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

NucPred

Fetching Q5W274 from www.uniprot.org...

The NucPred score for your sequence is 0.49 (see score help below)

   1  MAQLVGSDEIESFRMDLAEIGRSLRSSFRGQSSSFRSNSALSASQKDDAV    50
  51  DEENMLAWAAIERLPTFDRLRSSLFEEINGNDANVKRKRVTDVTKLGALE   100
 101  RHVFIEKMIKHIEHDNLQLLHKIRKRIDKVGVELPTVEVRYKNLTIEAEC   150
 151  ELVHGKPLPTLWNSLKSITMNLARLPGLQSELAKIKILNDVSGVIKPGRM   200
 201  TLLLGPPGCGKTSLLKALSGNLDKSLKVSGEISYNGYKLEEFVPQKTSAY   250
 251  VSQNDLHIPEMTVRETLDYSSRFQGVGSRAEIMTDLSRREKEAGVVPDPD   300
 301  IDTYMKAISIEGQKKNLQTDYILKILGLDICADTLVGDAMRRGISGGQKK   350
 351  RLTTGELIVGPIKALFMDEISNGLDSSTTYQIVACLQQLAHITDATILVS   400
 401  LLQPAPETFDLFDDIILMAEGKILYHGPRNSALEFFESCGFKCPERKGVA   450
 451  DFLQEVTSKKDQAQYWHGTKETYKFVSVDMLSRKFKESPYRKKLNEELSV   500
 501  PYDNSRSHRNSITFRDYSLPKWELFRACMSREFLLMKRNSFIYIFKTVQL   550
 551  AIIASITMTVFLRTRMDTDLVHANYYLGALFYALIILLVDGFPELSMTIT   600
 601  RLAVFYKQSELCFYPAWAYTIPATILKIPLSLLESVIWASMTYYVIGFSP   650
 651  EAGRFFRQLLLLFAVHMTSISMFRFLASVCRTIVASTAAGGLSILFVLCF   700
 701  SGFIIPRPSMPIWLKWGFWISPLTYGEIGLAVNEFLAPRWQKTLPTNTSI   750
 751  GNEVLESRGLNFDGYFYWISVCALFGFTILFNIGFTLALTFLKAPGSRAI   800
 801  ISTDKYSQIEGSSDSIDKADAAENSKATMDSHERAGRMVLPFEPLSLVFQ   850
 851  DVQYYVDTPAAMTELGFTQKRLQLLSDITGALRPGILTALMGVSGAGKTT   900
 901  LLDVLAGRKTTGYVEGEIKVGGYPKVQETFARVSGYCEQTDIHSPQITVE   950
 951  ESVIFSAWLRLHPQIDSKTKYEFVKEVIETIELDGIKGMLVGMPGVSGLS  1000
1001  TEQRKRLTIAVELVANPSIIFMDEPTTGLDARSAAIVMRAVKNVADTGRT  1050
1051  IVCTIHQPSIDIFEAFDELILLKTGGRMIYWGHLGRNSCKMIEYFEGISC  1100
1101  VPKIKNNHNPATWMLEVTSTSSEADISIDFAEVYKNSALHKNNEELVKKL  1150
1151  SFPPAGSKDLHFPTRFSQNGWGQFKTCFWKQYWSYWRSPSYNLMRSLHML  1200
1201  FASLVSGLLFWDKGKKLDNQQSVFSVFGAMFTAVIFCGINNSSSVLPYVT  1250
1251  TERSVLYRERFAGMYASWAYALAQVAIEIPYLLAQALAFTVITYPMIGYY  1300
1301  WSAYKVFWYFYSMFCTLLYFTYLGMMLVSMTPSFPVAAILQSSFYTMFNL  1350
1351  FAGFLMPKAQIPKWWIWFYYLTPTSWTLNGMLTSQYGDIEKEITVFQEKK  1400
1401  TVAAFLGDYFGFHHNQLPIVAFVLIAYPLVFASLFAFFIGKLNFQRR     1447

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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