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 December 17, 2017. For both PDB and CSGID only the structures released as of December 17, 2017 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 8 0 0.0 0.0
Aeromonas Aeromonas hydrophila 7 25 0 0.0 0.0
Agrobacterium Agrobacterium tumefaciens 52 118 0 0.0 0.0
Aliivibrio Aliivibrio fischeri 1 15 1 6.7 7.1
Alphavirus Chikungunya virus 0 11 0 0.0 0.0
Aquifex Aquifex aeolicus 191 315 0 0.0 0.0
Aspergillus Aspergillus fumigatus 0 1 1 100.0 100.0
Bacillus Bacillus cereus 103 223 3 1.3 2.5
Bacillus Bacillus subtilis 451 883 1 0.1 0.2
Betacoronavirus Severe acute respiratory syndrome-related coronavirus 0 2 0 0.0 0.0
Bordetella Bordetella bronchiseptica 4 31 0 0.0 0.0
Bordetella Bordetella pertussis 17 33 1 3.0 6.2
Borrelia Borrelia burgdorferi 26 58 0 0.0 0.0
Borrelia Borrelia turicatae 1 1 0 0.0 0.0
Bos Bos taurus 1131 1698 0 0.0 0.0
Branhamella Moraxella catarrhalis 0 3 0 0.0 0.0
Brevibacillus Brevibacillus brevis 23 33 0 0.0 0.0
Brugia Brugia malayi 2 9 0 0.0 0.0
Burkholderia Burkholderia ambifaria 0 13 0 0.0 0.0
Burkholderia Burkholderia cenocepacia 0 46 0 0.0 0.0
Burkholderia Burkholderia cepacia 23 33 0 0.0 0.0
Burkholderia Burkholderia multivorans 0 13 0 0.0 0.0
Burkholderia Burkholderia pseudomallei 7 86 0 0.0 0.0
Burkholderia Burkholderia thailandensis 0 49 0 0.0 0.0
Burkholderia Burkholderia xenovorans 11 29 0 0.0 0.0
Candida Candida albicans 27 78 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 58 126 0 0.0 0.0
Clostridium Clostridium tetani 8 12 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 27 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 110 178 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 143 211 2 0.9 2.9
Haliangium Haliangium ochraceum 0 4 0 0.0 0.0
Hepacivirus Hepatitis C virus 60 231 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 32 144 8 5.6 7.1
Kluyveromyces Kluyveromyces lactis 11 35 0 0.0 0.0
Komagataella Komagataella pastoris 3 4 0 0.0 0.0
Lactococcus Lactococcus lactis 54 116 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 11 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 1886 3447 0 0.0 0.0
Mycobacterium Mycobacterium marinum 0 5 0 0.0 0.0
Mycobacterium Mycobacterium smegmatis 37 140 1 0.7 1.0
Mycobacterium Mycobacterium tuberculosis 401 1122 3 0.3 0.4
Neisseria Neisseria gonorrhoeae 19 43 0 0.0 0.0
Orthopoxvirus Vaccinia virus 39 70 0 0.0 0.0
Oryctolagus Oryctolagus cuniculus 236 421 0 0.0 0.0
Ovis Ovis aries 51 77 0 0.0 0.0
Photorhabdus Photorhabdus luminescens 0 1 0 0.0 0.0
Plasmodium (Laverania) Plasmodium falciparum 140 338 0 0.0 0.0
Plasmodium (Plasmodium) Plasmodium vivax 19 48 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 0 0.0 0.0
Pseudomonas Pseudomonas putida 173 318 2 0.6 1.4
Rattus Rattus norvegicus 803 1381 0 0.0 0.0
Rhadinovirus Human herpesvirus 8 9 19 0 0.0 0.0
Rhadinovirus Murid herpesvirus 4 6 7 0 0.0 0.0
Rhadinovirus Saimiriine herpesvirus 2 6 7 0 0.0 0.0
Rhodobacter Rhodobacter sphaeroides 117 165 0 0.0 0.0
Rickettsia Rickettsia prowazekii 0 6 0 0.0 0.0
root synthetic construct 4965 8419 1 0.0 0.0
root uncultured bacterium 2 35 1 2.9 3.0
Saccharomyces Saccharomyces cerevisiae 1050 2078 0 0.0 0.0
Schizosaccharomyces Schizosaccharomyces pombe 69 187 0 0.0 0.0
Serratia Serratia marcescens 48 72 0 0.0 0.0
Shewanella Shewanella oneidensis 24 60 0 0.0 0.0
Shigella Shigella dysenteriae 1 2 0 0.0 0.0
Simplexvirus Human herpesvirus 1 38 58 0 0.0 0.0
Stenotrophomonas Stenotrophomonas maltophilia 17 26 0 0.0 0.0
Streptococcus Streptococcus dysgalactiae 7 7 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 11 0 0.0 0.0
Streptococcus Streptococcus mutans 14 90 1 1.1 1.3
Streptococcus Streptococcus pyogenes 59 125 0 0.0 0.0
Streptococcus Streptococcus sanguinis 0 2 0 0.0 0.0
Streptococcus Streptococcus sp. 'group G' 15 28 0 0.0 0.0
Streptococcus Streptococcus suis 12 26 0 0.0 0.0
Streptococcus Streptococcus thermophilus 1 20 1 5.0 5.3
Streptococcus Streptococcus uberis 0 2 0 0.0 0.0
Streptomyces Streptomyces fradiae 3 9 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 378 485 0 0.0 0.0
Treponema Treponema pallidum 12 19 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 11 36 0 0.0 0.0
Zygosaccharomyces Zygosaccharomyces rouxii 0 1 0 0.0 0.0
Actinobacteria (class) Bifidobacterium Bifidobacterium longum 7 32 1 3.1 4.0
Bacilli Bacillus Bacillus anthracis 64 251 71 28.3 38.0
Bacilli Enterococcus Enterococcus faecalis 92 189 6 3.2 6.2
Bacilli Enterococcus Enterococcus faecium 14 28 8 28.6 57.1
Bacilli Enterococcus Enterococcus gallinarum 0 6 4 66.7 66.7
Bacilli Listeria Listeria monocytogenes 37 146 34 23.3 31.2
Bacilli Staphylococcus Staphylococcus aureus 378 954 18 1.9 3.1
Bacilli Staphylococcus Staphylococcus epidermidis 8 53 0 0.0 0.0
Bacilli Staphylococcus Staphylococcus haemolyticus 1 6 2 33.3 40.0
Bacilli Streptococcus Streptococcus agalactiae 12 47 0 0.0 0.0
Bacilli Streptococcus Streptococcus pneumoniae 130 380 16 4.2 6.4
Bacteroidia Bacteroides Bacteroides thetaiotaomicron 25 150 0 0.0 0.0
Betaproteobacteria Neisseria Neisseria meningitidis 59 180 3 1.7 2.5
Chlamydiae Chlamydia Chlamydia trachomatis 6 28 2 7.1 9.1
Clostridia Clostridium Clostridium difficile 6 87 12 13.8 14.8
Clostridia Clostridium Clostridium perfringens 31 145 7 4.8 6.1
Coccidia Cryptosporidium Cryptosporidium parvum 10 32 7 21.9 31.8
Coccodia Toxoplasma Toxoplasma gondii 39 95 6 6.3 10.7
Epsilonproteobacteria Campylobacter Campylobacter jejuni 17 125 29 23.2 26.9
Epsilonproteobacteria Helicobacter Helicobacter pylori 91 276 1 0.4 0.5
Gammaproteobacteria Acinetobacter Acinetobacter baumannii 4 82 10 12.2 12.8
Gammaproteobacteria Acinetobacter Acinetobacter haemolyticus 0 2 2 100.0 100.0
Gammaproteobacteria Coxiella Coxiella burnetii 0 26 6 23.1 23.1
Gammaproteobacteria Escherichia Escherichia coli 3257 5159 10 0.2 0.5
Gammaproteobacteria Francisella Francisella tularensis 3 65 35 53.8 56.5
Gammaproteobacteria Legionella Legionella pneumophila 9 97 4 4.1 4.5
Gammaproteobacteria Pseudomonas Pseudomonas aeruginosa 328 858 6 0.7 1.1
Gammaproteobacteria Pseudomonas Pseudomonas fluorescens 49 118 0 0.0 0.0
Gammaproteobacteria Salmonella Salmonella enterica 318 651 30 4.6 9.0
Gammaproteobacteria Shigella Shigella flexneri 23 99 4 4.0 5.3
Gammaproteobacteria Vibrio Vibrio cholerae 84 320 43 13.4 18.2
Gammaproteobacteria Vibrio Vibrio parahaemolyticus 17 54 1 1.9 2.7
Gammaproteobacteria Vibrio Vibrio vulnificus 5 31 6 19.4 23.1
Gammaproteobacteria Yersinia Yersinia enterocolitica 29 55 2 3.6 7.7
Gammaproteobacteria Yersinia Yersinia pestis 19 114 44 38.6 46.3
Mammalia Homo Homo sapiens 9087 19631 1 0.0 0.0
Spirochaetia Leptospira Leptospira interrogans 11 24 0 0.0 0.0
Viruses Ebolavirus Zaire ebolavirus 2 15 1 6.7 7.7
Viruses Flavivirus Dengue virus 27 73 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 121 528 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