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

NucPred

Fetching Q9R1B9 from www.uniprot.org...

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

   1  MSGIGWQTLSLSLGLVLSILNKVAPQACPAQCSCSGSTVDCHGLALRSVP    50
  51  RNIPRNTERLDLNGNNITRITKIDFAGLRHLRVLQLMENRISTIERGAFQ   100
 101  DLKELERLRLNRNNLQLFPELLFLGTAKLYRLDLSENQIQAIPRKAFRGA   150
 151  VDIKNLQLDYNQISCIEDGAFRALRDLEVLTLNNNNITRLSVASFNHMPK   200
 201  LRTFRLHSNNLYCDCHLAWLSDWLRQRPRVGLYTQCMGPSHLRGHNVAEV   250
 251  QKREFVCSGHQSFMAPSCSVLHCPAACTCSNNIVDCRGKGLTEIPTNLPE   300
 301  TITEIRLEQNSIRVIPPGAFSPYKKLRRLDLSNNQISELAPDAFQGLRSL   350
 351  NSLVLYGNKITELPKSLFEGLFSLQLLLLNANKINCLRVDAFQDLHNLNL   400
 401  LSLYDNKLQTVAKGTFSALRAIQTMHLAQNPFICDCHLKWLADYLHTNPI   450
 451  ETSGARCTSPRRLANKRIGQIKSKKFRCSGTEDYRSKLSGDCFADLACPE   500
 501  KCRCEGTTVDCSNQRLNKIPDHIPQYTAELRLNNNEFTVLEATGIFKKLP   550
 551  QLRKINFSNNKITDIEEGAFEGASGVNEILLTSNRLENVQHKMFKGLESL   600
 601  KTLMLRSNRISCVGNDSFIGLGSVRLLSLYDNQITTVAPGAFDSLHSLST   650
 651  LNLLANPFNCNCHLAWLGEWLRRKRIVTGNPRCQKPYFLKEIPIQDVAIQ   700
 701  DFTCDDGNDDNSCSPLSRCPSECTCLDTVVRCSNKGLKVLPKGIPKDVTE   750
 751  LYLDGNQFTLVPKELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLIL   800
 801  SYNRLRCIPPRTFDGLKSLRLLSLHGNDISVVPEGAFNDLSALSHLAIGA   850
 851  NPLYCDCNMQWLSDWVKSEYKEPGIARCAGPGEMADKLLLTTPSKKFTCQ   900
 901  GPVDITIQAKCNPCLSNPCKNDGTCNNDPVDFYRCTCPYGFKGQDCDVPI   950
 951  HACISNPCKHGGTCHLKEGENAGFWCTCADGFEGENCEVNIDDCEDNDCE  1000
1001  NNSTCVDGINNYTCLCPPEYTGELCEEKLDFCAQDLNPCQHDSKCILTPK  1050
1051  GFKCDCTPGYIGEHCDIDFDDCQDNKCKNGAHCTDAVNGYTCVCPEGYSG  1100
1101  LFCEFSPPMVLPRTSPCDNFDCQNGAQCIIRINEPICQCLPGYLGEKCEK  1150
1151  LVSVNFVNKESYLQIPSAKVRPQTNITLQIATDEDSGILLYKGDKDHIAV  1200
1201  ELYRGRVRASYDTGSHPASAIYSVETINDGNFHIVELLTLDSSLSLSVDG  1250
1251  GSPKVITNLSKQSTLNFDSPLYVGGMPGKNNVASLRQAPGQNGTSFHGCI  1300
1301  RNLYINSELQDFRKMPMQTGILPGCEPCHKKVCAHGMCQPSSQSGFTCEC  1350
1351  EEGWMGPLCDQRTNDPCLGNKCVHGTCLPINAFSYSCKCLEGHGGVLCDE  1400
1401  EEDLFNPCQMIKCKHGKCRLSGVGQPYCECNSGFTGDSCDREISCRGERI  1450
1451  RDYYQKQQGYAACQTTKKVSRLECRGGCAGGQCCGPLRSKRRKYSFECTD  1500
1501  GSSFVDEVEKVVKCGCARCAS                               1521

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.)

Go back to the NucPred Home Page.