ArticleNucleic acids research2009
HHomp--prediction and classification of outer membrane proteins.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- General features of transmembrane beta barrels from a large database.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A unique antigen against SARS-CoV-2, Acinetobacter baumannii, and Pseudomonas aeruginosa.Scientific reports · 2022Article
- Surface proteomics and label-free quantification of Leptospira interrogans serovar Pomona.PLoS neglected tropical diseases · 2021Article
- How do I get the most out of my protein sequence using bioinformatics tools?Acta crystallographica. Section D, Structural biology · 2021Article
- OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins.Frontiers in bioinformatics · 2021Article
- Computational prediction of secreted proteins in gram-negative bacteria.Computational and structural biotechnology journal · 2021Review
- Article
- Integrative approach for detecting membrane proteins.BMC bioinformatics · 2020Article
- Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica.BMC microbiology · 2020Article
- A Brief History of Protein Sorting Prediction.The protein journal · 2019Review
- Transcriptome and Comparative Genomics Analyses Reveal New Functional Insights on Key Determinants of Pathogenesis and Interbacterial Competition inApplied and environmental microbiology · 2019Article
- In silico proteomic and phylogenetic analysis of the outer membrane protein repertoire of gastric Helicobacter species.Scientific reports · 2018Article
- A unified model for BAM function that takes into account type Vc secretion and species differences in BAM composition.AIMS microbiology · 2018Article
- Discovery of Novel Leptospirosis Vaccine Candidates Using Reverse and Structural Vaccinology.Frontiers in immunology · 2017Article
- Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes.BMC microbiology · 2016Article
- The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis.Nucleic acids research · 2016Article
- Transport protein evolution deduced from analysis of sequence, topology and structure.Current opinion in structural biology · 2016Review
- Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins.PloS one · 2016Article
- Divergence between the Highly Virulent Zoonotic Pathogen Helicobacter heilmannii and Its Closest Relative, the Low-Virulence "Helicobacter ailurogastricus" sp. nov.Infection and immunity · 2016Article
- Cyclic di-GMP modulates gene expression in Lyme disease spirochetes at the tick-mammal interface to promote spirochete survival during the blood meal and tick-to-mammal transmission.Infection and immunity · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Outer membrane proteins (OMPs) are the transmembrane proteins found in the outer membranes of Gram-negative bacteria, mitochondria and plastids. Most prediction methods have focused on analogous features, such as alternating hydrophobicity patterns. Here, we start from the observation that almost all beta-barrel OMPs are related by common ancestry. We identify proteins as OMPs by detecting their homologous relationships to known OMPs using sequence similarity. Given an input sequence, HHomp builds a profile hidden Markov model (HMM) and compares it with an OMP database by pairwise HMM comparison, integrating OMP predictions by PROFtmb. A crucial ingredient is the OMP database, which contains profile HMMs for over 20,000 putative OMP sequences. These were collected with the exhaustive, transitive homology detection method HHsenser, starting from 23 representative OMPs in the PDB database. In a benchmark on TransportDB, HHomp detects 63.5% of the true positives before including the first false positive. This is 70% more than PROFtmb, four times more than BOMP and 10 times more than TMB-Hunt. 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.
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Registered trials
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