Organism Information
| 0rganism Name | Mycobacterium ulcerans Agy99 |
|---|---|
| Taxon Object ID | 642555140 |
| NCBI Taxon ID | 362242 |
| RefSeq Project ID | 16230 |
| GenBank Project ID | 16230 |
| GOLD ID in IMG Database | Gc00469 |
| External Links | NCBI/RefSeq:NC_005916; NCBI/RefSeq:NC_008611; PUBMED:14736915; PUBMED:17210928 |
| Genome type | isolate |
| Lineage | Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; Mycobacteriaceae; Mycobacterium; ulcerans |
| Sequencing Status | Finished |
| IMG Release | IMG/W 2.7 |
| Comment | |
| Project Information | |
| Geographic Location | ulcerative lesion on the right elbow of a female patient from the Ga district of Ghana in 1999 |
| GOLD ID | Gc00469 |
| Isolation Country | Ghana |
| Isolation Year | July, 1999 |
| NCBI Project ID | 16230 |
| Publication Journal | Genome Research (17, 192-200) |
| Sequencing Center | Institut Pasteur |
| Project Sequencing Method | Sanger |
| Metadata | |
| Assembly Method | Phrap, GAP4 |
| Biotic Relationships | Free living |
| Cell Shape | Rod-shaped |
| Gram Staining | Gram+ |
| Host Name | Homo sapiens |
| Host Gender | Female |
| Host Health | Patient |
| Isolation | ulcerative lesion on the right elbow of a female patient from the Ga district of Ghana in 1999 |
| Library Method | 2-3Kb, 3-5Kb, 5-10Kb |
| Motility | Nonmotile |
| Oxygen Requirement | Aerobe |
| Sporulation | Nonsporulating |
| Temperature Range | Mesophile |
| Temperature Optimum | 32 |
| Cell Arrangement | Singles |
| Diseases | Buruli ulcer |
| Energy Source | Chemoorganotroph |
| Habitat | Host, Fresh water |
| Phenotype | Pathogen, Antibiotic resistant |
| Relevance | Medical, Human Pathogen |
| Body Site | Skin |
| Phenotypes/Metabolism from Pathway Assertion | |
| Metabolism | Auxotroph (L-lysine auxotroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-alanine prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-aspartate prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-glutamate prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Auxotroph (L-phenylalanine auxotroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Auxotroph (L-tyrosine auxotroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Auxotroph (L-tryptophan auxotroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Auxotroph (L-histidine auxotroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Auxotroph (Glycine prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-arginine prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-asparagine prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-cysteine prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-glutamine prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-isoleucine prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Auxotroph (L-leucine auxotroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-proline prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-serine prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-threonine prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (L-valine prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | (Non-selenocysteine synthesizer) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (Biotin prototroph) (IMG_PIPELINE; 2011-01-04) |
| Metabolism | Prototrophic (Coenzyme A prototroph) (IMG_PIPELINE; 2011-01-04) |
| Number | % of Total | |
|---|---|---|
| DNA, total number of bases | 5805761 | 100.00% |
| DNA coding number of bases | 4236262 | 72.97% |
| DNA G+C number of bases | 3796479 | 65.39% 1 |
| | | |
| DNA scaffolds | 2 | 100.00% |
| Plasmid Count | 1 | |
| | | |
| Genes total number | 4306 | 100.00% |
| Protein coding genes | 4241 | 98.49% |
| RNA genes | 65 | 1.51% |
| rRNA genes | 3 | 0.07% |
| 5S rRNA | 1 | 0.02% |
| 16S rRNA | 1 | 0.02% |
| 23S rRNA | 1 | 0.02% |
| tRNA genes | 45 | 1.05% |
| Other RNA genes | 17 | 0.39% |
| Protein coding genes with function prediction | 2792 | 64.84% |
| Protein coding genes without function prediction | 1449 | 33.65% |
| Genes w/o function with similarity | 1443 | 33.51% |
| Genes w/o function w/o similarity | 6 | 0.14% |
| Protein coding genes connected to SwissProt Protein Product | 331 | 7.69% |
| not connected to SwissProt Protein Product | 3910 | 90.80% |
| Protein coding genes connected to SEED | 353 | 8.20% |
| not connected to SEED | 3888 | 90.29% |
| Protein coding genes with enzymes | 983 | 22.83% |
| w/o enzymes but with candidate KO based enzymes | 276 | 6.41% |
| Protein coding genes connected to Transporter Classification | 305 | 7.08% |
| Protein coding genes connected to KEGG pathways3 | 1055 | 24.50% |
| not connected to KEGG pathways | 3186 | 73.99% |
| Protein coding genes connected to KEGG Orthology (KO) | 1790 | 41.57% |
| not connected to KEGG Orthology (KO) | 2451 | 56.92% |
| Protein coding genes connected to MetaCyc pathways | 761 | 17.67% |
| not connected to MetaCyc pathways | 3480 | 80.82% |
| Protein coding genes with COGs3 | 2853 | 66.26% |
| with Pfam3 | 3420 | 79.42% |
| with TIGRfam3 | 1071 | 24.87% |
| with InterPro | 1798 | 41.76% |
| with IMG Terms | 777 | 18.04% |
| with IMG Pathways | 313 | 7.27% |
| with IMG Parts List | 265 | 6.15% |
| Protein coding genes in ortholog clusters | 3982 | 92.48% |
| in paralog clusters | 959 | 22.27% |
| in Chromosomal Cassette | 3976 | 92.34% |
| Number of Chromosomal Cassettes | 673 | - |
| Fused Protein coding genes | 352 | 8.17% |
| as fusion components | 2108 | 48.95% |
| Protein coding genes coding signal peptides | 1141 | 26.50% |
| Protein coding genes coding transmembrane proteins | 839 | 19.48% |
| COG clusters | 1379 | 28.30% |
| Pfam clusters | 1542 | 12.94% |
| TIGRfam clusters | 879 | 21.85% |
| Paralogous groups | 235 | 100.00% |
| Orthologous groups | 3905 | 1.02% |
Notes:
1 - GC percentage shown as count of G's and C's divided by a total number of G's, C's, A's, and T's.
This is not necessarily synonymous with the total number of bases.
2 - Pseudogenes may also be counted as protein coding or RNA genes,
so is not additive under total gene count.
3 - Graphical view available.
