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 April 19, 2018. For both PDB and CSGID only the structures released as of April 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
Aeromonas Aeromonas hydrophila 7 25 0 0.0 0.0
Agrobacterium Agrobacterium tumefaciens 50 114 0 0.0 0.0
Aliivibrio Aliivibrio fischeri 1 14 1 7.1 7.7
Alphavirus Chikungunya virus 0 11 0 0.0 0.0
Aquifex Aquifex aeolicus 185 308 0 0.0 0.0
Bacillus Bacillus cereus 99 219 3 1.4 2.5
Bacillus Bacillus subtilis 420 836 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 32 1 3.1 6.2
Borrelia Borrelia burgdorferi 23 47 0 0.0 0.0
Borrelia Borrelia turicatae 1 1 0 0.0 0.0
Bos Bos taurus 1072 1619 0 0.0 0.0
Branhamella Moraxella catarrhalis 0 3 0 0.0 0.0
Brevibacillus Brevibacillus brevis 20 30 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 43 0 0.0 0.0
Burkholderia Burkholderia cepacia 23 33 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 47 0 0.0 0.0
Burkholderia Burkholderia xenovorans 11 28 0 0.0 0.0
Candida Candida albicans 26 76 0 0.0 0.0
Capra Capra hircus 20 33 0 0.0 0.0
Cavia Cavia porcellus 7 15 0 0.0 0.0
Chlamydia Chlamydia pneumoniae 1 3 0 0.0 0.0
Citrobacter Citrobacter rodentium 0 1 0 0.0 0.0
Clostridium Clostridium botulinum 56 120 0 0.0 0.0
Clostridium Clostridium tetani 7 11 0 0.0 0.0
Corynebacterium Corynebacterium diphtheriae 34 59 1 1.7 4.0
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 51 0 0.0 0.0
Enterovirus Enterovirus B 9 24 0 0.0 0.0
Equus Equus caballus 107 173 0 0.0 0.0
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 134 200 2 1.0 3.0
Haliangium Haliangium ochraceum 0 3 0 0.0 0.0
Hepacivirus Hepatitis C virus 56 225 0 0.0 0.0
Hepevirus Hepatitis E virus 0 4 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 26 131 7 5.3 6.7
Kluyveromyces Kluyveromyces lactis 9 30 0 0.0 0.0
Komagataella Komagataella pastoris 3 4 0 0.0 0.0
Lactococcus Lactococcus lactis 49 105 0 0.0 0.0
Leporipoxvirus Myxoma virus 4 4 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 1762 3242 0 0.0 0.0
Mycobacterium Mycobacterium marinum 0 5 0 0.0 0.0
Mycobacterium Mycobacterium smegmatis 37 132 1 0.8 1.1
Mycobacterium Mycobacterium tuberculosis 373 1026 2 0.2 0.3
Neisseria Neisseria gonorrhoeae 19 43 0 0.0 0.0
Orthopoxvirus Vaccinia virus 37 65 0 0.0 0.0
Oryctolagus Oryctolagus cuniculus 227 403 0 0.0 0.0
Ovis Ovis aries 48 74 0 0.0 0.0
Photorhabdus Photorhabdus luminescens 0 1 0 0.0 0.0
Plasmodium (Laverania) Plasmodium falciparum 127 319 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 21 0 0.0 0.0
Pseudomonas Pseudomonas putida 162 286 2 0.7 1.6
Rattus Rattus norvegicus 765 1316 0 0.0 0.0
Rhadinovirus Human herpesvirus 8 8 18 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 99 145 0 0.0 0.0
Rickettsia Rickettsia prowazekii 0 5 0 0.0 0.0
root synthetic construct 4733 8088 1 0.0 0.0
root uncultured bacterium 2 34 1 2.9 3.1
Saccharomyces Saccharomyces cerevisiae 994 1979 0 0.0 0.0
Schizosaccharomyces Schizosaccharomyces pombe 65 180 0 0.0 0.0
Serratia Serratia marcescens 46 70 0 0.0 0.0
Shewanella Shewanella oneidensis 21 53 0 0.0 0.0
Shigella Shigella dysenteriae 1 2 0 0.0 0.0
Simplexvirus Human herpesvirus 1 37 57 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 9 0 0.0 0.0
Streptococcus Streptococcus mutans 14 89 1 1.1 1.3
Streptococcus Streptococcus pyogenes 58 123 0 0.0 0.0
Streptococcus Streptococcus sanguinis 0 1 0 0.0 0.0
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 33 0 0.0 0.0
Sus Sus scrofa 357 460 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 13 37 0 0.0 0.0
Yellow fever virus group Yellow fever virus 4 10 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 30 1 3.3 4.3
Bacilli Bacillus Bacillus anthracis 56 230 64 27.8 36.8
Bacilli Enterococcus Enterococcus faecalis 85 179 6 3.4 6.4
Bacilli Enterococcus Enterococcus faecium 14 27 7 25.9 53.8
Bacilli Enterococcus Enterococcus gallinarum 0 6 4 66.7 66.7
Bacilli Listeria Listeria monocytogenes 30 129 32 24.8 32.3
Bacilli Staphylococcus Staphylococcus aureus 352 908 18 2.0 3.2
Bacilli Staphylococcus Staphylococcus epidermidis 7 52 0 0.0 0.0
Bacilli Staphylococcus Staphylococcus haemolyticus 1 5 1 20.0 25.0
Bacilli Streptococcus Streptococcus agalactiae 12 47 0 0.0 0.0
Bacilli Streptococcus Streptococcus pneumoniae 122 358 16 4.5 6.8
Bacteroidia Bacteroides Bacteroides thetaiotaomicron 25 142 0 0.0 0.0
Betaproteobacteria Neisseria Neisseria meningitidis 55 167 3 1.8 2.7
Chlamydiae Chlamydia Chlamydia trachomatis 4 26 2 7.7 9.1
Clostridia Clostridium Clostridium difficile 6 78 12 15.4 16.7
Clostridia Clostridium Clostridium perfringens 29 141 7 5.0 6.2
Coccidia Cryptosporidium Cryptosporidium parvum 9 30 7 23.3 33.3
Coccodia Toxoplasma Toxoplasma gondii 38 93 6 6.5 10.9
Epsilonproteobacteria Campylobacter Campylobacter jejuni 16 121 28 23.1 26.7
Epsilonproteobacteria Helicobacter Helicobacter pylori 87 262 1 0.4 0.6
Gammaproteobacteria Acinetobacter Acinetobacter baumannii 4 80 10 12.5 13.2
Gammaproteobacteria Acinetobacter Acinetobacter haemolyticus 0 2 2 100.0 100.0
Gammaproteobacteria Coxiella Coxiella burnetii 0 25 5 20.0 20.0
Gammaproteobacteria Escherichia Escherichia coli 3035 4871 10 0.2 0.5
Gammaproteobacteria Francisella Francisella tularensis 3 58 31 53.4 56.4
Gammaproteobacteria Legionella Legionella pneumophila 8 95 4 4.2 4.6
Gammaproteobacteria Pseudomonas Pseudomonas aeruginosa 308 808 6 0.7 1.2
Gammaproteobacteria Pseudomonas Pseudomonas fluorescens 47 114 0 0.0 0.0
Gammaproteobacteria Salmonella Salmonella enterica 300 625 30 4.8 9.2
Gammaproteobacteria Shigella Shigella flexneri 19 88 4 4.5 5.8
Gammaproteobacteria Vibrio Vibrio cholerae 79 302 41 13.6 18.4
Gammaproteobacteria Vibrio Vibrio parahaemolyticus 16 51 1 2.0 2.9
Gammaproteobacteria Vibrio Vibrio vulnificus 5 30 6 20.0 24.0
Gammaproteobacteria Yersinia Yersinia enterocolitica 27 50 2 4.0 8.7
Gammaproteobacteria Yersinia Yersinia pestis 16 103 40 38.8 46.0
Mammalia Homo Homo sapiens 8469 18340 0 0.0 0.0
Spirochaetia Leptospira Leptospira interrogans 11 22 0 0.0 0.0
Viruses Ebolavirus Zaire ebolavirus 1 14 1 7.1 7.7
Viruses Flavivirus Dengue virus 26 71 1 1.4 2.2
Viruses Flavivirus Japanese encephalitis virus 2 7 1 14.3 20.0
Viruses Flavivirus West Nile virus 13 21 1 4.8 12.5
Viruses Influenzavirus A Influenza A virus 119 519 2 0.4 0.5
Viruses Orthopoxvirus Cowpox virus 3 3 0 0.0 0.0
Viruses Orthopoxvirus Ectromelia virus 2 7 1 14.3 20.0