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

NucPred

Fetching P81021 from www.uniprot.org...

The NucPred score for your sequence is 0.64 (see score help below)

   1  MSSVAVLTQESFAEHRSGLTQQQVKVTALNSEEENDPPTYKEAFPPLPEK    50
  51  APCLEAAQEPSGPWSKIRPIKASVITQVFHVPLEERKYKDMNQFGEGEQA   100
 101  KICLDIMQKTGAHLELSLAKDQGLSIMVSGKLEAVMKARKEIVARLQTQA   150
 151  SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGT   200
 201  KEGIEKARHEILLISAEQDKRAVERLDVEKVYHPFIAGPYNKLVSELMQD   250
 251  TGTRINIPPPSVNKTEIVFTGEKEQLAQAVARVKKIYEEKKKKTTTIAVE   300
 301  VKKSQHKYVIGRKGNSLQEILEKTGVSVEIPPTDSSSETVILRGEPEKLG   350
 351  QALTEVYAKANSFTVSSVSAPSWLHRFIIGLFGQNLAKITQQMPKIHIEF   400
 401  TEGEDKITSEGPTEDVNVAQEQIEVMVKDLINRTDYAEINVDHKFHRHLI   450
 451  GKNGANINRIKDLYKVSVRIPPDNEKSNLIRIEGDPQGVQQAKKELLELA   500
 501  SRMENERTKDLIIEQKFHRTIIGQKGERIREIREKFPEVIINFPDPAHKS   550
 551  DIVQLRGPKNEVEKCTKYMQKMVADLVENSFSISVPIFKQFHKNIIGKGG   600
 601  ANIKKIREESNTKIDLPGREQATQRQLLSQGREQTVKLLRHRILAIQKEL   650
 651  ANITEVEVSIPSKLHNSLIGAKGRFIRSIMEECGGVHIHFPTEGSGSATV   700
 701  TIRAQPRTWRKPRSSCCTWAEEKQTKSYTVDLRAKPEYHKFLIGKGGGNI   750
 751  RKVRDNTGARIIFPTSEDKDQELITIMGTEEAVKEAQKELEALIKNLDNV   800
 801  VEDSMVVDPKHHRHFVIRRGQVLREIADEYGGVMVRLPTVSGTQSDKVTL   850
 851  KGAKDCVEAAKKRIQEIIEDLEAQVTIECTIPQKFHRSIMGPKGSRIQQI   900
 901  TRDYGVQIKFPDREENPAPVAEPALQENGEEGGEGKDGKDADPSSPRKCD   950
 951  IIIISGRREKCEAAKEALQALVPVTIEVEVPFDLHRYIIGQKGSGIRKMM  1000
1001  DEFEVNIQVPAPELQSSDIITITGLAANLDRAKAGLLERVKELQAEQEDR  1050
1051  ALRSFKLTVTVDPKYHPKIIGRKGAVITQIRTEHEVNIQFPDKDDESQAQ  1100
1101  DQITITGYEKNAEAARDAIMKIVGELEQMVSEDVTLDHRVHARIIGARGK  1150
1151  AIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEYL  1200
1201  ADVVDNEAMQVYMKPSSHEESKVPSKGFVVRDAPCGTVNNEKAPDMSSSE  1250
1251  DFPSFGAQVAPKTLPWGPKR                                1270

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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