ArticleMicrobiology (Reading, England)2006
Lipoprotein computational prediction in spirochaetal genomes.
Article in Microbiology (Reading, England), 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
123 citing papers in PubMed, 1 synthesis or guideline pooled it, 211 citations in OpenAlex.
- Trends and advances inFrontiers in microbiology · 2024Pooled it
- Curiouser and curiouser: understanding the intersection of inter- and intra-specific diversity during theInfection and immunity · 2026Review
- Role of dual specificity phosphatase 1 in influencing inflammatory pathways in macrophages modulated byFrontiers in immunology · 2026Article
- Biofilms and oral health: nanotechnology for biofilm control.Discover nano · 2025Review
- Role of Dual Specificity Phosphatase 1 (DUSP1) in influencing inflammatory pathways in macrophages modulated bybioRxiv : the preprint server for biology · 2025Article
- Complex exchanges among plasmids and clonal expansion of lineages shape the population structure and virulence ofbioRxiv : the preprint server for biology · 2025Article
- Serovar-specific genomic features ofFrontiers in molecular biosciences · 2025Article
- Hitchhiker's Guide toJournal of bacteriology · 2024Review
- Analysis of the Borreliaceae Pangenome Reveals a Distinct Genomic Architecture Conserved Across Phylogenetic Scales.The Journal of infectious diseases · 2024Article
- Identification and characterization of CIM-1, a carbapenemase that adds to the family of resistance factors against last resort antibiotics.Communications biology · 2024Article
- Leptospiral adhesins: from identification to future perspectives.Frontiers in microbiology · 2024Review
- Pathogenicity and virulence ofVirulence · 2023Review
- Review
- Review
- Locus Coeruleus Dysfunction and Trigeminal Mesencephalic Nucleus Degeneration: A Cue for Periodontal Infection Mediated Damage in Alzheimer's Disease?International journal of environmental research and public health · 2023Review
- Lipoproteome screening of the Lyme disease agent identifies inhibitors of antibody-mediated complement killing.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Structural Analysis of the Outer Membrane Lipoprotein BBA14 (OrfD) and the Corresponding Paralogous Gene Family 143 (PFam143) fromPathogens (Basel, Switzerland) · 2022Article
- Development of Human Recombinant Leptospirosis Vaccines.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The FUR-like regulators PerRA and PerRB integrate a complex regulatory network that promotes mammalian host-adaptation and virulence of Leptospira interrogans.PLoS pathogens · 2021Article
- Recent Progress in Lyme Disease and Remaining Challenges.Frontiers in medicine · 2021Review
63 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Lipoproteins are of great interest in understanding the molecular pathogenesis of spirochaetes. Because spirochaete lipobox sequences exhibit more plasticity than those of other bacteria, application of existing prediction algorithms to emerging sequence data has been problematic. In this paper a novel lipoprotein prediction algorithm is described, designated SpLip, constructed as a hybrid of a lipobox weight matrix approach supplemented by a set of lipoprotein signal peptide rules allowing for conservative amino acid substitutions. Both the weight matrix and the rules are based on a training set of 28 experimentally verified spirochaetal lipoproteins. The performance of the SpLip algorithm was compared to that of the hidden Markov model-based LipoP program and the rules-based algorithm Psort for all predicted protein-coding genes of Leptospira interrogans sv. Copenhageni, L. interrogans sv. Lai, Borrelia burgdorferi, Borrelia garinii, Treponema pallidum and Treponema denticola. Psort sensitivity (13-35 %) was considerably less than that of SpLip (93-100 %) or LipoP (50-84 %) due in part to the requirement of Psort for Ala or Gly at the -1 position, a rule based on E. coli lipoproteins. The percentage of false-positive lipoprotein predictions by the LipoP algorithm (8-30 %) was greater than that of SpLip (0-1 %) or Psort (4-27 %), due in part to the lack of rules in LipoP excluding unprecedented amino acids such as Lys and Arg in the -1 position. This analysis revealed a higher number of predicted spirochaetal lipoproteins than was previously known. The improved performance of the SpLip algorithm provides a more accurate prediction of the complete lipoprotein repertoire of spirochaetes. The hybrid approach of supplementing weight matrix scoring with rules based on knowledge of protein secretion biochemistry may be a general strategy for development of improved prediction algorithms.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.