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

NucPred

Fetching P41820 from www.uniprot.org...

The NucPred score for your sequence is 0.45 (see score help below)

   1  MNQNSDTTHGQALGSTLNHTTEVTRISNSSDHFEDSSSNVDESLDSSNPS    50
  51  SNEKASHTNEEYRSKGNQSYVPSSSNEPSPESSSNSDSSSSDDSSVDRLA   100
 101  GDPFELGENFNLKHYLRAYKDSLQRDDIITRSSGVCMRDHSVYGVGSGYE   150
 151  FLKTFPDIFLQPYRAITEKQVVEKAILSHCHALANAGELVMVLGQPGSGC   200
 201  STFLRSVTSDTVHYKRVEGTTHYDGIDKADMKKFFPGDLLYSGENDVHFP   250
 251  SLTTAETLDFAAKCRTPNNRPCNLTRQEYVSRERHLIATAFGLTHTFNTK   300
 301  VGNDFVRGVSGGERKRVTISEGFATRPTIACWDNSTRGLDSSTAFEFVNV   350
 351  LRTCANELKMTSFVTAYQASEKIYKLFDRICVLYAGRQIYYGPADKAKQY   400
 401  FLDMGFDCHPRETTPDFLTAISDPKARFPRKGFENRVPRTPDEFEQMWRN   450
 451  SSVYADLMAEMESYDKRWTETTPASSEAPEKDNFGSDISATTKHELYRQS   500
 501  AVAEKSKRVKDTSPYTVTFSQQLWYCLARSWERYINDPAYIGSMAFAFLF   550
 551  QSLIIGSIFYDMKLNTVDVFSRGGVLFFSILFCALQSLSEIANMFSQRPI   600
 601  IAKHRASALYHPAADVISSLIVDLPFRFINISVFSIVLYFLTNLKRTAGG   650
 651  FWTYFLFLFIGATCMSAFFRSLAGIMPNVESASALGGIGVLAIAIYTGYA   700
 701  IPNIDVGWWFRWIAYLDPLQFGFESLMINEFKARQFECSQLIPYGSGYDN   750
 751  YPVANKICPVTSAEPGTDYVDGSTYLYISFNYKTRQLWRNLAIIIGYYAF   800
 801  LVFVNIVASETLNFNDLKGEYLVFRRGHAPDAVKAAVNEGGKPLDLETGQ   850
 851  DTQGGDVVKESPDNEEELNKEYEGIEKGHDIFSWRNLNYDIQIKGEHRRL   900
 901  LNGVQGFVVPGKLTALMGESGAGKTTLLNVLAQRVDTGVVTGDMLVNGRG   950
 951  LDSTFQRRTGYVQQQDVHIGESTVREALRFSAALRQPASVPLSEKYEYVE  1000
1001  SVIKLLEMESYAEAIIGTPGSGLNVEQRKRATIGVELAAKPALLLFLDEP  1050
1051  TSGLDSQSAWSIVCFLRKLADAGQAILCTIHQPSAVLFDQFDRLLLLQKG  1100
1101  GKTVYFGDIGEHSKTLLNYFESHGAVHCPDDGNPAEYILDVIGAGATATT  1150
1151  NRDWHEVWNNSEERKAISAELDKINASFSNSEDKKTLSKEDRSTYAMPLW  1200
1201  FQVKMVMTRNFQSYWREPSILMSKLALDIFAGLFIGFTFYNQGLGVQNIQ  1250
1251  NKLFAVFMATVLAVPLINGLQPKFIELRNVFEVREKPSNIYSWVAFVFSA  1300
1301  IIVEIPFNLVFGTLFFLCWFYPIKFYKHIHHPGDKTGYAWLLYMFFQMYF  1350
1351  STFGQAVASACPNAQTASVVNSLLFTFVITFNGVLQPNSNLVGFWHWMHS  1400
1401  LTPFTYLIEGLLSDLVHGLPVECKSHEMLTINPPSGQTCGEYMSAFLTNN  1450
1451  TAAGNLLNPNATTSCSYCPYQTADQFLERFSMRYTHRWRNLGIFVGYVFF  1500
1501  NIFAVLLLFYVFRVMKLRSTWLGKKITGTG                      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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