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

NucPred

Fetching Q9W539 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MTLSRGPYSELDKMSLFQDLKLKRRKIDSRCSSDGESIADTSTSSPDLLA    50
  51  PMSPKLCDSGSAGASLGASLPLPLALPLPMALPLPMSLPLPLTAASSAVT   100
 101  VSLAAVVAAVAETGGAGAGGAGTAVTASGAGPCVSTSSTTAAAATSSTSS   150
 151  LSSSSSSSSSTSSSTSSASPTAGASSTATCPASSSSSSGNGSGGKSGSIK   200
 201  QEHTEIHSSSSAISAAAASTVMSPPPAEATRSSPATPEGGGPAGDGSGAT   250
 251  GGGNTSGGSTAGVAINEHQNNGNGSGGSSRASPDSLEEKPSTTTTTGRPT   300
 301  LTPTNGVLSSASAGTGISTGSSAKLSEAGMSVIRSVKEERLLNVSSKMLV   350
 351  FHQQREQETKAVAAAAAAAAAGHVTVLVTPSRIKSEPPPPASPSSTSSTQ   400
 401  RERERERDRERDRERERERDRDREREREQSISSSQQHLSRVSASPPTQLS   450
 451  HGSLGPNIVQTHHLHQQLTQPLTLRKSSPPTEHLLSQSMQHLTQQQAIHL   500
 501  HHLLGQQQQQQQASHPQQQQQQQHSPHSLVRVKKEPNVGQRHLSPHHQQQ   550
 551  SPLLQHHQQQQQQQQQQQQHLHQQQQQQQHHQQQPQALALMHPASLALRN   600
 601  SNRDAAILFRVKSEVHQQVAAGLPHLMQSAGGAAAAAAAAVAAQRMVCFS   650
 651  NARINGVKPEVIGGPLGNLRPVGVGGGNGSGSVQCPSPHPSSSSSSSQLS   700
 701  PQTPSQTPPRGTPTVIMGESCGVRTMVWGYEPPPPSAGQSHGQHPQQQQQ   750
 751  SPHHQPQQQQQQQQQQSQQQQQQQQQQSLGQQQHCLSSPSAGSLTPSSSS   800
 801  GGGSVSGGGVGGPLTPSSVAPQNNEEAAQLLLSLGQTRIQDMRSRPHPFR   850
 851  TPHALNMERLWAGDYSQLPPGQLQALNLSAQQQQWGSSNSTGLGGVGGGM   900
 901  GGRNLEAPHEPTDEDEQPLVCMICEDKATGLHYGIITCEGCKGFFKRTVQ   950
 951  NRRVYTCVADGTCEITKAQRNRCQYCRFKKCIEQGMVLQAVREDRMPGGR  1000
1001  NSGAVYNLYKVKYKKHKKTNQKQQQQAAQQQQQQAAAQQQHQQQQQHQQH  1050
1051  QQHQQQQLHSPLHHHHHQGHQSHHAQQQHHPQLSPHHLLSPQQQQLAAAV  1100
1101  AAAAQHQQQQQQQQQQQQQAKLMGGVVDMKPMFLGPALKPELLQAPPMHS  1150
1151  PAQQQQQQQQQQQQQQASPHLSLSSPHQQQQQQQGQHQNHHQQQGGGGGG  1200
1201  AGGGAQLPPHLVNGTILKTALTNPSEIVHLRHRLDSAVSSSKDRQISYEH  1250
1251  ALGMIQTLIDCDAMEDIATLPHFSEFLEDKSEISEKLCNIGDSIVHKLVS  1300
1301  WTKKLPFYLEIPVEIHTKLLTDKWHEILILTTAAYQALHGKRRGEGGGSR  1350
1351  HGSPASTPLSTPTGTPLSTPIPSPAQPLHKDDPEFVSEVNSHLSTLQTCL  1400
1401  TTLMGQPIAMEQLKLDVGHMVDKMTQITIMFRRIKLKMEEYVCLKVYILL  1450
1451  NKEVELESIQERYVQVLRSYLQNSSPQNPQARLSELLSHIPEIQAAASLL  1500
1501  LESKMFYVPFVLNSASIR                                  1518

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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