The Pathema-Bacillus resource provides updated gene model and functional curation following standardized protocols for all publicly available Bacillus genomes. more >>

For each genome both coding and non-coding features are predicted, and have been made available for retrieval and analysis. Each coding region is assigned descriptive functional curation using one of three distinct methods, distinguishable on individual gene pages, and as outlined in the protocols section. << hide

• Gene Model and Functional Curation Protocols
• Gene Naming Conventions
• Explanation of Pathema Terms

Community members are encouraged to participate in our annotation effort by registering and submitting updates from individual gene pages. Sign up using the link below to register for community annotation.

• Register For Community Tools
• List of Community Participants
• List of All Community Annotations

Search by: Gene Annotation Locus Gene Symbol Common Name

Match: Exact Inexact

Curation Type: All methods Manual Mapped Automated

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• BLAST
• Curated Gene List
• Retrieve Genes/Sequence by Coordinates
• Region View
• Organism Gene List
• Advanced Gene Search
• Gene Attribute Download

Bacillus anthracis produces a number of virulence factors that promote host pathogenesis. They are generally responsible for host adhesion, host invasion and colonization, and evasion of host defense mechanisms. Plasmid pXO1 encodes the major toxin genes specific to Bacillus anthracis: lef and cya express the secreted proteins lethal factor and edema factor which are delivered into host cells by a third plasmid-encoded protein, protective antigen. Lethal factor and edema factor are enzymes which modulate host signal transduction pathways to impair the host immune response and facilitate pathogenesis. more >>

Lethal factor is a metaloproteinase that cleaves mitogen-activated protein kinase, while edema factor is an adenylate cyclase that increases cAMP levels in host cells. Also located on pXO1 is an operon of spore germination proteins which are thought to allow the bacterium to germinate within phagocytic cells. Two regulatory genes important in virulence also reside on pXO1: AtxA activates transcription of both toxin and capsule biosyntheis genes, while PagR represses the expression of AtxA. The polyglutamate capsule biosynthesis operon capABCDE is located on plasmid pXO2. Expression of proteins from this operon is important to virulence as they synthesize a capsule that allows the bacterium to resist phagocytosis by the host. Two postive regulators of the cap operon, AcpA and AcpB, are also located on pXO2.

The chromosome encodes virulence factors orthologous to those in other gram positive bacteria. These include fibronectin-binding proteins involved in host adhesion; potential cytolysins and a putative internalin involved in host invasion; and a siderophore biosynthesis operon asbABCDEF crucial to scavenging iron from the host and allowing successful colonization. Several additional genes located on the chromosome allow the bacterium to evade host defense mechanisms. Two immune inhibitor A metalloproteinases degrade antibacterial proteins secreted by the host; a putative lysylphosphatidylglycerol synthetase MprF and peptidoglycan biosynthesis operon are also thought to contribute to host defense evasion. Recent analysis of the Bacillus anthracis secretome has identified secreted chromosomal proteins with features characteristic of virulence factors. << hide

• CDC/OHS Biosafety Information
• CDC/OHS Biosafety in Microbiological and Biomedical Laboratories (BMBL) 5th Edition
• CDC Laboratory Information for Bioterrorism Emergencies
• B. anthracis Protocols

Below you can display a list of curated known and potential virulence factors, or BLAST Bacillus genome sequences against the Lawrence Livermore National Laboratory (LLNL) Virulence Database.

JCVI Curated Virulence Factors

• B. anthracis pXO1 VFs
• B. anthracis pXO2 VFs
• B. anthracis Chromosome VFs
• B. anthracis Putative VFs
• B. anthracis Structures

The Pathema-Bacillus resource offers several whole-genome and multi-genome comparative tools to help identify regions and proteins of interest. Homologous protein results are pre-computed using blastp and can be viewed using a number of our homology tools under the Comparative Tools menu. Sequence alignment of specific molecules can be obtained using MUMmer.

• Multi-Genome Homology Graph
• Genome Homology Graph
• Genome Scatter Plot
• MUMmer Whole Genome Alignment
• Genome Properties

The Pathema-Bacillus resource provides pre-computed blastp results for each protein against every other protein in the database. Detailed results can be obtained via the individual gene pages' Protein vs. All Alignment link. ClustalW and BER alignments are also acccesible from this gene page tool.

• Genome Region Comparision
• Protein Motif Search

• Restriction Digest
• Pseudo 2-D Gel
• Codon Usage Tables
• %GC Content Display

Functional genomics attempts to make use of the vast wealth of data produced by genomic projects to describe gene and protein functions and interactions. Functional genomics focuses on dynamic aspects such as gene transcription, translation, and protein-protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. Below we list the current tools available for functional genomics studies of Bacillus.

• Bacillus Anthracis Microarray Description
• Request a Microarray

Genome Properties consists of a suite of "Properties" which are defined attributes of prokaryotic organisms including presence/absence of metabolic pathways and characteristics of a genome such as "human pathogen". These properties are evaluated by manual curation or computer algorithms.

• Genome Properties
• Genome Properties Details Comparison

KEGG Pathways are manually drawn pathway maps representing the molecular interaction and reaction networks for metabolism, other cellular processes, and human diseases.

• KEGG Pathway Display

Several types of vaccines are currently under development. These include: recombinant Protective Antigen (rPA)-based anthrax vaccines; protective antigen (PA) plus capsular poly-gamma-D-glutamic acid (PGA) based anthrax vaccine (designed to attack both bacilli and toxin); and epicutaneous and intranasal vaccine (developed for needle-free administration). Anthrax vaccine research is working toward developing a vaccine that will confer simultaneous protection against spores, bacilli, and toxins.

• B. anthracis Vaccines
• B. anthracis Antibodies

The evaluation of epitopes is an important aspect in characterizing immune responses for vaccine development.

• B. anthracis epitopes

Metalloprotease inhibitors composed of peptides and small molecules are being identified and developed to neutralize anthrax toxin and treat Bacillus anthracis infection.

Inhibitors of lethal factor may rescue cells by inhibiting toxin actions such as receptor binding, mitogen-activated protein kinase (MAPK) kinase cleavage, enzymatic functions, blocking of pore formation or translocation.

• B. anthracis Inhibitors

• B. anthracis Structures

Here the top used tools and searches in Pathema are listed. In the future users will be able to put their own customized favorite tools in this box.

• All Organism List
• Organism Gene List
• Strain List
• TIGRFAM Evidence List
• Pfam Evidence List
• EC Number List

• Batch Download
• Gene Attribute Download
• Pathema FTP Download

• Genome Cart
• Gene Cart