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Showing 1 - 20 of 12,153 items

NameEMDBPDBSASBDB
Homo sapiens (human)2217582314529
synthetic construct (others)42131230439
Escherichia coli (E. coli)35101161584
Mus musculus (house mouse)39771100274
Severe acute respiratory syndrome coronavirus 2265161760
Saccharomyces cerevisiae (brewer's yeast)281948177
Rattus norvegicus (Norway rat)1379471617
Bos taurus (domestic cattle)1257413836
Escherichia coli K-12 (bacteria)1369309387
Human immunodeficiency virus 1112727000
Arabidopsis thaliana (thale cress)605279534
Saccharomyces cerevisiae S288C (yeast)1058230137
Gallus gallus (chicken)254282410
Mycobacterium tuberculosis (bacteria)268245911
Sus scrofa (pig)99316540
Oryctolagus cuniculus (rabbit)112114882
Pseudomonas aeruginosa (bacteria)21322453
Staphylococcus aureus (bacteria)195199113
Lama glama (llama)67611950
Bacillus subtilis (bacteria)27115701

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Yorodumi Speices

Taxonomy data in EMDB/PDB/SASBDB

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