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

NucPred

Fetching Q03350 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MLWALALLALGIGPRASAGDHVKDTSFDLFSISNINRKTIGAKQFRGPDP    50
  51  GVPAYRFVRFDYIPPVNTDDLNRIVKLARRKEGFFLTAQLKQDRKSRGTL   100
 101  LVLEGPGTSQRQFEIVSNGPGDTLDLNYWVEGNQHTNFLEDVGLADSQWK   150
 151  NVTVQVASDTYSLYVGCDLIDSVTLEEPFYEQLEVDRSRMYVAKGASRES   200
 201  HFRGLLQNVHLVFADSVEDILSKKGCQHSQGAEVNTISEHTETLHLSPHI   250
 251  TTDLVVQGVEKAQEVCTHSCEELSNMMNELSGLHVMVNQLSKNLERVSSD   300
 301  NQFLLELIGGPLKTRNMSACVQEGRIFAENETWVVDSCTTCTCKKFKTVC   350
 351  HQITCSPATCANPSFVEGECCPSCSHSADSDEGWSPWAEWTECSVTCGSG   400
 401  TQQRGRSCDVTSNTCLGPSIQTRTCSLGKCDTRIRQNGGWSHWSPWSSCS   450
 451  VTCGVGNVTRIRLCNSPVPQMGGKNCKGSGRETKPCQRDPCPIDGRWSPW   500
 501  SPWSACTVTCAGGIRERSRVCNSPEPQYGGKDCVGDVTEHQMCNKRSCPI   550
 551  DGCLSNPCFPGAKCNSFPDGSWSCGSCPVGFLGNGTHCEDLDECAVVTDI   600
 601  CFSTNKAPRCVNTNPGFHCLPCPPRYKGNQPFGVGLEDARTEKQVCEPEN   650
 651  PCKDKTHSCHKNAECIYLGHFSDPMYKCECQIGYAGDGLICGEDSDLDGW   700
 701  PNNNLVCATNATYHCIKDNCPKLPNSGQEDFDKDGIGDACDEDDDNDGVS   750
 751  DEKDNCQLLFNPRQLDYDKDEVGDRCDNCPYVHNPAQIDTDNNGEGDACS   800
 801  VDIDGDDVFNERDNCPYVYNTDQRDTDGDGVGDHCDNCPLMHNPDQIDQD   850
 851  NDLVGDQCDNNEDIDDDGHQNNQDNCPYISNSNQADHDNDGKGDACDSDD   900
 901  DNDGVPDDRDNCRLVFNPDQEDSDGDGRGDICKDDFDNDNVPDIDDVCPE   950
 951  NNAITETDFRNFQMVPLDPKGTTQIDPNWVIRHQGKELVQTANSDPGIAV  1000
1001  GFDEFGSVDFSGTFYVNTDRDDDYAGFVFGYQSSSRFYVVMWKQVTQTYW  1050
1051  EDKPSRAYGYSGVSLKVVNSTTGTGEHLRNALWHTGNTEGQVRTLWHDPK  1100
1101  NIGWKDYTAYRWHLIHRPKTGYMRVLVHEGKQVMADSGPIYDQTYAGGRL  1150
1151  GLFVFSQEMVYFSDLKYECRDA                              1172

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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