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Table 1 Distribution of the select serine protease families across the representative genomes of the prokaryotic lineages.

From: Genome-wide survey of prokaryotic serine proteases: Analysis of distribution and domain architectures of five serine protease families in prokaryotes

Prokaryotic Genomes Tryp Subt DDpept Clp Lon
Archaea
Crenarchaeota      
Aeropyrum_pernix (Chromosome) - 3 1 2 -
Pyrobaculum_aerophilum (Chromosome) 1 2 1 1 -
Sulfolobus_acidocaldarius_DSM_639 (Chromosome) 2 5 - - -
Sulfolobus_solfataricus (Chromosome) 1 2 - - -
Sulfolobus_tokodaii (Chromosome) 1 3 - - -
Euryarchaeota      
Archaeoglobus_fulgidus (Chromosome) - 2 - - 2
Halobacterium_sp_NRC1 (1Chromosome + 2 plasmids) 1 2 - - 1
Methanococcoides_burtonii_DSM_6 (Chromosome) - 2 - - 1
Methanococcus_jannaschii (3Chromosomes) - - - - 2
Methanosarcina_acetivorans (Chromosome) - 3 1 - 2
Methanosarcina_mazei (Chromosome) - 2 1 - 2
Natronomonas_pharaonis (Chromosome + 2 plasmids) 1 3 - - 1
Pyrococcus_abyssi (Chromosome + 1 plasmid) - - 1 1 2
Pyrococcus_furiosus (Chromosome) - 3 - 1 2
Thermococcus_kodakaraensis_KOD1 (Chromosome) - 3 - - 2
Thermoplasma_acidophilum (Chromosome) - 2 - - 1
Nanoarchaeota      
Nanoarchaeum_equitans (Chromosome) - - - - 1
Bacteria
Actinobacteria      
Corynebacterium_efficiens_YS-314 (Chromosome) 7 1 2 2 -
Corynebacterium_glutamicum_ATCC_13032_Bielefeld (Chromosome) 7 1 2 2 -
Mycobacterium_leprae (Chromosome) 4 3 2 2 1
Mycobacterium_tuberculosis_CDC1551 (Chromosome) 6 4 13 2 1
Propionibacterium_acnes_KPA17120 (Chromosome) 2 1 2 2 1
Rubrobacter_xylanophilus_DSM_9941(Chromosome) 7 3 3 1 1
Streptomyces_avermitilis (1Chromosome + 1 plasmid) 14 15 13 5 2
Symbiobacterium_thermophilum_IAM14863 (Chromosome) 4 5 9 3 3
Alphaproteobacteria      
Agrobacterium_tumefaciens_C58_Cereon (2 Chromosomes + 2 plasmids) 3 - 3 3 1
Bradyrhizobium_japonicum (Chromosome) 10 2 17 2 2
Mesorhizobium_loti (1Chromosome + 2 plasmids) 8 2 7 3 1
Novosphingobium_aromaticivorans_DSM_12444 (1 Chromosome + 2 plasmids) 2 2 7 1 1
Rhodopseudomonas_palustris_CGA009 (1 Chromosome +1 plasmid) 8 2 7 1 1
Sinorhizobium_meliloti (1 Chromosome +2 plasmids) 1 2 2 - -
Betaproteobacteria      
Azoarcus_sp_EbN1 (Chromosome) 4 3 - 2 3
Bordetella_bronchiseptica (Chromosome) 2 2 2 2 2
Bordetella_parapertussis (Chromosome) 2 1 2 1 2
Burkholderia_cenocepacia_AU_1054 (3 Chromosomes) 3 1 1 - -
Burkholderia_mallei_ATCC_23344 (2 Chromosomes) 3 2 1 1 1
Burkholderia_thailandensis_E264 (2 Chromosomes) - 6 3 1 1
Chromobacterium_violaceum (Chromosome) 6 4 2 2 1
Neisseria_meningitidis_MC58 (Chromosome) 1 1 - 1 1
Ralstonia_eutropha_JMP134 (2 Chromosomes + 2 plasmids) - 1 1 - -
Ralstonia_solanacearum (1 Chromosome + 1 plasmid) 3 3 1 1 1
Chlorobi      
Bacteroides_thetaiotaomicron_VPI-5482 (1 Chromosome + 1 plasmid) 3 2 2 1 1
Pelodictyon_luteolum_DSM_273 (Chromosome) 3 1 1 1 1
Salinibacter_ruber_DSM_13855 (1 Chromosome + 1 plasmid) 2 5 4 2 -
Cyanobacteria      
Gloeobacter_violaceus (Chromosome) 7 4 4 2 -
Synechococcus_CC9605 (Chromosome) 3 1 3 3 -
Synechocystis_PCC6803 (1 Chromosome + 4 plasmids) 3 1 3 4 -
Deinococcus-Thermus      
Deinococcus_radiodurans (2 Chromosomes + 2 plasmids) - 1 - - -
Deltaproteobacteria      
Bdellovibrio_bacteriovorus (Chromosome) 24 15 2 1 3
Geobacter_sulfurreducens (Chromosome) 2 3 2 1 5
Epsilonproteobacteria      
Thiomicrospira_crunogena_XCL-2 (Chromosome) 1 1 2 1 3
Firmicutes      
Bacillus_anthracis_Ames (Chromosome) 2 4 14 4 3
Bacillus_clausii_KSM-K16 (Chromosome) 2 5 4 3 3
Bacillus_halodurans (Chromosome) 2 9 2 3 3
Bacillus_subtilis (Chromosome) 4 7 4 2 3
Bacillus_thuringiensis_konkukian (1 Chromosome + 1 plasmid) 2 5 17 3 3
Enterococcus_faecalis_V583 (1 Chromosome + 3 plasmids) 2 - 3 1 -
Lactobacillus_acidophilus_NCFM (Chromosome) 1 1 6 1 1
Lactobacillus_johnsonii_NCC_533 (Chromosome) 1 1 3 1 1
Lactobacillus_sakei_23K (Chromosome) 1 - 3 1 -
Lactococcus_lactis (Chromosome) 1 - 1 1 1
Oceanobacillus_iheyensis (Chromosome) 3 8 4 2 1
Staphylococcus_aureus_COL (Chromosome) 9 1 2 2 -
Staphylococcus_epidermidis_ATCC_12228 (1 Chromosome + 1 plasmid) 3 - 3 1 -
Streptococcus_agalactiae_2603 (Chromosome) 1 3 2 1 -
Streptococcus_mutans (Chromosome) 1 - 2 1 -
Streptococcus_pneumoniae_TIGR4 (Chromosome) 2 1 1 1 -
Thermoanaerobacter_tengcongensis (Chromosome) 2 3 2 2 2
Thermus_thermophilus_HB27 (1 Chromosome + 1 plasmid) 3 1 2 1 3
Fusobacteria      
Fusobacterium_nucleatum (Chromosome) 1 2 - 1 1
Gammaproteobacteria      
Escherichia_coli_O157H7_EDL933 (1 Chromosome + 1 plasmid) 4 - 3 4 2
Haemophilus_influenzae (Chromosome) 2 - - 1 2
Hahella_chejuensis_KCTC_2396 (Chromosome) 8 4 4 2 3
Idiomarina_loihiensis_L2TR (Chromosome) 2 2 3 1 2
Photorhabdus_luminescens (Chromosome) 3 3 7 1 1
Pseudoalteromonas_haloplanktis_TAC125 (2 Chromosomes) 2 2 3 1 2
Pseudomonas_aeruginosa (Chromosome) 2 2 7 3 3
Pseudomonas_fluorescens_Pf-5 (Chromosome) 2 2 7 3 4
Pseudomonas_putida_KT2440 (Chromosome) 2 2 4 3 4
Pseudomonas_syringae_phaseolicola_1448A (1 Chromosome + 2 plasmids) 3 2 4 1 4
Shewanella_oneidensis (1 Chromosome + 1 plasmid) 2 6 2 2 2
Xanthomonas_campestris (Chromosome) 3 10 3 1 1
Xylella_fastidiosa (Chromosome) 2 3 1 2 1
Spirochaetes      
Treponema_denticola_ATCC_35405 (Chromosome) 5 - 1 2 1
Total 247 227 254 121 117
  1. Tryp- Trypsin (Pfam accession – PF00089); Subt- Subtilisin (PF00082); DDPept- D-Ala-D-Ala carboxypeptidase B (DD-peptidase) (PF00144); Clp- ClP protease (PF00574); Lon- Lon protease (PF05362).
  2. Genomes where no serine protease-like proteins were identified: Bacteroides_fragilis_YCH46 Haloarcula_marismortui_ATCC_43049; Legionella_pneumophila_Lens; Nostoc_sp.; Salmonella_enterica_Choleraesuis; Clostridium_acetobutylicum; Clostridium_perfringens