KALAHITGGGLWDNIPRVLPYNLTAELDAKKINISPVFAWLSLNGNIDKL  1100
1101  ELLKTFNCGIGMIMIASKEHELEILKSLYGSRASVIGKIIPTKPHGHQVI  1150
1151  VRHFATCFERVERLLSIPKKRVGVLISGSGSNLQALIDATKSTNMGMCSE  1200
1201  IVFVLSNKAGIFGLERAAKANIPSTVISNKDYATREAFDVALHNELIKHN  1250
1251  VEIICLAGFMRILTPCFVNKWKGKLLNIHPSLLPKYKGITAQKDALESGD  1300
1301  NESGCTVHFVDENVDTGAIIVQEIVPIFENDTVESLTERIHVAEHIAFPK  1350
1351  ALRLVASGYVRLNDKCETEWA                               1371

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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