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HHomp—prediction and classification of outer membrane proteins

Michael Remmert, Dirk Linke, Andrei N. Lupas, Johannes Söding
2009 Nucleic Acids Research  
Outer membrane proteins (OMPs) are the transmembrane proteins found in the outer membranes of Gram-negative bacteria, mitochondria and plastids.  ...  In Escherichia coli, HHomp identifies 57 out of 59 known OMPs and correctly assigns them to their functional subgroups. HHomp can be accessed at http://toolkit. tuebingen.mpg.de/hhomp.  ...  ACKNOWLEDGEMENTS We thank Oliver Kohlbacher for support during MR's diploma thesis and all users who helped to improve our webserver with their questions, feedback and bug reports.  ... 
doi:10.1093/nar/gkp325 pmid:19429691 pmcid:PMC2703889 fatcat:j7bpnnw4fzb67p2oylq2cpfhhq

Is the C-terminal insertional signal in Gram-negative bacterial outer membrane proteins species-specific or not?

Nagarajan Paramasivam, Michael Habeck, Dirk Linke
2012 BMC Genomics  
In Gram-negative bacteria, the outer membrane is composed of an asymmetric lipid bilayer of phopspholipids and lipopolysaccharides, and the transmembrane proteins that reside in this membrane are almost  ...  It recognizes its substrates, unfolded outer membrane proteins (OMPs), through a C-terminal motif that has been speculated to be species-specific, based on theoretical and experimental results from only  ...  Acknowledgements We are grateful for helpful discussions with Vikram Alva, Iwan Grin, Jack Leo and other department members; continuing support by the Max Planck Society, and specifically by Andrei Lupas  ... 
doi:10.1186/1471-2164-13-510 pmid:23013516 pmcid:PMC3582582 fatcat:wfwexk2w2vhpzn2hbrwsbmlm3e

Outer membrane proteins can be simply identified using secondary structure element alignment

Ren-Xiang Yan, Zhen Chen, Ziding Zhang
2011 BMC Bioinformatics  
Outer membrane proteins (OMPs) are frequently found in the outer membranes of gram-negative bacteria, mitochondria and chloroplasts and have been found to play diverse functional roles.  ...  Computational discrimination of OMPs from globular proteins and other types of membrane proteins is helpful to accelerate new genome annotation and drug discovery.  ...  Acknowledgements We thank the anonymous referees whose constructive and insightful comments were very helpful in improving the quality of this work. We are also grateful to Dr.  ... 
doi:10.1186/1471-2105-12-76 pmid:21414186 pmcid:PMC3072342 fatcat:khwsqujvwbhqrnqqyyjgkvubge

OMPdb: a database of -barrel outer membrane proteins from Gram-negative bacteria

K. D. Tsirigos, P. G. Bagos, S. J. Hamodrakas
2010 Nucleic Acids Research  
We describe here OMPdb, which is currently the most complete and comprehensive collection of integral b-barrel outer membrane proteins from Gram-negative bacteria.  ...  and test sets for predictive algorithms regarding transmembrane b-barrels.  ...  ACKNOWLEDGEMENTS The authors would like to thank the anonymous referees whose comments helped in improving the quality of the article.  ... 
doi:10.1093/nar/gkq863 pmid:20952406 pmcid:PMC3013764 fatcat:j7dyqmqe3bespfziyou6umd3xm

Genomic Analysis Indicates the Presence of an Asymmetric Bilayer Outer Membrane in Planctomycetes and Verrucomicrobia

Daan R. Speth, Muriel C. F. van Teeseling, Mike S. M. Jetten
2012 Frontiers in Microbiology  
S. profunda" and could confirm high expression of several predicted OMPs, including the biomarkers of outer membrane biogenesis.  ...  However, recent work on outer membrane biogenesis has provided several marker genes in the outer membrane protein (OMP) assembly and the lipopolysaccharide (LPS) insertion complexes.  ...  BamA were detectable in all genomes searched, as were at least eight predicted outer membrane proteins (OMP).  ... 
doi:10.3389/fmicb.2012.00304 pmid:22934092 pmcid:PMC3422733 fatcat:nupvvhu2drcjfort3bqcatkxgq

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

Vikram Alva, Seung-Zin Nam, Johannes Söding, Andrei N. Lupas
2016 Nucleic Acids Research  
The MPI Bioinformatics Toolkit (http://toolkit. tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis.  ...  It offers a wide array of interconnected, state-of-the-art bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAST+, HMMER3, MUSCLE) and internally (e.g.  ...  Kopec, Jörn Marialke, Christian Mayer, Markus Meier, Andre Noll, Michael Remmert, Tina Streich, Christina Wassermann and Johannes Wörner for their contributions to the development and maintenance of the  ... 
doi:10.1093/nar/gkw348 pmid:27131380 pmcid:PMC4987908 fatcat:ffsm76krd5hhvctyfgr5gnu4ne

ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea

Nagarajan Paramasivam, Dirk Linke
2011 Frontiers in Microbiology  
On top of the consensus prediction at the level of single sequences, the tool uses clusters of homologous proteins from Gram-negative bacteria and from Archaea to eliminate false-positive and false-negative  ...  ClubSub-P can assign the SCL of proteins from Gram-negative bacteria and Archaea with high precision.  ...  We are also thankful to the many authors that provided us with offline version of their tools. This work was funded by the Bill & Melinda Gates Foundation, Grand Challenges Explorations program.  ... 
doi:10.3389/fmicb.2011.00218 pmid:22073040 pmcid:PMC3210502 fatcat:6elzwfzrvve2xjh762ixt4cjsa

Surface Immunolabeling and Consensus Computational Framework To Identify Candidate Rare Outer Membrane Proteins of Treponema pallidum

D. L. Cox, A. Luthra, S. Dunham-Ems, D. C. Desrosiers, J. C. Salazar, M. J. Caimano, J. D. Radolf
2010 Infection and Immunity  
Treponema pallidum reacts poorly with the antibodies present in rabbit and human syphilitic sera, a property attributed to the paucity of proteins in its outer membrane.  ...  Using a consensus computational framework that combined subcellular localization and ␤-barrel structural prediction tools, we generated ranked groups of candidate rare OMPs, the predicted T. pallidum outer  ...  ACKNOWLEDGMENTS We acknowledge the excellent technical assistance of Morgan LeDoyt.  ... 
doi:10.1128/iai.00834-10 pmid:20876295 pmcid:PMC2981305 fatcat:l4fj4zgqhrdk5ptyeiwh7xdb5m

Computational prediction of secreted proteins in gram-negative bacteria

Xinjie Hui, Zewei Chen, Junya Zhang, Moyang Lu, Xuxia Cai, Yuping Deng, Yueming Hu, Yejun Wang
2021 Computational and Structural Biotechnology Journal  
algorithms and tools for their prediction.  ...  Proteins can be exported to periplasmic space, integrated into membrane, transported into extracellular milieu, or translocated into cytoplasm of contacting cells.  ...  Acknowledgements Y.W. was supported by Natural Science Funds of Shenzhen (JCYJ201607115221141; JCYJ20190808165205582) and a fund for Youth Innovation Team of Shenzhen University (no. 406/0000080805).  ... 
doi:10.1016/j.csbj.2021.03.019 pmid:33897982 pmcid:PMC8047123 fatcat:xvj4vcrnujbpzgzx3ait62s2dy

Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica

Michael L. Clawson, Gennie Schuller, Aaron M. Dickey, James L. Bono, Robert W. Murray, Michael T. Sweeney, Michael D. Apley, Keith D. DeDonder, Sarah F. Capik, Robert L. Larson, Brian V. Lubbers, Brad J. White (+4 others)
2020 BMC Microbiology  
Seven genes encoding predicted OMPs; a peptidase S6, a ligand-gated channel, an autotransporter outer membrane beta-barrel domain-containing protein (AOMB-BD-CP), a porin, and three different trimeric  ...  Additionally, genes encoding outer membrane proteins (OMPs) specific to genotype 2 M. haemolytica were identified, and the diversity of their protein isoforms was characterized with predominantly unassembled  ...  The use of product and company names is necessary to accurately report the methods and results; however, the USDA neither guarantees nor warrants the standard of the products, and the use of names by the  ... 
doi:10.1186/s12866-020-01932-2 pmid:32787780 fatcat:2squ566luzefdjsbvo234i63fu

In silico proteomic and phylogenetic analysis of the outer membrane protein repertoire of gastric Helicobacter species

Eva Bauwens, Myrthe Joosten, Joemar Taganna, Mirko Rossi, Ayla Debraekeleer, Alfred Tay, Fanny Peters, Steffen Backert, James Fox, Richard Ducatelle, Han Remaut, Freddy Haesebrouck (+1 others)
2018 Scientific Reports  
By means of a comprehensive survey of the diversity and distribution of predicted outer membrane proteins (OMPs) identified in all known gastric Helicobacter species with fully annotated genome sequences  ...  Its outer membrane proteome takes an important role in colonization of the human gastric mucosa.  ...  Acknowledgements We thank Nathalie Van Rysselberghe and Sofie De Bruyckere for their skilled technical assistance. This work was supported by the  ... 
doi:10.1038/s41598-018-32476-1 pmid:30337679 pmcid:PMC6194013 fatcat:7xcyv3xqlfagjb3bubucelpqgq

Discovery of Novel Leptospirosis Vaccine Candidates Using Reverse and Structural Vaccinology

André Alex Grassmann, Frederico Schmitt Kremer, Júlia Cougo dos Santos, Jéssica Dias Souza, Luciano da Silva Pinto, Alan John Alexander McBride
2017 Frontiers in Immunology  
The Leptospira interrogans serovar Copenhageni strain L1-130 genome was mined in silico for the enhanced identification of conserved β-barrel (βb) transmembrane proteins and outer membrane (OM) lipoproteins  ...  These proteins were conserved among the pathogenic Leptospira spp. and were predicted to have epitopes for several variants of MHC-II receptors.  ...  FigUre 3 | The gene Ontology (gO) terms predicted by cOFacTOr were based on the structural models of the βb-outer membrane proteins (OMPs) and outer membrane (OM) lipoproteins.  ... 
doi:10.3389/fimmu.2017.00463 pmid:28496441 pmcid:PMC5406399 fatcat:ijdp4iea65dyxgmmuoic7xmw2u

Intimin and Invasin Export Their C-Terminus to the Bacterial Cell Surface Using an Inverse Mechanism Compared to Classical Autotransport

Philipp Oberhettinger, Monika Schütz, Jack C. Leo, Nadja Heinz, Jürgen Berger, Ingo B. Autenrieth, Dirk Linke, Mikael Skurnik
2012 PLoS ONE  
We conclude that proteins of the intimin and invasin family constitute a novel group of autotransported proteins, and propose that this class of autotransporters be termed Type Ve secretion.  ...  Invasin and intimin are major virulence factors of enteropathogenic Yersiniae and Escherichia coli, mediating invasion into and intimate adherence to host cells, respectively.  ...  We also would like to thank Gad Frankel (Imperial College, London) for providing intimin antibodies and the E. coli E2348/69 DeaeA EPEC strain, Ian Henderson (School of Immunity and Infection, Birmingham  ... 
doi:10.1371/journal.pone.0047069 pmid:23056583 pmcid:PMC3467248 fatcat:m72goglfczgqjp7rljrgghkjcm

OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins

Ahmed F. Roumia, Konstantinos D. Tsirigos, Margarita C. Theodoropoulou, Ioannis A. Tamposis, Stavros J. Hamodrakas, Pantelis G. Bagos
2021 Frontiers in Bioinformatics  
OMPdb (www.ompdb.org) was introduced as a database for β-barrel outer membrane proteins from Gram-negative bacteria in 2011 and then included 69,354 entries classified into 85 families.  ...  Here, we present the upgrade of OMPdb, which from now on aims to become a global repository for all transmembrane β-barrel proteins, both eukaryotic and bacterial.  ...  TP0969 was predicted as an outer membrane beta barrel by CELLO (Yu et al., 2006) , PSORT (Yu et al., 2010) , HHomp (Remmert et al., 2009) , and PRED-TMBB (Bagos et al., 2004) prediction algorithms  ... 
doi:10.3389/fbinf.2021.646581 fatcat:kjz5emdbgbcihjrankm42ht7k4

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

David Goudenege, Stephane Avner, Celine Lucchetti-Miganeh, Frederique Barloy-Hubler
2010 BMC Microbiology  
A fast and low-cost alternative approach is in silico prediction, based on features of the protein primary sequences.  ...  The functions of proteins are strongly related to their localization in cell compartments (for example the cytoplasm or membranes) but the experimental determination of the sub-cellular localization of  ...  prediction of alpha-transmembrane segments (TM-Box); and one box, only available for diderms (Gram-negatives), for outer membrane localization through prediction of betabarrels.  ... 
doi:10.1186/1471-2180-10-88 pmid:20331850 pmcid:PMC2850352 fatcat:tfffhv4kkbhbrd62iuqepzsfii
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