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 January 16, 2019. For both PDB and CSGID only the structures released as of January 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 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 5 23 0 0.0 0.0
Agrobacterium Agrobacterium tumefaciens 41 105 1 1.0 1.6
Aliivibrio Aliivibrio fischeri 1 17 4 23.5 25.0
Alphavirus Chikungunya virus 0 8 0 0.0 0.0
Aquifex Aquifex aeolicus 155 278 0 0.0 0.0
Aspergillus Aspergillus fumigatus 0 1 1 100.0 100.0
Bacillus Bacillus cereus 85 194 4 2.1 3.7
Bacillus Bacillus subtilis 329 735 1 0.1 0.2
Betacoronavirus Severe acute respiratory syndrome-related coronavirus 0 2 0 0.0 0.0
Bordetella Bordetella bronchiseptica 0 24 0 0.0 0.0
Bordetella Bordetella pertussis 13 30 3 10.0 17.6
Borrelia Borrelia burgdorferi 13 33 0 0.0 0.0
Borrelia Borrelia turicatae 1 1 0 0.0 0.0
Bos Bos taurus 987 1501 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 16 26 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 20 30 0 0.0 0.0
Burkholderia Burkholderia multivorans 0 8 0 0.0 0.0
Burkholderia Burkholderia pseudomallei 2 76 0 0.0 0.0
Burkholderia Burkholderia thailandensis 0 46 0 0.0 0.0
Burkholderia Burkholderia xenovorans 10 24 0 0.0 0.0
Candida Candida albicans 21 75 6 8.0 11.1
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 50 107 0 0.0 0.0
Clostridium Clostridium tetani 7 10 0 0.0 0.0
Corynebacterium Corynebacterium diphtheriae 30 57 4 7.0 14.8
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 27 52 4 7.7 16.0
Enterovirus Enterovirus B 7 21 0 0.0 0.0
Equus Equus caballus 106 173 3 1.7 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 7 0 0.0 0.0
Haemophilus Haemophilus influenzae 120 188 8 4.3 11.8
Haliangium Haliangium ochraceum 0 3 0 0.0 0.0
Hepacivirus Hepatitis C virus 52 217 0 0.0 0.0
Hepevirus Hepatitis E virus 0 3 0 0.0 0.0
Influenzavirus B Influenza B virus 9 27 0 0.0 0.0
Japanese encephalitis virus group Murray Valley encephalitis virus 0 1 0 0.0 0.0
Klebsiella Klebsiella pneumoniae 23 136 19 14.0 16.8
Kluyveromyces Kluyveromyces lactis 8 28 0 0.0 0.0
Komagataella Komagataella pastoris 3 4 0 0.0 0.0
Lactococcus Lactococcus lactis 41 96 0 0.0 0.0
Leporipoxvirus Myxoma virus 1 1 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 1400 2809 0 0.0 0.0
Mycobacterium Mycobacterium marinum 0 5 0 0.0 0.0
Mycobacterium Mycobacterium smegmatis 36 129 1 0.8 1.1
Mycobacterium Mycobacterium tuberculosis 318 965 12 1.2 1.9
Neisseria Neisseria gonorrhoeae 15 39 1 2.6 4.2
Orthopoxvirus Vaccinia virus 31 58 0 0.0 0.0
Oryctolagus Oryctolagus cuniculus 199 364 0 0.0 0.0
Ovis Ovis aries 40 65 0 0.0 0.0
Photorhabdus Photorhabdus luminescens 0 1 0 0.0 0.0
Plasmodium (Laverania) Plasmodium falciparum 101 289 0 0.0 0.0
Plasmodium (Plasmodium) Plasmodium vivax 14 43 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 134 253 6 2.4 5.0
Rattus Rattus norvegicus 683 1205 0 0.0 0.0
Rhadinovirus Human herpesvirus 8 7 16 0 0.0 0.0
Rhadinovirus Murid herpesvirus 4 3 4 0 0.0 0.0
Rhadinovirus Saimiriine herpesvirus 2 5 6 0 0.0 0.0
Rhodobacter Rhodobacter sphaeroides 89 131 0 0.0 0.0
Rickettsia Rickettsia prowazekii 0 5 0 0.0 0.0
root synthetic construct 4001 7241 1 0.0 0.0
root uncultured bacterium 2 35 2 5.7 6.1
Saccharomyces Saccharomyces cerevisiae 830 1785 0 0.0 0.0
Schizosaccharomyces Schizosaccharomyces pombe 62 175 1 0.6 0.9
Serratia Serratia marcescens 42 66 1 1.5 4.2
Shewanella Shewanella oneidensis 17 47 0 0.0 0.0
Shigella Shigella dysenteriae 1 1 0 0.0 0.0
Simplexvirus Human herpesvirus 1 29 48 0 0.0 0.0
Stenotrophomonas Stenotrophomonas maltophilia 13 22 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 9 75 1 1.3 1.5
Streptococcus Streptococcus pyogenes 43 108 2 1.9 3.1
Streptococcus Streptococcus sp. 'group G' 8 20 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 29 43 0 0.0 0.0
Streptomyces Streptomyces toyocaensis 1 1 0 0.0 0.0
Streptomyces Streptomyces venezuelae 16 31 2 6.5 13.3
Sus Sus scrofa 328 426 0 0.0 0.0
Treponema Treponema pallidum 7 14 0 0.0 0.0
Trueperella Trueperella pyogenes 0 4 4 100.0 100.0
Vibrio Vibrio harveyi 10 34 0 0.0 0.0
Yellow fever virus group Yellow fever virus 1 7 0 0.0 0.0
Yersinia Yersinia pseudotuberculosis 8 32 0 0.0 0.0
Zygosaccharomyces Zygosaccharomyces rouxii 0 1 0 0.0 0.0
Actinobacteria (class) Bifidobacterium Bifidobacterium longum 6 30 2 6.7 8.3
Bacilli Bacillus Bacillus anthracis 71 411 158 38.4 46.5
Bacilli Enterococcus Enterococcus faecalis 65 160 10 6.2 10.5
Bacilli Enterococcus Enterococcus faecium 12 26 9 34.6 64.3
Bacilli Enterococcus Enterococcus gallinarum 0 6 4 66.7 66.7
Bacilli Listeria Listeria monocytogenes 41 255 58 22.7 27.1
Bacilli Staphylococcus Staphylococcus aureus 300 897 68 7.6 11.4
Bacilli Staphylococcus Staphylococcus epidermidis 5 51 1 2.0 2.2
Bacilli Staphylococcus Staphylococcus haemolyticus 1 6 2 33.3 40.0
Bacilli Streptococcus Streptococcus agalactiae 11 43 2 4.7 6.2
Bacilli Streptococcus Streptococcus pneumoniae 107 346 22 6.4 9.2
Bacteroidia Bacteroides Bacteroides thetaiotaomicron 20 130 1 0.8 0.9
Betaproteobacteria Neisseria Neisseria meningitidis 52 159 4 2.5 3.7
Chlamydiae Chlamydia Chlamydia trachomatis 6 57 3 5.3 5.9
Clostridia Clostridium Clostridium difficile 6 125 25 20.0 21.0
Clostridia Clostridium Clostridium perfringens 35 186 13 7.0 8.6
Coccidia Cryptosporidium Cryptosporidium parvum 8 32 10 31.2 41.7
Coccodia Toxoplasma Toxoplasma gondii 35 104 20 19.2 29.0
Epsilonproteobacteria Campylobacter Campylobacter jejuni 29 258 69 26.7 30.1
Epsilonproteobacteria Helicobacter Helicobacter pylori 65 238 5 2.1 2.9
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 2662 4450 37 0.8 2.1
Gammaproteobacteria Francisella Francisella tularensis 3 119 65 54.6 56.0
Gammaproteobacteria Legionella Legionella pneumophila 1 83 4 4.8 4.9
Gammaproteobacteria Pseudomonas Pseudomonas aeruginosa 256 743 9 1.2 1.8
Gammaproteobacteria Pseudomonas Pseudomonas fluorescens 39 97 1 1.0 1.7
Gammaproteobacteria Salmonella Salmonella enterica 267 711 76 10.7 17.1
Gammaproteobacteria Shigella Shigella flexneri 30 131 4 3.1 4.0
Gammaproteobacteria Vibrio Vibrio cholerae 95 505 111 22.0 27.1
Gammaproteobacteria Vibrio Vibrio parahaemolyticus 14 48 3 6.2 8.8
Gammaproteobacteria Vibrio Vibrio vulnificus 4 45 22 48.9 53.7
Gammaproteobacteria Yersinia Yersinia enterocolitica 27 57 9 15.8 30.0
Gammaproteobacteria Yersinia Yersinia pestis 12 148 90 60.8 66.2
Mammalia Homo Homo sapiens 6697 16255 1 0.0 0.0
Spirochaetia Leptospira Leptospira interrogans 11 23 1 4.3 8.3
Viruses Ebolavirus Zaire ebolavirus 0 15 3 20.0 20.0
Viruses Flavivirus Dengue virus 20 62 6 9.7 14.3
Viruses Flavivirus Japanese encephalitis virus 2 7 1 14.3 20.0
Viruses Flavivirus West Nile virus 8 14 2 14.3 33.3
Viruses Influenzavirus A Influenza A virus 106 777 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 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