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

NucPred

Fetching Q6URW6 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MAAVTMSVSGRKVASRPGPVPEAAQSFLYAPRTPNVGGPGGPQVEWTARR    50
  51  MVWVPSELHGFEAAALRDEGEEEAEVELAESGRRLRLPRDQIQRMNPPKF   100
 101  SKAEDMAELTCLNEASVLHNLRERYYSGLIYTYSGLFCVVINPYKQLPIY   150
 151  TEAIVEMYRGKKRHEVPPHVYAVTEGAYRSMLQDREDQSILCTGESGAGK   200
 201  TENTKKVIQYLAHVASSPKGRKEPGVPASVSTMSYGELERQLLQANPILE   250
 251  AFGNAKTVKNDNSSRFGKFIRINFDIAGYIVGANIETYLLEKSRAIRQAK   300
 301  DECSFHIFYQLLGGAGEQLKADLLLEPCSHYRFLTNGPSSSPGQERELFQ   350
 351  ETLESLRVLGLLPEEITAMLRTVSAVLQFGNIVLKKERNTDQATMPDNTA   400
 401  AQKLCRLLGLGVTDFSRALLTPRIKVGRDYVQKAQTKEQADFALEALAKA   450
 451  TYERLFRWLVLRLNRALDRSPRQGASFLGILDIAGFEIFQLNSFEQLCIN   500
 501  YTNEKLQQLFNHTMFVLEQEEYQREGIPWTFLDFGLDLQPCIDLIERPAN   550
 551  PPGLLALLDEECWFPKATDKSFVEKVAQEQGSHPKFQRPRNLRDQADFSV   600
 601  LHYAGKVDYKASEWLMKNMDPLNDNVAALLHQSTDRLTAEIWKDVEGIVG   650
 651  LEQVSSLGDGPPGGRPRRGMFRTVGQLYKESLSRLMATLSNTNPSFVRCI   700
 701  VPNHEKRAGKLEPRLVLDQLRCNGVLEGIRICRQGFPNRILFQEFRQRYE   750
 751  ILTPNAIPKGFMDGKQACEKMIQALELDPNLYRVGQSKIFFRAGVLAQLE   800
 801  EERDLKVTDIIVSFQAAARGYLARRAFQRRQQQQSALRVMQRNCAAYLKL   850
 851  RNWQWWRLFIKVKPLLQVTRQDEVLQARAQELQKVQELQQQSAREVGELQ   900
 901  GRVAQLEEERTRLAEQLRAEAELCSEAEETRARLAARKQELELVVTELEA   950
 951  RVGEEEECSRQLQSEKKRLQQHIQELESHLEAEEGARQKLQLEKVTTEAK  1000
1001  MKKFEEDLLLLEDQNSKLSKERRLLEERLAEFSSQAAEEEEKVKSLNKLR  1050
1051  LKYEATISDMEDRLKKEEKGRQELEKLKRRLDGESSELQEQMVEQKQRAE  1100
1101  ELLAQLGRKEDELQAALLRAEEEGGARAQLLKSLREAQAGLAEAQEDLEA  1150
1151  ERVARAKAEKQRRDLGEELEALRGELEDTLDSTNAQQELRSKREQEVTEL  1200
1201  KKALEEESRAHEVSMQELRQRHSQALVEMAEQLEQARRGKGVWEKTRLSL  1250
1251  EAEVSELKAELSSLQTSRQEGEQKRRRLESQLQEVQGRSSDSERARSEAA  1300
1301  EKLQRAQAELESVSTALSEAESKAIRLGKELSSAESQLHDTQELLQEETR  1350
1351  AKLALGSRVRALEAEAAGLREQMEEEVVARERAGRELQSTQAQLSEWRRR  1400
1401  QEEEAAVLEAGEEARRRAAREAETLTQRLAEKTEAVERLERARRRLQQEL  1450
1451  DDATVDLGQQKQLLSTLEKKQRKFDQLLAEEKAAVLRAVEDRERIEAEGR  1500
1501  EREARALSLTRALEEEQEAREELERQNRALRAELEALLSSKDDVGKNVHE  1550
1551  LERARKAAEQAASDLRTQVTELEDELTAAEDAKLRLEVTVQALKAQHERD  1600
1601  LQGRDDAGEERRRQLAKQLRDAEVERDEERKQRALAMAARKKLELELEEL  1650
1651  KAQTSAAGQGKEEAVKQLKKMQVQMKELWREVEETRSSRDEMFTLSRENE  1700
1701  KKLKGLEAEVLRLQEELAASDRARRQAQQDRDEMAEEVASGNLSKAATLE  1750
1751  EKRQLEGRLSQLEEELEEEQNNSELLKDHYRKLVLQVESLTTELSAERSF  1800
1801  SAKAESGRQQLERQIQELRARLGEEDAGARARQKMLIAALESKLAQAEEQ  1850
1851  LEQESRERILSGKLVRRAEKRLKEVVLQVDEERRVADQVRDQLEKSNLRL  1900
1901  KQLKRQLEEAEEEASRAQAGRRRLQRELEDVTESAESMNREVTTLRNRLR  1950
1951  RGPLTFTTRTVRQVFRLEEGVASDEEEAEGAEPGSAPGQEPEAPPPATPQ  2000

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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