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

NucPred

Fetching P40818 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MPAVASVPKELYLSSSLKDLNKKTEVKPEKISTKSYVHSALKIFKTAEEC    50
  51  RLDRDEERAYVLYMKYVTVYNLIKKRPDFKQQQDYFHSILGPGNIKKAVE   100
 101  EAERLSESLKLRYEEAEVRKKLEEKDRQEEAQRLQQKRQETGREDGGTLA   150
 151  KGSLENVLDSKDKTQKSNGEKNEKCETKEKGAITAKELYTMMTDKNISLI   200
 201  IMDARRMQDYQDSCILHSLSVPEEAISPGVTASWIEAHLPDDSKDTWKKR   250
 251  GNVEYVVLLDWFSSAKDLQIGTTLRSLKDALFKWESKTVLRNEPLVLEGG   300
 301  YENWLLCYPQYTTNAKVTPPPRRQNEEVSISLDFTYPSLEESIPSKPAAQ   350
 351  TPPASIEVDENIELISGQNERMGPLNISTPVEPVAASKSDVSPIIQPVPS   400
 401  IKNVPQIDRTKKPAVKLPEEHRIKSESTNHEQQSPQSGKVIPDRSTKPVV   450
 451  FSPTLMLTDEEKARIHAETALLMEKNKQEKELRERQQEEQKEKLRKEEQE   500
 501  QKAKKKQEAEENEITEKQQKAKEEMEKKESEQAKKEDKETSAKRGKEITG   550
 551  VKRQSKSEHETSDAKKSVEDRGKRCPTPEIQKKSTGDVPHTSVTGDSGSG   600
 601  KPFKIKGQPESGILRTGTFREDTDDTERNKAQREPLTRARSEEMGRIVPG   650
 651  LPSGWAKFLDPITGTFRYYHSPTNTVHMYPPEMAPSSAPPSTPPTHKAKP   700
 701  QIPAERDREPSKLKRSYSSPDITQAIQEEEKRKPTVTPTVNRENKPTCYP   750
 751  KAEISRLSASQIRNLNPVFGGSGPALTGLRNLGNTCYMNSILQCLCNAPH   800
 801  LADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKALWTGQYRYISPKDF   850
 851  KITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYKEENNDH   900
 901  LDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFM   950
 951  YLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEI  1000
1001  WKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPLENLDLSQYVIGPKNNLKK  1050
1051  YNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSA  1100
1101  AYILFYTSLGPRVTDVAT                                  1118

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.)

Go back to the NucPred Home Page.