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

NucPred

Fetching Q9NXL9 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MNSDQVTLVGQVFESYVSEYHKNDILLILKERDEDAHYPVVVNAMTLFET    50
  51  NMEIGEYFNMFPSEVLTIFDSALRRSALTILQSLSQPEAVSMKQNLHARI   100
 101  SGLPVCPELVREHIPKTKDVGHFLSVTGTVIRTSLVKVLEFERDYMCNKC   150
 151  KHVFVIKADFEQYYTFCRPSSCPSLESCDSSKFTCLSGLSSSPTRCRDYQ   200
 201  EIKIQEQVQRLSVGSIPRSMKVILEDDLVDSCKSGDDLTIYGIVMQRWKP   250
 251  FQQDVRCEVEIVLKANYIQVNNEQSSGIIMDEEVQKEFEDFWEYYKSDPF   300
 301  AGRNVILASLCPQVFGMYLVKLAVAMVLAGGIQRTDATGTRVRGESHLLL   350
 351  VGDPGTGKSQFLKYAAKITPRSVLTTGIGSTSAGLTVTAVKDSGEWNLEA   400
 401  GALVLADAGLCCIDEFNSLKEHDRTSIHEAMEQQTISVAKAGLVCKLNTR   450
 451  TTILAATNPKGQYDPQESVSVNIALGSPLLSRFDLILVLLDTKNEDWDRI   500
 501  ISSFILENKGYPSKSEKLWSMEKMKTYFCLIRNLQPTLSDVGNQVLLRYY   550
 551  QMQRQSDCRNAARTTIRLLESLIRLAEAHARLMFRDTVTLEDAITVVSVM   600
 601  ESSMQGGALLGGVNALHTSFPENPGEQYQRQCELILEKLELQSLLSEELR   650
 651  RLERLQNQSVHQSQPRVLEVETTPGSLRNGPGEESNFRTSSQQEINYSTH   700
 701  IFSPGGSPEGSPVLDPPPHLEPNRSTSRKHSAQHKNNRDDSLDWFDFMAT   750
 751  HQSEPKNTVVVSPHPKTSGENMASKISNSTSQGKEKSEPGQRSKVDIGLL   800
 801  PSPGETGVPWRADNVESNKKKRLALDSEAAVSADKPDSVLTHHVPRNLQK   850
 851  LCKERAQKLCRNSTRVPAQCTVPSHPQSTPVHSPDRMLDSPKRKRPKSLA   900
 901  QVEEPAIENVKPPGSPVAKLAKFTFKQKSKLIHSFEDHSHVSPGATKIAV   950
 951  HSPKISQRRTRRDAALPVKRPGKLTSTPGNQISSQPQGETKEVSQQPPEK  1000
1001  HGPREKVMCAPEKRIIQPELELGNETGCAHLTCEGDKKEEVSGSNKSGKV  1050
1051  HACTLARLANFCFTPPSESKSKSPPPERKNRGERGPSSPPTTTAPMRVSK  1100
1101  RKSFQLRGSTEKLIVSKESLFTLPELGDEAFDCDWDEEMRKKS         1143

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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