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

NucPred

Fetching Q9C438 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MDSSRHGLHPLQNSLLHQSQMDIYNSITGIRISAIPYNFNSYDQFKQYIS    50
  51  ASFGIAPADLFLLTAFGIKLKFSMIMNGDVREVYVFDRRFYDGQQMVDDK   100
 101  LDTALESLNQCEMLNMIKPMRSPLENADILRFVSYLKDITNRPNLSTEDL   150
 151  DLNKLRLVLNSLKRSSGWAAALLSDLKKTNYYKKVNEEVLCDNKKEIEII   200
 201  LISHNALIQYTNLMFKTLEKSFNESVDSLIMLQEQSLLENWKSYYQILKG   250
 251  VRFKGNYVLSDLLDEKMLENVAADSKALMGNVNDKLTRLRSRIDSEIISK   300
 301  RVMINDLYESLKKKYLDVPNLNSNSRTENDSDTLNRLTELVNQVVKDSKE   350
 351  LPILDELLTTSGGNSTTLSAESVKKINVLVSVFETHSSTIIPQITELSNK   400
 401  LYDEKVEALNLKQDLQRTLLSDTIHKIVGVQLSILKATNLINNDLSKNIS   450
 451  NLDFNELKMSIVKDLPLVFGLWLAGNLKKLKWLENFNKVAFKANEILEML   500
 501  KFIESNYRSKWIDGFSKTNPCVNSNQGQRILALQINEDLKQQFVRDHLAS   550
 551  SRIVLKTGSNVPTPGGSKGNSRAPTPEHDPHPPHLNAINKLLHNFNKDYN   600
 601  FGNLRQASEEVVRTHSPATKRDDRFGNQFWLTLIDNITTEDFYHYIDSLK   650
 651  ENKVNIKVIKQLEKNLTDLGLGRIYETSNDKVISAGGGTIGPLNSQDTSY   700
 701  MNLLKKFLKNFEINDVTIQINISTLETENGNNNEKEKEPSFSNHELLQGY   750
 751  QRRVKKLESLLYQQSLHQSGPPPINMAYPPIRDYQQRSSANLMTSATATE   800
 801  MLMDTHARIHDTDMKQKRENVDEIQVLQTRIEQLQANLEQTSKERDDERE   850
 851  QKEILHLKLMKRDEEGDEDEKINGLVAANHQLQIRLEALQKQNQELQSLQ   900
 901  ERNNNEIHASQEREIEALKKQVVQLTEEKTQMSDEKDRLDLSNEHWKTQY   950
 951  EEAAMMKKDLLDNMTAQEQEYKNELNTHIKEVEDLKVKVENLEDEEANLI  1000
1001  EIKENYESKLAQNESHFEELESIIKSLYGKLRLVIERTFQNVVTVCLMLE  1050
1051  AIGLLMKRDEQYEENDPSNGIRIHRVKGLRSRRRSTTSKAASPLGNDEIL  1100
1101  ELSSQIVAEADKQLVYFHQEPVKELESLETVLDFKFNQDFDKFTRLTYMD  1150
1151  QKLLVESVTKRFKDVEQLARKLQKESNYSKTEIDGLIKEVNTRISIKDFK  1200
1201  VGDLVLFLPTRDDTINMNMANTVEAVNRRASTVASFETYQPWAAFNVGAP  1250
1251  HYFLINDVSKIDLNGRDWVLARIESMEEHKVTREGHRRNVGNPYNLNPDA  1300
1301  VWYGVRAKEETVG                                       1313

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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