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 September 19, 2018. For both PDB and CSGID only the structures released as of September 19, 2018 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 3 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 7 25 0 0.0 0.0
Agrobacterium Agrobacterium tumefaciens 50 115 1 0.9 1.5
Aliivibrio Aliivibrio fischeri 1 17 4 23.5 25.0
Alphavirus Chikungunya virus 0 11 0 0.0 0.0
Aquifex Aquifex aeolicus 184 307 0 0.0 0.0
Aspergillus Aspergillus fumigatus 0 1 1 100.0 100.0
Bacillus Bacillus cereus 97 213 4 1.9 3.4
Bacillus Bacillus subtilis 419 830 1 0.1 0.2
Betacoronavirus Severe acute respiratory syndrome-related coronavirus 0 2 0 0.0 0.0
Bordetella Bordetella bronchiseptica 3 30 0 0.0 0.0
Bordetella Bordetella pertussis 16 34 3 8.8 16.7
Borrelia Borrelia burgdorferi 21 42 0 0.0 0.0
Borrelia Borrelia turicatae 1 1 0 0.0 0.0
Bos Bos taurus 1045 1574 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 17 27 0 0.0 0.0
Brugia Brugia malayi 2 8 0 0.0 0.0
Burkholderia Burkholderia ambifaria 0 13 0 0.0 0.0
Burkholderia Burkholderia cenocepacia 0 44 1 2.3 2.3
Burkholderia Burkholderia cepacia 22 32 0 0.0 0.0
Burkholderia Burkholderia multivorans 0 8 0 0.0 0.0
Burkholderia Burkholderia pseudomallei 7 81 0 0.0 0.0
Burkholderia Burkholderia thailandensis 0 46 0 0.0 0.0
Burkholderia Burkholderia xenovorans 11 28 0 0.0 0.0
Candida Candida albicans 26 81 6 7.4 10.9
Capra Capra hircus 20 32 0 0.0 0.0
Cavia Cavia porcellus 6 14 0 0.0 0.0
Chlamydia Chlamydia pneumoniae 1 3 0 0.0 0.0
Citrobacter Citrobacter rodentium 0 2 1 50.0 50.0
Clostridium Clostridium botulinum 56 117 0 0.0 0.0
Clostridium Clostridium tetani 7 11 0 0.0 0.0
Corynebacterium Corynebacterium diphtheriae 34 62 4 6.5 14.3
Corynebacterium Corynebacterium matruchotii 0 1 1 100.0 100.0
Cryptosporidium Cryptosporidium hominis 1 4 0 0.0 0.0
Cytomegalovirus Human herpesvirus 5 16 26 0 0.0 0.0
Enterobacter Enterobacter aerogenes 3 10 0 0.0 0.0
Enterobacter Enterobacter cloacae 30 55 4 7.3 16.0
Enterovirus Enterovirus B 7 21 0 0.0 0.0
Equus Equus caballus 106 172 2 1.2 3.0
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 7 0 0.0 0.0
Haemophilus Haemophilus influenzae 132 204 8 3.9 11.1
Haliangium Haliangium ochraceum 0 3 0 0.0 0.0
Hepacivirus Hepatitis C virus 56 224 0 0.0 0.0
Hepevirus Hepatitis E virus 0 3 0 0.0 0.0
Influenzavirus B Influenza B virus 10 28 0 0.0 0.0
Japanese encephalitis virus group Murray Valley encephalitis virus 0 1 0 0.0 0.0
Klebsiella Klebsiella pneumoniae 26 139 15 10.8 13.3
Kluyveromyces Kluyveromyces lactis 9 30 0 0.0 0.0
Komagataella Komagataella pastoris 3 4 0 0.0 0.0
Lactococcus Lactococcus lactis 47 103 0 0.0 0.0
Leporipoxvirus Myxoma virus 3 3 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 8 10 0 0.0 0.0
Millerozyma Millerozyma farinosa 2 2 0 0.0 0.0
Modoc virus group Modoc virus 0 2 0 0.0 0.0
Morbillivirus Measles virus 2 12 0 0.0 0.0
Mus Mus musculus 1742 3185 0 0.0 0.0
Mycobacterium Mycobacterium marinum 0 5 0 0.0 0.0
Mycobacterium Mycobacterium smegmatis 37 130 1 0.8 1.1
Mycobacterium Mycobacterium tuberculosis 367 1027 12 1.2 1.8
Neisseria Neisseria gonorrhoeae 18 42 0 0.0 0.0
Orthopoxvirus Vaccinia virus 34 62 0 0.0 0.0
Oryctolagus Oryctolagus cuniculus 214 381 0 0.0 0.0
Ovis Ovis aries 43 68 0 0.0 0.0
Photorhabdus Photorhabdus luminescens 0 1 0 0.0 0.0
Plasmodium (Laverania) Plasmodium falciparum 127 316 0 0.0 0.0
Plasmodium (Plasmodium) Plasmodium vivax 18 47 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 9 22 1 4.5 7.7
Providencia Providencia stuartii 0 1 1 100.0 100.0
Pseudomonas Pseudomonas putida 156 276 5 1.8 4.2
Rattus Rattus norvegicus 752 1289 0 0.0 0.0
Rhadinovirus Human herpesvirus 8 8 17 0 0.0 0.0
Rhadinovirus Murid herpesvirus 4 6 7 0 0.0 0.0
Rhadinovirus Saimiriine herpesvirus 2 5 6 0 0.0 0.0
Rhodobacter Rhodobacter sphaeroides 97 142 0 0.0 0.0
Rickettsia Rickettsia prowazekii 0 5 0 0.0 0.0
root synthetic construct 4671 8003 1 0.0 0.0
root uncultured bacterium 2 35 2 5.7 6.1
Saccharomyces Saccharomyces cerevisiae 978 1953 0 0.0 0.0
Schizosaccharomyces Schizosaccharomyces pombe 64 180 1 0.6 0.9
Serratia Serratia marcescens 44 69 1 1.4 4.0
Shewanella Shewanella oneidensis 21 52 0 0.0 0.0
Shigella Shigella dysenteriae 1 2 0 0.0 0.0
Simplexvirus Human herpesvirus 1 35 55 0 0.0 0.0
Stenotrophomonas Stenotrophomonas maltophilia 17 26 0 0.0 0.0
Streptococcus Streptococcus dysgalactiae 6 6 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 2 10 1 10.0 12.5
Streptococcus Streptococcus mutans 12 79 1 1.3 1.5
Streptococcus Streptococcus pyogenes 58 124 1 0.8 1.5
Streptococcus Streptococcus sp. 'group G' 15 28 0 0.0 0.0
Streptococcus Streptococcus suis 9 23 0 0.0 0.0
Streptococcus Streptococcus thermophilus 1 19 1 5.3 5.6
Streptococcus Streptococcus uberis 0 1 0 0.0 0.0
Streptomyces Streptomyces fradiae 2 8 0 0.0 0.0
Streptomyces Streptomyces griseus 38 52 0 0.0 0.0
Streptomyces Streptomyces toyocaensis 1 1 0 0.0 0.0
Streptomyces Streptomyces venezuelae 20 35 2 5.7 13.3
Sus Sus scrofa 347 445 0 0.0 0.0
Treponema Treponema pallidum 11 18 0 0.0 0.0
Trueperella Trueperella pyogenes 0 4 4 100.0 100.0
Vibrio Vibrio harveyi 12 36 0 0.0 0.0
Yellow fever virus group Yellow fever virus 3 9 0 0.0 0.0
Yersinia Yersinia pseudotuberculosis 10 35 0 0.0 0.0
Zygosaccharomyces Zygosaccharomyces rouxii 0 1 0 0.0 0.0
Actinobacteria (class) Bifidobacterium Bifidobacterium longum 7 31 2 6.5 8.3
Bacilli Bacillus Bacillus anthracis 76 418 158 37.8 46.2
Bacilli Enterococcus Enterococcus faecalis 83 180 10 5.6 10.3
Bacilli Enterococcus Enterococcus faecium 14 29 9 31.0 60.0
Bacilli Enterococcus Enterococcus gallinarum 0 6 4 66.7 66.7
Bacilli Listeria Listeria monocytogenes 46 263 60 22.8 27.6
Bacilli Staphylococcus Staphylococcus aureus 349 955 69 7.2 11.4
Bacilli Staphylococcus Staphylococcus epidermidis 6 52 1 1.9 2.2
Bacilli Staphylococcus Staphylococcus haemolyticus 1 6 2 33.3 40.0
Bacilli Streptococcus Streptococcus agalactiae 12 46 2 4.3 5.9
Bacilli Streptococcus Streptococcus pneumoniae 120 361 22 6.1 9.1
Bacteroidia Bacteroides Bacteroides thetaiotaomicron 25 143 1 0.7 0.8
Betaproteobacteria Neisseria Neisseria meningitidis 54 166 4 2.4 3.6
Chlamydiae Chlamydia Chlamydia trachomatis 6 56 3 5.4 6.0
Clostridia Clostridium Clostridium difficile 6 126 24 19.0 20.0
Clostridia Clostridium Clostridium perfringens 37 189 14 7.4 9.2
Coccidia Cryptosporidium Cryptosporidium parvum 9 33 10 30.3 41.7
Coccodia Toxoplasma Toxoplasma gondii 38 107 20 18.7 29.0
Epsilonproteobacteria Campylobacter Campylobacter jejuni 30 252 68 27.0 30.6
Epsilonproteobacteria Helicobacter Helicobacter pylori 86 263 5 1.9 2.8
Gammaproteobacteria Acinetobacter Acinetobacter baumannii 4 85 15 17.6 18.5
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 2962 4789 31 0.6 1.7
Gammaproteobacteria Francisella Francisella tularensis 6 123 64 52.0 54.7
Gammaproteobacteria Legionella Legionella pneumophila 7 93 4 4.3 4.7
Gammaproteobacteria Pseudomonas Pseudomonas aeruginosa 299 795 10 1.3 2.0
Gammaproteobacteria Pseudomonas Pseudomonas fluorescens 45 111 1 0.9 1.5
Gammaproteobacteria Salmonella Salmonella enterica 302 747 77 10.3 17.3
Gammaproteobacteria Shigella Shigella flexneri 38 143 5 3.5 4.8
Gammaproteobacteria Vibrio Vibrio cholerae 103 515 116 22.5 28.2
Gammaproteobacteria Vibrio Vibrio parahaemolyticus 16 53 3 5.7 8.1
Gammaproteobacteria Vibrio Vibrio vulnificus 5 46 22 47.8 53.7
Gammaproteobacteria Yersinia Yersinia enterocolitica 27 55 7 12.7 25.0
Gammaproteobacteria Yersinia Yersinia pestis 16 154 91 59.1 65.9
Mammalia Homo Homo sapiens 8329 18062 1 0.0 0.0
Spirochaetia Leptospira Leptospira interrogans 11 23 1 4.3 8.3
Viruses Ebolavirus Zaire ebolavirus 1 17 4 23.5 25.0
Viruses Flavivirus Dengue virus 21 64 6 9.4 14.0
Viruses Flavivirus Japanese encephalitis virus 2 7 1 14.3 20.0
Viruses Flavivirus West Nile virus 12 18 2 11.1 33.3
Viruses Influenzavirus A Influenza A virus 124 780 3 0.4 0.5
Viruses Japanese encephalitis virus group St. Louis encephalitis virus 0 1 1 100.0 100.0
Viruses Orthopoxvirus Cowpox virus 3 6 3 50.0 100.0
Viruses Orthopoxvirus Ectromelia virus 2 7 1 14.3 20.0
Viruses Orthopoxvirus Monkeypox virus 0 1 1 100.0 100.0
Viruses Vibrio phage Vibrio phage ICP1 0 1 1 100.0 100.0