{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T21:54:09Z","timestamp":1787003649083,"version":"build-2736575974"},"reference-count":63,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T00:00:00Z","timestamp":1768867200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T00:00:00Z","timestamp":1770768000000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM136396"],"award-info":[{"award-number":["R35GM136396"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-026-36188-9","type":"journal-article","created":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T15:19:23Z","timestamp":1768922363000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["The Lysis cassette of jumbophage PhiKZ"],"prefix":"10.1038","volume":"16","author":[{"given":"Prasanth","family":"Manohar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Wan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriella","family":"Ganser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiersten","family":"Sharp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ry","family":"Young","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,1,20]]},"reference":[{"key":"36188_CR1","first-page":"678","volume":"14","author":"VN Krylov","year":"1978","unstructured":"Krylov, V. N. & Zhazykov, I. Z. [Pseudomonas bacteriophage phiKZ\u2013possible model for studying the genetic control of morphogenesis]. Genetika 14, 678\u2013685 (1978).","journal-title":"Genetika"},{"key":"36188_CR2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1006\/jmbi.2001.5396","volume":"317","author":"VV Mesyanzhinov","year":"2002","unstructured":"Mesyanzhinov, V. V. et al. The genome of bacteriophage phiKZ of Pseudomonas aeruginosa. J. Mol. Biol. 317, 1\u201319 (2002).","journal-title":"J. Mol. Biol."},{"key":"36188_CR3","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1038\/s41586-019-1786-y","volume":"577","author":"SD Mendoza","year":"2020","unstructured":"Mendoza, S. D. et al. A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases. Nature 577, 244\u2013248 (2020).","journal-title":"Nature"},{"key":"36188_CR4","doi-asserted-by":"publisher","unstructured":"Cahill, J. & Young, R. Phage lysis: multiple genes for multiple barriers. in 33\u201370. https:\/\/doi.org\/10.1016\/bs.aivir.2018.09.003 (2019).","DOI":"10.1016\/bs.aivir.2018.09.003"},{"key":"36188_CR5","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1007\/s12275-014-4087-z","volume":"52","author":"R Young","year":"2014","unstructured":"Young, R. Phage lysis: three steps, three choices, one outcome. J. Microbiol. 52, 243\u2013258 (2014).","journal-title":"J. Microbiol."},{"key":"36188_CR6","doi-asserted-by":"publisher","unstructured":"Cahill, J. & Young, R. Release of Phages From Prokaryotic Cells. in Encyclopedia of Virology 501\u2013518 https:\/\/doi.org\/10.1016\/B978-0-12-814515-9.00074-6 (Elsevier, 2021).","DOI":"10.1016\/B978-0-12-814515-9.00074-6"},{"key":"36188_CR7","doi-asserted-by":"publisher","first-page":"9348","DOI":"10.1073\/pnas.151247598","volume":"98","author":"A Gr\u00fcndling","year":"2001","unstructured":"Gr\u00fcndling, A., Manson, M. D. & Young, R. Holins kill without warning. Proc. Natl. Acad. Sci. U S A. 98, 9348\u20139352 (2001).","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"36188_CR8","doi-asserted-by":"crossref","unstructured":"Cahill, J. et al. Spatial and temporal control of lysis by the lambda holin. mBio 15, (2024).","DOI":"10.1128\/mbio.01290-23"},{"key":"36188_CR9","doi-asserted-by":"publisher","first-page":"1967","DOI":"10.1002\/pro.485","volume":"19","author":"J Berry","year":"2010","unstructured":"Berry, J., Savva, C., Holzenburg, A. & Young, R. The lambda spanin components Rz and Rz1 undergo tertiary and quaternary rearrangements upon complex formation. Protein Sci. 19, 1967\u20131977 (2010).","journal-title":"Protein Sci."},{"key":"36188_CR10","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1534\/g3.116.037192","volume":"7","author":"J Cahill","year":"2017","unstructured":"Cahill, J. et al. Genetic analysis of the lambda spanins Rz and Rz1: identification of functional domains. G3 Genes|Genomes|Genetics. 7, 741\u2013753 (2017).","journal-title":"G3 Genes|Genomes|Genetics"},{"key":"36188_CR11","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1111\/mmi.12167","volume":"88","author":"JD Berry","year":"2013","unstructured":"Berry, J. D., Rajaure, M. & Young, R. Spanin function requires subunit homodimerization through intermolecular disulfide bonds. Mol. Microbiol. 88, 35\u201347 (2013).","journal-title":"Mol. Microbiol."},{"key":"36188_CR12","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1134\/S0006297906030102","volume":"71","author":"KA Miroshnikov","year":"2006","unstructured":"Miroshnikov, K. A., Faizullina, N. M., Sykilinda, N. N. & Mesyanzhinov, V. V. Properties of the endolytic transglycosylase encoded by gene 144 of Pseudomonas aeruginosa bacteriophage PhiKZ. Biochem. (Mosc). 71, 300\u2013305 (2006).","journal-title":"Biochem. (Mosc)"},{"key":"36188_CR13","doi-asserted-by":"publisher","first-page":"7242","DOI":"10.1074\/jbc.M709398200","volume":"283","author":"A Fokine","year":"2008","unstructured":"Fokine, A., Miroshnikov, K. A., Shneider, M. M., Mesyanzhinov, V. V. & Rossmann, M. G. Structure of the bacteriophage phiKZ lytic transglycosylase gp144. J. Biol. Chem. 283, 7242\u20137250 (2008).","journal-title":"J. Biol. Chem."},{"key":"36188_CR14","first-page":"149","volume":"13","author":"V Krylov","year":"2021","unstructured":"Krylov, V. et al. Phage phiKZ\u2014The First of Giants. Viruses 13, 149 (2021).","journal-title":"Phage phiKZ\u2014The First Giants Viruses"},{"key":"36188_CR15","doi-asserted-by":"crossref","unstructured":"Paradis-Bleau, C. et al. Peptidoglycan lytic activity of the Pseudomonas aeruginosa phage phiKZ gp144 lytic transglycosylase. FEMS Microbiol. Lett. 266, 201\u2013209 (2007).","DOI":"10.1111\/j.1574-6968.2006.00523.x"},{"key":"36188_CR16","doi-asserted-by":"publisher","first-page":"81","DOI":"10.32607\/20758251-2017-9-1-81-87","volume":"9","author":"OV Chertkov","year":"2017","unstructured":"Chertkov, O. V. et al. Dual active site in the endolytic transglycosylase gp144 of bacteriophage PhiKZ. Acta Naturae. 9, 81\u201387 (2017).","journal-title":"Acta Naturae"},{"key":"36188_CR17","doi-asserted-by":"publisher","first-page":"1334","DOI":"10.1111\/j.1365-2958.2007.05870.x","volume":"65","author":"Y Briers","year":"2007","unstructured":"Briers, Y. et al. Muralytic activity and modular structure of the endolysins of Pseudomonas aeruginosa bacteriophages \u03c6KZ and EL. Mol. Microbiol. 65, 1334\u20131344 (2007).","journal-title":"Mol. Microbiol."},{"key":"36188_CR18","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1186\/s12859-018-2342-8","volume":"19","author":"R Kongari","year":"2018","unstructured":"Kongari, R. et al. Phage spanins: diversity, topological dynamics and gene convergence. BMC Bioinform. 19, 326 (2018).","journal-title":"BMC Bioinform."},{"key":"36188_CR19","doi-asserted-by":"publisher","first-page":"1652","DOI":"10.1110\/ps.0303703","volume":"12","author":"AS Juncker","year":"2003","unstructured":"Juncker, A. S. et al. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci. 12, 1652\u20131662 (2003).","journal-title":"Protein Sci."},{"key":"36188_CR20","doi-asserted-by":"publisher","unstructured":"Braun, V. & Wu, H. C. Chapter 14 Lipoproteins, structure, function, biosynthesis and model for protein export. in 319\u2013341 https:\/\/doi.org\/10.1016\/S0167-7306(08)60417-2 (1994).","DOI":"10.1016\/S0167-7306(08)60417-2"},{"key":"36188_CR21","doi-asserted-by":"crossref","unstructured":"Park, T., Struck, D. K., Deaton, J. F. & Young, R. Topological dynamics of holins in programmed bacterial lysis. Proceedings of the National Academy of Sciences 103, 19713\u201319718 (2006).","DOI":"10.1073\/pnas.0600943103"},{"key":"36188_CR22","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1016\/0092-8674(82)90260-4","volume":"30","author":"EJ Grayhack","year":"1982","unstructured":"Grayhack, E. J. & Roberts, J. W. The phage \u03bb Q gene product: activity of a transcription antiterminator in vitro. Cell 30, 637\u2013648 (1982).","journal-title":"Cell"},{"key":"36188_CR23","doi-asserted-by":"publisher","unstructured":"Cahill, J. et al. Suppressor analysis of the fusogenic lambda Spanins. J. Virol. 91,  https:\/\/doi.org\/10.1128\/jvi.00413-17 (2017).","DOI":"10.1128\/jvi.00413-17"},{"key":"36188_CR24","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1007\/s11274-024-04063-2","volume":"40","author":"SV Chernyshov","year":"2024","unstructured":"Chernyshov, S. V., Masulis, I. S. & Mikoulinskaia, G. V. From DNA to lytic proteins: transcription and translation of the bacteriophage T5 holin\/endolysin Operon. World J. Microbiol. Biotechnol. 40, 256 (2024).","journal-title":"World J. Microbiol. Biotechnol."},{"key":"36188_CR25","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.1016\/j.jmb.2007.08.045","volume":"373","author":"EJ Summer","year":"2007","unstructured":"Summer, E. J. et al. Rz\/Rz1 Lysis gene equivalents in phages of Gram-negative hosts. J. Mol. Biol. 373, 1098\u20131112 (2007).","journal-title":"J. Mol. Biol."},{"key":"36188_CR26","doi-asserted-by":"publisher","first-page":"2201","DOI":"10.1128\/JB.01548-14","volume":"196","author":"SH Moussa","year":"2014","unstructured":"Moussa, S. H., Lawler, J. L. & Young, R. Genetic dissection of T4 Lysis. J. Bacteriol. 196, 2201\u20132209 (2014).","journal-title":"J. Bacteriol."},{"key":"36188_CR27","doi-asserted-by":"publisher","first-page":"6631","DOI":"10.1128\/JB.187.19.6631-6640.2005","volume":"187","author":"TAT Tran","year":"2005","unstructured":"Tran, T. A. T., Struck, D. K. & Young, R. Periplasmic domains define Holin-Antiholin interactions in T4 Lysis Inhibition. J. Bacteriol. 187, 6631\u20136640 (2005).","journal-title":"J. Bacteriol."},{"key":"36188_CR28","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/S0378-1119(01)00365-1","volume":"265","author":"E Ramanculov","year":"2001","unstructured":"Ramanculov, E. & Young, R. Genetic analysis of the T4 holin: timing and topology. Gene 265, 25\u201336 (2001).","journal-title":"Gene"},{"key":"36188_CR29","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1046\/j.1365-2958.2001.02491.x","volume":"41","author":"E Ramanculov","year":"2001","unstructured":"Ramanculov, E. & Young, R. An ancient player unmasked: T4 rI encodes a t -specific antiholin. Mol. Microbiol. 41, 575\u2013583 (2001).","journal-title":"Mol. Microbiol."},{"key":"36188_CR30","first-page":"21","volume":"4","author":"R Young","year":"2002","unstructured":"Young, R. Bacteriophage holins: deadly diversity. J. Mol. Microbiol. Biotechnol. 4, 21\u201336 (2002).","journal-title":"J. Mol. Microbiol. Biotechnol."},{"key":"36188_CR31","doi-asserted-by":"publisher","first-page":"4623","DOI":"10.1016\/j.jmb.2020.06.013","volume":"432","author":"IV Krieger","year":"2020","unstructured":"Krieger, I. V. et al. The structural basis of T4 phage lysis control: DNA as the signal for lysis inhibition. J. Mol. Biol. 432, 4623\u20134636 (2020).","journal-title":"J. Mol. Biol."},{"key":"36188_CR32","doi-asserted-by":"publisher","first-page":"1419106","DOI":"10.3389\/fmicb.2024.1419106","volume":"15","author":"JMF Schwarzkopf","year":"2024","unstructured":"Schwarzkopf, J. M. F., Mehner-Breitfeld, D. & Br\u00fcser, T. A dimeric holin\/antiholin complex controls lysis by phage T4. Front. Microbiol. 15, 1419106 (2024).","journal-title":"Front. Microbiol."},{"key":"36188_CR33","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1146\/annurev.micro.54.1.799","volume":"54","author":"IN Wang","year":"2000","unstructured":"Wang, I. N., Smith, D. L. & Young, R. Holins: the protein clocks of bacteriophage infections. Annu. Rev. Microbiol. 54, 799\u2013825 (2000).","journal-title":"Annu. Rev. Microbiol."},{"key":"36188_CR34","doi-asserted-by":"crossref","unstructured":"Bavda, V. R. & Jain, V. Deciphering the role of holin in mycobacteriophage D29 physiology. Front Microbiol 11, 883 (2020).","DOI":"10.3389\/fmicb.2020.00883"},{"key":"36188_CR35","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1128\/jb.167.3.1035-1042.1986","volume":"167","author":"R Raab","year":"1986","unstructured":"Raab, R. et al. Mutational analysis of bacteriophage lambda lysis gene S. J. Bacteriol. 167, 1035\u20131042 (1986).","journal-title":"J. Bacteriol."},{"key":"36188_CR36","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1016\/0042-6822(71)90287-X","volume":"43","author":"RW Reader","year":"1971","unstructured":"Reader, R. W. & Siminovitch, L. Lysis defective mutants of bacteriophage lambda: on the role of the S function in Lysis. Virology 43, 623\u2013637 (1971).","journal-title":"Virology"},{"key":"36188_CR37","doi-asserted-by":"publisher","first-page":"25","DOI":"10.4161\/bact.1.1.14868","volume":"1","author":"Y Briers","year":"2011","unstructured":"Briers, Y., Peeters, L. M., Volckaert, G. & Lavigne, R. The Lysis cassette of bacteriophage \u0444KMV encodes a signal-arrest-release endolysin and a Pinholin. Bacteriophage 1, 25\u201330 (2011).","journal-title":"Bacteriophage"},{"key":"36188_CR38","doi-asserted-by":"publisher","first-page":"JB0021421","DOI":"10.1128\/JB.00214-21","volume":"204","author":"A Holt","year":"2021","unstructured":"Holt, A. et al. Phage-encoded cationic antimicrobial peptide required for Lysis. J. Bacteriol. 204, JB0021421 (2021).","journal-title":"J. Bacteriol."},{"key":"36188_CR39","doi-asserted-by":"crossref","unstructured":"Kongari, R., Snowden, J., Berry, J. D. & Young, R. Localization and regulation of the T1 unimolecular Spanin. J. Virol. 92, e00380\u201318 (2018).","DOI":"10.1128\/JVI.00380-18"},{"key":"36188_CR40","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1111\/mmi.12439","volume":"91","author":"CG Savva","year":"2014","unstructured":"Savva, C. G. et al. Stable micron-scale holes are a general feature of canonical holins. Mol. Microbiol. 91, 57\u201365 (2014).","journal-title":"Mol. Microbiol."},{"key":"36188_CR41","doi-asserted-by":"publisher","first-page":"1346","DOI":"10.1128\/JB.01986-12","volume":"195","author":"KH To","year":"2013","unstructured":"To, K. H., Dewey, J., Weaver, J., Park, T. & Young, R. Functional analysis of a class I holin, P2 Y. J. Bacteriol. 195, 1346\u20131355 (2013).","journal-title":"J. Bacteriol."},{"key":"36188_CR42","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1111\/j.1365-2958.2010.07362.x","volume":"78","author":"T Pang","year":"2010","unstructured":"Pang, T., Park, T. & Young, R. Mapping the pinhole formation pathway of S21. Mol. Microbiol. 78, 710\u2013719 (2010).","journal-title":"Mol. Microbiol."},{"key":"36188_CR43","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1128\/JB.01174-09","volume":"192","author":"EJ Summer","year":"2010","unstructured":"Summer, E. J. et al. Genomic and biological analysis of phage Xfas53 and related prophages of Xylella fastidiosa. J. Bacteriol. 192, 179\u2013190 (2010).","journal-title":"J. Bacteriol."},{"key":"36188_CR44","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1046\/j.1365-2958.1996.331395.x","volume":"21","author":"U Bl\u00e4si","year":"1996","unstructured":"Bl\u00e4si, U. & Young, R. Two beginnings for a single purpose: the dual-start holins in the regulation of phage Lysis. Mol. Microbiol. 21, 675\u2013682 (1996).","journal-title":"Mol. Microbiol."},{"key":"36188_CR45","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1046\/j.1365-2958.1999.01385.x","volume":"32","author":"M Barenboim","year":"1999","unstructured":"Barenboim, M., Chang, C., Hajj, D., Young, R. & F. & Characterization of the dual start motif of a class II Holin gene. Mol. Microbiol. 32, 715\u2013727 (1999).","journal-title":"Mol. Microbiol."},{"key":"36188_CR46","doi-asserted-by":"publisher","DOI":"10.1101\/2025.11.23.690004","author":"A Chan","year":"2025","unstructured":"Chan, A. et al. Bacteriophage genome-wide transposon mutagenesis. Preprint at. https:\/\/doi.org\/10.1101\/2025.11.23.690004 (2025).","journal-title":"Preprint at."},{"key":"36188_CR47","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1128\/jb.178.4.1099-1104.1996","volume":"178","author":"C Schmidt","year":"1996","unstructured":"Schmidt, C., Velleman, M. & Arber, W. Three functions of bacteriophage P1 involved in cell Lysis. J. Bacteriol. 178, 1099\u20131104 (1996).","journal-title":"J. Bacteriol."},{"key":"36188_CR48","first-page":"100064","volume":"2","author":"SK Niazi","year":"2025","unstructured":"Niazi, S. K. Critical assessment of AI-based protein structure prediction: fundamental challenges and future directions in drug discovery. Comput. Struct. Biotechnol. Rep. 2, 100064 (2025).","journal-title":"Comput. Struct. Biotechnol. Rep."},{"key":"36188_CR49","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","volume":"630","author":"J Abramson","year":"2024","unstructured":"Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold3. Nature 630, 493\u2013500 (2024).","journal-title":"Nature"},{"key":"36188_CR50","doi-asserted-by":"publisher","first-page":"950","DOI":"10.1038\/s41589-024-01638-w","volume":"20","author":"V Agarwal","year":"2024","unstructured":"Agarwal, V. & McShan, A. C. The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins. Nat. Chem. Biol. 20, 950\u2013959 (2024).","journal-title":"Nat. Chem. Biol."},{"key":"36188_CR51","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1134\/S1022795410010047","volume":"46","author":"EA Pleteneva","year":"2010","unstructured":"Pleteneva, E. A. et al. Pseudolysogeny of Pseudomonas aeruginosa bacteria infected with \u03c6KZ-like bacteriophages. Russ J. Genet. 46, 20\u201325 (2010).","journal-title":"Russ J. Genet."},{"key":"36188_CR52","doi-asserted-by":"publisher","first-page":"8073","DOI":"10.1128\/jb.174.24.8073-8080.1992","volume":"174","author":"ST Abedon","year":"1992","unstructured":"Abedon, S. T. Lysis of lysis-inhibited bacteriophage T4-infected cells. J. Bacteriol. 174, 8073\u20138080 (1992).","journal-title":"J. Bacteriol."},{"key":"36188_CR53","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1128\/jb.177.14.4121-4130.1995","volume":"177","author":"LM Guzman","year":"1995","unstructured":"Guzman, L. M., Belin, D., Carson, M. J. & Beckwith, J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose pBAD promoter. J. Bacteriol. 177, 4121\u20134130 (1995).","journal-title":"J. Bacteriol."},{"key":"36188_CR54","doi-asserted-by":"publisher","first-page":"e0021123","DOI":"10.1128\/aem.00211-23","volume":"89","author":"A Klotz","year":"2023","unstructured":"Klotz, A., Kaczmarczyk, A. & Jenal, U. A. Synthetic Cumate-Inducible promoter for graded and homogenous gene expression in Pseudomonas aeruginosa. Appl. Environ. Microbiol. 89, e0021123 (2023).","journal-title":"Appl. Environ. Microbiol."},{"key":"36188_CR55","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1093\/bioinformatics\/btr703","volume":"28","author":"T Carver","year":"2012","unstructured":"Carver, T., Harris, S. R., Berriman, M., Parkhill, J. & McQuillan, J. A. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28, 464\u2013469 (2012).","journal-title":"Bioinformatics"},{"key":"36188_CR56","doi-asserted-by":"publisher","DOI":"10.1101\/2022.04.08.487609","author":"J Hallgren","year":"2022","unstructured":"Hallgren, J. et al. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. Preprint at. https:\/\/doi.org\/10.1101\/2022.04.08.487609 (2022).","journal-title":"Preprint at."},{"key":"36188_CR57","doi-asserted-by":"publisher","first-page":"W401","DOI":"10.1093\/nar\/gkv485","volume":"43","author":"KD Tsirigos","year":"2015","unstructured":"Tsirigos, K. D., Peters, C., Shu, N., K\u00e4ll, L. & Elofsson, A. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res. 43, W401\u2013W407 (2015).","journal-title":"Nucleic Acids Res."},{"key":"36188_CR58","doi-asserted-by":"publisher","first-page":"2237","DOI":"10.1016\/j.jmb.2017.12.007","volume":"430","author":"L Zimmermann","year":"2018","unstructured":"Zimmermann, L. et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237\u20132243 (2018).","journal-title":"J. Mol. Biol."},{"key":"36188_CR59","doi-asserted-by":"publisher","first-page":"D351","DOI":"10.1093\/nar\/gky1100","volume":"47","author":"AL Mitchell","year":"2019","unstructured":"Mitchell, A. L. et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47, D351\u2013D360 (2019).","journal-title":"Nucleic Acids Res."},{"key":"36188_CR60","doi-asserted-by":"publisher","first-page":"1023","DOI":"10.1038\/s41587-021-01156-3","volume":"40","author":"F Teufel","year":"2022","unstructured":"Teufel, F. et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat. Biotechnol. 40, 1023\u20131025 (2022).","journal-title":"Nat. Biotechnol."},{"key":"36188_CR61","doi-asserted-by":"publisher","first-page":"767","DOI":"10.1093\/bioinformatics\/btu700","volume":"31","author":"D Simm","year":"2015","unstructured":"Simm, D., Hatje, K. & Kollmar, M. Waggawagga: comparative visualization of coiled-coil predictions and detection of stable single \u03b1-helices (SAH domains). Bioinformatics 31, 767\u2013769 (2015).","journal-title":"Bioinformatics"},{"key":"36188_CR62","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1007\/s004380051128","volume":"262","author":"N Zhang","year":"1999","unstructured":"Zhang, N. & Young, R. Complementation and characterization of the nested Rz and Rz1 reading frames in the genome of bacteriophage \u03bb. Mol. Gen. Genet. 262, 659\u2013667 (1999).","journal-title":"Mol. Gen. Genet."},{"key":"36188_CR63","doi-asserted-by":"publisher","first-page":"1453","DOI":"10.1126\/science.277.5331.1453","volume":"277","author":"FR Blattner","year":"1997","unstructured":"Blattner, F. R. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453\u20131462 (1997).","journal-title":"Science"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-36188-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-36188-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-36188-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T22:02:27Z","timestamp":1770847347000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-36188-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,20]]},"references-count":63,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["36188"],"URL":"https:\/\/doi.org\/10.1038\/s41598-026-36188-9","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.11.11.687635","asserted-by":"object"}]},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,20]]},"assertion":[{"value":"12 November 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 January 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 January 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"5840"}}