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

NucPred

Fetching Q3UGF1 from www.uniprot.org...

The NucPred score for your sequence is 0.35 (see score help below)

   1  MKRVFSLLEKSWLGAPIQFAWQKSSGNYLAVTGADYIVKIFDRHGQKRSE    50
  51  ISLPGNCVTMDWDKDGDILAVIAEKSSCIYLWDANTNKTSQLDNGMRDQM   100
 101  SFLLWSKIGSFLAVGTIKGNLLIYNHQTSRKIPVLGKHTKKITCGCWNSE   150
 151  NLLALGGEDKMITVSNQEGDTIRQTPVKSEPSDIKFSMSKTDERISSAEN   200
 201  TISAVVGKKMLFLFHLNEPDNPVDLEFQQAYGNIVCYSWYGDGYIMIGFS   250
 251  RGTFLAISTHFPEVGQEIFKARDHKDNLTSVALSQTLNKAATCGDNCIKI   300
 301  HDLTELRDMYAIINLDDENKGLGTLSWTDDGQLLALSTQRGSLHVFLTKL   350
 351  PILGDACHTRIAYLTSLLEVTVANLIEGEPPITVSVDVEPTFVAVGLYHL   400
 401  AVGMNNRAWFYVLGENVVKKLKDVEYLGTVASICLHSDYAAALFEGKIQL   450
 451  HLIENEMLDAQEERETRLFPAVDDKCRILCHALTSDFLIYGTDTGIIHYF   500
 501  FIEDWQFVNDYRHPVGVKKLFPDPNGTRLVFIDEKSDGFVYCPVNDATYE   550
 551  IPDFSPTIKGVLWENWPMDKGVFIAYDDDKVYTYAFHKDTIQGSKVILAG   600
 601  STKLPFSHKPLLLYNGELTCQTQSGKINSIYLSTHSFLGSMKDTEPTDLR   650
 651  QMLTQTLLLKRFSDAWDICKMLNDRTSWSELAKACLHHMEVEFAIRVSRT   700
 701  MGDVGTVMSLEQIKGIEDYNLLAGHLAMFTNDFNLAQDLYLASNCPVAAL   750
 751  EMRRDLQHWDSALQLAKRLAPDQIPFISKEYAIQLEFTGDYVNALAHYEK   800
 801  GITGDNKEHDEVCLAGVAQMSIRMGDIRRGANQALKHPSRVLKRDCGAIL   850
 851  ENMKQFSEAAQLYEKGQYYDRAASVYIRCKNWAKVGELLPHVSSPKIHLQ   900
 901  YAKAKEADGRYKEAVVAYENAKQWNSVIRIYLDHLNNPEKAVSIVRETQS   950
 951  LDGAKMVARFFLQLGDYGSAIQFLVLSKCNNEAFTLAQQHNKMEIYADII  1000
1001  GAEDTTNEDYQSIALYFEGEKRHFQAGKFFLLCGQYSRALKHFLKCPSSE  1050
1051  DNVAIEMAIETVGQAKDELLTNQLIDHLMGESDGMPKDAKYLFRLYMALK  1100
1101  QYREAARTAIIIAREEQSAGNYRNAHDVLFSMYAELKAQKIKIPSEMATN  1150
1151  LMILHSYILVKIHVKSGDHMKGARMLIRVANNISKFPSHIVPILTSTVIE  1200
1201  CHRAGLKNSAFSFAAMLMRPEYRNKIDAKYKKKIEAMVRRPDTSETEEAT  1250
1251  TPCPFCQFLLPECELLCPGCKNNIPYCIATGRHMLKDDWTMCPHCGFPAL  1300
1301  YSEFKILLNSESTCPMCSERLNSSQLKKITDCSQYLRTEME           1341

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.)

Go back to the NucPred Home Page.