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

NucPred

Fetching Q7PC84 from www.uniprot.org...

The NucPred score for your sequence is 0.49 (see score help below)

   1  MAAMLGRDEDPVGALSGRVSLASTSHRSLVGASKSFRDVFMPQTDEVFGR    50
  51  SERREEDDMELRWAAIERLPTFDRLRKGMLPQTSANGKIELEDIDLTRLE   100
 101  PKDKKHLMEMILSFVEEDNEKFLRDLRERTDRVGIEVPKIEVRYENISVE   150
 151  GDVRSASRALPTLFNVTLNTLESILGFFHLLPSKRKKIQILKDISGIVKP   200
 201  SRMTLLLGPPSSGKTTLLQALAGKLDDTLQMSGRITYCGHEFREFVPQKT   250
 251  CAYISQHDLHFGEMTVREILDFSGRCLGVGSRYQLMSELSRREKEEGIKP   300
 301  DPKIDAFMKSIAISGQETSLVTDYVLKILGLDICADILAGDVMRRGISGG   350
 351  QKKRLTTGEMLVGPARALFMDEISTGLDSSTTFQICKFMRQLVHISDVTM   400
 401  IISLLQPAPETFELFDDIILLSEGQIVYQGPRDNVLEFFEYFGFQCPERK   450
 451  GVADFLQEVTSKKDQEQYWNKREQPYNYVSVSDFSSGFSTFHTGQKLTSE   500
 501  FRVPYDKAKTHSAALVTQKYGISNWELFKACFDREWLLMKRNSFVYVFKT   550
 551  VQITIMSLITMTVYLRTEMHVGTVRDGQKFYGAMFFSLINVMFNGLAELA   600
 601  FTVMRLPVFYKQRDFLFYPPWAFALPAWLLKIPLSLIESGIWIGLTYYTI   650
 651  GFAPSAARFFRQLLAYFCVNQMALSLFRFLGAIGRTEVISNSIGTFTLLI   700
 701  VFTLGGFIIAKDDIRPWMTWAYYMSPMMYGQTAIVMNEFLDERWSSPNYD   750
 751  TRINAKTVGEVLLKSRGFFTEPYWFWICIVALLGFSLLFNLFYILALMYL   800
 801  NPLGNSKATVVEEGKDKQKGENRGTEGSVVELNSSSNKGPKRGMVLPFQP   850
 851  LSLAFNNVNYYVDMPSEMKAQGVEGDRLQLLRDVGGAFRPGILTALVGVS   900
 901  GAGKTTLMDVLAGRKTGGYIEGSISISGYPKNQTTFARVSGYCEQNDIHS   950
 951  PHVTVYESLIYSAWLRLSTDIDIKTRELFVEEVMELVELKPLRNSIVGLP  1000
1001  GVDGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNT  1050
1051  VDTGRTVVCTIHQPSIDIFESFDELLLMKRGGQVIYAGSLGHHSQKLVEY  1100
1101  FEAVEGVPKINDGYNPATWMLDVTTPSMESQMSLDFAQIFSNSSLYRRNQ  1150
1151  ELIKDLSTPPPGSKDVYFKTKYAQSFSTQTKACFWKQYWSYWRHPQYNAI  1200
1201  RFLMTVVIGVLFGLIFWQIGTKTENEQDLNNFFGAMYAAVLFLGALNAAT  1250
1251  VQPAIAIERTVFYREKAAGMYSAIPYAISQVAVEIMYNTIQTGVYTLILY  1300
1301  SMIGCNWTMAKFLWFYYYMLTSFIYFTLYGMMLMALTPNYQIAGICMSFF  1350
1351  LSLWNLFSGFLIPRPQIPIWWRWYYWATPVAWTLYGLITSQVGDKDSMVH  1400
1401  ISGIGDIDLKTLLKEGFGFEHDFLPVVAVVHIAWILLFLFVFAYGIKFLN  1450
1451  FQRR                                                1454

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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