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

NucPred

Fetching Q3UHD1 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MRGQAAAPGPIWILAPLLLLLLLLGRWARAASGADIGPGTEQCTTLVQGK    50
  51  FFGYFSAAAVFPANASRCSWTLRNPDPRRYTLYMKVAKAPAPCSGPGRVR   100
 101  TYQFDSFLESTRTYLGVESFDEVLRLCDSSAPLAFLQASKQFLQMQRQQP   150
 151  PQDGDLGPQGEFPSSSDDFSVEYLVVGNRNPSHAACQMLCRWLDACLAGS   200
 201  RSSHPCGIMQTPCACLGGDVGDPASSPLVPRGDVCLRDGVAGGPENCLTS   250
 251  LTQDRGGHGSAGGWKLWSLWGECTRDCGGGLQTRTRTCLPTLGVEGGGCE   300
 301  GVLEEGRLCNRKACGPTGRSSSRSQSLRSTDARRREEFGDELQQFGFPSP   350
 351  QTGDPAAEEWSPWSVCSSTCGEGWQTRTRFCVSSSYSTQCSGPLREQRLC   400
 401  NNSAVCPVHGAWDEWSPWSLCSSTCGRGFRDRTRTCRPPQFGGNPCEGPE   450
 451  KQTKFCNIALCPGRAVDGNWNEWSSWSTCSASCSQGRQQRTRECNGPSYG   500
 501  GAECQGHWVETRDCFLQQCPVDGKWQAWASWGSCSVTCGGGSQRRERVCS   550
 551  GPFFGGAACQGPQDEYRQCGAQRCPEPHEICDEDNFGAVVWKETPAGEVA   600
 601  AVRCPRNATGLILRRCELDEEGIAFWEPPTYIRCVSIDYRNIQMMTREHL   650
 651  AKAQRGLPGEGVSEVIQTLLEISQDGTSYSGDLLSTIDVLRNMTEIFRRA   700
 701  YYSPTPGDVQNFVQIISNLLAEENRDKWEEAQLMGPNAKELFRLVEDFVD   750
 751  VIGFRMKDLRDAYQVTDNLVLSIHKLPASGATDISFPMKGWRATGDWAKV   800
 801  PEDRVTVSKSVFSTGLAEADDSSVFVVGTVLYRNLGSFLALQRNTTVLNS   850
 851  KVISVTVKPPPRSLLTPLEIEFAHMYNGTTNQTCILWDETDGPSSSAPPQ   900
 901  LGPWSWRGCRTVPLDALRTRCLCDRLSTFAILAQLSADATMDKVTVPSVT   950
 951  LIVGCGVSSLTLLMLVIIYVSVWRYIRSERSVILINFCLSIISSNALILI  1000
1001  GQTQTRNKVVCTLVAAFLHFFFLSSFCWVLTEAWQSYMAVTGRLRSRLVR  1050
1051  KRFLCLGWGLPALVVAISVGFTKAKGYSTMNYCWLSLEGGLLYAFVGPAA  1100
1101  AVVLVNMVIGILVFNKLVSKDGITDKKLKERAGASLWSSCVVLPLLALTW  1150
1151  MSAVLAVTDRRSALFQILFAVFDSLEGFVIVMVHCILRREVQDAVKCRVV  1200
1201  DRQEEGNGDSGGSFQNGHAQLMTDFEKDVDLACRSVLNKDIAACRTATIT  1250
1251  GTFKRPSLPEEEKMKLAKGPPPTFNSLPANVSKLHLHGSPRYPGGPLPDF  1300
1301  PNHSLTLKKDKAPKSSFIGDGDIFKKLDSELSRAQEKALDTSYVILPTAT  1350
1351  ATLRPKPKEEPKYSINIDQMPQTRLIHLSMAPDASFPTRSPPAREPPGGA  1400
1401  PPEVPPVQPPPPPPPPPPPPQQPIPPPPTLEPAPPSLGDTGEPAAHPGPS  1450
1451  SGAGAKNENVATLSVSSLERRKSRYAELDFEKIMHTRKRHQDMFQDLNRK  1500
1501  LQHAAEKEKEVPGADSKPEKQQTPNKRAWESLRKPHGTPAWVKKELEPLP  1550
1551  PSPLELRSVEWEKAGATIPLVGQDIIDLQTEV                    1582

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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