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

NucPred

Fetching P48553 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MDASEEPLPPVIYTMENKPIVTCAGDQNLFTSVYPTLSQQLPREPMEWRR    50
  51  SYGRAPKMIHLESNFVQFKEELLPKEGNKALLTFPFLHIYWTECCDTEVY   100
 101  KATVKDDLTKWQNVLKAHSSVDWLIVIVENDAKKKNKTNILPRTSIVDKI   150
 151  RNDFCNKQSDRCVVLSDPLKDSSRTQESWNAFLTKLRTLLLMSFTKNLGK   200
 201  FEDDMRTLREKRTEPGWSFCEYFMVQEELAFVFEMLQQFEDALVQYDELD   250
 251  ALFSQYVVNFGAGDGANWLTFFCQPVKSWNGLILRKPIDMEKRESIQRRE   300
 301  ATLLDLRSYLFSRQCTLLLFLQRPWEVAQRALELLHNCVQELKLLEVSVP   350
 351  PGALDCWVFLSCLEVLQRIEGCCDRAQIDSNIAHTVGLWSYATEKLKSLG   400
 401  YLCGLVSEKGPNSEDLNRTVDLLAGLGAERPETANTAQSPYKKLKEALSS   450
 451  VEAFEKHYLDLSHATIEMYTSIGRIRSAKFVGKDLAEFYMRKKAPQKAEI   500
 501  YLQGALKNYLAEGWALPITHTRKQLAECQKHLGQIENYLQTSSLLASDHH   550
 551  LTEEERKHFCQEILDFASQPSDSPGHKIVLPMHSFAQLRDLHFDPSNAVV   600
 601  HVGGVLCVEITMYSQMPVPVHVEQIVVNVHFSIEKNSYRKTAEWLTKHKT   650
 651  SNGIINFPPETAPFPVSQNSLPALELYEMFERSPSDNSLNTTGIICRNVH   700
 701  MLLRRQESSSSLEMPSGVALEEGAHVLRCSHVTLEPGANQITFRTQAKEP   750
 751  GTYTLRQLCASVGSVWFVLPHIYPIVQYDVYSQEPQLHVEPLADSLLAGI   800
 801  PQRVKFTVTTGHYTIKNGDSLQLSNAEAMLILCQAESRAVVYSNTREQSS   850
 851  EAALRIQSSDKVTSISLPVAPAYHVIEFELEVLSLPSAPALGGESDMLGM   900
 901  AEPHRKHKDKQRTGRCMVTTDHKVSIDCPWSIYSTVIALTFSVPFRTTHS   950
 951  LLSSGTRKYVQVCVQNLSELDFQLSDSYLVDTGDSTDLQLVPLNTQSQQP  1000
1001  IYSKQSVFFVWELKWTEEPPPSLHCRFSVGFSPASEEQLSISLKPYTYEF  1050
1051  KVENFFTLYNVKAEIFPPSGMEYCRTGSLCSLEVLITRLSDLLEVDKDEA  1100
1101  LTESDEHFSTKLMYEVVDNSSNWAVCGKSCGVISMPVAARATHRVHMEVM  1150
1151  PLFAGYLPLPDVRLFKYLPHHSAHSSQLDADSWIENDSLSVDKHGDDQPD  1200
1201  SSSLKSRGSVHSACSSEHKGLPMPRLQALPAGQVFNSSSGTQVLVIPSQD  1250
1251  DHVLEVSVT                                           1259

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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