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

NucPred

Fetching Q7PC80 from www.uniprot.org...

The NucPred score for your sequence is 0.33 (see score help below)

   1  MSSAGVVEMQKAASFRREGGGSMASMWLSADGNGAFSRSSSSSSRRMRGE    50
  51  EDDEEALRWAALQKLPTYDRVRAAILPMVEGEGGEAGGGGGGRRVVVDVH   100
 101  SLGPHERRALLERLVRVADDDNERFLLKLKERISRVGIDMPTIEVRFEHL   150
 151  EVEAEVRVGNSGIPTVLNSITNKIEEAANALGILPTRKQTLRILHDISGI   200
 201  IKPKRMTLLLGPPGSGKTTFLLALAGRLKDLKFSGQVTYNGHQMEDFVPQ   250
 251  RTAAYISQHDLHIGEMTVRETLSFSARCQGVGSRFDMLTELTRREKAANI   300
 301  KPDADVDAFMKASAMEGQESNLITDYILKILGLEICADTMVGDDMVRGIS   350
 351  GGQRKRVTTGEMLVGPANAFFMDEISTGLDSSTTFQIVKSLRQTIHILGG   400
 401  TAVISLLQPAPETYDLFDDIILLSDGHIVYQGPRENVLEFFELMGFKCPE   450
 451  RKGVADFLQEVTSRKDQKQYWAQHDKPYRYVPIKEFASAFQSFHTGRSIA   500
 501  NELATPFDKSKSHPAALTTSRYGVSAMELLKANIDRELLLIKRNSFVYIF   550
 551  RTIQLMTVSAMAMTVFFRTKMHRDSVADGVIFMGALFFAVMMIMLNGLSE   600
 601  LPLTIFKLPVFFKQRDLLFFPAWTYTIPSWILKSPMSFIEVGGFCFMSYY   650
 651  VIGFDPNVGRFFKQYLLMLAVSQMAAALFRFVGGAARNLIVANVFGSFML   700
 701  LIFMVLGGFILARDKVNKWWIWGYWISPMMYAQNAVSVNEFLGHSWDKVL   750
 751  NNSLSNETLGVQALMSRGIFPEAKWYWIGFGALLGFIMLFNILFTLALTY   800
 801  LKPDGKSQPSISEEELKEKQANINGNVLDVDTMASSNNLAIVGSTGTGSE   850
 851  IADNSQPTQRGMVLPFTPLSLTFEDIKYSVDMPQEMKAHGIVEDRLELLK   900
 901  GVSGCFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIEGNISISGYPKK   950
 951  QETFARVSGYCEQNDIHSPQVTVSESLLFSAWLRLPKDVDSNTRKMFIEE  1000
1001  VMELVELKPLRDALVGLPGVNGLSIEQRKRLTIAVELVANPSIIFMDEPT  1050
1051  SGLDARAAAIVMRTVRNTVNTGRTVVCTIHQPSIDIFEAFDELFLMKRGG  1100
1101  EEIYVGPLGHHSSELIKYFEGIQGVSKITDGYNPATWMLEVTTVSQEQAL  1150
1151  DVDFCDIYRKSELFQRNKALIQELSTPPPGSSELYFPTQYSQSFLIQCLA  1200
1201  CLWKQHLSYWRNPPYNAIRLFFTTVIALIFGTIFWDLGGKMGQSQDLFNA  1250
1251  MGSMYAAVLFIGVLNGQSVQPVVSVERTVFYRERAAGMYSALPYAFGQVA  1300
1301  IEFPYTLVQSVIYSIIVYSMIGFQWTVAKFFWYLFFMFFTLLYFTFYGMM  1350
1351  AVGLTPSYHVASIVSSAFYAIWNLFTGFVISRPATPVWWRWYCWICPVAW  1400
1401  TLYGLIVSQYGDIVTPMDDGIPVNVFVENYFDFKHSWLGFVAVVIVAFTM  1450
1451  LFAFLFGFAIMKLNFQKR                                  1468

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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