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

NucPred

Fetching O94477 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MTSGIYYKGLQCWIPDEQSQWIPGSIKDCRVEGEKAFLTVQDENENETVI    50
  51  TVKPDDLNYEGRNGLPFLRSINSDADDLTDLSYLNEPSVLDALSTRYNQL   100
 101  QIYTYSGIVLIAVNPFQRLPNLYTHEIVRAYSEKSRDELDPHLYAIAEDS   150
 151  YKCMNQEHKNQTIIISGESGAGKTVSARYIMRYFASVQALIQSTDSNFHE   200
 201  APQLTAVENEILATNPIMEAFGNSKTSRNDNSSRFGKYIQILFDGNATII   250
 251  GAKIQTYLLERSRLVFQPNQERNYHIFYQILAGSSSEQLEKWKLVENSQE   300
 301  FNYLKQGNCSTIEGVNDKEEFKATVDALKTVGIDNDTCECIFSLLAALLH   350
 351  IGNIEVKHSRNDAYIDSKNENLINATSLLGVDPSSLVKWLTKRKIKMASE   400
 401  GILKPLNEFQAVVARDSVAKFLYASLFDWLVATINKALMYSADKSNQTAK   450
 451  SFIGVLDIYGFEHFKKNSFEQFCINYANEKLQQEFYRHVFKLEQEEYAAE   500
 501  GLNWSYIDYQDNQQCISMIESRLGILSLLDEECRMPTNSDENWVSKLNDA   550
 551  FSKPEFKNSYQKSRFGNKEFTIKHYALDVVYCAEGFIDKNRDTISDELLE   600
 601  LFTNSDVPFVKDLVLFRLEQTAPPADTKKIKTKPKSNTLGSMFKSSLVSL   650
 651  MSTINETNAHYIRCIKPNEEKEAWKFDNQMVVSQLRACGVLETIKISCAG   700
 701  FPSRWTFDEFVSRYYMLVPSAVRTTESLTFSKAILEKHADPTKYQIGKTK   750
 751  IFFRSGVTPLLESARDKALKHAAHLLYEAFAVNYYRTRFLLSRKRVRSFQ   800
 801  AVAHGFLSRRHTEYELLSSNIIKLQSLWRTALKRKEFIQTKNSILKVQSI   850
 851  IRGFLLRQTLEEKTKHDATLIIQSLWLTFKAHKHYKELQYYAVRIQSLWR   900
 901  MKLAKRQLTELKIESTKASHLKQVSYRLESRLFEISKQLDNSEQENNKFR   950
 951  ERIAELESHLSNYAEAKLAQERELEQTRVLISDQSQDGELKELLEEKENA  1000
1001  LIMMEEEMRQVNDANTELLRVNATLKSQLKNYDMIIVEQTSQLKEKNRII  1050
1051  ASLTKATKILNSASSIEQSRNSEEKSRRDSSLMEMRTQKEMLVLLMNDGL  1100
1101  KHDLDKLTEYAGRTFTTLKTLLLKDNDVEAQKLDHLFLAKLLFIIISQMW  1150
1151  KSNLCQESVALVERYCVHTLEYVFQKTSSANERPDIGFWVANTHALLAFV  1200
1201  YTKQQAFKHSSAFTLLSTESHESVQTIFEMIESHLSKIFFEWVRQVNNFL  1250
1251  KPLIVQAMIITGTNTDAGDENRKLRIKFFEKPKYKITDVIHVLNKVHDSC  1300
1301  QAYKVNYEIYNALIRSIYRFINVEAFNSLFIDERGSWKRGTNISYNYHVL  1350
1351  KDWCLESGVPEAYLQLEELLQTSKILQFVKDDPNYVARVRDFYALNFLQI  1400
1401  KTLLHRYDYADYEAHVPKKTMSELSKNIVAEGINQREQLTYEVLDYRLQD  1450
1451  SFEESPSLEKIKIPDDCNVTYLRRIIDLASAEESVEQALITVGNVADNDV  1500
1501  QNSSDEENQVPNGIKV                                    1516

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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