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

NucPred

Fetching Q5H8C1 from www.uniprot.org...

The NucPred score for your sequence is 0.32 (see score help below)

   1  MNSLSWGAANAVLLLLLLAWASPTFISINRGVRVMKGHSAFLSGDDLKFA    50
  51  IPKEKDACKVEVVMNEPITQRVGKLTPQVFDCHFLPNEVKYVHNGCPILD   100
 101  EDTVKLRLYRFTERDTFIETFILWVYLLEPDCNIIHMSNNVLEVPEFNGL   150
 151  SQAIDKNLLRFDYDRMASLECTVSLDTARTRLPAHGQMVLGEPRPEEPRG   200
 201  DQPHSFFPESQLRAKLKCPGGSCTPGLKKIGSLKVSCEEFLLMGLRYQHL   250
 251  DPPSPNIDYISIQLDLTDTRSKIVYKSESAWLPVYIRAGIPNQIPKAAFM   300
 301  AVFILEVDQFILTSLTTSVLDCEEDETPKPLLVFNITKAPLQGYVTHLLD   350
 351  HTRPISSFTWKDLSDMQIAYQPPNSSHSERRHDEVELEVYDFFFERSAPM   400
 401  TVHISIRTADTNAPRVSWNTGLSLLEGQSRAITWEQFQVVDNDDIGAVRL   450
 451  VTVGGLQHGWLTLRGGKGFLFTVADLQAGVVRYHHDDSDSTKDFVVFRIF   500
 501  DGHHSIRHKFPINVLPKDDSPPFLITNVVIELEEGQTILIQGSMLRASDV   550
 551  DASDDYIFFNITKPPQAGEIMKKPGPGLIGYPVHGFLQRDLFNGIIYYRH   600
 601  FGGEIFEDSFQFVLWDSHEPPNLSVPQVATIHITPVDDQLPKEAPGVSRH   650
 651  LVVKETEVAYITKKQLHFIDSESYDRELVYTITTPPFFSFSHRHLDAGKL   700
 701  FMVDSIPKVVKNPTALELRSFTQHAVNYMKVAYMPPMQDIGPHCRDVQFT   750
 751  FSVSNQHGGTLHGICFNITILPVDNQVPEAFTNPLKVTEGGQSIISTEHI   800
 801  LISDADTKLDNIDLSLRELPLHGRVELNGFPLNSGGTFSWGDLHTLKVRY   850
 851  QHDGTEVLQDDLLLEVTDGTNSAEFVLHVEVFPVNDEPPVLKADLMPVMN   900
 901  CSEGGEVVITSEYIFATDVDSDNLKLMFVIAREPQHGVVRRAGVTVDQFS   950
 951  QRDVISEAVTYKHTGGEIGLMPCFDTITLVVSDGEAGPFVNGCCYNGPNP  1000
1001  SVPLHASFPVYDLNITVYPVDNQPPSIAIGPVFVVDEGCSTALTVNHLSA  1050
1051  TDPDTAADDLEFVLVSPPQFGYLENILPSVGFEKSNIGISIDSFQWKDMN  1100
1101  AFHINYVQSRHLRIEPTADQFTVYVTDGKHHSLEIPFSIIINPTNDEAPD  1150
1151  FVVQNITVCEGQMKELDSSIISAVDLDIPQDALLFSITQKPRHGLLIDRG  1200
1201  FSKDFSENKQPANPHQKHAPVHSFSMELLKTGMRLTYMHDDSESLADDFT  1250
1251  IQLSDGKHKILKTISVEVIPVNDEKPMLSKKAEIAMNMGETRIISSAILS  1300
1301  AIDEDSPREKIYYVFERLPQNGQLQLKIGRDWVPLSPGMKCTQEEVDLNL  1350
1351  LRYTHTGAMDSQNQDSFTFYLWDGNNRSPALDCQITIKDMEKGDIVILTK  1400
1401  PLVVSKGDRGFLTTTTLLAVDGTDKPEELLYVITSPPRYGQIEYVHYPGV  1450
1451  PITNFSQMDVVGQTVCYVHKSKVTVSSDRFRFIISNGLRTEHGVFEITLE  1500
1501  TVDRALPVVTRNKGLRLAQGAVGLLSPDLLQLTDPDTPAENLTFLLVQLP  1550
1551  QHGQLYLWGTGLLQHNFTQQDVDSKNVAYRHSGGDSQTDCFTFMATDGTN  1600
1601  QGFIVNGRVWEEPVLFTIQVDQLDKTAPRITLLHSPSQVGLLKNGCYGIY  1650
1651  ITSRVLKASDPDTEDDQIIFKILQGPKHGHLENTTTGEFIHEKFSQKDLN  1700
1701  SKTILYIINPSLEVNSDTVEFQIMDPTGNSATPQILELKWSHIEWSQTEY  1750
1751  EVCENVGLLPLEIIRRGYSMDSAFVGIKVNQVSAAVGKDFTVIPSKLIQF  1800
1801  DPGMSTKMWNIAITYDGLEEDDEVFEVILNSPVNAVLGTKTKAAVKILDS  1850
1851  KGGQCHPSYSSNQSKHSTWEKGIWHLLPPGSSSSTTSGSFHLERRPLPSS  1900
1901  MQLAVIRGDTLRGFDSTDLSQRKLRTRGNGKTVRPSSVYRNGTDIIYNYH  1950
1951  GIVSLKLEDDSFPTHKRKAKVSIISQPQKTIKVAELPQADKVESTTDSHF  2000
2001  PRQDQLPSFPKNCTLELKGLFHFEEGIQKLYQCNGIAWKAWSPQTKDVED  2050
2051  KSCPAGWHQHSGYCHILITEQKGTWNAAAQACREQYLGNLVTVFSRQHMR  2100
2101  WLWDIGGRKSFWIGLNDQVHAGHWEWIGGEPVAFTNGRRGPSQRSKLGKS  2150
2151  CVLVQRQGKWQTKDCRRAKPHNYVCSRKL                       2179

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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