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 July 17, 2019. For both PDB and CSGID only the structures released as of July 17, 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 84 194 0 0.0 0.0
Aspergillus Aspergillus fumigatus 0 1 1 100.0 100.0
Bacillus Bacillus cereus 61 163 5 3.1 4.9
Bacillus Bacillus subtilis 229 610 3 0.5 0.8
Betacoronavirus Severe acute respiratory syndrome-related coronavirus 0 2 0 0.0 0.0
Bordetella Bordetella bronchiseptica 0 21 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 732 1217 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 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 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 15 71 8 11.3 14.3
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
Clostridium Clostridium botulinum 42 99 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 52 5 9.6 19.2
Enterovirus Enterovirus B 6 13 0 0.0 0.0
Equus Equus caballus 93 158 3 1.9 4.6
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 43 200 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 17 127 23 18.1 20.9
Kluyveromyces Kluyveromyces lactis 4 23 0 0.0 0.0
Komagataella Komagataella pastoris 2 3 0 0.0 0.0
Lactococcus Lactococcus lactis 38 91 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 831 2146 0 0.0 0.0
Mycobacterium Mycobacterium marinum 0 4 0 0.0 0.0
Mycobacterium Mycobacterium smegmatis 23 107 1 0.9 1.2
Mycobacterium Mycobacterium tuberculosis 197 792 12 1.5 2.0
Neisseria Neisseria gonorrhoeae 11 31 1 3.2 5.0
Orthopoxvirus Vaccinia virus 25 48 0 0.0 0.0
Oryctolagus Oryctolagus cuniculus 135 294 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 54 226 0 0.0 0.0
Plasmodium (Plasmodium) Plasmodium vivax 10 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 98 210 6 2.9 5.4
Rattus Rattus norvegicus 463 951 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 75 116 0 0.0 0.0
Rickettsia Rickettsia prowazekii 0 4 0 0.0 0.0
root synthetic construct 2342 5391 1 0.0 0.0
root uncultured bacterium 2 32 2 6.2 6.7
Saccharomyces Saccharomyces cerevisiae 555 1443 0 0.0 0.0
Schizosaccharomyces Schizosaccharomyces pombe 44 146 1 0.7 1.0
Serratia Serratia marcescens 34 56 1 1.8 4.5
Shewanella Shewanella oneidensis 6 30 1 3.3 4.2
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 17 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 84 2 2.4 3.2
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 14 26 2 7.7 16.7
Sus Sus scrofa 233 329 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 26 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 72 420 160 38.1 46.0
Bacilli Enterococcus Enterococcus faecalis 32 115 10 8.7 12.0
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 43 269 60 22.3 26.5
Bacilli Staphylococcus Staphylococcus aureus 170 752 69 9.2 11.9
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 60 291 23 7.9 10.0
Bacteroidia Bacteroides Bacteroides thetaiotaomicron 7 111 1 0.9 1.0
Betaproteobacteria Neisseria Neisseria meningitidis 30 127 4 3.1 4.1
Chlamydiae Chlamydia Chlamydia trachomatis 6 66 3 4.5 5.0
Clostridia Clostridium Clostridium difficile 6 134 25 18.7 19.5
Clostridia Clostridium Clostridium perfringens 37 194 14 7.2 8.9
Coccidia Cryptosporidium Cryptosporidium parvum 6 28 10 35.7 45.5
Coccodia Toxoplasma Toxoplasma gondii 20 82 20 24.4 32.3
Epsilonproteobacteria Campylobacter Campylobacter jejuni 30 261 69 26.4 29.9
Epsilonproteobacteria Helicobacter Helicobacter pylori 40 204 6 2.9 3.7
Gammaproteobacteria Acinetobacter Acinetobacter baumannii 4 85 16 18.8 19.8
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 1723 3374 42 1.2 2.5
Gammaproteobacteria Francisella Francisella tularensis 6 130 66 50.8 53.2
Gammaproteobacteria Legionella Legionella pneumophila 1 77 4 5.2 5.3
Gammaproteobacteria Pseudomonas Pseudomonas aeruginosa 167 640 13 2.0 2.7
Gammaproteobacteria Pseudomonas Pseudomonas fluorescens 31 86 1 1.2 1.8
Gammaproteobacteria Salmonella Salmonella enterica 198 655 79 12.1 17.3
Gammaproteobacteria Shigella Shigella flexneri 40 158 6 3.8 5.1
Gammaproteobacteria Vibrio Vibrio cholerae 103 542 119 22.0 27.1
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 22 46 9 19.6 37.5
Gammaproteobacteria Yersinia Yersinia pestis 8 143 92 64.3 68.1
Mammalia Homo Homo sapiens 4506 13388 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 123 826 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 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