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

NucPred

Fetching Q6FP05 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MAFWLPQNIQRRLILYVLQQITLFSNVDITKLDVSLGSHSKFTFQDVDLN    50
  51  ISEMNISGCEVNSGMLGKLMLGLTVSGDVHISGDNIDFMITMINEDDFND   100
 101  MNSFSLAKSFYDLTSSIMQFKPDAHLKNEISGSGSDSPRIPDDYTNPSSA   150
 151  GGNPTTNTYDIIVDDTASSTTESDDSSPIDSIPTSRFNIMQQKVIATALA   200
 201  KLKITLQSVRIRINLGKRKDCNCLDVVVKRIDMSTSEGHVRNFDANGISI   250
 251  AYINNEPSVVPPNNMDMAESLYFSQADASSIYMSALSDANTDIKSLDASV   300
 301  FNSERYELLSINGMSFSFVGISSIDDFAISRIKINLGTLQVNIPFLLKVR   350
 351  EDIILTMIFKLISPRHTDKVDVKNSPAYKRFQNELHSNDTNLFSNLAIEE   400
 401  ILIGLSSNQKIILRAVDLESNEINGINLSVGDIDLVGLDMDWISETRPCF   450
 451  NASFGKSNTIIELANTIIRVSEHDLILFLKIYYEIMDFIDFVLSKWKILG   500
 501  VKQVSQLRNDEKFSLNVGSLVIEIPLDNSILEINIPNIEHDSLNQDLKLY   550
 551  EVNMTHIVESIKISSLKLKEVSIDLSSARKKMKCYNEHFSQYFVFTHYKV   600
 601  QITGIDSQINLKSLWIIGAVIEQFYIASPVQEYPEATNKNSVRFHDNNKR   650
 651  LLSTSLMINKRAILAKYIIELDDIKVCISGFDADQIRHCKFSLQRLLFLN   700
 701  QIDKGLLFNIFQPHVEIKFFSGSLNDIIRSTNIGVSGQPHLILCIFADKK   750
 751  IKVSIKDIMIFYQAKWLDSVQRNASLDQEKGQNVEYSELPEFSISIRDSA   800
 801  INFLPFRINPSLVILFESIIVTKSGNDALINMHSKVGRFYLTDNYDHLKT   850
 851  TQVMNKTICDSLIKSGYSQIGKFEGLSMTLNKKHKIVNCNGCLEKVILSV   900
 901  CSDSFHTLVQLCMDLKVPVTFPDDKKYQPVPSVAVDLFETIEENEFNLSN   950
 951  LDNKDIDKSIGSDSDSLHIVNSFLDEVEDFQFHEDYNSGTVWSHTTSDTH  1000
1001  SSSDILPISLKEEYLDSRRTEVQKHSQSNDRNIISEIDFDIKNADIRLYD  1050
1051  GYDWRYTRKNVSSAISELEEGLLSGIQRQEQTESELSRTTVFDSICIATK  1100
1101  QKDLGNLKQIISEQVQGKHDHLNSDKVYLYPSKHYKSLIKANELIFKIKI  1150
1151  YDSNSPRNEEFNNHAAKLFQITASISTYEVLDNLPTSTWNKFVTLLKKEA  1200
1201  WPKSEPMLYFDFMLFKPINSLEATEATINIRSAPLRIHADQYMVDFLLRF  1250
1251  FQFNDKRFELIDEYPEILFLQKFKSNTIKLRIDYKPNKTSSGMYSGKISD  1300
1301  LINLFVLDESKVTLKGVVLHGINGFNELSEQLVKIWGNDVTSKQIFNILQ  1350
1351  GFAPVKSFIALGAGAQTFITVLLAEYKRDRSISRSVKKSGNIFIKTTTGD  1400
1401  FIKLGAKLAVGTQALLENTEGILSGNATQNRTLADVSQTNKVLDLDSLLQ  1450
1451  QDQVLIGRNPKIRNKSPSAIIIDAADLEESGRPKVVSLYSEQPLDLHKGL  1500
1501  EEAYHALEKHIQIAYNTIWQTNQELRGEESRSAKAAAVTIAKAAPVAVIR  1550
1551  PMIGATEAIAKTLQGIYNQLDKSNIEEINDKYKKEDN               1587

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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