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HHomp—prediction and classification of outer membrane proteins
2009
Nucleic Acids Research
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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?
2012
BMC Genomics
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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
2011
BMC Bioinformatics
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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
2010
Nucleic Acids Research
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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
2012
Frontiers in Microbiology
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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
2016
Nucleic Acids Research
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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
2011
Frontiers in Microbiology
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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
2010
Infection and Immunity
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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
2021
Computational and Structural Biotechnology Journal
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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
2020
BMC Microbiology
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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
2018
Scientific Reports
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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
2017
Frontiers in Immunology
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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
2012
PLoS ONE
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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
2021
Frontiers in Bioinformatics
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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
2010
BMC Microbiology
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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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