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

NucPred

Fetching Q8NEZ3 from www.uniprot.org...

The NucPred score for your sequence is 0.17 (see score help below)

   1  MKRIFSLLEKTWLGAPIQFAWQKTSGNYLAVTGADYIVKIFDRHGQKRSE    50
  51  INLPGNCVAMDWDKDGDVLAVIAEKSSCIYLWDANTNKTSQLDNGMRDQM   100
 101  SFLLWSKVGSFLAVGTVKGNLLIYNHQTSRKIPVLGKHTKRITCGCWNAE   150
 151  NLLALGGEDKMITVSNQEGDTIRQTQVRSEPSNMQFFLMKMDDRTSAAES   200
 201  MISVVLGKKTLFFLNLNEPDNPADLEFQQDFGNIVCYNWYGDGRIMIGFS   250
 251  CGHFVVISTHTGELGQEIFQARNHKDNLTSIAVSQTLNKVATCGDNCIKI   300
 301  QDLVDLKDMYVILNLDEENKGLGTLSWTDDGQLLALSTQRGSLHVFLTKL   350
 351  PILGDACSTRIAYLTSLLEVTVANPVEGELPITVSVDVEPNFVAVGLYHL   400
 401  AVGMNNRAWFYVLGENAVKKLKDMEYLGTVASICLHSDYAAALFEGKVQL   450
 451  HLIESEILDAQEERETRLFPAVDDKCRILCHALTSDFLIYGTDTGVVQYF   500
 501  YIEDWQFVNDYRHPVSVKKIFPDPNGTRLVFIDEKSDGFVYCPVNDATYE   550
 551  IPDFSPTIKGVLWENWPMDKGVFIAYDDDKVYTYVFHKDTIQGAKVILAG   600
 601  STKVPFAHKPLLLYNGELTCQTQSGKVNNIYLSTHGFLSNLKDTGPDELR   650
 651  PMLAQNLMLKRFSDAWEMCRILNDEAAWNELARACLHHMEVEFAIRVYRR   700
 701  IGNVGIVMSLEQIKGIEDYNLLAGHLAMFTNDYNLAQDLYLASSCPIAAL   750
 751  EMRRDLQHWDSALQLAKHLAPDQIPFISKEYAIQLEFAGDYVNALAHYEK   800
 801  GITGDNKEHDEACLAGVAQMSIRMGDIRRGVNQALKHPSRVLKRDCGAIL   850
 851  ENMKQFSEAAQLYEKGLYYDKAASVYIRSKNWAKVGDLLPHVSSPKIHLQ   900
 901  YAKAKEADGRYKEAVVAYENAKQWQSVIRIYLDHLNNPEKAVNIVRETQS   950
 951  LDGAKMVARFFLQLGDYGSAIQFLVMSKCNNEAFTLAQQHNKMEIYADII  1000
1001  GSEDTTNEDYQSIALYFEGEKRYLQAGKFFLLCGQYSRALKHFLKCPSSE  1050
1051  DNVAIEMAIETVGQAKDELLTNQLIDHLLGENDGMPKDAKYLFRLYMALK  1100
1101  QYREAAQTAIIIAREEQSAGNYRNAHDVLFSMYAELKSQKIKIPSEMATN  1150
1151  LMILHSYILVKIHVKNGDHMKGARMLIRVANNISKFPSHIVPILTSTVIE  1200
1201  CHRAGLKNSAFSFAAMLMRPEYRSKIDAKYKKKIEGMVRRPDISEIEEAT  1250
1251  TPCPFCKFLLPECELLCPGCKNSIPYCIATGRHMLKDDWTVCPHCDFPAL  1300
1301  YSELKIMLNTESTCPMCSERLNAAQLKKISDCTQYLRTEEEL          1342

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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