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

NucPred

Fetching Q8VDC1 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MASSSTETQLQRIIRDLQDAATELSHEFKEGGEPITDDSTSLHKFSYKLE    50
  51  YLLQFDQKEKASLLGSKKDYWDYFCACLAKVKGANDGIRFVRSISELRTS   100
 101  LGKGRAFIRYSLVHQRLADTLQQCFMNTKVTSDWYYARSPFLKPKLSSDI   150
 151  VGQLYELTEVQFDLAPRGYDLDAAWPTFARRTLATSTSAYMWKPPSRSSS   200
 201  MSSLVSNYLQTQEMASSLDLNCSLNNEALESFDEMRLELDQLEVREKQLQ   250
 251  ERVQQLDRENQALRMLVSRQGGQLQVEKEMGYLAVEDSIGLVSLVAELQK   300
 301  QGDVSQATVKKLQSCLQALELNVDKKEYSPSALQLENMAKELDTVRGSLG   350
 351  RENQLLASLSERLARAEKGEKTPPDTELHQEPVPADLVLKFQELKGKLQA   400
 401  LEGENTEAQELNRQQSIKLEQLAKELQLKEEARASLAHLVKDVVPLQEEL   450
 451  SGKKQESAQLRRQLQESLAHLSSVEEELAEARQQEKQHREEKQLLEQEAT   500
 501  SLTWQLQLLETQLGQVSQLVSDLEEQKKQLMQERDHLSQRVGTLEQLAEV   550
 551  HGPPQSAEMPEKRQQCLREEQVNNSTVSEAEQEELQKELQNMVDRNQLLE   600
 601  GKLQALQTDYKALQQREAAIQGSLASLEAEQASIRHLGNQMEASLLAVKK   650
 651  AKETMKAQVAEKEAALQSKESECQRLQEEADQCRLQAEAQAQELRALENQ   700
 701  CQQQIQLIEVLSAEKGQQGLSLPQVNTDQLALSQAQLEIHQGEAQRLQNE   750
 751  VVDLQAKLQVALGDRDKLQSQLGVAETVLREHKTLVQQLKEQNEALNRAH   800
 801  VQELLQCSEREGILQEESIYKAQKQEQELRALQAELSQVRCSSEGAHLEH   850
 851  AELQDQLHRANTDTAELGIQVCALTAEKDRMEEALASLAQELQDSKEAAL   900
 901  QERKGLELQVMQLQQEKEKLQEKVKAAEEAASSFSGLQAQLAQAEQLAQS   950
 951  LQETAHQEQDALKFQLSAEIMDHQNRLKTANEECGHLRAQLEEQGQQLQM  1000
1001  TKEAVQELEITKAAMEEKLNCTSSHLAECQATLLRKDEESTMLQTSLERT  1050
1051  QKELEKATSKIQEYYNKLCQEVTNRERNDQKMLADLDDLNRTKKYLEERL  1100
1101  IELLRDKDALWQKSDALEFQQKLSAEEKCLGDMEVNHCHDCKREFSWIVR  1150
1151  RHHCRICGRIFCYYCCNNYVVTKPSGKKERCCRACFQKFGEGSGSNDSSG  1200
1201  SGTSQGEPSPMVSPAEASPQSIGSQGINSVCRPPDDAVFDIITDEELCQI  1250
1251  QESGSSLPETPTETDSMDPNTAEQDTTSNSLTPEDTEDVPMGQDAEICLL  1300
1301  KSGELMIKLPLTVEEVASFGEGSRELFVRSSTYSLITITVAEPGLTISWV  1350
1351  FSSDPKSISFSVVFQETEDTPLDQCKVLIPTTRCNSHKENIRGQLKVRIP  1400
1401  GIYLLIFDNTFSRFISKKVLYHLTVDRPVIYDGSDFP               1437

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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