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

NucPred

Fetching Q99P47 from www.uniprot.org...

The NucPred score for your sequence is 0.43 (see score help below)

   1  MNMGSVAGAVLKMLLLLSTQNWNRVEAGNSYDCDEPLVSALPQASFSSSS    50
  51  ELSSSHGPGFARLNRRDGAGGWSPLVSNKYQWLQIDLGERMEVTSVATQG   100
 101  GYGSSNWVTSYLLMFSDSGRNWKQYRQEDSIWGFSGNANADSVVYYRLQP   150
 151  SIKARFLRFIPLEWNPKGRIGMRIEVFGCAYRSVVIDLDGKSSLLYRFDQ   200
 201  NSLSPIRDIISLKFKTMESDGILLHRAGPAGDHITLELRRGKLFLLINSG   250
 251  DARLTSSSTLINLTLGSLLDDQHWHSVLIQRLGKQVNFTVDEHRRHFHAQ   300
 301  GEFNYLDLDYEISFGGISAPAKSVSLPYKHFHGCLENLFYNGVDVIGLVK   350
 351  EHSPQIITMGNASFSCSQPQSMPLTFLSPRSYLVLPASTKEEAISASFQF   400
 401  RTWNKAGLLLFSELQLVSGSLLLLLSDGKLKLTLYQPGKSPSDITAGAGL   450
 451  GDGQWHSVSLSAKRNHLSVVVDGHISPASPWLGPEQVNSGGVFYFGGCPD   500
 501  KGFGSKCKSPLGGFQGCMRLISINNKMVDLIAVQQGALGNFSDLQIDSCG   550
 551  ISDRCLPNSCEHGGECSQSWSTFHCNCTNTGYTGATCHSSVYEQSCEAYK   600
 601  HQGNASGFYYIDSDGSGPLQPFLLYCNMTETAWTVMQHNGSDLMRVRNTH   650
 651  SENAHTGVFEYTASMEQLQAAINRAEHCQQELVYYCKKSRLVNQQDGSPR   700
 701  SWWVGRTNETQTYWGGSLPVHQKCTCGLEGNCIDAQYHCNCDADLNEWTN   750
 751  DTGFLSYKEHLPVTKIVITDTGRPHSEAAYKLGPLLCRGDRPFWNAASFN   800
 801  TEASYLHFPTFHGELSADVSFFFKTTALSGVFLENLGITDFIRIELRSPT   850
 851  TVTFSFDVGNGPFELSVHSPTHFNDNQWHHVRVERNMKEASLRVDELPPK   900
 901  IQAAPTDGHVLLQLNSQLFVGGTATRQRGFLGCIRSLQLNGMALDLEERA   950
 951  TVTPGVQPGCRGHCGSYGKLCRHGGKCREKPSGFFCDCSSSAYAGPFCSK  1000
1001  EISAYFGSGSSVIYNFQENYSLSKNSSFHAASFHGDMKLSREMIKFSFRT  1050
1051  TRAPSLLLHMSSFYKEYLSIIIAKNGSLQIRYKLNKYHEPDVISFDLKSM  1100
1101  ADGQLHHIKINREEGMVFVEIDENTRRQTYLSSGTEFSAVKSLVLGRMLE  1150
1151  YSDVDQETALAAAHGFTGCLSAVQFSHIAPLKAALQPGPPAPVTVTGHVT  1200
1201  ESSCVAPSGTDATSRERTHSFADHSGTMDDREPLTHAIKSDSAVIGGLIA  1250
1251  VVIFILLCVSAIAVRIYQQKRLYKRNEAKRSENVDSAEAVLKSELHIQNA  1300
1301  VGENQKEYFF                                          1310

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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