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

NucPred

Fetching Q5K651 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MAKQLNLPENTDDWTKEDVNQWLESHKIDQKHREILTEQDVNGAVLKWLK    50
  51  KEHLVDMGITHGPAIQIEELFKELRKTAIEDSIQTSKMGKPSKNAPKDQT   100
 101  VSQKERRETSKQKQKGKENPDMANPSAMSTTAKGSKSLKVELIEDKIDYT   150
 151  KERQPSIDLTCVSYPFDEFSNPYRYKLDFSLQPETGPGNLIDPIHEFKAF   200
 201  TNTATATEEDVKMKFSNEVFRFASACMNSRTNGTIHFGVKDKPHGKIVGI   250
 251  KVTNDTKEALINHFNLMINKYFEDHQVQQAKKCIREPRFVEVLLPNSTLS   300
 301  DRFVIEVDIIPQFSECQYDYFQIKMQNYNNKIWEQSKKFSLFVRDGTSSK   350
 351  DITKNKVDFRAFKADFKTLAESRKAAEEKFRAKTNKKEREGPKLVKLLTG   400
 401  NQDLLDNSYYEQYILVTNKCHPDQTKHLDFLKEIKWFAVLEFDPESNING   450
 451  VVKAYKESRVANLHFPSVYVEQKTTPNETISTLNLYHQPSWIFCNGRLDL   500
 501  DSEKYKPFDPSSWQRERASDVRKLISFLTHEDIMPRGKFLVVFLLLSSVD   550
 551  DPRDPLIETFCAFYQDLKGMENILCICVHPHIFQGWKDLLEARLIKHQDE   600
 601  ISSQCISALSLEEINGTILKLKSVTQSSKRLLPSIGLSTVLLKKEEDIMT   650
 651  ALEIICENECEGTLLEKDKNKFLEFKASKEEDFYRGGKVSWWNFYFSSES   700
 701  YSSPFVKRDKYERLEAMIQNCADSSKPTSTKIIHLYHHPGCGGTTLAMHI   750
 751  LWELRKKFRCAVLKNKTVDFSEIGEQVTSLITYGAMNRQEYVPVLLLVDD   800
 801  FEEQDNVYLLQYSIQTAIAKKYIRYEKPLVIILNCMRSQNPEKSARIPDS   850
 851  IAVIQQLSPKEQRAFELKLKEIKEQHKNFEDFYSFMIMKTNFNKEYIENV   900
 901  VRNILKGQNIFTKEAKLFSFLALLNSYVPDTTISLSQCEKFLGIGNKKAF   950
 951  WGTEKFEDKMGTYSTILIKTEVIECGNYCGVRIIHSLIAEFSLEELKKSY  1000
1001  HLNKSQIMLDMLTENLFFDTGMGKSKFLQDMHTLLLTRHRDEHEGETGNW  1050
1051  FSPFIEALHKDEGNEAVEAVLLESIHRFNPNAFICQALARHFYIKKKDFG  1100
1101  NALNWAKQAKIIEPDNSYISDTLGQVYKSKIRWWIEENGGNGNISVDDLI  1150
1151  ALLDLAEHASSAFKESQQQSEDREYEVKERLYPKSKRRYDTYNIAGYQGE  1200
1201  IEVGLYTIQILQLIPFFDNKNELSKRYMVNFVSGSSDIPGDPNNEYKLAL  1250
1251  KNYIPYLTKLKFSLKKSFDFFDEYFVLLKPRNNIKQNEEAKTRRKVAGYF  1300
1301  KKYVDIFCLLEESQNNTGLGSKFSEPLQVERCRRNLVALKADKFSGLLEY  1350
1351  LIKSQEDAISTMKCIVNEYTFLLEQCTVKIQSKEKLNFILANIILSCIQP  1400
1401  TSRLVKPVEKLKDQLREVLQPIGLTYQFSEPYFLASLLFWPENQQLDQHS  1450
1451  EQMKEYAQALKNSFKGQYKHMHRTKQPIAYFFLGKGKRLERLVHKGKIDQ  1500
1501  CFKKTPDINSLWQSGDVWKEEKVQELLLRLQGRAENNCLYIEYGINEKIT  1550
1551  IPITPAFLGQLRSGRSIEKVSFYLGFSIGGPLAYDIEIV             1589

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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