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 February 17, 2018. For both PDB and CSGID only the structures released as of February 17, 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 51 115 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 187 310 0 0.0 0.0
Bacillus Bacillus cereus 101 221 3 1.4 2.5
Bacillus Bacillus subtilis 432 851 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 17 33 1 3.0 6.2
Borrelia Borrelia burgdorferi 24 49 0 0.0 0.0
Borrelia Borrelia turicatae 1 1 0 0.0 0.0
Bos Bos taurus 1116 1676 0 0.0 0.0
Branhamella Moraxella catarrhalis 0 3 0 0.0 0.0
Brevibacillus Brevibacillus brevis 21 31 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 83 0 0.0 0.0
Burkholderia Burkholderia thailandensis 0 48 0 0.0 0.0
Burkholderia Burkholderia xenovorans 11 28 0 0.0 0.0
Candida Candida albicans 27 77 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 56 122 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 108 175 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 136 202 2 1.0 3.0
Haliangium Haliangium ochraceum 0 3 0 0.0 0.0
Hepacivirus Hepatitis C virus 59 228 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 51 110 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 1823 3327 0 0.0 0.0
Mycobacterium Mycobacterium marinum 0 5 0 0.0 0.0
Mycobacterium Mycobacterium smegmatis 37 133 1 0.8 1.0
Mycobacterium Mycobacterium tuberculosis 384 1053 2 0.2 0.3
Neisseria Neisseria gonorrhoeae 19 43 0 0.0 0.0
Orthopoxvirus Vaccinia virus 39 67 0 0.0 0.0
Oryctolagus Oryctolagus cuniculus 234 415 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 130 323 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 167 292 2 0.7 1.6
Rattus Rattus norvegicus 789 1360 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 105 151 0 0.0 0.0
Rickettsia Rickettsia prowazekii 0 5 0 0.0 0.0
root synthetic construct 4861 8247 1 0.0 0.0
root uncultured bacterium 2 34 1 2.9 3.1
Saccharomyces Saccharomyces cerevisiae 1019 2017 0 0.0 0.0
Schizosaccharomyces Schizosaccharomyces pombe 65 181 0 0.0 0.0
Serratia Serratia marcescens 48 72 0 0.0 0.0
Shewanella Shewanella oneidensis 21 56 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 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 9 0 0.0 0.0
Streptococcus Streptococcus mutans 14 90 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 20 1 5.0 5.3
Streptococcus Streptococcus uberis 0 1 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 368 474 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 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 88 182 6 3.3 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 35 140 32 22.9 30.5
Bacilli Staphylococcus Staphylococcus aureus 365 933 18 1.9 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 126 370 16 4.3 6.6
Bacteroidia Bacteroides Bacteroides thetaiotaomicron 25 142 0 0.0 0.0
Betaproteobacteria Neisseria Neisseria meningitidis 56 177 3 1.7 2.5
Chlamydiae Chlamydia Chlamydia trachomatis 6 28 2 7.1 9.1
Clostridia Clostridium Clostridium difficile 6 78 12 15.4 16.7
Clostridia Clostridium Clostridium perfringens 31 144 7 4.9 6.2
Coccidia Cryptosporidium Cryptosporidium parvum 9 30 7 23.3 33.3
Coccodia Toxoplasma Toxoplasma gondii 39 94 6 6.4 10.9
Epsilonproteobacteria Campylobacter Campylobacter jejuni 16 122 28 23.0 26.4
Epsilonproteobacteria Helicobacter Helicobacter pylori 89 265 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 3124 4984 10 0.2 0.5
Gammaproteobacteria Francisella Francisella tularensis 3 58 31 53.4 56.4
Gammaproteobacteria Legionella Legionella pneumophila 8 96 4 4.2 4.5
Gammaproteobacteria Pseudomonas Pseudomonas aeruginosa 320 823 6 0.7 1.2
Gammaproteobacteria Pseudomonas Pseudomonas fluorescens 48 115 0 0.0 0.0
Gammaproteobacteria Salmonella Salmonella enterica 306 632 30 4.7 9.2
Gammaproteobacteria Shigella Shigella flexneri 21 91 4 4.4 5.7
Gammaproteobacteria Vibrio Vibrio cholerae 79 307 41 13.4 18.0
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 28 51 2 3.9 8.7
Gammaproteobacteria Yersinia Yersinia pestis 18 106 40 37.7 45.5
Mammalia Homo Homo sapiens 8784 18843 0 0.0 0.0
Spirochaetia Leptospira Leptospira interrogans 11 22 0 0.0 0.0
Viruses Ebolavirus Zaire ebolavirus 2 15 1 6.7 7.7
Viruses Flavivirus Dengue virus 26 72 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 120 523 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