GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting.
GP4
Gram-positive
homology-based prediction
prediction methods
protein subcellular localization prediction
sorting signals
Journal
Briefings in bioinformatics
ISSN: 1477-4054
Titre abrégé: Brief Bioinform
Pays: England
ID NLM: 100912837
Informations de publication
Date de publication:
20 07 2021
20 07 2021
Historique:
received:
29
07
2020
revised:
08
10
2020
accepted:
09
10
2020
pubmed:
24
11
2020
medline:
20
11
2021
entrez:
23
11
2020
Statut:
ppublish
Résumé
Subcellular localization is a critical aspect of protein function and the potential application of proteins either as drugs or drug targets, or in industrial and domestic applications. However, the experimental determination of protein localization is time consuming and expensive. Therefore, various localization predictors have been developed for particular groups of species. Intriguingly, despite their major representation amongst biotechnological cell factories and pathogens, a meta-predictor based on sorting signals and specific for Gram-positive bacteria was still lacking. Here we present GP4, a protein subcellular localization meta-predictor mainly for Firmicutes, but also Actinobacteria, based on the combination of multiple tools, each specific for different sorting signals and compartments. Novelty elements include improved cell-wall protein prediction, including differentiation of the type of interaction, prediction of non-canonical secretion pathway target proteins, separate prediction of lipoproteins and better user experience in terms of parsability and interpretability of the results. GP4 aims at mimicking protein sorting as it would happen in a bacterial cell. As GP4 is not homology based, it has a broad applicability and does not depend on annotated databases with homologous proteins. Non-canonical usage may include little studied or novel species, synthetic and engineered organisms, and even re-use of the prediction data to develop custom prediction algorithms. Our benchmark analysis highlights the improved performance of GP4 compared to other widely used subcellular protein localization predictors. A webserver running GP4 is available at http://gp4.hpc.rug.nl/.
Identifiants
pubmed: 33227814
pii: 5998864
doi: 10.1093/bib/bbaa302
pmc: PMC8294519
pii:
doi:
Substances chimiques
Bacterial Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
Références
BMC Bioinformatics. 2007 May 22;8:170
pubmed: 17519041
Mol Microbiol. 2013 Sep;89(6):1154-66
pubmed: 23869560
Bioinformatics. 2007 Jul 15;23(14):1728-36
pubmed: 17488755
BMC Bioinformatics. 2005 Jul 02;6:167
pubmed: 15992409
Protein Sci. 2002 Dec;11(12):2836-47
pubmed: 12441382
J Mol Biol. 2004 May 14;338(5):1027-36
pubmed: 15111065
Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15898-903
pubmed: 26578815
Mol Microbiol. 2020 Mar;113(3):659-671
pubmed: 31975449
Sci Rep. 2017 Mar 16;7:44598
pubmed: 28300209
Methods Mol Biol. 2017;1615:23-57
pubmed: 28667600
Math Biosci. 2005 Feb;193(2):223-34
pubmed: 15748731
Protein Sci. 2003 Aug;12(8):1652-62
pubmed: 12876315
Proteomics. 2016 Jan;16(2):226-40
pubmed: 26773550
Microb Genom. 2020 Mar;6(3):
pubmed: 32124724
Proteins. 2006 Aug 15;64(3):643-51
pubmed: 16752418
Curr Opin Struct Biol. 2005 Jun;15(3):267-74
pubmed: 15922590
Bioinformatics. 2010 Jul 1;26(13):1608-15
pubmed: 20472543
Stand Genomic Sci. 2015 Nov 19;10:108
pubmed: 26594309
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W350-5
pubmed: 24848019
Nat Rev Microbiol. 2006 Oct;4(10):741-51
pubmed: 16964270
Proteins. 1991;11(2):95-110
pubmed: 1946347
BMC Genomics. 2018 Dec 19;19(1):948
pubmed: 30567498
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
BMC Genomics. 2014;15 Suppl 6:S16
pubmed: 25573073
Bioinformatics. 2004 Mar 1;20(4):547-56
pubmed: 14990451
Mol Microbiol. 1999 Oct;34(1):195
pubmed: 10540297
BMC Genomics. 2019 Jul 16;20(Suppl 8):547
pubmed: 31307390
J Mol Biol. 2009 Mar 27;387(2):416-30
pubmed: 19135455
J Bacteriol. 2006 Sep;188(18):6652-60
pubmed: 16952957
Bioinformatics. 2017 Apr 15;33(8):1224-1226
pubmed: 28057683
Genomics. 2019 Jul;111(4):886-892
pubmed: 29842950
Nat Methods. 2011 Sep 29;8(10):785-6
pubmed: 21959131
Nucleic Acids Res. 2018 Jul 2;46(W1):W459-W466
pubmed: 29718411
Protein J. 2019 Jun;38(3):200-216
pubmed: 31119599
PLoS Pathog. 2007 Aug 3;3(8):e105
pubmed: 17676952
Curr Top Microbiol Immunol. 2017;404:129-158
pubmed: 26728066
Nucleic Acids Res. 2019 Jan 8;47(D1):D351-D360
pubmed: 30398656
J Proteome Res. 2013 Sep 6;12(9):4101-10
pubmed: 23937099
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
Biochim Biophys Acta. 2012 Dec;1824(12):1425-33
pubmed: 22705560
Genomics. 1992 Dec;14(4):897-911
pubmed: 1478671
Proteins. 2000 Oct 1;41(1):98-107
pubmed: 10944397
Front Microbiol. 2011 Nov 08;2:218
pubmed: 22073040
Bioinformatics. 2014 Dec 1;30(23):3356-64
pubmed: 25150248
Nat Biotechnol. 2019 Apr;37(4):420-423
pubmed: 30778233
Bioinformatics. 2017 Nov 1;33(21):3387-3395
pubmed: 29036616
Bioinformatics. 2017 Mar 15;33(6):843-853
pubmed: 27993784
Trends Microbiol. 2009 Apr;17(4):139-45
pubmed: 19299134
Microb Biotechnol. 2018 Jul;11(4):588-605
pubmed: 29806194
Proteomics. 2010 Nov;10(22):3970-83
pubmed: 21080490
J Gen Microbiol. 1992 May;138(5):861-9
pubmed: 1645127
BMC Bioinformatics. 2015 Sep 18;16:297
pubmed: 26384938
Nucleic Acids Res. 2007;35(15):e96
pubmed: 17670799
Biomed Res Int. 2019 Nov 19;2019:5617153
pubmed: 31886228
Mol Biol Res Commun. 2019 Mar;8(1):17-26
pubmed: 31528640
J Mol Biol. 2001 Jan 19;305(3):567-80
pubmed: 11152613
Bioinformatics. 2010 Mar 1;26(5):680-2
pubmed: 20053844
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W379-81
pubmed: 16845030
Bioinformatics. 2002 Dec;18(12):1641-9
pubmed: 12490449
Bioinformatics. 2019 Aug 15;35(16):2757-2765
pubmed: 30590410
Genomics Proteomics Bioinformatics. 2004 Nov;2(4):209-15
pubmed: 15901249
Science. 1998 Sep 4;281(5382):1457
pubmed: 9750114
Protein Expr Purif. 2005 Jan;39(1):1-7
pubmed: 15596354
Microb Biotechnol. 2016 Sep;9(5):530-40
pubmed: 27435445