Coverage of Infectious Pathogens*

Stages of targets according to unified status codes

Classification Genus Species # of structures in PDB at CSGID start # of structures in PDB # of CSGID structures CSGID as % of all entries CSGID as % of new entries
* "Number of Structures in PDB at CSGID start" denotes number of protein structures for a given species deposited in the PDB before October 1, 2007. "Current number of structures in PDB" denotes the number of structures deposited in the PDB as of November 16, 2019. For both PDB and CSGID only the structures released as of November 16, 2019 are taken into account (thus structures that have been deposited but are not yet released by the PDB are omitted). Assignment of species for PDB structures is based on taxonomy id and scientific name provided by depositors; the assignment may be imprecise in cases where only scientific name and no taxonomy id was given.
Acinetobacter Acinetobacter sp. ADP1 0 2 0 0.0 0.0
Actinobacillus Actinobacillus pleuropneumoniae 1 6 0 0.0 0.0
Actinomyces Actinomyces oris 0 1 1 100.0 100.0
Aeromonas Aeromonas hydrophila 1 17 0 0.0 0.0
Agrobacterium Agrobacterium tumefaciens 24 81 1 1.2 1.8
Aliivibrio Aliivibrio fischeri 1 15 4 26.7 28.6
Alphavirus Chikungunya virus 0 6 0 0.0 0.0
Aquifex Aquifex aeolicus 81 188 0 0.0 0.0
Aspergillus Aspergillus fumigatus 0 1 1 100.0 100.0
Bacillus Bacillus cereus 59 145 5 3.4 5.8
Bacillus Bacillus subtilis 218 592 3 0.5 0.8
Betacoronavirus Severe acute respiratory syndrome-related coronavirus 0 2 0 0.0 0.0
Bordetella Bordetella bronchiseptica 0 20 0 0.0 0.0
Bordetella Bordetella pertussis 12 27 3 11.1 20.0
Borrelia Borrelia burgdorferi 3 22 0 0.0 0.0
Bos Bos taurus 705 1148 0 0.0 0.0
Brachybacterium Brachybacterium faecium 0 3 3 100.0 100.0
Branhamella Moraxella catarrhalis 0 7 4 57.1 57.1
Brevibacillus Brevibacillus brevis 12 18 0 0.0 0.0
Brugia Brugia malayi 0 5 0 0.0 0.0
Burkholderia Burkholderia ambifaria 0 13 0 0.0 0.0
Burkholderia Burkholderia cenocepacia 0 40 1 2.5 2.5
Burkholderia Burkholderia cepacia 13 20 0 0.0 0.0
Burkholderia Burkholderia multivorans 0 8 0 0.0 0.0
Burkholderia Burkholderia pseudomallei 0 72 0 0.0 0.0
Burkholderia Burkholderia thailandensis 0 47 1 2.1 2.1
Burkholderia Burkholderia xenovorans 3 17 0 0.0 0.0
Candida Candida albicans 15 72 9 12.5 15.8
Capra Capra hircus 14 26 0 0.0 0.0
Cavia Cavia porcellus 6 11 0 0.0 0.0
Chlamydia Chlamydia pneumoniae 0 2 0 0.0 0.0
Citrobacter Citrobacter rodentium 0 2 1 50.0 50.0
Clavispora Candida auris 0 1 1 100.0 100.0
Clostridium Clostridium botulinum 38 97 0 0.0 0.0
Clostridium Clostridium tetani 6 8 0 0.0 0.0
Corynebacterium Corynebacterium diphtheriae 22 44 4 9.1 18.2
Corynebacterium Corynebacterium matruchotii 0 1 1 100.0 100.0
Cryptosporidium Cryptosporidium hominis 1 3 0 0.0 0.0
Cytomegalovirus Human herpesvirus 5 8 18 0 0.0 0.0
Enterobacter Enterobacter aerogenes 3 8 0 0.0 0.0
Enterobacter Enterobacter cloacae 24 50 5 10.0 19.2
Enterovirus Enterovirus B 5 12 0 0.0 0.0
Equus Equus caballus 76 139 6 4.3 9.5
Eremothecium Eremothecium gossypii 0 2 0 0.0 0.0
Erythrobacter Erythrobacter litoralis 0 1 0 0.0 0.0
Flavivirus Zika virus 0 6 6 100.0 100.0
Fusobacterium Fusobacterium nucleatum 0 6 0 0.0 0.0
Haemophilus Haemophilus influenzae 76 135 9 6.7 15.3
Haliangium Haliangium ochraceum 0 3 0 0.0 0.0
Hepacivirus Hepatitis C virus 43 197 0 0.0 0.0
Hepevirus Hepatitis E virus 0 3 0 0.0 0.0
Influenzavirus B Influenza B virus 5 21 0 0.0 0.0
Japanese encephalitis virus group Murray Valley encephalitis virus 0 1 0 0.0 0.0
Klebsiella Klebsiella pneumoniae 14 123 24 19.5 22.0
Kluyveromyces Kluyveromyces lactis 4 23 0 0.0 0.0
Komagataella Komagataella pastoris 2 3 0 0.0 0.0
Lactococcus Lactococcus lactis 37 90 0 0.0 0.0
Lodderomyces Lodderomyces elongisporus 0 1 0 0.0 0.0
Malassezia Malassezia globosa 0 2 0 0.0 0.0
Mesocricetus Mesocricetus auratus 0 2 0 0.0 0.0
Millerozyma Millerozyma farinosa 1 1 0 0.0 0.0
Modoc virus group Modoc virus 0 2 0 0.0 0.0
Morbillivirus Measles virus 1 10 0 0.0 0.0
Mus Mus musculus 795 2089 0 0.0 0.0
Mycobacterium Mycobacterium marinum 0 4 0 0.0 0.0
Mycobacterium Mycobacterium smegmatis 22 104 1 1.0 1.2
Mycobacterium Mycobacterium tuberculosis 192 758 12 1.6 2.1
Neisseria Neisseria gonorrhoeae 11 30 1 3.3 5.3
Orthopoxvirus Vaccinia virus 25 48 0 0.0 0.0
Oryctolagus Oryctolagus cuniculus 128 266 0 0.0 0.0
Ovis Ovis aries 27 49 0 0.0 0.0
Photorhabdus Photorhabdus luminescens 0 1 0 0.0 0.0
Plasmodium (Laverania) Plasmodium falciparum 54 222 0 0.0 0.0
Plasmodium (Plasmodium) Plasmodium vivax 9 39 0 0.0 0.0
Polyomavirus BK polyomavirus 0 1 0 0.0 0.0
Polyomavirus JC polyomavirus 0 7 0 0.0 0.0
Proteus Proteus mirabilis 4 15 1 6.7 9.1
Providencia Providencia stuartii 0 1 1 100.0 100.0
Pseudomonas Pseudomonas putida 88 200 6 3.0 5.4
Rattus Rattus norvegicus 445 918 0 0.0 0.0
Rhadinovirus Human herpesvirus 8 3 8 0 0.0 0.0
Rhadinovirus Murid herpesvirus 4 1 1 0 0.0 0.0
Rhadinovirus Saimiriine herpesvirus 2 1 2 0 0.0 0.0
Rhodobacter Rhodobacter sphaeroides 55 93 0 0.0 0.0
Rickettsia Rickettsia prowazekii 0 4 0 0.0 0.0
root synthetic construct 2276 5259 1 0.0 0.0
root uncultured bacterium 2 32 2 6.2 6.7
Saccharomyces Saccharomyces cerevisiae 534 1405 0 0.0 0.0
Schizosaccharomyces Schizosaccharomyces pombe 40 140 1 0.7 1.0
Serratia Serratia marcescens 32 54 1 1.9 4.5
Shewanella Shewanella oneidensis 5 28 1 3.6 4.3
Shigella Shigella dysenteriae 1 1 0 0.0 0.0
Simplexvirus Human herpesvirus 1 20 39 0 0.0 0.0
Stenotrophomonas Stenotrophomonas maltophilia 8 25 9 36.0 52.9
Streptococcus Streptococcus dysgalactiae 2 2 0 0.0 0.0
Streptococcus Streptococcus equi 1 2 0 0.0 0.0
Streptococcus Streptococcus equinus 0 1 0 0.0 0.0
Streptococcus Streptococcus gordonii 1 8 1 12.5 14.3
Streptococcus Streptococcus mutans 5 64 1 1.6 1.7
Streptococcus Streptococcus pyogenes 18 70 2 2.9 3.8
Streptococcus Streptococcus sp. 'group G' 0 12 0 0.0 0.0
Streptococcus Streptococcus suis 5 15 0 0.0 0.0
Streptococcus Streptococcus thermophilus 0 12 1 8.3 8.3
Streptococcus Streptococcus uberis 0 1 0 0.0 0.0
Streptomyces Streptomyces fradiae 1 7 0 0.0 0.0
Streptomyces Streptomyces griseus 20 33 0 0.0 0.0
Streptomyces Streptomyces venezuelae 14 26 2 7.7 16.7
Sus Sus scrofa 223 318 0 0.0 0.0
Treponema Treponema pallidum 5 11 0 0.0 0.0
Trueperella Trueperella pyogenes 0 4 4 100.0 100.0
Vibrio Vibrio harveyi 8 32 0 0.0 0.0
Yellow fever virus group Yellow fever virus 1 7 0 0.0 0.0
Yersinia Yersinia pseudotuberculosis 3 25 0 0.0 0.0
Zygosaccharomyces Zygosaccharomyces rouxii 0 1 0 0.0 0.0
Actinobacteria (class) Bifidobacterium Bifidobacterium longum 4 27 2 7.4 8.7
Bacilli Bacillus Bacillus anthracis 70 426 159 37.3 44.7
Bacilli Enterococcus Enterococcus faecalis 30 111 10 9.0 12.3
Bacilli Enterococcus Enterococcus faecium 8 20 9 45.0 75.0
Bacilli Enterococcus Enterococcus gallinarum 0 6 4 66.7 66.7
Bacilli Listeria Listeria monocytogenes 42 275 60 21.8 25.8
Bacilli Staphylococcus Staphylococcus aureus 168 742 69 9.3 12.0
Bacilli Staphylococcus Staphylococcus epidermidis 3 46 1 2.2 2.3
Bacilli Staphylococcus Staphylococcus haemolyticus 1 4 2 50.0 66.7
Bacilli Streptococcus Streptococcus agalactiae 3 28 2 7.1 8.0
Bacilli Streptococcus Streptococcus pneumoniae 54 284 24 8.5 10.4
Bacteroidia Bacteroides Bacteroides thetaiotaomicron 7 110 1 0.9 1.0
Betaproteobacteria Neisseria Neisseria meningitidis 28 122 4 3.3 4.3
Chlamydiae Chlamydia Chlamydia trachomatis 6 69 3 4.3 4.8
Clostridia Clostridium Clostridium difficile 6 136 25 18.4 19.2
Clostridia Clostridium Clostridium perfringens 37 204 14 6.9 8.4
Coccidia Cryptosporidium Cryptosporidium parvum 5 26 10 38.5 47.6
Coccodia Toxoplasma Toxoplasma gondii 17 76 20 26.3 33.9
Epsilonproteobacteria Campylobacter Campylobacter jejuni 30 264 69 26.1 29.5
Epsilonproteobacteria Helicobacter Helicobacter pylori 40 203 6 3.0 3.7
Gammaproteobacteria Acinetobacter Acinetobacter baumannii 4 82 16 19.5 20.5
Gammaproteobacteria Acinetobacter Acinetobacter haemolyticus 0 2 2 100.0 100.0
Gammaproteobacteria Coxiella Coxiella burnetii 0 63 11 17.5 17.5
Gammaproteobacteria Escherichia Escherichia coli 1631 3239 43 1.3 2.7
Gammaproteobacteria Francisella Francisella tularensis 4 132 67 50.8 52.3
Gammaproteobacteria Legionella Legionella pneumophila 1 77 4 5.2 5.3
Gammaproteobacteria Pseudomonas Pseudomonas aeruginosa 157 622 13 2.1 2.8
Gammaproteobacteria Pseudomonas Pseudomonas fluorescens 31 85 1 1.2 1.9
Gammaproteobacteria Salmonella Salmonella enterica 192 656 80 12.2 17.2
Gammaproteobacteria Shigella Shigella flexneri 38 151 6 4.0 5.3
Gammaproteobacteria Vibrio Vibrio cholerae 101 560 122 21.8 26.6
Gammaproteobacteria Vibrio Vibrio parahaemolyticus 2 29 3 10.3 11.1
Gammaproteobacteria Vibrio Vibrio vulnificus 1 42 23 54.8 56.1
Gammaproteobacteria Yersinia Yersinia enterocolitica 21 45 9 20.0 37.5
Gammaproteobacteria Yersinia Yersinia pestis 8 143 92 64.3 68.1
Mammalia Homo Homo sapiens 4341 13048 1 0.0 0.0
Spirochaetia Leptospira Leptospira interrogans 8 19 1 5.3 9.1
Viruses Ebolavirus Zaire ebolavirus 0 11 4 36.4 36.4
Viruses Flavivirus Dengue virus 11 53 6 11.3 14.3
Viruses Flavivirus Japanese encephalitis virus 1 6 1 16.7 20.0
Viruses Flavivirus West Nile virus 4 10 2 20.0 33.3
Viruses Influenzavirus A Influenza A virus 123 842 7 0.8 1.0
Viruses Japanese encephalitis virus group St. Louis encephalitis virus 0 1 1 100.0 100.0
Viruses Orthopoxvirus Cowpox virus 0 3 3 100.0 100.0
Viruses Orthopoxvirus Ectromelia virus 2 6 1 16.7 25.0
Viruses Orthopoxvirus Monkeypox virus 0 1 1 100.0 100.0
Viruses Vibrio phage Vibrio phage ICP1 0 1 1 100.0 100.0