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

NucPred

Fetching Q9NQ11 from www.uniprot.org...

The NucPred score for your sequence is 0.35 (see score help below)

   1  MSADSSPLVGSTPTGYGTLTIGTSIDPLSSSVSSVRLSGYCGSPWRVIGY    50
  51  HVVVWMMAGIPLLLFRWKPLWGVRLRLRPCNLAHAETLVIEIRDKEDSSW   100
 101  QLFTVQVQTEAIGEGSLEPSPQSQAEDGRSQAAVGAVPEGAWKDTAQLHK   150
 151  SEEAVSVGQKRVLRYYLFQGQRYIWIETQQAFYQVSLLDHGRSCDDVHRS   200
 201  RHGLSLQDQMVRKAIYGPNVISIPVKSYPQLLVDEALNPYYGFQAFSIAL   250
 251  WLADHYYWYALCIFLISSISICLSLYKTRKQSQTLRDMVKLSMRVCVCRP   300
 301  GGEEEWVDSSELVPGDCLVLPQEGGLMPCDAALVAGECMVNESSLTGESI   350
 351  PVLKTALPEGLGPYCAETHRRHTLFCGTLILQARAYVGPHVLAVVTRTGF   400
 401  CTAKGGLVSSILHPRPINFKFYKHSMKFVAALSVLALLGTIYSIFILYRN   450
 451  RVPLNEIVIRALDLVTVVVPPALPAAMTVCTLYAQSRLRRQGIFCIHPLR   500
 501  INLGGKLQLVCFDKTGTLTEDGLDVMGVVPLKGQAFLPLVPEPRRLPVGP   550
 551  LLRALATCHALSRLQDTPVGDPMDLKMVESTGWVLEEEPAADSAFGTQVL   600
 601  AVMRPPLWEPQLQAMEEPPVPVSVLHRFPFSSALQRMSVVVAWPGATQPE   650
 651  AYVKGSPELVAGLCNPETVPTDFAQMLQSYTAAGYRVVALASKPLPTVPS   700
 701  LEAAQQLTRDTVEGDLSLLGLLVMRNLLKPQTTPVIQALRRTRIRAVMVT   750
 751  GDNLQTAVTVARGCGMVAPQEHLIIVHATHPERGQPASLEFLPMESPTAV   800
 801  NGVKDPDQAASYTVEPDPRSRHLALSGPTFGIIVKHFPKLLPKVLVQGTV   850
 851  FARMAPEQKTELVCELQKLQYCVGMCGDGANDCGALKAADVGISLSQAEA   900
 901  SVVSPFTSSMASIECVPMVIREGRCSLDTSFSVFKYMALYSLTQFISVLI   950
 951  LYTINTNLGDLQFLAIDLVITTTVAVLMSRTGPALVLGRVRPPGALLSVP  1000
1001  VLSSLLLQMVLVTGVQLGGYFLTLAQPWFVPLNRTVAAPDNLPNYENTVV  1050
1051  FSLSSFQYLILAAAVSKGAPFRRPLYTNVPFLVALALLSSVLVGLVLVPG  1100
1101  LLQGPLALRNITDTGFKLLLLGLVTLNFVGAFMLESVLDQCLPACLRRLR  1150
1151  PKRASKKRFKQLERELAEQPWPPLPAGPLR                      1180

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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