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

NucPred

Fetching Q85FG7 from www.uniprot.org...

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

   1  MNTKILLSLPWPKLMDPYMLLGFYYGLLTTLPVGPSQILCVRSFLLGGNL    50
  51  SGLISISGSVLAQLITASSIYCSPIYLLLLRPHLLTIVAIPYTLLFCLVI   100
 101  KDFPNYQILRPVTSLRDSRVARLFLISFFFQILNPIMLPNSVLTRLIYLY   150
 151  FFRYSTNTVFMVSTFMGWLTGQAAFNFFSRLLLSRVKGDSPILYLVAKRF   200
 201  IYATFSIVSISYAVAYLGRAPVSFWTKKFMNESHDREMNLWEIAEYSDLL   250
 251  WWFFKPWPTSFFDPSRANRSNRFVKNRRFHMNNTFYKGRTSTYFFEKCLT   300
 301  DGKERLSFLALPSLSIFGKEMYQSMAKSRRSFGIRLSYQNWVSKKLAKTK   350
 351  FFEKELTDQIKLLDTGSSFSKTMSRKTRLMGGKRRRIPRTYDPFVNNFRI   400
 401  RIPVSQTFLLEDDLGLSLWEWDKLATERKNRKAKKTVRINAIKDKIFTKD   450
 451  RRWKHGYGNPLPWEPLPSRSKRMFYFIFENRALYDYDLQNILKKIKSSPT   500
 501  LDVTWKEIMDLDYEDHILFLTYLEVGCCHRFGWISPLKAFLRKSSKSLSN   550
 551  VERRIRRLNKIGNLSMDLARYTILYFENNFDIPGGDGDFRYRKLRNVGIT   600
 601  FAKGKPRSERLMKRYAKVSDFRRKFLKGSMRSRRRKTLLWKALQEKIRSS   650
 651  FFLRSAERTILFQSLIERLTTSSREEKFSELEKDTDYEFQKQLLDISLSA   700
 701  KRSLIGESKLTRSAIAARSDIGPIHNGRGYMLVFQSRFRKFIKLPVLIVL   750
 751  KNIGRILLRQNSEWNKDWTGWKKEIHINCTFDGEDFSQDELPPRWLREGI   800
 801  QIKIVYPFQLKPWHTDGNEKQHTLQRKHKEIGSKSRELKSKRKLKQKKHK   850
 851  FTYLTVLGYQTDIPFGTIQKKTSFWKPVRRKLIRICKRSLPRQIKQAYQF   900
 901  IHSRFEKVSKLNSTPSKKLNLISNLRQGGKLLSDYSLDEKSWMKTSSTNY   950
 951  VNEKTKPNCNVISNSERFIAIGGEMSPANVTRKQLVTRDQVEREFLMSIV  1000
1001  AVDSKNLLDEKIDDPYSKITSKDLETGDTTSGDINLVNSTKFERKQLVDS  1050
1051  EEAGLSLYLLVRELIETFVSVLINLPFTINRIFVHYFTEFLALYTKLAGI  1100
1101  LDNINEGSNLSTRSKSLQFDLPSQTCIYIDMWNIGMRGSLNLDLLVNDKR  1150
1151  SSSNCGVKNRQSGIYVETDGVSNLYQPKMYEKQTPVHYNLIATKFLSPEI  1200
1201  RNNHVNDLTMCFDTETGKTDEEFFDEKVARSIENWGFLNKSCKLDEINWN  1250
1251  EWLYSLSRYNLPLTAWRNIAPRKWKVCLSELSSIETNTITELKDQVSQNK  1300
1301  LHSYYSIYTKKSFLRNKISNFSKLRKHRNLLQNLTDSVQNGDVENLSVQR  1350
1351  DIMEQRFHCKSCIQKSSRGGRNRISKFVHFLSSNVESKNNLNLQIDLLSW  1400
1401  LDPDIAKTKIFLKKKKKAKQLKNPLLRNHYRYRYVLDISGRFQKVLNQLN  1450
1451  DLTLDEREDADYIFRWKFKFETELEKFRNLISLTRMLGDDQDLITLCTNI  1500
1501  EVNSDLLNLQFNAKTKRDMFHNLSVVSAHRLRLVFDDQDLLYKIINPLLK  1550
1551  FKGRLRGIFRRRLYRNVYNGSYISNLSHILTERNCKQSCLYNIDDLLSPR  1600
1601  RRREFRFLYCLLSPKIEYSQYISRIKKIDNAEKKQTLYHLPRPIRIQKIK  1650
1651  RFLWPSHRLEEAACTGRSCVGVMTGSRFVTLRIRMYPIPLN           1691

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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