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

NucPred

Fetching Q9DB00 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MLPCKKRRLSVTESSQQQDDQEGDDLDLEAAVKPDTDQLPDSASESLSWG    50
  51  QSQDSAVCPEGLSMQDGDDQLRAEGLSLNSKMLAQHVNLAVLEAVDVAVS   100
 101  QEIPLPSLESSHSLPVHVDKGRLQVSASKKGKRVVFTPGQVTREDRGDHP   150
 151  VPEEPPSGEPAEEAKTEGGELELRSDGEVPLLSSSSQSAKPGAQPRKSVQ   200
 201  PDGSAFPQDKPLGPLVRQAEEEMEDGGLFIPTEEQDSEESDKKKKTKKGT   250
 251  KRKRDGKGPEQGTMVYDPKLDDMLDRTLEDGAKQHNLTAVNVRNILHEVI   300
 301  TNEHVVAMMKAAISETEDMPLFEPKMTRSKLKEVVEKGVVIPTWNISPIK   350
 351  KASEIKQPPQFVDIHLEEDDSSDEEYSPDEEEEDETAEESLLESDVESTA   400
 401  SSPRGVKRSRLRLSSEVAETDEESGMLSEVEKAATPALRHISAEVVPMGP   450
 451  PPPPKPKQSRDSVFMEKLDAVDEELASSPVCMDSFQPMEDSLIAFRTRSK   500
 501  MPLKDVPLGQLEAELQAPDITPDMYDPNTADDEDWKQWLGGLINDDVENE   550
 551  DEADDDDDPEYNFLEDLDEPDTEDFRTDRAVRITKKEVNGLMEELFETVQ   600
 601  SVVPSKFQDEMGFSNMEDDGPEEEERATESRPSFNTPQALRFEEPLANLL   650
 651  NERHRTVKELLEQLKMKKPSVRQQPEVEKLKPQEEAAHQTLVLDPAQRSR   700
 701  LQQQMQQHVQLLTQIYLLTTSNPNLSSEASTTRIFLKELGTFAENSIALH   750
 751  QQFNPRFQTLFQPCNWMGAMRLIEDFTQVSIDCSPHKTAKKTASEFPCLP   800
 801  KQVAWILATNKVFMYPELLPICSLKANNPRDKTIFTKAEDNLLALGLKHF   850
 851  EGTEFPKPLISKYLVTCKTAHQLTVRIKNLNLNRAPNNVIKFYKKTKQLP   900
 901  VLVRCCEEIQPHQWKPPFEKEEHRLPFWLKASLQSIQDELRNISEGATEG   950
 951  GSVTTATESSTDQHLQKASPALGDEPQYPLLLPKGVVLKLKPGSKRFSRK  1000
1001  AWRQKRPLVQKPLLIQPSPSVQPVFNPGKMATWPTQSEVPPSNTVVQIPH  1050
1051  LIQPAAVLQTLPGFPSVGVRGEDGFESPTALPAMPCGSEARTTFPLSETQ  1100
1101  SAPPSCSAPKLMLPSLAPSKFRKPYVRRKPTRRKGAKVSPCVKPAPIIHP  1150
1151  TPVIFTVPATTVKVVSIGGGCNMIQPVSAAVAPSPQTIPITTLLVNPTTF  1200
1201  PCSLNQPLVASSISPLIVSSNPLTLPVTSIPEDKAQVKLDVAEGKNAPQN  1250
1251  PESKLKPQELTPLCTTVFSKEEPKSWHSSADTGSQEAFSESSACSWAVVK  1300
1301  TESQEGSSEKSACGWTVVKTEDGGHAVEPLPQNLQDSLSSSSKDLLNMVK  1350
1351  MEAQDCMVEISSNFPKQDIGEEVKEECSMELDSESPQEKPSSASEMSKQT  1400
1401  VLQREDMQAAKSPSVPQDAAAEGRTSSHASRGLPKSTLSSMGQGGGLSGP  1450
1451  PGKLEDSANADGQSVGTPAGPDTGGEKDGPEEEEEEDFDDLTQDEEDELS  1500
1501  SASEESVLSVPELQETMEKLTWLASERRMSQEGESEEENSQEENSEPEEE  1550
1551  EEEEAEGMETLQKEDEVNDEAVGDAAKKPPSTLASPQTAPEIETSIAPAG  1600
1601  ESIKAAGKGRSSHRARNKRGSRARASKDTSKLLLLYDEDILDRDPLREQK  1650
1651  DLAFAQAYLTRVREALQHTPGKYEDFLQIIYEFESSTQMHSAVDLFKSLQ  1700
1701  TLLQDWPQLLKDFAAFLLPEQALSCGLFEEQQAFEKSRKFLRQLEICFAE  1750
1751  NPSHHQKIIKVLQGCADCLPQDIAELKTQMWQLLRGHDHLQDEFSIFFDH  1800
1801  LRPAASRMGDFEEINWTEEKEYEFDGFEEVILPDVEEDEEPAKVSTASKS  1850
1851  KRRKEIGVQHQDKDTEWPEAAKDCSCSCHEGGPESKLKKSKRRNCHCSSK  1900
1901  VCDSKPYKSKEPPELVGSGPLHEASTVPGSKEAGQGKDMLEEEILEEQEN  1950
1951  MEVTQSKTARTTRKGEAPAPGSTIGSTLLCPAEVTPMELLLEGPALCSAE  2000
2001  TPRLPPQTGAVVCSVRRNQAGPEVVSCLSTSSLPPEEGEDQRAAANSETI  2050
2051  APHREASETERLPETVEHSAPLPSPVSTRTRDTGRRHICGKAGSQSWLIE  2100
2101  SRAEAEAAHVAAPICEKSSGARASEAAPKTAREVLAEDSGTQGMGPEGAL  2150
2151  PKASEATVCANNSKVSSTGEKVVLWTREADRVILTMCQEQGAQPHTFSVI  2200
2201  SQQLGNKTPVEVSHRFRELMQLFHTACEASSEDEDDATSTSNADQLSDHG  2250
2251  DLLSEEELDE                                          2260

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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