References
- Altekruse SF, Stern NJ, Fields PI, Swerdlow DL. Campylobacter jejuni: an emerging foodborne pathogen. Emerg Infect Dis 1999;5:28-35. https://doi.org/10.3201/eid0501.990104
- Balaban M, Hendrixson DR. Polar flagellar biosynthesis and a regulator of flagellar number influence spatial parameters of cell division in Campylobacter jejuni. PLoS Pathog 2011;7:e1002420. https://doi.org/10.1371/journal.ppat.1002420
- Young KT, Davis LM, Dirita VJ. Campylobacter jejuni: molecular biology and pathogenesis. Nat Rev Microbiol 2007;5:665-679. https://doi.org/10.1038/nrmicro1718
- Allos BM. Campylobacter jejuni infections: update on emerging issues and trends. Clin Infect Dis 2001;32:1201-1206. https://doi.org/10.1086/319760
- Snelling WJ, Matsuda M, Moore JE, Dooley JS. Campylobacter jejuni. Lett Appl Microbiol 2005;41:297-302. https://doi.org/10.1111/j.1472-765X.2005.01788.x
- Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, Basham D, et al. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 2000;403:665-668. https://doi.org/10.1038/35001088
- Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, et al. Exploration of uncharted regions of the protein universe. PLoS Biol 2009;7:e1000205. https://doi.org/10.1371/journal.pbio.1000205
- Nimrod G, Schushan M, Steinberg DM, Ben-Tal N. Detection of functionally important regions in "hypothetical proteins" of known structure. Structure 2008;16:1755-1763. https://doi.org/10.1016/j.str.2008.10.017
- Ferdous N, Reza MN, Emon MT, Islam MS, Mohiuddin AKM, Hossain MU. Molecular characterization and functional annotation of a hypothetical protein (SCO0618) of Streptomyces coelicolor A3(2). Genomics Inform 2020;18:e28. https://doi.org/10.5808/GI.2020.18.3.e28
- Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2019;47:D607-D613. https://doi.org/10.1093/nar/gky1131
- Jez JM. Revisiting protein structure, function, and evolution in the genomic era. J Invertebr Pathol 2017;142:11-15. https://doi.org/10.1016/j.jip.2016.07.013
- Stahl M, Butcher J, Stintzi A. Nutrient acquisition and metabolism by Campylobacter jejuni. Front Cell Infect Microbiol 2012;2:5.
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402. https://doi.org/10.1093/nar/25.17.3389
- Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792-1797. https://doi.org/10.1093/nar/gkh340
- Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018;35:1547-1549. https://doi.org/10.1093/molbev/msy096
- Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003;31:3784-3788. https://doi.org/10.1093/nar/gkg563
- Yu CS, Lin CJ, Hwang JK. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci 2004;13:1402-1406. https://doi.org/10.1110/ps.03479604
- Bhasin M, Garg A, Raghava GP. PSLpred: prediction of subcellular localization of bacterial proteins. Bioinformatics 2005;21:2522-2524. https://doi.org/10.1093/bioinformatics/bti309
- Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 2010;26:1608-1615. https://doi.org/10.1093/bioinformatics/btq249
- Secondary structure analysis of a protein using SOPMA. Ettimadai: Amrita Vishwa Vidyapeetham Virtual Lab, 2012. Accessed 2021 Nov 30. Available from: https://vlab.amrita.edu/?sub-=3&brch=275&sim=1454&cnt=1.
- Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202. https://doi.org/10.1006/jmbi.1999.3091
- Zimmermann L, Stephens A, Nam SZ, Rau D, Kubler J, Lozajic M, et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J Mol Biol 2018;430:2237-2243. https://doi.org/10.1016/j.jmb.2017.12.007
- Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, et al. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: four approaches that performed well in CASP8. Proteins 2009;77 Suppl 9:114-122. https://doi.org/10.1002/prot.22570
- Likova E, Petkov P, Ilieva N, Litov L. The PyMOL Molecular Graphics System, version 2.0. New York: Schrodinger, LLC, 2015.
- Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PRO-CHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291. https://doi.org/10.1107/s0021889892009944
- Eisenberg D, Luthy R, Bowie JU. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 1997;277:396-404. https://doi.org/10.1016/S0076-6879(97)77022-8
- Colovos C, Yeates TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 1993;2:1511-1519. https://doi.org/10.1002/pro.5560020916
- Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, et al. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 2011;39:D225-D229. https://doi.org/10.1093/nar/gkq1189
- Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 2014;30:1236-1240. https://doi.org/10.1093/bioinformatics/btu031
- Tian W, Chen C, Lei X, Zhao J, Liang J. CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Res 2018;46:W363-W367. https://doi.org/10.1093/nar/gky473
- Eng J. ROC analysis: web-based calculator for ROC curves. Baltimore: Johns Hopkins University, 2014. Accessed 2021 Nov 30. Available from: http://www.jrocfit.org.
- Halarnkar PP, Blomquist GJ. Comparative aspects of propionate metabolism. Comp Biochem Physiol B 1989;92:227-231. https://doi.org/10.1016/0305-0491(89)90270-8
- Suvorova IA, Ravcheev DA, Gelfand MS. Regulation and evolution of malonate and propionate catabolism in proteobacteria. J Bacteriol 2012;194:3234-3240. https://doi.org/10.1128/JB.00163-12
- Horswill AR, Escalante-Semerena JC. In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate. Biochemistry 2001;40:4703-4713. https://doi.org/10.1021/bi015503b
- Blank L, Green J, Guest JR. AcnC of Escherichia coli is a 2-methylcitrate dehydratase (PrpD) that can use citrate and isocitrate as substrates. Microbiology (Reading) 2002;148:133-146. https://doi.org/10.1099/00221287-148-1-133
- Lohkamp B, Bauerle B, Rieger PG, Schneider G. Three-dimensional structure of iminodisuccinate epimerase defines the fold of the MmgE/PrpD protein family. J Mol Biol 2006;362:555-566. https://doi.org/10.1016/j.jmb.2006.07.051
- Kanamasa S, Dwiarti L, Okabe M, Park EY. Cloning and functional characterization of the cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus. Appl Microbiol Biotechnol 2008;80:223-229. https://doi.org/10.1007/s00253-008-1523-1
- Reddick JJ, Sirkisoon S, Dahal RA, Hardesty G, Hage NE, Booth WT, et al. First biochemical characterization of a methylcitric acid cycle from Bacillus subtilis strain 168. Biochemistry 2017;56:5698-5711. https://doi.org/10.1021/acs.biochem.7b00778