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

NucPred

Fetching Q769J6 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MSQLCLWLTCQPCYAVSVRGILTGAIFILGCWGLSDFQKSLLQDLEPKDV    50
  51  SSYFGHHAAPFTGHPPSHLQRLRRRRTLEDILHLELLVAVGPDVSRAHQE   100
 101  DTERYVLTNLNIGSELLRNPSLGVQFQVHLVKLITLSDSESTPNITANIT   150
 151  SSLMSVCEWSQTINPHDDRDPSHADLILYITRFDLELPDGNQQVRGVTQL   200
 201  GGACSLSWSCLITEDTGFDLGVTIAHEIGHSFGLDHDGAPGSGSTCKASG   250
 251  HVMAADGATPTGGTLEWSACSQRQLQHLLSTGQMHCFQDPPGLQSGLTRH   300
 301  QLMAQPGLYYSADDQCRVAFGSGAVACTFSREGLDVCQALSCHTDPLDQS   350
 351  SCSRLLVPLLDGTECGVEKWCSKARCRSLAELAPVAAVHGHWSSWGPHSP   400
 401  CSRSCGGGVITRRRWCNNPRPAFGGRACVGEDLQAKMCNTQACEKTQLEF   450
 451  MSEQCAQTDRQPLQLSQGTASFYHWDAAVQYSQGDTLCRHMCWAVGESFI   500
 501  VSRGDRFLDGTRCVPSGPQDDGTLSLCLLGSCRTFGCDGRMDSQKVWDAC   550
 551  QVCGGDNSTCSSRNGSFTAGRAREYVTFLIVTPNMTNAHIVNRRPLFTHL   600
 601  AVRIQGHYIVAGKTSISPNTTYPSLLEDYRVEYRVTLTEDQLPHLEEIHI   650
 651  RGPVRDDIEIQVYRRYGGEYGDLTHPDITFSYFQLKQQAAWVWTAKRGPC   700
 701  SVSCGAGLRWVTYSCQDQAQDKWVKNAQCQGSPQPPAWQEPCVSAPCSPY   750
 751  WVAGDFSPCSVSCGGGLRERSLRCVETQDGFLKTLPPARCRAVAQQPAAE   800
 801  VENCNSQPCPTRWEVSDPGPCMSSACEAGLDSRNVTCVSRAGDPEKPETA   850
 851  GPCRTDEMSAMLEPCSRSLCSPGLGQVDNTMSLGEEAPSPVGSDKPGAQA   900
 901  EHVWTPLVGLCSISCGRGLKELYFLCMDSVLKMPVQEELCGLASKPPSRW   950
 951  EVCRARPCPARWETQVLAPCPVTCGGGRVPLSVRCVQLDRGHPISVPHSK  1000
1001  CSPVPKPGSFEDCSPEPCPARWKVLSLGPCSASCGLGTATQMVACMQLDQ  1050
1051  GHDNEVNETFCKALVRPQASVPCLIADCAFRWHISAWTECSVSCGDGIQR  1100
1101  RHDTCLGPQAQVPVPANFCQHLPKPMTVRGCWAGPCAGQETSSSLPHKEA  1150
1151  TLPSQTQAAATVASLQWSQPRARTPTLFSASQSLGLQENLEEHGACGRQY  1200
1201  LEPTGTIHMRDQGRLDCVVAIGRPLGEVVTLQILESSLKCSAGEQLLLWG  1250
1251  RFTWRKTCRKMPGMTFSTKTNTVVVKQHRVLPGGGVLLRYWSQPAPGTFY  1300
1301  KECDRQLFGPRGEIVSPSLSPDGRKAGTCRVFISVAPQARIAIRALASDM  1350
1351  GTASEGTNANYVSIRDIHSLRTTTFWGQQVLYWESEGSEAELEFSPGFLE  1400
1401  AHASLQGEYWTISPRTSEQDDSLALS                          1426

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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