Identification and functional annotation of hypothetical proteins of uropathogenic Escherichia coli strain CFT073 towards designing antimicrobial drug targets

References

• Ahn, R. E. J. (1998). Conserved structural features of the synaptic fusion complex: SNARE proteins reclassified as Q- and R-SNAREs. Proceedings of the National Academy of Sciences of the United States of America, 95(26), 15781–15786.
   PubMed Web of Science ®Google Scholar
• Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., Lipman, D. J., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., Lipman, D., Arciszewska, L., Drake, D., Craig, N., Chauvatcharin, N., Atichartpongkul, S., Utamapongchai, S., … Craig, N. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389–3402. https://doi.org/10.1111/j.1574-6968.2009.01707.x
   PubMed Web of Science ®Google Scholar
• Amato, S. M., Fazen, C. H., Henry, T. C., Mok, W. W. K., Orman, M. A., Sandvik, E. L., Volzing, K. G., & Brynildsen, M. P. (2014). The role of metabolism in bacterial persistence. Frontiers in Microbiology, 5(MAR), 70–79. https://doi.org/10.3389/fmicb.2014.00070
   PubMedGoogle Scholar
• Beacham, I. R. (1979). Periplasmic enzymes in gram-negative bacteria. International Journal of Biochemistry, 10(11), 877–883. https://doi.org/10.1016/0020-711X(79)90117-4
   PubMedGoogle Scholar
• Carfi, A., Pares, S., Duée, E., Galleni, M., Duez, C., Frère, J. M., & Dideberg, O. (1995). The 3-D structure of a zinc metallo-β-lactamase from Bacillus cereus reveals a new type of protein fold. The EMBO Journal, 14(20), 4914–4921. https://doi.org/10.1002/j.1460-2075.1995.tb00174.x
   PubMed Web of Science ®Google Scholar
• Cegelski, L., Marshall, G. R., Eldridge, G. R., & Hultgren, S. J. (2008). The biology and future prospects of antivirulence therapies. Nature Reviews. Microbiology, 6(1), 17–27. https://doi.org/10.1038/nrmicro2244
   PubMed Web of Science ®Google Scholar
• Choi, U., & Lee, C. R. (2019). Distinct Roles of Outer Membrane Porins in Antibiotic Resistance and Membrane Integrity in Escherichia coli. Frontiers in Microbiology, 10(APR), 953–959. https://doi.org/10.3389/fmicb.2019.00953
   PubMedGoogle Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science: A Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Crowther, G. J., Shanmugam, D., Carmona, S. J., Doyle, M. A., Hertz-Fowler, C., Berriman, M., Nwaka, S., Ralph, S. A., Roos, D. S., Van Voorhis, W. C., & Agüero, F. (2010). Identification of attractive drug targets in neglected-disease pathogens using an in silico approach. PLoS Neglected Tropical Diseases, 4(8), e804. https://doi.org/10.1371/journal.pntd.0000804
   PubMed Web of Science ®Google Scholar
• de Castro, E., Sigrist, C. J. a., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P. S., Gasteiger, E., Bairoch, A., & Hulo, N. (2006). ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Research, 34(Web Server), W362–365. https://doi.org/10.1093/nar/gkl124
   PubMedGoogle Scholar
• Delcour, A. H. (2009). Outer membrane permeability and antibiotic resistance. Biochim Biophys Acta, 1794(5), 808–816. https://doi.org/10.1016/j.bbapap.2008.11.005
   PubMed Web of Science ®Google Scholar
• Derbyshire, M. K., Gonzales, N. R., Lu, S., He, J., Marchler, G. H., Wang, Z., & Marchler-Bauer, A. (2015). Improving the consistency of domain annotation within the Conserved Domain Database. Database, 2015(7), 1–8. https://doi.org/10.1093/database/bav012
   Google Scholar
• Desler, C., Suravajhala, P., Sanderhoff, M., Rasmussen, M., & Rasmussen, L. J. (2009). In Silico screening for functional candidates amongst hypothetical proteins. BMC Bioinformatics, 10(1), 289. https://doi.org/10.1186/1471-2105-10-289
   PubMedGoogle Scholar
• Dillon, S. C., & Bateman, A. (2004). The Hotdog fold: Wrapping up a superfamily of thioesterases and dehydratases. BMC Bioinformatics, 5, 109. https://doi.org/10.1186/1471-2105-5-109
   PubMed Web of Science ®Google Scholar
• Emanuelsson, O., Brunak, S., von Heijne, G., & Nielsen, H. (2007). Locating proteins in the cell using TargetP, SignalP and related tools. Nature Protocols, 2(4), 953–971. https://doi.org/10.1038/nprot.2007.131
   PubMed Web of Science ®Google Scholar
• Fleitas Martínez, O., Cardoso, M. H., Ribeiro, S. M., & Franco, O. L. (2019). Recent advances in anti-virulence therapeutic strategies with a focus on dismantling bacterial membrane microdomains, toxin neutralization, quorum-sensing interference and biofilm inhibition. Frontiers in Cellular and Infection Microbiology, 9(APR), 74. https://doi.org/10.3389/fcimb.2019.00074
   PubMedGoogle Scholar
• Flores-Mireles, A. L., Walker, J. N., Caparon, M., & Hultgren, S. J. (2015). Urinary tract infections: Epidemiology, mechanisms of infection and treatment options. Nature Reviews Microbiology , 13(5), 269–284. https://doi.org/10.1038/nrmicro3432
   PubMed Web of Science ®Google Scholar
• Frisinger, F. S., Jana, B., Donadio, S., & Guardabassi, L. (2021). In Silico Prediction and Prioritisation of Novel Selective Antimicrobial Drug Targets in Escherichia Coli. Antibiotics (Basel), 10(6), 1–19.
   Web of Science ®Google Scholar
• Fumagalli, M., Lecca, D., Abbracchio, M. P., & Ceruti, S. (2017). Pathophysiological role of purines and pyrimidines in neurodevelopment: Unveiling new pharmacological approaches to congenital brain diseases. Frontiers in Pharmacology, 8(DEC), 918–941. https://doi.org/10.3389/fphar.2017.00941
   PubMedGoogle Scholar
• Garg, A., & Gupta, D. (2008). VirulentPred: A SVM based prediction method for virulent proteins in bacterial pathogens. BMC Bioinformatics, 9(1), 62. https://doi.org/10.1186/1471-2105-9-62
   PubMedGoogle Scholar
• Gough, J., Karplus, K., Hughey, R., & Chothia, C. (2001). Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure1. Journal of Molecular Biology , 313(4), 903–919. https://doi.org/10.1006/jmbi.2001.5080
   PubMed Web of Science ®Google Scholar
• Green, D. M., Trifillis, A. L., Johnson, D. E., Chippendale, G. R., Lockatell, C. V., Jones, B. D., & Warren, J. W. (1990). Pyelonephritogenic Escherichia coli and killing of cultured human renal proximal tubular epithelial cells: Role of hemolysin in some strains. Infection and Immunity, 58(5), 1281–1289.
   PubMed Web of Science ®Google Scholar
• Green, E. R., & Mecsas, J. (2016). Bacterial secretion systems: An overview. Virulence Mechanisms of Bacterial Pathogens, 4(1), 213–239. https://doi.org/10.1128/9781555819286.ch8
   Google Scholar
• Hantke, K. (2001). Iron and metal regulation in bacteria. Current Opinion in Microbiology, 4(2), 172–177. https://doi.org/10.1016/S1369-5274(00)00184-3
   PubMed Web of Science ®Google Scholar
• Hiller, K., Grote, A., Maneck, M., Münch, R., & Jahn, D. (2006). JVirGel 2.0: Computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins. Bioinformatics (Oxford, England), 22(19), 2441–2443. https://doi.org/10.1093/bioinformatics/btl409
   PubMed Web of Science ®Google Scholar
• Hua, S., & Sun, Z. (2001). Support vector machine approach for protein subcellular localization prediction. Bioinformatics (Oxford, England), 17(8), 721–728. https://doi.org/10.1093/bioinformatics/17.8.721
   PubMed Web of Science ®Google Scholar
• Humann, J., & Lenz, L. L. (2009). Bacterial peptidoglycan degrading enzymes and their impact on host muropeptide detection . Journal of Innate Immunity, 1(2), 88–97. https://doi.org/10.1159/000181181
   PubMed Web of Science ®Google Scholar
• Johnson, J. R. (1991). Virulence factors in Escherichia coli urinary tract infection. Clinical Microbiology Reviews, 4(1), 80–128. https://doi.org/10.1128/CMR.4.1.80.Updated
   PubMed Web of Science ®Google Scholar
• Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A. F., Sangrador-Vegas, A., Scheremetjew, M., Yong, S. Y., Lopez, R., & Hunter, S. (2014). InterProScan 5: Genome-scale protein function classification. Bioinformatics (Oxford, England), 30(9), 1236–1240. https://doi.org/10.1093/bioinformatics/btu031
   PubMed Web of Science ®Google Scholar
• Kalia, M., Yadav, V. K., Singh, P. K., Sharma, D., Narvi, S. S., & Agarwal, V. (2018). Exploring the impact of parthenolide as anti-quorum sensing and anti-biofilm agent against Pseudomonas aeruginosa. Life Sciences, 199, 96–103. https://doi.org/10.1016/j.lfs.2018.03.013
   PubMed Web of Science ®Google Scholar
• Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., & Tanabe, M. (2014). Data, information, knowledge and principle: Back to metabolism in KEGG. Nucleic Acids Research, 42(D1), D199–205. https://doi.org/10.1093/nar/gkt1076
   PubMed Web of Science ®Google Scholar
• Kaper, J. B., Nataro, J. P., & Mobley, H. L. (2004). Pathogenic Escherichia coli. Nature Reviews. Microbiology, 2(2), 123–140. https://doi.org/10.1038/nrmicro818
   PubMed Web of Science ®Google Scholar
• Kaur, H., Kalia, M., & Taneja, N. (2021). Identification of novel non-homologous drug targets against Acinetobacter baumannii using subtractive genomics and comparative metabolic pathway analysis. Microbial Pathogenesis, 152(July), 104608. https://doi.org/10.1016/j.micpath.2020.104608
   PubMedGoogle Scholar
• Kawai, Y., Mercier, R., Mickiewicz, K., Serafini, A., Sório de Carvalho, L. P., & Errington, J. (2019). Crucial role for central carbon metabolism in the bacterial L-form switch and killing by β-lactam antibiotics. Nature Microbiology, 4(10), 1716–1726. https://doi.org/10.1038/s41564-019-0497-3
   PubMed Web of Science ®Google Scholar
• Khan, A. U., Maryam, L., & Zarrilli, R. (2017). Structure, Genetics and Worldwide Spread of New Delhi Metallo-β-lactamase (NDM): A threat to public health. BMC Microbiology, 17(1), 101–112. https://doi.org/10.1186/s12866-017-1012-8
   PubMedGoogle Scholar
• Kilstrup, M., Hammer, K., Jensen, P. R., & Martinussen, J. (2005). Nucleotide metabolism and its control in lactic acid bacteria. FEMS Microbiology Reviews, 29(3), 555–590. https://doi.org/10.1016/j.femsre.2005.04.006
   PubMed Web of Science ®Google Scholar
• Krogh, a., Larsson, B., von Heijne, G., & Sonnhammer, E. L. L. (2001). Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. Journal of Molecular Biology, 305(3), 567–580. https://doi.org/10.1006/jmbi.2000.4315
   PubMed Web of Science ®Google Scholar
• Kumar, K., Prakash, A., Tasleem, M., Islam, A., Ahmad, F., & Hassan, M. I. (2014). Functional annotation of putative hypothetical proteins from Candida dubliniensis. Gene, 543(1), 93–100. https://doi.org/10.1016/j.gene.2014.03.060
   PubMed Web of Science ®Google Scholar
• Kushwaha, S. K., & Shakya, M. (2010). Protein interaction network analysis-Approach for potential drug target identification in Mycobacterium tuberculosis. Journal of Theoretical Biology, 262(2), 284–294. https://doi.org/10.1016/j.jtbi.2009.09.029
   PubMed Web of Science ®Google Scholar
• Laskowski, R. a., Rullmannn, J. a., MacArthur, M. W., Kaptein, R., & Thornton, J. M. (1996). AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR, 8(4), 477–486. https://doi.org/10.1007/BF00228148
   PubMed Web of Science ®Google Scholar
• Law, V., Knox, C., Djoumbou, Y., Jewison, T., Guo, A. C., Liu, Y., MacIejewski, A., Arndt, D., Wilson, M., Neveu, V., Tang, A., Gabriel, G., Ly, C., Adamjee, S., Dame, Z. T., Han, B., Zhou, Y., & Wishart, D. S. (2014). DrugBank 4.0: Shedding new light on drug metabolism. Nucleic Acids Research, 42(D1), D1091–D1097. https://doi.org/10.1093/nar/gkt1068
   PubMed Web of Science ®Google Scholar
• Leithner, K., Triebl, A., Trötzmüller, M., Hinteregger, B., Leko, P., Wieser, B. I., Grasmann, G., Bertsch, A. L., Züllig, T., Stacher, E., Valli, A., Prassl, R., Olschewski, A., Harris, A. L., Köfeler, H. C., Olschewski, H., & Hrzenjak, A. (2018). The glycerol backbone of phospholipids derives from noncarbohydrate precursors in starved lung cancer cells. Proceedings of the National Academy of Sciences of the United States of America, 115(24), 6225–6230. https://doi.org/10.1073/pnas.1719871115
   PubMed Web of Science ®Google Scholar
• Letunic, I., Doerks, T., & Bork, P. (2015). SMART: Recent updates, new developments and status in 2015. Nucleic Acids Research, 43(D1), D257–D260. https://doi.org/10.1093/nar/gku949
   PubMed Web of Science ®Google Scholar
• Luo, H., Lin, Y., Gao, F., Zhang, C. T., & Zhang, R. (2014). DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Research, 42(D1), D574–D580. https://doi.org/10.1093/nar/gkt1131
   PubMed Web of Science ®Google Scholar
• Miyoshi, S. I., & Shinoda, S. (1997). Bacterial metalloprotease as the toxic factor in infection. Journal of Toxicology: Toxin Reviews, 16(4), 177–194. https://doi.org/10.3109/15569549709016455
   Web of Science ®Google Scholar
• Mohan, R., & Venugopal, S. (2012). Computational structural and functional analysis of hypothetical proteins of Staphylococcus aureus. Bioinformation, 8(15), 722–728. https://doi.org/10.6026/97320630008722
   PubMedGoogle Scholar
• Nicholson, T. F., Watts, K. M., & Hunstad, D. A. (2009). OmpA of uropathogenic Escherichia coli promotes postinvasion pathogenesis of cystitis. Infection and Immunity, 77(12), 5245–5251. https://doi.org/10.1128/IAI.00670-09
   PubMed Web of Science ®Google Scholar
• Nicolle, L. E. (2005). Complicated urinary tract infection in adults. The Canadian Journal of Infectious Diseases & Medical Microbiology = Journal Canadien Des Maladies Infectieuses et de la Microbiologie Medicale, 16(6), 349–360. https://doi.org/10.1155/2005/385768
   PubMedGoogle Scholar
• Pao, S. S., Paulsen, I. T., & Saier, M. H. (1998). Major facilitator superfamily. Microbiology and Molecular Biology Reviews: MMBR, 62(1), 1–34. https://doi.org/10.1128/MMBR.62.1.1-34.1998
   PubMed Web of Science ®Google Scholar
• Pedruzzi, I., Rivoire, C., Auchincloss, A. H., Coudert, E., Keller, G., De Castro, E., Baratin, D., Cuche, B. a., Bougueleret, L., Poux, S., Redaschi, N., Xenarios, I., & Bridge, A. (2015). HAMAP in 2015: Updates to the protein family classification and annotation system. Nucleic Acids Research, 43(D1), D1064–D1070. https://doi.org/10.1093/nar/gku1002
   PubMed Web of Science ®Google Scholar
• Pranavathiyani, G., Prava, J., Rajeev, A. C., & Pan, A. (2020). Novel target exploration from hypothetical proteins of Klebsiella pneumoniae MGH 78578 reveals a protein involved in host-pathogen interaction. Frontiers in Cellular and Infection Microbiology, 10(April), 109–113. https://doi.org/10.3389/fcimb.2020.00109
   PubMedGoogle Scholar
• Punta, M., Coggill, P., Eberhardt, R., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E., Eddy, S., Bateman, A., & Finn, R. (2012). The Pfam protein families databases. Nucleic Acids Research, 40, D290–D301. https://doi.org/10.1093/nar/gkp985
   Google Scholar
• Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., & Lopez, R. (2005). InterProScan: Protein domains identifier. Nucleic Acids Research, 33(SUPPL. 2), W116–120. https://doi.org/10.1093/nar/gki442
   PubMedGoogle Scholar
• Rabbi, M. F., Akter, S. A., Hasan, M. J., & Amin, A. (2021). In silico characterization of a hypothetical protein from Shigella dysenteriae ATCC 12039 reveals a pathogenesis-related protein of the type-VI secretion system. Bioinformatics and Biology Insights, 15, 11779322211011140. https://doi.org/10.1177/11779322211011140
   Web of Science ®Google Scholar
• Rappas, M., Niwa, H., & Zhang, X. (2005). Mechanisms of ATPases-a multi-disciplinary approach. Current Protein and Peptide Science, 5(2), 89–105. https://doi.org/10.2174/1389203043486874
   Web of Science ®Google Scholar
• Rice, P., Longden, I., & Bleasby, A. (2000). EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics, 16(6), 276–277.
   PubMed Web of Science ®Google Scholar
• Saha, S., & Raghava, G. P. S. (2006). VICMpred: An SVM-based method for the prediction of functional proteins of gram-negative bacteria using amino acid patterns and composition. Genomics, Proteomics & Bioinformatics, 4(1), 42–47. https://doi.org/10.1016/S1672-0229(06)60015-6
   PubMedGoogle Scholar
• Samant, S., Lee, H., Ghassemi, M., Chen, J., Cook, J. L., Mankin, A. S., & Neyfakh, A. a. (2008). Nucleotide biosynthesis is critical for growth of bacteria in human blood. PLoS Pathogens, 4(2), e37. https://doi.org/10.1371/journal.ppat.0040037
   PubMed Web of Science ®Google Scholar
• Sarkar, M., Maganti, L., Ghoshal, N., & Dutta, C. (2012). In silico quest for putative drug targets in Helicobacter pylori HPAG1: Molecular modeling of candidate enzymes from lipopolysaccharide biosynthesis pathway. Journal of Molecular Modeling, 18(5), 1855–1865. https://doi.org/10.1007/s00894-011-1204-3
   PubMed Web of Science ®Google Scholar
• Selvaraj, S. K., Periandythevar, P., & Prasadarao, N. V. (2007). Outer membrane protein A of Escherichia coli K1 selectively enhances the expression of intercellular adhesion molecule-1 in brain microvascular endothelial cells. Microbes and Infection, 9(5), 547–557. https://doi.org/10.1016/j.micinf.2007.01.020
   PubMed Web of Science ®Google Scholar
• Sen, T., & Verma, N. K. (2020). Functional annotation and curation of hypothetical proteins present in A newly emerged serotype 1c of Shigella flexneri: Emphasis on selecting targets for virulence and vaccine design studies. Genes, 11(3), 340. https://doi.org/10.3390/genes11030340
   PubMed Web of Science ®Google Scholar
• Sigrist, C. J. a., Cerutti, L., De Castro, E., Langendijk-Genevaux, P. S., Bulliard, V., Bairoch, A., & Hulo, N. (2009). PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Research, 38(suppl_1), D161–166. https://doi.org/10.1093/nar/gkp885
   PubMedGoogle Scholar
• Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., Kuhn, M., Bork, P., Jensen, L. J., & Von Mering, C. (2015). STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research, 43(Database issue), D447–D452. https://doi.org/10.1093/nar/gku1003
   PubMed Web of Science ®Google Scholar
• Tang, K. H., Tang, Y. J., & Blankenship, R. E. (2011). Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications. Frontiers in Microbiology, 2(AUG), 123–165. https://doi.org/10.3389/fmicb.2011.00165
   PubMedGoogle Scholar
• Teh, B. A., Choi, S. B., Musa, N., Ling, F. L., Cun, S. T. W., Salleh, A. B., Najimudin, N., Wahab, H. a., & Normi, Y. M. (2014). Structure to function prediction of hypothetical protein KPN_00953 (Ycbk) from Klebsiella pneumoniae MGH 78578 highlights possible role in cell wall metabolism. BMC Structural Biology, 14(1), 7. https://doi.org/10.1186/1472-6807-14-7
   PubMedGoogle Scholar
• Terlizzi, M. E., Gribaudo, G., & Maffei, M. E. (2017). UroPathogenic Escherichia coli (UPEC) infections: Virulence factors, bladder responses, antibiotic, and non-antibiotic antimicrobial strategies. Frontiers in Microbiology, 8(AUG), 1566. https://doi.org/10.3389/fmicb.2017.01566
   PubMedGoogle Scholar
• Tsirigos, K. D., Peters, C., Shu, N., Käll, L., & Elofsson, A. (2015). The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res, 43(W1), W401–7. https://doi.org/10.1093/nar/gkv485
   PubMed Web of Science ®Google Scholar
• Tusnády, G. E., & Simon, I. (2001). The HMMTOP transmembrane topology prediction server. Bioinformatics (Oxford, England), 17(9), 849–850. https://doi.org/10.1093/bioinformatics/17.9.849
   PubMed Web of Science ®Google Scholar
• Vemula, M. H., Ganji, R., Sivangala, R., Jakkala, K., Gaddam, S., Penmetsa, S., & Banerjee, S. (2016). Mycobacterium tuberculosis zinc metalloprotease-1 elicits tuberculosis-specific humoral immune response independent of mycobacterial load in pulmonary and extra-pulmonary tuberculosis patients. Frontiers in Microbiology, 7(MAR), 412–418. https://doi.org/10.3389/fmicb.2016.00418
   PubMedGoogle Scholar
• Wang, W., Arshad, M. I., Khurshid, M., Rasool, M. H., Nisar, M. A., Aslam, M. A., & Qamar, M. U. (2018). Antibiotic resistance: A rundown of a global crisis. Infection and Drug Resistance, 11, 1645–1658.
   PubMed Web of Science ®Google Scholar
• Welch, R. A., Burland, V., Plunkett, G., Redford, P., Roesch, P., Rasko, D., Buckles, E. L., Liou, S.-R., Boutin, A., Hackett, J., Stroud, D., Mayhew, G. F., Rose, D. J., Zhou, S., Schwartz, D. C., Perna, N. T., Mobley, H. L. T., Donnenberg, M. S., & Blattner, F. R. (2002). Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proceedings of the National Academy of Sciences, 99(26), 17020–17024. https://doi.org/10.1073/pnas.252529799
   PubMed Web of Science ®Google Scholar
• Wesolowski, J., & Paumet, F. (2008). SNARE motif: A common motif used by pathogens to manipulate membrane fusion. Virulence, 1(4), 319–324. https://doi.org/10.4161/viru.1.4.12195
   Google Scholar
• Xi, H., Schneider, B. L., & Reitzer, L. (2000). Purine catabolism in Escherichia coli and function of xanthine dehydrogenase in purine salvage. Journal of Bacteriology, 182(19), 5332–5341. https://doi.org/10.1128/JB.182.19.5332-5341.2000
   PubMed Web of Science ®Google Scholar
• Yu, C., Lin, C., & Hwang, J.-K. (2004). Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n -peptide compositions. Protein Science, 13(5), 1402–1406. https://doi.org/10.1110/ps.03479604
   PubMed Web of Science ®Google Scholar
• Yu, C.-S., Cheng, C.-W., Su, W.-C., Chang, K.-C., Huang, S.-W., Hwang, J.-K., & Lu, C.-H. (2014). CELLO2GO: A web server for protein subCELlular LOcalization Prediction with Functional Gene Ontology annotation. PloS One, 9(6), e99368. https://doi.org/10.1371/journal.pone.0099368
   PubMed Web of Science ®Google Scholar
• Yu, N. Y., Wagner, J. R., Laird, M. R., Melli, G., Rey, S., Lo, R., Dao, P., Cenk Sahinalp, S., Ester, M., Foster, L. J., & Brinkman, F. S. L. (2010). PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics (Oxford, England), 26(13), 1608–1615. https://doi.org/10.1093/bioinformatics/btq249
   PubMed Web of Science ®Google Scholar