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

NucPred

Fetching Q99NH2 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MKVTVCFGRTRVVVPCGDGRMKVFSLIQQAVTRYRKAVAKDPNYWIQVHR    50
  51  LEHGDGGILDLDDILCDVADDKDRLVAVFDEQDPHHGGDGTSASFTGTQS   100
 101  PEIFGSELGTNNVSAFQPYQATSEIEVTPSVLRANMPLHVRRSSDPALTG   150
 151  LSTSVSDNNFSSEEPSRKNPTRWSTTAGFLKQNTAGSPKTCDRKKDENYR   200
 201  SLPRDPSSWSNQFQRDNARSSLSASHPMVDRWLEKQEQDEEGTEEDSSRV   250
 251  EPVGHADTGLENMPNFSLDDMVKLVQVPNDGGPLGIHVVPFSARGGRTLG   300
 301  LLVKRLEKGGKAEQENLFHENDCIVRINDGDLRNRRFEQAQHMFRQAMRA   350
 351  RVIWFHVVPAANKEQYEQLSQREKNNYSPGRFSPDSHCVANRSVANNAPQ   400
 401  ALPRAPRLSQPPEQLDAHPRLPHSAHASTKPPAAPALAPPSVLSTNVGSV   450
 451  YNTKKVGKRLNIQLKKGTEGLGFSITSRDVTIGGSAPIYVKNILPRGAAI   500
 501  QDGRLKAGDRLIEVNGVDLAGKSQEEVVSLLRSTKMEGTVSLLVFRQEEA   550
 551  FHPREMNAEPSQMQTPKETKAEDEDVVLTPDGTREFLTFEVPLNDSGSAG   600
 601  LGVSVKGNRSKENHADLGIFVKSIINGGAASKDGRLRVNDQLIAVNGESL   650
 651  LGKANQEAMETLRRSMSTEGNKRGMIQLIVARRISRCNELRSPGSPAAPE   700
 701  LPIETELDDRERRISHSLYSGIEGLDESPTRNAALSRIMGKCQLSPTVNM   750
 751  PHDDTVMIEDDRLPVLPPHLSDQSSSSSHDDVGFIMTEAGTWAKATISDS   800
 801  ADCSLSPDVDPVLAFQREGFGRQSMSEKRTKQFSDASQLDFVKTRKSKSM   850
 851  DLVADETKLNTVDDQRAGSPSRDVGPSLGLKKSSSLESLQTAVAEVTLNG   900
 901  NIPFHRPRPRIIRGRGCNESFRAAIDKSYDKPMVDDDDEGMETLEEDTEE   950
 951  SSRSGRESVSTSSDQPSYSLERQMNGDPEKRDKTERKKDKAGKDKKKDRE  1000
1001  KEKDKLKAKKGMLKGLGDMFRFGKHRKDDKMEKMGRIKIQDSFTSEEDRV  1050
1051  RMKEEQERIQAKTREFRERQARERDYAEIQDFHRTFGCDDELLYGGMSSY  1100
1101  EGCLALNARPQSPREGHLMDTLYAQVKKPRSSKPGDSNRSTPSNHDRIQR  1150
1151  LRQEFQQAKQDEDVEDRRRTYSFEQSWSSSRPASQSGRHSVSVEVQVQRQ  1200
1201  RQEERESFQQAQRQYSSLPRQSRKNASSISQDSWEQNYAPGEGFQSAKEN  1250
1251  PRYSSYQGSRNGYLGGHGFNARVMLETQELLRQEQRRKEQQLKKQPPADG  1300
1301  VRGPFRQDVPPSPSQVARLNRLQTPEKGRPFYS                   1333

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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