Table 1 Bacterial genomes used for training and testing the SPSR methodology
From: Deriving enzymatic and taxonomic signatures of metagenomes from short read data
Organism Name | ID | Phyla | Total Uniprot Proteins | Total Uniprot Enzymes | Choice |
|---|---|---|---|---|---|
Mycobacterium tuberculosis. | B01 | Actinobacteria | 5,971 | 1,371 | Train |
Mycobacterium bovis. | B02 | Actinobacteria | 3,986 | 1,253 | Test |
Sulfurihydrogenibium azorense | B03 | Aquificae | 1,708 | 486 | Train |
Aquifex aeolicus. | B04 | Aquificae | 1,556 | 368 | Test |
Cytophaga hutchinsonii | B05 | Bacteroidetes | 3,771 | 895 | Test |
Gramella forsetii | B06 | Bacteroidetes | 3,554 | 992 | Train |
Pelodictyon luteolum | B07 | Chlorobi | 2,078 | 496 | Test |
Chlorobium chlorochromatii | B08 | Chlorobi | 1,991 | 609 | Train |
Nostoc punctiforme | B09 | Cyanobacteria | 6,601 | 1,534 | Train |
Anabaena variabilis | B10 | Cyanobacteria | 5,643 | 1,362 | Test |
Synechocystis sp | B11 | Cyanobacteria | 3,529 | 575 | Train |
Bacillus cereus (strain ZK). | B12 | Firmicutes | 5,638 | 1,469 | Test |
Bacillus cereus (strain ATCC). | B13 | Firmicutes | 5,248 | 1,546 | Train |
Pseudomonas aeruginosa. | B14 | Proteobacteria | 9,091 | 848 | Train |
Rhizobium meliloti | B15 | Proteobacteria | 7,107 | 1,583 | Test |
Salmonella typhimurium. | B16 | Proteobacteria | 5,768 | 1,279 | Train |
Shigella flexneri. | B17 | Proteobacteria | 5,395 | 813 | Test |
Salmonella typhi. | B18 | Proteobacteria | 5,351 | 942 | Test |
Escherichia coli (K12). | B19 | Proteobacteria | 4,412 | 1,443 | Train |
Caulobacter crescentus | B20 | Proteobacteria | 3,852 | 1,238 | Test |
Leptospira biflexa | B21 | Spirochaetes | 3,730 | 957 | Train |
Thermotoga petrophila | B22 | Thermotogae | 1,784 | 411 | Test |