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

NucPred

Fetching Q9SL02 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MSTVDKMLIKGIRSFDPENKNVVTFFRPLTLIVGANGAGKTTIIECLKVS    50
  51  CTGELPPNARSGHSFIHDPKVAGETETKAQIKLRFKTAAGKDVVCIRSFQ   100
 101  LTQKASKMEYKAIESVLQTINPHTGEKVCLSYRCADMDREIPALMGVSKA   150
 151  ILENVIFVHQDESNWPLQDPSTLKKKFDDIFSATRYTKALEVIKKLHKDQ   200
 201  AQEIKTFKLKLENLQTLKDAAYKLRESIAQDQERTESSKVQMLELETSVQ   250
 251  KVDAEVHNKEMMLKDLRKLQDQVSIKTAERSTLFKEQQRQYAALPEENED   300
 301  TIEELKEWKSKFEERLALLGTKIRKMEREMVDTETTISSLHNAKTNYMLE   350
 351  ISKLQTEAEAHMLLKNERDSTIQNIFFHYNLGNVPSTPFSTEVVLNLTNR   400
 401  IKSRLGELEMDLLDKKKSNETALSTAWDCYMDANDRWKSIEAQKRAKDEI   450
 451  KMGISKRIEEKEIERDSFEFEISTVDVKQTDEREKQVQVELERKTKQNSE   500
 501  RGFESKIEQKQHEIYSLEHKIKTLNRERDVMAGDAEDRVKLSLKKTEQEN   550
 551  LKKKHKKIIDECKDRIRGVLKGRLPPEKDMKREIVQALRSIEREYDDLSL   600
 601  KSREAEKEVNMLQMKIQEVNNSLFKHNKDTESRKRYIESKLQALKQESVT   650
 651  IDAYPKLLESAKDKRDDRKREYNMANGMRQMFEPFEKRARQEHSCPCCER   700
 701  SFTADEEASFIKKQRVKASSTGEHLKALAVESSNADSVFQQLDKLRAVFE   750
 751  EYSKLTTEIIPLAEKTLQEHTEELGQKSEALDDVLGISAQIKADKDSIEA   800
 801  LVQPLENADRIFQEIVSYQKQIEDLEYKLDFRGLGVKTMEEIQSELSSLQ   850
 851  SSKDKLHGELEKLRDDQIYMERDISCLQARWHAVREEKAKAANLLRDVTK   900
 901  AEEDLERLAEEKSQLDLDVKYLTEALGPLSKEKEQLLSDYNDMKIRRNQE   950
 951  YEELAEKKRNYQQEVEALLKASYKINEYHDLKKGERLDDIQEKQRLSDSQ  1000
1001  LQSCEARKNELAGELNRNKDLMRNQDQLRRNIEDNLNYRTTKAKVEELTR  1050
1051  EIESLEEQILNIGGIAAVEAEIVKILRERERLLSELNRCRGTVSVYESSI  1100
1101  SKNRVELKQAQYKDIDKRHFDQLIQLKTTEMANKDLDRYYNALDKALMRF  1150
1151  HTMKMEEINKIIRELWQQTYRGQDMDYIRIHSDSEGAGTRSYSYKVLMQT  1200
1201  GDTELEMRGRCSAGQKVLASLIIRLALAETFCLNCGILALDEPTTNLDGP  1250
1251  NSESLAGALLRIMEDRKGQENFQLIVITHDERFAQMIGQRQHAEKYYRVA  1300
1301  KDDMQHSIIEAQEIFD                                    1316

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.