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

NucPred

Fetching Q9JIL5 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MYAAVEHGPVLCSDSNILCLSWKGRVPKSEKEKPVCRRRYYEEGWLATGN    50
  51  GRGVVGVTFTSSHCRRDRSTPQRINFNLRGHNSEVVLVRWNEPYQKLATC   100
 101  DADGGIFVWIQYEGRWSVELVNDRGAQVSDFTWSHDGTQALISYRDGFVL   150
 151  VGSVSGQRHWSSEINLESQITCGIWTPDDQQVLFGTADGQVIVMDCHGRM   200
 201  LAHVLLHESDGILSMSWNYPIFLVEDSSESDTDSDDYSPPQDGPAAYPIP   250
 251  VQNTKPLLTVSFTSGDISLMNNYDDLSPTVIRSGLKEVVAQWCTQGDLLA   300
 301  VAGMEQQAQLSELPNGPLLKSAMVKFYNVRGEHIFTLDTLVQRPIISICW   350
 351  GHRDSRLLMASGPALYVVRVEHRVSSLQLLCQQAIASTLREDKDVNKLTL   400
 401  PPRLCSYLSTAFIPTIKPPIPDPNNMRDFVSYPSAGNERLHCTMKRTEDD   450
 451  PEVGGPCYTLYLEYLGGLVPILKGRRISKLRPEFVIMDPRTDSKSDEIYG   500
 501  NSLISTVIDSCNCSDSSDIELSDDWAAKKSPKISRSSKSPKLPRISIEAR   550
 551  KSPKLPRAAQEISRSPRLPMRKPSMGSPSLTRREFPFEDITQHNYLAQVT   600
 601  SNIWGTKFKIVGLAAFLPTNLGAVIYKTSLLHLQPRQMTIYLPEVRKISM   650
 651  DYINLPVFNPNVFSEDEDDLPVTGASGVPENNPPCTVNIPIAPIHSSAQA   700
 701  LSPTQSIGLVQSLLANQNVQLDVLTNQTTAVGSAEHAGDAATQYPVSSRY   750
 751  SNPGQVIFGGVEMGRIIQNPPQLPLPPPPPPPPQAPMQLSAVDHGDRDHE   800
 801  HLQKSAKALRPVPQLAAEGDAVVFSAPQEVQVAKMNPPPPYPGTIPAAPT   850
 851  TAAPPPPLPPPQPPVDVCLKKGDFSLYPTAAHYQPPLGYERITTFDSSGN   900
 901  VEEVCRPRTRMLCSQNTYTLPGPGSSATLRLTATEKKVPQPCTSATLNRL   950
 951  TVPRYSIPTGDPPPYPEIASQLAQGRSAAQRLDNSLIHATLRRNNREVAL  1000
1001  KMAQLADSSRAPLQPLAKPKGGAAGAVAQLPARPPPALYTCSQCSGAGPS  1050
1051  SQSGAALAHAISTSPLASQSSYNLLSPPDTSRDRTDYVNSAFTEDEALSQ  1100
1101  HCQLEKPLRHPPLPEAAVTMKRPPPYQWDPMLGEDVWVPQERTAQPTVPN  1150
1151  PLKLSPLMLGQGQHLDVARVPFVPPKSPSSPTATFPTGYGMGMPYPGSYN  1200
1201  NPSLPGVQAPCSPKDALSQAQFAQQESAVVLQPAYPPSLSYCTLPPTYPG  1250
1251  SSTCSSVQLPPIALHPWNSYSTCPPMQNTQGTLPPKPHLVVEKPLVSPPP  1300
1301  AELQSHMGTEVMVETADNFQEVLSLTESPVPQRTEKFGKKNRKRLDSRAE  1350
1351  EGSVQAITEGKVKKDARTLSDFNSLISSPRLGREKKKVKSQKDQLKSKKL  1400
1401  NKTNEFQDSSESEPELFISGDELMNQSQGSKKGWKSKRSLRTASELEEFK  1450
1451  CRKASEKEDGRLGSQGFVYVMANKQPLWNEATQVYQLDFGGRVTQESAKN  1500
1501  FQIELEGRQVMQFGRIDGNAYILDFQYPFSAVQAFAVALANVTQRLK     1547

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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