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

NucPred

Fetching Q76CU2 from www.uniprot.org...

The NucPred score for your sequence is 0.36 (see score help below)

   1  MEPANLSNLRGSSLRGSTRGSLRANSNSIWRNNGVEIFSRSSRDEDDEEA    50
  51  LKWAALEKLPTFDRLRKGLLFGSQGAAAEVDINDLGFQERKNLLERLVKV   100
 101  ADEDNEKFLLKLKNRIDRVGIDLPTIEVRYEHLNIDADAYVGSRSLPTFM   150
 151  NFMTNFVETLLNSLHILSSRKRQLTILKDISGIIKPCRMTLLLGPPSSGK   200
 201  TTLLLALAGKLDPALKVTGKVSYNGHELHEFVPQRTAAYISQHDLHIGEM   250
 251  TVRETLEFSARCQGVGSRFEMLAELSRREKAANIKPDADIDIYMKAAATE   300
 301  GQEANVVTDYVLKILGLDICADTMVGDDMIRGISGGQKKRVTTGEMLVGP   350
 351  SKALFMDEISTGLDSSTTYSIVNSLRQSVQILKGTAVISLLQPAPETYNL   400
 401  FDDIILLSDGYIVYQGPRDDVLEFFESMGFKCPQRKGVADFLQEVTSKKD   450
 451  QQQYWSKRNEPYRFITSKEFAEAYQSFHVGRKLGDELATPFDKTKCHPAA   500
 501  LTNEKYGIGKKELLKVCTERELLLMKRNSFVYMFKFSQLTIMALITMTLF   550
 551  FRTEMPRDTTDDGGIYAGALFFVVIMIMFNGMSELAMTIFKLPVFYKQRD   600
 601  LLFFPSWAYAIPSWILKIPVTLVEVGLWVILTYYVIGFDPNITRFLKQFL   650
 651  LLIVVNQMASGMFRFIGAVGRTMGVASTFGSFALLLQFALGGFVLSRDDV   700
 701  KSWWIWGYWISPMMYSVNSILVNEFDGKKWNHIVPGGNETLGSTVVKSRG   750
 751  FFPEAYWYWIGVGALVGFTVVFNFCYSLALAYLNPFDKPQAVLPEDGENA   800
 801  ENGEVSSQITSTDGGDSISESQNNKKGMVLPFEPHSITFDDVVYSVDMPQ   850
 851  EMKEQGAGEDRLVLLKGVSGAFRPGVLTALMGVSGAGKTTLMDVLAGRKT   900
 901  GGYIDGEIKISGYPKKQETFARISGYCEQNDIHSPYVTVYESLVYSAWLR   950
 951  LPQDVDEKTRKMFVDEVMELVELGPLRSALVGLPGVNGLSTEQRKRLTIA  1000
1001  VELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTGRTVVCTIHQPSI  1050
1051  DIFEAFDELFLMKRGGQEIYVGPLGRHSCHLIKYFESNPGVAKIKEGYNP  1100
1101  ATWMLEVTASAQEMMLGIDFTEVYKNSDLYRRNKALISELGVPRPGSKDL  1150
1151  HFETQYSQSFWTQCVACLWKQHWSYWRNPAYTAVRFIFTTFIALIFGTMF  1200
1201  WDLGTKVSKSQDLLNAMGSMYAAVLFLGVQNASSVQPVVAIERTVFYRER  1250
1251  AAGMYSAIPYAFGQVSIEIPYIFVQSVFYGIIVYAMIGFEWDVGKFFWYL  1300
1301  FIMFFTLLYFTFYGMMGVAVTPNQNVASIVAAFFYGVWNLFSGFIIPRPR  1350
1351  MPVWWRWYYWANPVAWTLYGLVASQFGDIQTKLSDNETVEQFLRRYFGFK  1400
1401  HDFLGVVAAVLTAYVFMFAFTFAFAIKAFNFQRR                  1434

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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