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

NucPred

Fetching Q6ZQF0 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MSRNDQEPFLVKFLKSSDNSECFFKALESIKELQSEDYLQIITDEEALKI    50
  51  RENDKSLYICDRFSGTVFDHLKQLGCRIVGPQVVTFCMRHQQCVPRAEHP   100
 101  VYNMIMSDVTVSCTSLDKDKREEVHKYVQMMGGRVYRDLNVSVTHLIAGE   150
 151  VGSKKYLVAANLKKPILLPSWIKTLWEKSQEKKITKYTDVNMEDFKCPIF   200
 201  LGCIICVTGLNGIHRKTVQQLTAKHGGQYMGQLKMNECTHLIVQEPKGQK   250
 251  YECARRWNVHCVTLQWFHDSIEKGFCQDESIYKAETRVEAKMVPDTSTPT   300
 301  AQSNAESHTLADVSHISNINGSCVNETMFGSTTSKLECSLENLENLDISM   350
 351  FQAPEDLLDGCRIYLCGFSGRKLDKLRRLINSGGGVRFNQLNEDVTHVIV   400
 401  GDYDDDVRQFWSKSSHRPHVVGAKWLLECFTKGYILPEESYIHTNYQPAG   450
 451  IAVSDQPGNQTAVLDKSGSFSKSALVPAERLQQADEDLLAQYGNDDSTMV   500
 501  EAKLSEALEPEVGPCPGSAHREPCDDSTHISVQEENKSSVSHCILDDSTV   550
 551  REEGLFSQKSFLVLGFSVENKCNIVDIIREHAGKIVSLPSRIVADYAVVP   600
 601  LLGCEVDVTVGEVVTNTWLVTCIDNQTLVDPKSNPLFTPVSVMSGVTPLE   650
 651  DCVISFSQCVGAERDSLVFLANHLGASVQEFFVRKANAKKGMLASTHLIV   700
 701  KEPTGSKYEAAKKWSLPAVNISWLLETARIGKRADENHFLVDNAPKQEQV   750
 751  LETKIPNGVSSNPDLPAHPDAHLEIHRKKAVTPLDMNRFQSRAFRAVISQ   800
 801  QRGQDPTFPPVRQPLTKEPSLHLDTPSKFLSKDKLFKPSFDVTDALAALE   850
 851  TPNAASQKRKLSSPLSEVIVRNLTVALANSSRNTDSHSASPQLKGAHLEE   900
 901  EETRKPLDSVVVCVSKKLSKKQSELNGVAASLGAEYRWSFDETVTHFIYQ   950
 951  GRANDSNREYKSAKERGVHIVSEHWLLECAQEYKHLPESLYPHTYNPKMS  1000
1001  LDINTVQDGRLCNSRAPLAVSASKDDGPDHLSVEGNETNTMGTNDKESPL  1050
1051  LNGSGRDDCKGALTQALEMRENFQKQLQEIMSATCIVKTPAQKTCMSRSS  1100
1101  CNSASSTPDSARSVRSGRSRVLEALRQSRQAVPDVNTEPSQNEQIIWDDP  1150
1151  TAREERARLASNLQWPSDPTQHSELQVEIKMPDDSPSRKPVYHSEIAEQA  1200
1201  SCVTQAPGHPGSEEPEPPVAERPLIPEPQAPAVASPLAKPPVAPQPADKI  1250
1251  ETQEETHRKVKKQYVFQMSSLNSQERIDYCRLIKDLGGSVIEKQCSDPSC  1300
1301  THMVVGYPLRNEKYLASMAAGKWVLHRSYLDACKTAGRFVQEEDYEWGSS  1350
1351  SILDALPDVTEHQQKLALAAMRWRKRIQQSQESGIVEGAFSGWKAILRVD  1400
1401  RPREAGFKRLLQAGGAKVLSGHPEPLLKDATHLFCDFNKLKPDDCRVFIA  1450
1451  EATAQNMVCLKTEYIADYLMLESPPCADNYRVSEAALFHNKKGGPGLPQK  1500
1501  RKTPAENVVKRPRVH                                     1515

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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