{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T19:42:47Z","timestamp":1774726967316,"version":"3.50.1"},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Chemotaxis is the process by which motile bacteria sense their chemical environment and move towards more favourable conditions. <jats:italic>Escherichia coli<\/jats:italic> utilises a single sensory pathway, but little is known about signalling pathways in species with more complex systems.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>To investigate whether chemotaxis pathways in other bacteria follow the <jats:italic>E. coli<\/jats:italic> paradigm, we analysed 206 species encoding at least 1 homologue of each of the 5 core chemotaxis proteins (CheA, CheB, CheR, CheW and CheY). 61 species encode more than one of all of these 5 proteins, suggesting they have multiple chemotaxis pathways. Operon information is not available for most bacteria, so we developed a novel statistical approach to cluster <jats:italic>che<\/jats:italic> genes into putative operons. Using operon-based models, we reconstructed putative chemotaxis pathways for all 206 species. We show that <jats:italic>cheA-cheW<\/jats:italic> and <jats:italic>cheR-cheB<\/jats:italic> have strong preferences to occur in the same operon as two-gene blocks, which may reflect a functional requirement for co-transcription. However, other <jats:italic>che<\/jats:italic> genes, most notably <jats:italic>cheY<\/jats:italic>, are more dispersed on the genome. Comparison of our operons with shuffled equivalents demonstrates that specific patterns of genomic location may be a determining factor for the observed <jats:italic>in vivo<\/jats:italic> chemotaxis pathways.<\/jats:p>\n            <jats:p>We then examined the chemotaxis pathways of <jats:italic>Rhodobacter sphaeroides<\/jats:italic>. Here, the PpfA protein is known to be critical for correct partitioning of proteins in the cytoplasmically-localised pathway. We found <jats:italic>ppfA<\/jats:italic> in <jats:italic>che<\/jats:italic> operons of many species, suggesting that partitioning of cytoplasmic Che protein clusters is common. We also examined the apparently non-typical chemotaxis components, CheA3, CheA4 and CheY6. We found that though variants of CheA proteins are rare, the CheY6 variant may be a common type of CheY, with a significantly disordered C-terminal region which may be functionally significant.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We find that many bacterial species potentially have multiple chemotaxis pathways, with grouping of <jats:italic>che<\/jats:italic> genes into operons likely to be a major factor in keeping signalling pathways distinct. Gene order is highly conserved with <jats:italic>cheA-cheW<\/jats:italic> and <jats:italic>cheR-cheB<\/jats:italic> blocks, perhaps reflecting functional linkage. CheY behaves differently to other Che proteins, both in its genomic location and its putative protein interactions, which should be considered when modelling chemotaxis pathways.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-4-3","type":"journal-article","created":{"date-parts":[[2010,1,12]],"date-time":"2010-01-12T07:16:05Z","timestamp":1263280565000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":65,"title":["Deciphering chemotaxis pathways using cross species comparisons"],"prefix":"10.1186","volume":"4","author":[{"given":"Rebecca","family":"Hamer","sequence":"first","affiliation":[]},{"given":"Pao-Yang","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Judith P","family":"Armitage","sequence":"additional","affiliation":[]},{"given":"Gesine","family":"Reinert","sequence":"additional","affiliation":[]},{"given":"Charlotte M","family":"Deane","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,1,11]]},"reference":[{"key":"392_CR1","doi-asserted-by":"publisher","first-page":"2016","DOI":"10.1128\/IAI.68.4.2016-2023.2000","volume":"68","author":"S Foynes","year":"2000","unstructured":"Foynes S, Dorrell N, Ward SJ, Stabler RA, McColm AA, Rycroft AN, Wren BW: Helicobacter pylori possesses two CheY response regulators and a histidine kinase sensor, CheA, which are essential for chemotaxis and colonization of the gastric mucosa. Infect Immun. 2000, 68: 2016-2023. 10.1128\/IAI.68.4.2016-2023.2000","journal-title":"Infect Immun"},{"key":"392_CR2","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1126\/science.284.5418.1318","volume":"284","author":"JW Costerton","year":"1999","unstructured":"Costerton JW, Stewart PS, Greenberg EP: Bacterial biofilms: a common cause of persistent infections. Science. 1999, 284: 1318-1322. 10.1126\/science.284.5418.1318","journal-title":"Science"},{"key":"392_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/bit.21838","volume":"100","author":"JD Bryers","year":"2008","unstructured":"Bryers JD: Medical biofilms. Biotechnol Bioeng. 2008, 100: 1-18. 10.1002\/bit.21838","journal-title":"Biotechnol Bioeng"},{"issue":"Pt 9","key":"392_CR4","doi-asserted-by":"publisher","first-page":"2599","DOI":"10.1099\/00221287-144-9-2599","volume":"144","author":"A Vande Broek","year":"1998","unstructured":"Broek Vande A, Lambrecht M, Vanderleyden J: Bacterial chemotactic motility is important for the initiation of wheat root colonization by Azospirillum brasilense. Microbiology. 1998, 144 (Pt 9): 2599-2606. 10.1099\/00221287-144-9-2599","journal-title":"Microbiology"},{"key":"392_CR5","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1016\/j.tim.2004.10.003","volume":"12","author":"V Sourjik","year":"2004","unstructured":"Sourjik V: Receptor clustering and signal processing in E. coli chemotaxis. Trends Microbiol. 2004, 12: 569-576. 10.1016\/j.tim.2004.10.003","journal-title":"Trends Microbiol"},{"key":"392_CR6","doi-asserted-by":"publisher","first-page":"1525","DOI":"10.1007\/s11538-008-9321-6","volume":"70","author":"MJ Tindall","year":"2008","unstructured":"Tindall MJ, Porter SL, Maini PK, Gaglia G, Armitage JP: Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell. Bull Math Biol. 2008, 70: 1525-1569. 10.1007\/s11538-008-9321-6","journal-title":"Bull Math Biol"},{"key":"392_CR7","doi-asserted-by":"publisher","first-page":"1570","DOI":"10.1007\/s11538-008-9322-5","volume":"70","author":"MJ Tindall","year":"2008","unstructured":"Tindall MJ, Maini PK, Porter SL, Armitage JP: Overview of mathematical approaches used to model bacterial chemotaxis II: bacterial populations. Bull Math Biol. 2008, 70: 1570-1607. 10.1007\/s11538-008-9322-5","journal-title":"Bull Math Biol"},{"key":"392_CR8","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.tim.2008.02.006","volume":"16","author":"SL Porter","year":"2008","unstructured":"Porter SL, Wadhams GH, Armitage JP: Rhodobacter sphaeroides : complexity in chemotactic signalling. Trends Microbiol. 2008, 16: 251-260. 10.1016\/j.tim.2008.02.006","journal-title":"Trends Microbiol"},{"key":"392_CR9","doi-asserted-by":"publisher","first-page":"1081","DOI":"10.1046\/j.1365-2958.2002.03218.x","volume":"46","author":"SL Porter","year":"2002","unstructured":"Porter SL, Warren AV, Martin AC, Armitage JP: The third chemotaxis locus of Rhodobacter sphaeroides is essential for chemotaxis. Mol Microbiol. 2002, 46: 1081-1094. 10.1046\/j.1365-2958.2002.03218.x","journal-title":"Mol Microbiol"},{"key":"392_CR10","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1046\/j.1365-2958.1997.6502022.x","volume":"26","author":"PA Hamblin","year":"1997","unstructured":"Hamblin PA, Maguire BA, Grishanin RN, Armitage JP: Evidence for two chemosensory pathways in Rhodobacter sphaeroides. Mol Microbiol. 1997, 26: 1083-1096. 10.1046\/j.1365-2958.1997.6502022.x","journal-title":"Mol Microbiol"},{"key":"392_CR11","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1046\/j.1365-2958.2001.02468.x","volume":"40","author":"AC Martin","year":"2001","unstructured":"Martin AC, Wadhams GH, Armitage JP: The roles of the multiple CheW and CheA homologues in chemotaxis and in chemoreceptor localization in Rhodobacter sphaeroides. Mol Microbiol. 2001, 40: 1261-1272. 10.1046\/j.1365-2958.2001.02468.x","journal-title":"Mol Microbiol"},{"key":"392_CR12","doi-asserted-by":"publisher","first-page":"7135","DOI":"10.1128\/JB.183.24.7135-7144.2001","volume":"183","author":"AC Martin","year":"2001","unstructured":"Martin AC, Wadhams GH, Shah DS, Porter SL, Mantotta JC, Craig TJ, Verdult PH, Jones H, Armitage JP: CheR- and CheB-dependent chemosensory adaptation system of Rhodobacter sphaeroides. J Bacteriol. 2001, 183: 7135-7144. 10.1128\/JB.183.24.7135-7144.2001","journal-title":"J Bacteriol"},{"key":"392_CR13","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1111\/j.1365-2958.1995.mmi_17020357.x","volume":"17","author":"MJ Ward","year":"1995","unstructured":"Ward MJ, Bell AW, Hamblin PA, Packer HL, Armitage JP: Identification of a chemotaxis operon with two cheY genes in Rhodobacter sphaeroides. Mol Microbiol. 1995, 17: 357-366. 10.1111\/j.1365-2958.1995.mmi_17020357.x","journal-title":"Mol Microbiol"},{"key":"392_CR14","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1046\/j.1365-2958.2003.03716.x","volume":"50","author":"GH Wadhams","year":"2003","unstructured":"Wadhams GH, Warren AV, Martin AC, Armitage JP: Targeting of two signal transduction pathways to different regions of the bacterial cell. Mol Microbiol. 2003, 50: 763-770. 10.1046\/j.1365-2958.2003.03716.x","journal-title":"Mol Microbiol"},{"key":"392_CR15","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1111\/j.1365-2958.2005.04880.x","volume":"58","author":"G Wadhams","year":"2005","unstructured":"Wadhams G, Martin A, Warren A, Armitage J: Requirements for chemotaxis protein localization in Rhodobacter sphaeroides. Mol Microbiol. 2005, 58: 895-902. 10.1111\/j.1365-2958.2005.04880.x","journal-title":"Mol Microbiol"},{"key":"392_CR16","doi-asserted-by":"publisher","first-page":"8209","DOI":"10.1073\/pnas.0600919103","volume":"103","author":"SR Thompson","year":"2006","unstructured":"Thompson SR, Wadhams GH, Armitage JP: The positioning of cytoplasmic protein clusters in bacteria. Proc Natl Acad Sci USA. 2006, 103: 8209-8214. 10.1073\/pnas.0600919103","journal-title":"Proc Natl Acad Sci USA"},{"key":"392_CR17","doi-asserted-by":"publisher","first-page":"7623","DOI":"10.1021\/bi00081a004","volume":"32","author":"RV Swanson","year":"1993","unstructured":"Swanson RV, Schuster SC, Simon MI: Expression of CheA fragments which define domains encoding kinase, phosphotransfer, and CheY binding activities. Biochemistry. 1993, 32: 7623-7629. 10.1021\/bi00081a004","journal-title":"Biochemistry"},{"key":"392_CR18","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/S0092-8674(00)80966-6","volume":"96","author":"AM Bilwes","year":"1999","unstructured":"Bilwes AM, Alex LA, Crane BR, Simon MI: Structure of CheA, a signal-transducing histidine kinase. Cell. 1999, 96: 131-141. 10.1016\/S0092-8674(00)80966-6","journal-title":"Cell"},{"key":"392_CR19","doi-asserted-by":"publisher","first-page":"18531","DOI":"10.1073\/pnas.0808010105","volume":"105","author":"SL Porter","year":"2008","unstructured":"Porter SL, Roberts MA, Manning CS, Armitage JP: A bifunctional kinase-phosphatase in bacterial chemotaxis. Proc Natl Acad Sci USA. 2008, 105: 18531-18536. 10.1073\/pnas.0808010105","journal-title":"Proc Natl Acad Sci USA"},{"key":"392_CR20","doi-asserted-by":"publisher","first-page":"5172","DOI":"10.1128\/JB.186.15.5172-5177.2004","volume":"186","author":"A Ferre","year":"2004","unstructured":"Ferre A, De La Mora J, Ballado T, Camarena L, Dreyfus G: Biochemical study of multiple CheY response regulators of the chemotactic pathway of Rhodobacter sphaeroides. J Bacteriol. 2004, 186: 5172-5177. 10.1128\/JB.186.15.5172-5177.2004","journal-title":"J Bacteriol"},{"key":"392_CR21","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/S0022-2836(02)01031-8","volume":"324","author":"SL Porter","year":"2002","unstructured":"Porter SL, Armitage JP: Phosphotransfer in Rhodobacter sphaeroides chemotaxis. J Mol Biol. 2002, 324: 35-45. 10.1016\/S0022-2836(02)01031-8","journal-title":"J Mol Biol"},{"key":"392_CR22","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1046\/j.1365-2958.2000.01680.x","volume":"35","author":"DS Shah","year":"2000","unstructured":"Shah DS, Porter SL, Harris DC, Wadhams GH, Hamblin PA, Armitage JP: Identification of a fourth cheY gene in Rhodobacter sphaeroides and interspecies interaction within the bacterial chemotaxis signal transduction pathway. Mol Microbiol. 2000, 35: 101-112. 10.1046\/j.1365-2958.2000.01680.x","journal-title":"Mol Microbiol"},{"key":"392_CR23","doi-asserted-by":"publisher","first-page":"4601","DOI":"10.1093\/emboj\/19.17.4601","volume":"19","author":"DS Shah","year":"2000","unstructured":"Shah DS, Porter SL, Martin AC, Hamblin PA, Armitage JP: Fine tuning bacterial chemotaxis: analysis of Rhodobacter sphaeroides behaviour under aerobic and anaerobic conditions by mutation of the major chemotaxis operons and cheY genes. Embo J. 2000, 19: 4601-4613. 10.1093\/emboj\/19.17.4601","journal-title":"Embo J"},{"key":"392_CR24","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1146\/annurev.micro.091208.073221","volume":"63","author":"JR Kirby","year":"2009","unstructured":"Kirby JR: Chemotaxis-like regulatory systems: unique roles in diverse bacteria. Annu Rev Microbiol. 2009, 63: 45-59. 10.1146\/annurev.micro.091208.073221","journal-title":"Annu Rev Microbiol"},{"key":"392_CR25","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1038\/35023079","volume":"406","author":"CK Stover","year":"2000","unstructured":"Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, et al.: Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature. 2000, 406: 959-964. 10.1038\/35023079","journal-title":"Nature"},{"key":"392_CR26","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1038\/nrmicro1770","volume":"5","author":"DR Zusman","year":"2007","unstructured":"Zusman DR, Scott AE, Yang Z, Kirby JR: Chemosensory pathways, motility and development in Myxococcus xanthus. Nat Rev Microbiol. 2007, 5: 862-872. 10.1038\/nrmicro1770","journal-title":"Nat Rev Microbiol"},{"key":"392_CR27","doi-asserted-by":"publisher","first-page":"6652","DOI":"10.1073\/pnas.110147297","volume":"97","author":"H Salgado","year":"2000","unstructured":"Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J: Operons in Escherichia coli : genomic analyses and predictions. Proc Natl Acad Sci USA. 2000, 97: 6652-6657. 10.1073\/pnas.110147297","journal-title":"Proc Natl Acad Sci USA"},{"key":"392_CR28","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1088\/1478-3975\/3\/3\/003","volume":"3","author":"A Zaslaver","year":"2006","unstructured":"Zaslaver A, Mayo A, Ronen M, Alon U: Optimal gene partition into operons correlates with gene functional order. Physical Biology. 2006, 3: 183-189. 10.1088\/1478-3975\/3\/3\/003","journal-title":"Physical Biology"},{"key":"392_CR29","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1073\/pnas.96.6.2896","volume":"96","author":"R Overbeek","year":"1999","unstructured":"Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N: The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA. 1999, 96: 2896-2901. 10.1073\/pnas.96.6.2896","journal-title":"Proc Natl Acad Sci USA"},{"key":"392_CR30","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1002\/prot.21021","volume":"64","author":"Y Yan","year":"2006","unstructured":"Yan Y, Moult J: Detection of operons. Proteins. 2006, 64: 615-628. 10.1002\/prot.21021","journal-title":"Proteins"},{"key":"392_CR31","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","volume":"Ac19","author":"H Akaike","year":"1974","unstructured":"Akaike H: New Look at Statistical-Model Identification. IEEE Transactions on Automatic Control. 1974, Ac19: 716-723. 10.1109\/TAC.1974.1100705.","journal-title":"IEEE Transactions on Automatic Control"},{"key":"392_CR32","doi-asserted-by":"publisher","first-page":"4374","DOI":"10.1128\/JB.184.16.4374-4383.2002","volume":"184","author":"A Ferrandez","year":"2002","unstructured":"Ferrandez A, Hawkins A, Summerfield D, Harwood C: Cluster II che Genes from Pseudomonas aeruginosa Are Required for an Optimal Chemotactic Response. J Bacteriol. 2002, 184: 4374-4383. 10.1128\/JB.184.16.4374-4383.2002","journal-title":"J Bacteriol"},{"key":"392_CR33","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.jbiotec.2007.01.024","volume":"129","author":"L Lovdok","year":"2007","unstructured":"Lovdok L, Kollmann M, Sourjik V: Co-expression of signaling proteins improves robustness of the bacterial chemotaxis pathway. J Biotechnol. 2007, 129: 173-180. 10.1016\/j.jbiotec.2007.01.024","journal-title":"J Biotechnol"},{"key":"392_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0076-6879(06)22001-9","volume":"422","author":"K Wuichet","year":"2007","unstructured":"Wuichet K, Alexander RP, Zhulin IB: Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis. Methods Enzymol. 2007, 422: 1-31. 10.1016\/S0076-6879(06)22001-9","journal-title":"Methods Enzymol"},{"key":"392_CR35","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1002\/bies.20343","volume":"28","author":"MD Baker","year":"2006","unstructured":"Baker MD, Wolanin PM, Stock JB: Signal transduction in bacterial chemotaxis. Bioessays. 2006, 28: 9-22. 10.1002\/bies.20343","journal-title":"Bioessays"},{"key":"392_CR36","unstructured":"NCBI Bacterial Genome Protein Sequences. ftp:\/\/ftp.ncbi.nlm.nih.gov\/genomes\/Bacteria\/all.faa.tar.gz"},{"key":"392_CR37","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.","journal-title":"J Mol Biol"},{"key":"392_CR38","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"key":"392_CR39","doi-asserted-by":"publisher","first-page":"1619","DOI":"10.1101\/gr.278202","volume":"12","author":"LY Geer","year":"2002","unstructured":"Geer LY, Domrachev M, Lipman DJ, Bryant SH: CDART: protein homology by domain architecture. Genome Res. 2002, 12: 1619-1623. 10.1101\/gr.278202","journal-title":"Genome Res"},{"key":"392_CR40","doi-asserted-by":"publisher","first-page":"871","DOI":"10.1111\/j.1365-2958.2006.05283.x","volume":"61","author":"K Terry","year":"2006","unstructured":"Terry K, Go AC, Ottemann KM: Proteomic mapping of a suppressor of non-chemotactic cheW mutants reveals that Helicobacter pylori contains a new chemotaxis protein. Mol Microbiol. 2006, 61: 871-882. 10.1111\/j.1365-2958.2006.05283.x","journal-title":"Mol Microbiol"},{"key":"392_CR41","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1128\/JB.185.1.285-294.2003","volume":"185","author":"IB Zhulin","year":"2003","unstructured":"Zhulin IB, Nikolskaya AN, Galperin MY: Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. J Bacteriol. 2003, 185: 285-294. 10.1128\/JB.185.1.285-294.2003","journal-title":"J Bacteriol"},{"key":"392_CR42","unstructured":"NCBI Bacterial Genome PTT files. ftp:\/\/ftp.ncbi.nlm.nih.gov\/genomes\/Bacteria\/all.ptt.tar.gz"},{"key":"392_CR43","volume-title":"Multivariate Analysis","author":"KV Mardia","year":"1979","unstructured":"Mardia KV, Kent JT, Bibby JM: Multivariate Analysis. 1979, London: Academic Press"},{"key":"392_CR44","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1093\/biomet\/76.2.297","volume":"76","author":"C Hurvich","year":"1989","unstructured":"Hurvich C, Tsai CL: Regression and Time-Series Model Selection in Small Samples. Biometrika. 1989, 76: 297-307. 10.1093\/biomet\/76.2.297.","journal-title":"Biometrika"},{"key":"392_CR45","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1016\/S0968-0004(98)01274-2","volume":"23","author":"T Dandekar","year":"1998","unstructured":"Dandekar T, Snel B, Huynen M, Bork P: Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci. 1998, 23: 324-328. 10.1016\/S0968-0004(98)01274-2","journal-title":"Trends Biochem Sci"},{"key":"392_CR46","doi-asserted-by":"publisher","first-page":"D449","DOI":"10.1093\/nar\/gkh086","volume":"32","author":"L Salwinski","year":"2004","unstructured":"Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004, 32: D449-451. 10.1093\/nar\/gkh086","journal-title":"Nucleic Acids Res"},{"key":"392_CR47","doi-asserted-by":"publisher","first-page":"3369","DOI":"10.1093\/bioinformatics\/bti534","volume":"21","author":"ZR Yang","year":"2005","unstructured":"Yang ZR, Thomson R, McNeil P, Esnouf RM: RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics. 2005, 21: 3369-3376. 10.1093\/bioinformatics\/bti534","journal-title":"Bioinformatics"},{"key":"392_CR48","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","volume":"302","author":"C Notredame","year":"2000","unstructured":"Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000, 302: 205-217. 10.1006\/jmbi.2000.4042","journal-title":"J Mol Biol"},{"key":"392_CR49","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1111\/j.1574-6968.1999.tb13575.x","volume":"174","author":"TA Tatusova","year":"1999","unstructured":"Tatusova TA, Madden TL: BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett. 1999, 174: 247-250. 10.1111\/j.1574-6968.1999.tb13575.x","journal-title":"FEMS Microbiol Lett"},{"key":"392_CR50","doi-asserted-by":"publisher","first-page":"D471","DOI":"10.1093\/nar\/gkn661","volume":"37","author":"T Lima","year":"2009","unstructured":"Lima T, Auchincloss AH, Coudert E, Keller G, Michoud K, Rivoire C, Bulliard V, de Castro E, Lachaize C, Baratin D, et al.: HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB\/Swiss-Prot. Nucleic Acids Res. 2009, 37: D471-478. 10.1093\/nar\/gkn661","journal-title":"Nucleic Acids Res"},{"key":"392_CR51","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28: 27-30. 10.1093\/nar\/28.1.27","journal-title":"Nucleic Acids Res"},{"key":"392_CR52","doi-asserted-by":"publisher","first-page":"7500","DOI":"10.1073\/pnas.0709764105","volume":"105","author":"AH Singh","year":"2008","unstructured":"Singh AH, Wolf DM, Wang P, Arkin AP: Modularity of stress response evolution. Proc Natl Acad Sci USA. 2008, 105: 7500-7505. 10.1073\/pnas.0709764105","journal-title":"Proc Natl Acad Sci USA"},{"key":"392_CR53","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1016\/0092-8674(92)90247-A","volume":"70","author":"JA Gegner","year":"1992","unstructured":"Gegner JA, Graham DR, Roth AF, Dahlquist FW: Assembly of an MCP receptor, CheW, and kinase CheA complex in the bacterial chemotaxis signal transduction pathway. Cell. 1992, 70: 975-982. 10.1016\/0092-8674(92)90247-A","journal-title":"Cell"},{"key":"392_CR54","doi-asserted-by":"publisher","first-page":"22251","DOI":"10.1074\/jbc.M110908200","volume":"277","author":"MS Boukhvalova","year":"2002","unstructured":"Boukhvalova MS, Dahlquist FW, Stewart RC: CheW binding interactions with CheA and Tar. Importance for chemotaxis signaling in Escherichia coli. J Biol Chem. 2002, 277: 22251-22259. 10.1074\/jbc.M110908200","journal-title":"J Biol Chem"},{"key":"392_CR55","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1038\/nsmb1085","volume":"13","author":"SY Park","year":"2006","unstructured":"Park SY, Borbat PP, Gonzalez-Bonet G, Bhatnagar J, Pollard AM, Freed JH, Bilwes AM, Crane BR: Reconstruction of the chemotaxis receptor-kinase assembly. Nat Struct Mol Biol. 2006, 13: 400-407. 10.1038\/nsmb1085","journal-title":"Nat Struct Mol Biol"},{"key":"392_CR56","doi-asserted-by":"publisher","first-page":"1717","DOI":"10.1126\/science.8456299","volume":"259","author":"JR Maddock","year":"1993","unstructured":"Maddock JR, Shapiro L: Polar location of the chemoreceptor complex in the Escherichia coli cell. Science. 1993, 259: 1717-1723. 10.1126\/science.8456299","journal-title":"Science"},{"key":"392_CR57","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1046\/j.1365-2958.2000.02044.x","volume":"37","author":"V Sourjik","year":"2000","unstructured":"Sourjik V, Berg HC: Localization of components of the chemotaxis machinery of Escherichia coli using fluorescent protein fusions. Mol Microbiol. 2000, 37: 740-751. 10.1046\/j.1365-2958.2000.02044.x","journal-title":"Mol Microbiol"},{"key":"392_CR58","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1016\/j.mib.2006.10.012","volume":"9","author":"D Kentner","year":"2006","unstructured":"Kentner D, Sourjik V: Spatial organization of the bacterial chemotaxis system. Curr Opin Microbiol. 2006, 9: 619-624. 10.1016\/j.mib.2006.10.012","journal-title":"Curr Opin Microbiol"},{"key":"392_CR59","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1046\/j.1365-2958.2000.01975.x","volume":"37","author":"K Gerdes","year":"2000","unstructured":"Gerdes K, Moller-Jensen J, Bugge Jensen R: Plasmid and chromosome partitioning: surprises from phylogeny. Mol Microbiol. 2000, 37: 455-466. 10.1046\/j.1365-2958.2000.01975.x","journal-title":"Mol Microbiol"},{"key":"392_CR60","first-page":"326","volume":"71","author":"M Galperin","year":"2005","unstructured":"Galperin M, Gomelsky M: Bacterial signal transduction modules: from genomics to biology. ASM News. 2005, 71: 326-333.","journal-title":"ASM News"},{"key":"392_CR61","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.jmb.2006.03.033","volume":"359","author":"R Barak","year":"2006","unstructured":"Barak R, Yan J, Shainskaya A, Eisenbach M: The chemotaxis response regulator CheY can catalyze its own acetylation. J Mol Biol. 2006, 359: 251-265. 10.1016\/j.jmb.2006.03.033","journal-title":"J Mol Biol"},{"key":"392_CR62","first-page":"183","volume":"4","author":"B Scharf","year":"2002","unstructured":"Scharf B, Schmitt R: Sensory transduction to the flagellar motor of Sinorhizobium meliloti. J Mol Microbiol Biotechnol. 2002, 4: 183-186.","journal-title":"J Mol Microbiol Biotechnol"},{"key":"392_CR63","doi-asserted-by":"publisher","first-page":"54573","DOI":"10.1074\/jbc.M408855200","volume":"279","author":"SL Porter","year":"2004","unstructured":"Porter SL, Armitage JP: Chemotaxis in Rhodobacter sphaeroides requires an atypical histidine protein kinase. J Biol Chem. 2004, 279: 54573-54580. 10.1074\/jbc.M408855200","journal-title":"J Biol Chem"},{"key":"392_CR64","doi-asserted-by":"publisher","first-page":"32694","DOI":"10.1074\/jbc.M606016200","volume":"281","author":"SL Porter","year":"2006","unstructured":"Porter SL, Wadhams GH, Martin AC, Byles ED, Lancaster DE, Armitage JP: The CheYs of Rhodobacter sphaeroides. J Biol Chem. 2006, 281: 32694-32704. 10.1074\/jbc.M606016200","journal-title":"J Biol Chem"},{"key":"392_CR65","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1093\/protein\/13.12.839","volume":"13","author":"CA Innis","year":"2000","unstructured":"Innis CA, Shi J, Blundell TL: Evolutionary trace analysis of TGF-beta and related growth factors: implications for site-directed mutagenesis. Protein Eng. 2000, 13: 839-847. 10.1093\/protein\/13.12.839","journal-title":"Protein Eng"},{"key":"392_CR66","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1093\/bioinformatics\/15.4.305","volume":"15","author":"P Gouet","year":"1999","unstructured":"Gouet P, Courcelle E, Stuart DI, Metoz F: ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics. 1999, 15: 305-308. 10.1093\/bioinformatics\/15.4.305","journal-title":"Bioinformatics"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-4-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T05:09:26Z","timestamp":1630472966000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-4-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,1,11]]},"references-count":66,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["392"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-4-3","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,1,11]]},"assertion":[{"value":"10 July 2009","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 January 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 January 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"3"}}