Welcome to the Mycoplasma genitalium database!

M. genitalium is a gram-positive bacterium and human pathogen. Among all freely-culturable organism, M. genitalium has the smallest genome, containing slightly more than 580 kb. Primarily due to its reduced genome size, M. genitalium has been the subject of intense research over the past thirty years. M. genitalium was the second organism to be completely sequenced, and the first organism to have its genome completely synthesized de novo and to be comprehensively modeled. M. genitalium's close relatives have also been the first to have their genome be transplated into a recipient cell. This PGDB provides a comprehensive description of M. genitalium molecular biology.

Cross references

Taxonomy: 243273, ATCC: 33530, BioProject: 97, CMR: gmg, GenBank: L43967, RefSeq: NC_000908

Genetic code

Mold, protozoa, coelenterate mitochondria, mycoplasma, and spiroplasma (4)

Content

Content Value Units   Content Value Units   Content Value Units  
Compartments 6     Proteins 683   Transcriptional regulation  
Chromosomes 1     Monomers 482     Interactions 30    
Length 580076 nt   DNA-binding 17   Transcriptional regulators 5  
GC-content 31.7 %   Integral membrane 85   Regulated promoters 26  
Transcription units 335     Lipoprotein 14     Pathways 17    
Monocistrons 231   Secreted 20     Stimuli 10    
Polycistrons 104   Terminal organelle 8   Quantitative parameters 1836  
Genes 525     Complexes 201     Cell composition 73  
mRNA 482     DNA-binding 39   Media composition 83  
rRNA 3     Reactions 1857     Reaction Keq 225  
sRNA 4     DNA damage 137     Reaction Km 483  
tRNA 36     DNA repair 32     Reaction Vmax 434  
Chromosome features 2305     Metabolic 645     RNA expression 525  
DnaA boxes 2283   Protein decay 40     RNA half-lives 525  
Short tandem repeats 19   Protein modification 63     Stimulus values 10  
Other 3   Replication Initiation 15     Transcr. reg. activity 2  
Metabolites 722     RNA decay 25     Transcr. reg. affinity 30  
Amino acids 29   RNA modification 91     Other 154    
Antibiotic 32   RNA processing 20     Processes 28    
Gases 4   Transcription 4     States 16    
Ions 19   Translation 20            
Lipids 82   tRNA aminoacylation 39            
Vitamins 27   Other 726          

Data sources

About WholeCellKB

WholeCellKB is a collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive, quantitative descriptions of individual species including:

  • Cellular chemical composition,
  • Growth medium composition,
  • Gene locations, lengths, and directions,
  • Transcription unit organization and transcriptional regulation,
  • Macromolecule composition,
  • Reaction stoichiometry, kinetics, and catalysis, and
  • Extensive links and cross-links to all references used to construct each database.

WholeCellKB currently contains a single database of Mycoplasma genitalium, an extremely small gram-positive bacterium and common human pathogen. This database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. The M. genitalium database was curated from over 900 primary research articles, reviews, books, and databases over four years by a team of three researchers at Stanford University.

Getting started

The best ways to get started are to browse or search this database using the menu or the search box at the top of this page. See the tutorial for additional help getting started.

More information

Please see the following for more information or to cite WholeCellKB:

Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW. WholeCellKB: Model Organism Databases for Comprehensive Whole-Cell Models. Nucleic Acids Research 41, D787-D792 (2013). Nucleic Acids Research | PubMed

Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW. A Whole-Cell Computational Model Predicts Phenotype from Genotype. Cell 150, 389-401 (2012). Cell | PubMed

Need help?

Please view the tutorial, about page, or contact us at wholecell@lists.stanford.edu.