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 March 23, 2019. For both PDB and CSGID only the structures released as of March 23, 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 2 7 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 25 85 1 1.2 1.7
Aliivibrio Aliivibrio fischeri 1 15 4 26.7 28.6
Alphavirus Chikungunya virus 0 8 0 0.0 0.0
Aquifex Aquifex aeolicus 85 195 0 0.0 0.0
Aspergillus Aspergillus fumigatus 0 1 1 100.0 100.0
Bacillus Bacillus cereus 68 172 5 2.9 4.8
Bacillus Bacillus subtilis 234 619 3 0.5 0.8
Betacoronavirus Severe acute respiratory syndrome-related coronavirus 0 2 0 0.0 0.0
Bordetella Bordetella bronchiseptica 0 22 0 0.0 0.0
Bordetella Bordetella pertussis 12 27 3 11.1 20.0
Borrelia Borrelia burgdorferi 4 24 0 0.0 0.0
Bos Bos taurus 744 1238 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 14 20 0 0.0 0.0
Brugia Brugia malayi 0 6 0 0.0 0.0
Burkholderia Burkholderia ambifaria 0 13 0 0.0 0.0
Burkholderia Burkholderia cenocepacia 0 43 1 2.3 2.3
Burkholderia Burkholderia cepacia 16 23 0 0.0 0.0
Burkholderia Burkholderia multivorans 0 8 0 0.0 0.0
Burkholderia Burkholderia pseudomallei 1 73 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 16 70 6 8.6 11.1
Capra Capra hircus 14 26 0 0.0 0.0
Cavia Cavia porcellus 6 14 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
Clostridium Clostridium botulinum 46 103 0 0.0 0.0
Clostridium Clostridium tetani 6 8 0 0.0 0.0
Corynebacterium Corynebacterium diphtheriae 22 47 4 8.5 16.0
Corynebacterium Corynebacterium matruchotii 0 1 1 100.0 100.0
Cryptosporidium Cryptosporidium hominis 1 4 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 26 51 4 7.8 16.0
Enterovirus Enterovirus B 6 17 0 0.0 0.0
Equus Equus caballus 97 163 3 1.8 4.5
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 80 135 8 5.9 14.5
Haliangium Haliangium ochraceum 0 3 0 0.0 0.0
Hepacivirus Hepatitis C virus 44 204 0 0.0 0.0
Hepevirus Hepatitis E virus 0 3 0 0.0 0.0
Influenzavirus B Influenza B virus 5 23 0 0.0 0.0
Japanese encephalitis virus group Murray Valley encephalitis virus 0 1 0 0.0 0.0
Klebsiella Klebsiella pneumoniae 18 131 23 17.6 20.4
Kluyveromyces Kluyveromyces lactis 4 23 0 0.0 0.0
Komagataella Komagataella pastoris 2 3 0 0.0 0.0
Lactococcus Lactococcus lactis 40 93 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 851 2204 0 0.0 0.0
Mycobacterium Mycobacterium marinum 0 5 0 0.0 0.0
Mycobacterium Mycobacterium smegmatis 25 110 1 0.9 1.2
Mycobacterium Mycobacterium tuberculosis 210 817 12 1.5 2.0
Neisseria Neisseria gonorrhoeae 11 31 1 3.2 5.0
Orthopoxvirus Vaccinia virus 25 52 0 0.0 0.0
Oryctolagus Oryctolagus cuniculus 139 300 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 56 230 0 0.0 0.0
Plasmodium (Plasmodium) Plasmodium vivax 11 40 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 5 16 1 6.2 9.1
Providencia Providencia stuartii 0 1 1 100.0 100.0
Pseudomonas Pseudomonas putida 101 213 6 2.8 5.4
Rattus Rattus norvegicus 477 968 0 0.0 0.0
Rhadinovirus Human herpesvirus 8 3 10 0 0.0 0.0
Rhadinovirus Murid herpesvirus 4 1 2 0 0.0 0.0
Rhadinovirus Saimiriine herpesvirus 2 1 2 0 0.0 0.0
Rhodobacter Rhodobacter sphaeroides 75 116 0 0.0 0.0
Rickettsia Rickettsia prowazekii 0 4 0 0.0 0.0
root synthetic construct 2358 5432 1 0.0 0.0
root uncultured bacterium 2 32 2 6.2 6.7
Saccharomyces Saccharomyces cerevisiae 584 1490 0 0.0 0.0
Schizosaccharomyces Schizosaccharomyces pombe 45 151 1 0.7 0.9
Serratia Serratia marcescens 35 59 1 1.7 4.2
Shewanella Shewanella oneidensis 6 32 1 3.1 3.8
Shigella Shigella dysenteriae 1 1 0 0.0 0.0
Simplexvirus Human herpesvirus 1 24 43 0 0.0 0.0
Stenotrophomonas Stenotrophomonas maltophilia 9 18 0 0.0 0.0
Streptococcus Streptococcus dysgalactiae 3 3 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 9 1 11.1 12.5
Streptococcus Streptococcus mutans 6 67 1 1.5 1.6
Streptococcus Streptococcus pyogenes 21 85 2 2.4 3.1
Streptococcus Streptococcus sp. 'group G' 0 12 0 0.0 0.0
Streptococcus Streptococcus suis 5 19 0 0.0 0.0
Streptococcus Streptococcus thermophilus 0 16 1 6.2 6.2
Streptococcus Streptococcus uberis 0 1 0 0.0 0.0
Streptomyces Streptomyces fradiae 1 7 0 0.0 0.0
Streptomyces Streptomyces griseus 21 35 0 0.0 0.0
Streptomyces Streptomyces venezuelae 15 30 2 6.7 13.3
Sus Sus scrofa 242 338 0 0.0 0.0
Treponema Treponema pallidum 6 12 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 26 0 0.0 0.0
Zygosaccharomyces Zygosaccharomyces rouxii 0 1 0 0.0 0.0
Actinobacteria (class) Bifidobacterium Bifidobacterium longum 4 28 2 7.1 8.3
Bacilli Bacillus Bacillus anthracis 72 416 160 38.5 46.5
Bacilli Enterococcus Enterococcus faecalis 32 121 10 8.3 11.2
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 45 265 60 22.6 27.3
Bacilli Staphylococcus Staphylococcus aureus 171 757 69 9.1 11.8
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 4 35 2 5.7 6.5
Bacilli Streptococcus Streptococcus pneumoniae 60 296 23 7.8 9.7
Bacteroidia Bacteroides Bacteroides thetaiotaomicron 7 111 1 0.9 1.0
Betaproteobacteria Neisseria Neisseria meningitidis 31 128 4 3.1 4.1
Chlamydiae Chlamydia Chlamydia trachomatis 6 62 3 4.8 5.4
Clostridia Clostridium Clostridium difficile 6 128 25 19.5 20.5
Clostridia Clostridium Clostridium perfringens 37 192 14 7.3 9.0
Coccidia Cryptosporidium Cryptosporidium parvum 6 28 10 35.7 45.5
Coccodia Toxoplasma Toxoplasma gondii 22 89 20 22.5 29.9
Epsilonproteobacteria Campylobacter Campylobacter jejuni 30 261 69 26.4 29.9
Epsilonproteobacteria Helicobacter Helicobacter pylori 41 206 6 2.9 3.6
Gammaproteobacteria Acinetobacter Acinetobacter baumannii 4 86 16 18.6 19.5
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 1771 3437 38 1.1 2.3
Gammaproteobacteria Francisella Francisella tularensis 6 129 65 50.4 52.8
Gammaproteobacteria Legionella Legionella pneumophila 1 77 4 5.2 5.3
Gammaproteobacteria Pseudomonas Pseudomonas aeruginosa 187 662 12 1.8 2.5
Gammaproteobacteria Pseudomonas Pseudomonas fluorescens 32 87 1 1.1 1.8
Gammaproteobacteria Salmonella Salmonella enterica 202 653 78 11.9 17.3
Gammaproteobacteria Shigella Shigella flexneri 40 146 6 4.1 5.7
Gammaproteobacteria Vibrio Vibrio cholerae 103 536 119 22.2 27.5
Gammaproteobacteria Vibrio Vibrio parahaemolyticus 2 29 3 10.3 11.1
Gammaproteobacteria Vibrio Vibrio vulnificus 1 41 22 53.7 55.0
Gammaproteobacteria Yersinia Yersinia enterocolitica 24 53 9 17.0 31.0
Gammaproteobacteria Yersinia Yersinia pestis 8 145 92 63.4 67.2
Mammalia Homo Homo sapiens 4647 13782 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 123 805 3 0.4 0.4
Viruses Japanese encephalitis virus group St. Louis encephalitis virus 0 1 1 100.0 100.0
Viruses Orthopoxvirus Cowpox virus 1 4 3 75.0 100.0
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