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

NucPred

Fetching Q9U6A1 from www.uniprot.org...

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

   1  MSSAAAAAAGAAGGALYTNNNITNNNNNNSNNNNSNITSSSNLSPTAATI    50
  51  ATTAAATTATALSGSISPGSRESASSLLSAAFGNLFGGSSGENVKRAVRA   100
 101  TNEAGPGCHQWAAQSLDNAMLAAAMETATSADLLNAAGLVSSLNTSKLLN   150
 151  NVNNNNNNNTPLSNGNNNNNNNASISPGSAHSSTTKGGSSRRVSNCSDRS   200
 201  LDGNLAAAATTAATDAAGGSPPRAASVSSLNGGASTQTKQQQLQHDLMAH   250
 251  HMLRNILQGKKELMQLDQELRTAMQQQQQQQQQQQNHEKHQQELHSKLNN   300
 301  NTTTNNNNNVVSESINLIEDSEMPEIKIKSEPELMASATQAPHSPHGGSS   350
 351  NSSSSHSHNSSNNSIASNGSLRRKSSDSLDSMQREERATPATTVEPQLQN   400
 401  EVLPTKKEAVDDMLDEVELLGLSGHGHSRNSDLESLASPSHSDMLLLDNS   450
 451  KDEVLDNDDIIEDDEDDDDDDDDCIETKRESNTSGSNCLKKPGMELKRAR   500
 501  VEHIVSSMRCSPSATAQAGQLQVNGCKKRKLYQPQQHAMERYVAAAAGLN   550
 551  FGLNLQSMMLDQEDSESNELESPQIQQKRVEKNALKSQLRSMQEQLAEMQ   600
 601  QKYVQLCSRMEQESECQELDNEHEQDMDSMEQEQEQELEQEQEQEPEPLQ   650
 651  QHNDDIELSHSPTLSKSTPKESSERAGSSSPYIEATEQQQLLRAAATMLL   700
 701  PPRPICSLQMMSKMMSSKLQHQHNPLVGVAHPALPQGFPPLLQHMGDMSH   750
 751  AAAMYQQFFFEQEARMAKEAAEQQQQQQQQQQQQQQQQQQQQQQQEQQRR   800
 801  YEQEQEQQRRMEEQQQQLHRQQQHLQQLQQQQQQMEHHVAAAVPRVQLHP   850
 851  PARLPTRMGGAAAAAAAAAHSVLKSELSEKFQMLRQHNSSSNSNNSSSNN   900
 901  NNSNNNSSMMRMSGTDLEGLADVLKSEITTSLSALVDTIVTRFVHQRRLF   950
 951  SKQADSVTAAAEQLNKDLMLASQILDRKSPRTKVVADRGLSGNSGHPGAQ  1000
1001  NGPTPATQSAAAMFQAPKTPQGMNPVAAAALYNSMASPFCLPPDQQQQQQ  1050
1051  QQQQAAQQQQQQAVQQQHQSAQQTQQQLEQNEALSLVVTPKKKRHKVTDT  1100
1101  RITPRTVSRILASGWRCAAQWTGSCRSSCCRTTTTTTTTAAAAAATTTAA  1150
1151  ATEQQWQQQQQQQCNAGTEPNGSRPGRRHILSTATTTTTHDAGVFAHLSG  1200
1201  HTKSIAARIQSLFAVQSILQSACGAGPHGPPHGGQPTAAQLHHQHHHQMQ  1250
1251  LSSSPPGSLGALMDSRDSPPLPHPPTMLHPALLAAAHHGGSPDYKTCLRA  1300
1301  VMDAQDRQSECNSADMTFDGMQPTISFLKQQQQQQSQLSGAHSVPMVNLW  1350
1351  SLAPTHTLGTNVETSWVETALTIITIYHTIYDIYTFSNHCESLTPLHSST  1400
1401  LTPMHLRKAKLMFFWVRYPSSAVLKMYFPDIKFNKNNTAQLVKWFSNFRE  1450
1451  FYYIQMEKYARQAVTEGIKTPDDLLIAGDSELYRVLNLHYNRNNHIEVPQ  1500
1501  NFRFVVEQTLREFFRAIQGGKDTEQSWKKSIYKIISRMDDPVPEYFKSPN  1550
1551  FLEQLE                                              1556

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.