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

NucPred

Fetching Q04182 from www.uniprot.org...

The NucPred score for your sequence is 0.51 (see score help below)

   1  MSSDIRDVEERNSRSSSSSSSSNSAAQSIGQHPYRGFDSEAAERVHELAR    50
  51  TLTSQSLLYTANSNNSSSSNHNAHNADSRSVFSTDMEGVNPVFTNPDTPG   100
 101  YNPKLDPNSDQFSSTAWVQNMANICTSDPDFYKPYSLGCVWKNLSASGDS   150
 151  ADVSYQSTFANIVPKLLTKGLRLLKPSKEEDTFQILKPMDGCLNPGELLV   200
 201  VLGRPGSGCTTLLKSISSNSHGFKIAKDSIVSYNGLSSSDIRKHYRGEVV   250
 251  YNAESDIHLPHLTVYQTLFTVARMKTPQNRIKGVDREAYANHVTEVAMAT   300
 301  YGLSHTRDTKVGNDLVRGVSGGERKRVSIAEVAICGARFQCWDNATRGLD   350
 351  SATALEFIRALKTQADIGKTAATVAIYQCSQDAYDLFDKVCVLDDGYQLY   400
 401  FGPAKDAKKYFQDMGYYCPPRQTTADFLTSITSPTERIISKEFIEKGTRV   450
 451  PQTPKDMAEYWLQSESYKNLIKDIDSTLEKNTDEARNIIRDAHHAKQAKR   500
 501  APPSSPYVVNYGMQVKYLLIRNFWRMKQSASVTLWQVIGNSVMAFILGSM   550
 551  FYKVMKKNDTSTFYFRGAAMFFAILFNAFSCLLEIFSLYETRPITEKHRT   600
 601  YSLYHPSADAFASVLSEMPPKLITAVCFNIIFYFLVDFRRNGGVFFFYFL   650
 651  INVIATFTLSHLFRCVGSLTKTLQEAMVPASMLLLAISMYTGFAIPKTKI   700
 701  LGWSIWIWYINPLAYLFESLMINEFHDRRFPCAQYIPAGPAYQNITGTQR   750
 751  VCSAVGAYPGNDYVLGDDFLKESYDYEHKHKWRGFGIGMAYVVFFFFVYL   800
 801  ILCEYNEGAKQKGEMVVFLRSKIKQLKKEGKLQEKHRPGDIENNAGSSPD   850
 851  SATTEKKILDDSSEGSDSSSDNAGLGLSKSEAIFHWRDLCYDVPIKGGQR   900
 901  RILNNVDGWVKPGTLTALMGASGAGKTTLLDCLAERVTMGVITGNIFVDG   950
 951  RLRDESFPRSIGYCQQQDLHLKTATVRESLRFSAYLRQPSSVSIEEKNRY  1000
1001  VEEVIKILEMQQYSDAVVGVAGEGLNVEQRKRLTIGVELAARPKLLVFLD  1050
1051  EPTSGLDSQTAWDTCQLMRKLATHGQAILCTIHQPSAILMQQFDRLLFLQ  1100
1101  KGGQTVYFGDLGEGCKTMIDYFESKGAHKCPPDANPAEWMLEVVGAAPGS  1150
1151  HATQDYNEVWRNSDEYKAVQEELDWMEKNLPGRSKEPTAEEHKPFAASLY  1200
1201  YQFKMVTIRLFQQYWRSPDYLWSKFILTIFNQVFIGFTFFKADRSLQGLQ  1250
1251  NQMLSIFMYTVIFNPILQQYLPSFVQQRDLYEARERPSRTFSWLAFFLSQ  1300
1301  IIVEIPWNILAGTIAYCIYYYAVGFYANASAAGQLHERGALFWLFSIAFY  1350
1351  VYIGSMGLLMISFNEVAETAAHMGTLLFTMALSFCGVMATPKVMPRFWIF  1400
1401  MYRVSPLTYMIDALLALGVANVDVKCSNYEMVKFTPPSGTTCGDYMASYI  1450
1451  KLAGTGYLSDPSATDICSFCAVSTTNAFLATFSSHYYRRWRNYGIFICYI  1500
1501  AFDYIAATFLYWLSRVPKKNGKISEKPKK                       1529

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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