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

NucPred

Fetching Q810U4 from www.uniprot.org...

The NucPred score for your sequence is 0.26 (see score help below)

   1  MQLKIMPKKKHLSAGGVPLILFLCQMISALDVPLDLVQPPTITQQSPKDY    50
  51  IIDPRENIVIQCEAKGKPPPSFSWTRNGTHFDIDKDPLVTMKPGSGTLVI   100
 101  NIMSEGKAETYEGVYQCTARNERGAAVSNNIVVRPSRSPLWTKERLEPIV   150
 151  LQNGQSLVLPCRPPIGLPPAIIFWMDNSFQRLPQSERVSQGLNGDLYFSN   200
 201  VLPEDTREDYICYARFNHTQTIQQKQPISLKVISVDELNDTIAANLSDTE   250
 251  FYGAKSSKERPPTFLTPEGNESHKEELRGNVLSLECIAEGLPTPIIYWIK   300
 301  EDGMLPANRTFYRNFKKTLQITHVSEADSGNYQCIAKNALGAVHHTISVT   350
 351  VKAAPYWIVAPQNLVLSPGENGTLICRANGNPKPRISWLTNGVPIEIALD   400
 401  DPSRKIDGDTIIFSNVQESSSAVYQCNASNKYGYLLANAFVNVLAEPPRI   450
 451  LTSANTLYQVIANRPALLDCAFFGSPMPTIEWFKGTKGSALHEDIYVLHD   500
 501  NGTLEIPVAQKDSTGTYTCVARNKLGMAKNEVHLEIKDPTRIIKQPEYAV   550
 551  VQRGSKVSFECRVKHDHTLIPTIMWLKDNGELPNDERFSTDKDHLVVSDV   600
 601  KDDDGGTYTCTANTTLDSASASAVLRVVAPTPTPAPIYDVPNPPFDLELT   650
 651  NQLDKSVQLTWTPGDDNNSPITKFIIEYEDAMHDAGLWRHQAEVSGTQTT   700
 701  AQLKLSPYVNYSFRVMAENSIGRSMPSEASEQYLTKAAEPDQNPMAVEGL   750
 751  GTEPDNLVITWKPLNGFQSNGPGLQYKVSWRQKDGDDEWTSVVVANVSKY   800
 801  IVSGTPTFVPYLIKVQALNDVGFAPEPAAVMGHSGEDLPMVAPGNVRVSV   850
 851  VNSTLAEVHWDPVPPKSVRGHLQGYRIYYWKTQSSSKRNRRHIEKKILTF   900
 901  QGTKTHGMLPGLQPYSHYALNVRVVNGKGEGPASTDRGFHTPEGVPSAPS   950
 951  SLKIVNPTLDSLTLEWDPPSHPNGILTEYILQYQPINSTHELGPLVDLKI  1000
1001  PANKTRWTLKNLNFSTRYKFYFYAQTSVGPGSQITEEAITTVDEAGIPPP  1050
1051  DVGAGKGKEEWRKEIVNGSRSFFGLKGLMPGTAYKVRVGAEGDSGFVSSE  1100
1101  DVFETGPAMASRQVDIATQGWFIGLMCAVALLILILLIVCFIRRNKGGKY  1150
1151  PVKEKEDAHADPEIQPMKEDDGTFGEYSDAEDHKPLKKGSRTPSDRTVKK  1200
1201  EDSDDSLVDYGEGVNGQFNEDGSFIGQYSGKKEKEPAEGNESSEAPSPVN  1250
1251  AMNSFV                                              1256

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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