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

NucPred

Fetching Q28146 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MGTALLQRGGCFLLCLSLLLLGCWAELGSGLEFPGAEGQWTRFPKWNACC    50
  51  ESEMSFQLKTRSARGLVLYFDDEGFCDFLELILTRGGRLQLSFSIFCAEP   100
 101  ATLLTDTPVNDGAWHNVRIRRQFRNTTLFIDQVEAKWVEVKSKRRDMTVF   150
 151  SGLFVGGLPPELRAAALKLTLASVREREPFKGWIRDVRVNSSLALPVDSG   200
 201  EVKLDDEPPNSGGGSPCEAGEEGEGGVCLNGGVCSVVDDQAVCDCSRTGF   250
 251  RGKDCSQEDNNVEGLAHLMMGDQGKSKEDNNVEGLAHLMMGDQGKEEYIA   300
 301  TFKGSEYFCYDLSQNPIQSSSDEITLSFKTLQRNGLMLHTGKSADYVNLA   350
 351  LKNGAVSLVINLGSGAFEALVEPVNGKFNDNAWHDVKVTRNLRQTSGIGH   400
 401  AMVNKLHCSVTISVDGILTTTGYTQEDYTMLGSDDFFYVGGSPSTADLPG   450
 451  SPVSNNFMGCLKEVVYKNNDVRLELSRLAKQGDPKMKIHGVVAFKCENVA   500
 501  TLDPITFETPESFISLPKWNAKKTGSISFDFRTTEPNGLILFSHGKPRHQ   550
 551  KDAKHPQMIKVDFFAIEMLDGHLYLLLDMGSGTIKIKALQKKVNDGEWYH   600
 601  VDFQRDGRSGTISVNTLRTPYTAPGESQILDLDDELYLGGLPENKAGLVF   650
 651  PTEVWTALLNYGYVGCIRDLFIDGQSKDIRQMAEVQSTAGVKPSCSRETA   700
 701  KPCLSNPCKNNGMCRDGWNRYVCDCSGTGYLGRSCEREATVLSYDGSMFM   750
 751  KIQLPVVMHTEAEDVSLRFRSQRAYGILMATTSRDSADTLRLELDAGRVK   800
 801  LTVNLDCIRINCNSSKGPETLFAGYNLNDNEWHTVRVVRRGKSLKLTVDD   850
 851  QQAMTGQMAGDHTRLEFHNIETGIITERRYLSSVPSNFIGHLQSLTFNGM   900
 901  AYIDLCKNGDIDYCELNARFGFRNIIADPVTFKTKSSYVALATLQAYTSM   950
 951  HLFFQFKTTSLDGLILYNSGDGNDFIVVELVKGYLHYVFDLGNGANLIKG  1000
1001  SSNKPLNDNQWHNVMISRDTSNLHTVKIDTKITTQITAGARNLDLKSDLY  1050
1051  IGGVAKETYKSLPKLVHAKEGFQGCLASVDLNGRLPDLISDALFCNGQIE  1100
1101  RGCEGPSTTCQEDSCSNQGVCLQQWDGISCDCSMTSFSGPLCNDPGTTYI  1150
1151  FSKGGGQITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDY  1200
1201  LELHIHQGKIGVKFNVGTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQ  1250
1251  VDSWPVIERYPAGNNDNERLAIARQRIPYRLGRVVDEWLLDKGRQLTIFN  1300
1301  SQATIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLV  1350
1351  GEVPSSMTTESTATAMQSEMSTSIMETTTTLATSTARRGKPPTKEPVSQT  1400
1401  TDDILVASAECPSDDEDIDPCEPSSGGLANPTRAGGREPYPGSAEVIRES  1450
1451  SSTTGMVVGIVAAAALCILILLYAMYKYRNRDEGSYHVDESRNYISNSAQ  1500
1501  SNGAVVKEKQPSSAKSANKNKKNKDKEYYV                      1530

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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