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

NucPred

Fetching Q5A950 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MSFYKKVTRGLATPLQGSINLFSGSPNVSGDEGTDADNENPEHRTTYHSL    50
  51  SGRVNHDDDDEDVAKLEDIVGFFTGLLNTTTVCAGLGSLNNLKKHYLDEF   100
 101  IKKSALNPLRPQNYGPETSSKLNNNSIEELLNNGDTSLEKVRKMSLYDFD   150
 151  EHTSDSEEEDSADKEEESIAENLKPGKSGKARNHPRDSRTTATLITTQIT   200
 201  RTKTATTATPTPTPTSSVDTDVTDVTEPIGKVTTKIPEEQLQGLNPLQKS   250
 251  VVKNLDPHHVREGVLIKVKNSETPLKNDRQELLEKIQLRLKIADKLQRVF   300
 301  DLSDEDTFCGNYSAWLIKDVLLQGHVYLTKDALLYFAFLPKRFSLENSSE   350
 351  VLDEDNSSSIVYSGNLGLKSAKYGEVVLNTVLQHRYWAVLRAETLSIYSS   400
 401  STNLYFPVLVIDIKKCLYTEIIDKEKLNREAISPVNRGTYSPNGGLSGTA   450
 451  TPRASTLENTASELNSMLSGDSYSPTEDNVETTASTVWFKLVTKKKTYKF   500
 501  SCDSSFSARQWCNNITKLIFQHNNANSNGEVLIKIPISKIAEYNKRALFS   550
 551  EEEEEDRTLDVTMNDIPLNVTIKYLGDNDNERKRDKLKRKYKGEEPTIEE   600
 601  VHFLFPKSGVEFFETFDKLVNPVVSDNDNQSSKSSITSTNFSEKAISTLS   650
 651  KSPNHLVQTVLDFNKPVDDDISAFKKFGTTITSPTRIFKATITSPEMTSI   700
 701  DETSLRDSFDSDRLHLPRDMSERALKNLEVSFVTSLKKLEDASKRYEKPH   750
 751  MEHSQTNLASILSDPSEVKKESKTAISKSIKALYSVGTHWSATPNHYFEL   800
 801  GKYYVNKVQDRDSSQRNFQSHFSTNSKLLASYYGHLLRTVPVYGKIYVSE   850
 851  TDVCFRSLLPGVSTKMVLPMTDIEEVRASRGSRLTYHGLRLIVRGSEELD   900
 901  LEFGSSKSRDDFQKVVLSVLERLHSKEGFRPEPYQWGSNFEVELYKTRME   950
 951  YSDSENREIQQYDNSIDIKFAEKKIEMARVRMFEDRLMAASGLDVPIILE  1000
1001  DSPFFKTELRPSTSYNITLLTIGSRGDVQPYIALGKGLVKEGHNVTIATH  1050
1051  AEFGDWIKTFGLGFKEIAGDPAELMSFMVTHNSMSVGFLKNAQQKFRSWI  1100
1101  SKLLTTSWEACQGSDILIESPSAMSGIHIAEALGIPYFRAFTMPWTRTRA  1150
1151  YPHAFFVPEQKKGGSYNYLTHVLFENIFWKGISGQVNKWRVEELDLPKTN  1200
1201  LYRLQQTRVPFLYNVSPAILPPSVDFPDWIKVTGYWFLDEGSGDYKPPEE  1250
1251  LVQFMKKASRDKKKIVYIGFGSIVVKDAKSLTKAVVSAVRRADVRCILNK  1300
1301  GWSDRLDNKDKNEIEIELPPEIYNSGTIPHDWLFPRIDAAVHHGGSGTTG  1350
1351  ATMRAGIPTIIKPFFGDQFFYATRIEDLGAGIALKKLTAKTLGDALVKAT  1400
1401  HDLKIIDKAKRVSQQIKHEHGVLSAIESIYSELEYSRNLILIKDIHNQNY  1450
1451  KRHHPVPSGVQTPAYDTDSDDYDDDEDDDESDKDDEEEEEENSYDGYDGN  1500
1501  GVNNSPSQNSSN                                        1512

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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