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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
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