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Table 3 Distribution of domain architectures in prokaryotic SPs; their occurrence in major lineages (indicated by +) and inferred functional associations based on co-existing domains and literature.

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

    Lineage*  
Domain Architecture# Representative sequence No. of SPs A B E Postulated Biological Functional Associations (see text)
Trypsin family (S1; Tryp(sin)- PF00089)
Tryp YP_643608.1 112 + + + Proteolysis
Tryp-PDZ NP_441326.1 63 + + + Signalling
Tryp-PDZ-PDZ NP_107958.1 49 - + - Signalling, Heat Shock response
Colicin_V-Tryp NP_338325.1 8 - + - Pathogenesis, Defense
Pro_Al_prot-Tryp NP_827728.1 2 - + - Proteolysis
Tryp-Endonuclease_NS NP_604177.1 1 - + - Nucleic acid metabolism
Tryp-(FG-GAP)3 NP_825221.1 1 - + - Ligand binding and processing
Tryp-(Sel1)6 YP_374752.1 1 - + - Proteolysis
Tryp-CW_binding_1-CW_binding_1 NP_344916.1 1 - + - Cell recognition, pathogenesis
FHA-FHA-Tryp NP_811686.1 1 - + - Metabolism and signalling
Pro_Al_prot-Tryp-CBM_5_12 NP_822175.1 1 - + - Carbohydrate metabolism
(Pro_Al_prot)2-Tryp NP_827729.1 1 - + - Proteolysis
Tryp-ANF_receptor YP_073997.1 1 - + - Ligand binding and processing
Tryp-PPC-SCP YP_434226.1 1 - + - Calcium chelating, signalling
Tryp-PPC-PPC YP_437990.1 1 - + - Carbohydrate metabolism, signalling
TerD-Tryp YP_273108.1 1 - + - Growth in unfavourable environment
Subtilisin family (S8; Subt(ilisin)- PF00082)
Subt NP_147093.1 142 + + + Proteolysis
Subt-Autotransporter YP_260308.1 15 - + - Transport, Cell adhesion, Virulence
Subtilisin_N-Subt NP_241550.1 14 + + + Proteolysis
Subt-PPC YP_154554.1 9 + + - Carbohydrate metabolism, signalling
Subtilisin_N-Subt-PA NP_391688.1 4 + + + Proteolysis
Subt-PPC-PPC YP_341139.1 4 + + - Carbohydrate metabolism, signalling
Subt-P_proprotein NP_967370.1 3 - + - Proteolysis
Subt-Big_2 NP_969490.1 2 - + - Cell adhesion, pathogenesis
Subt-DUF1034 YP_194362.1 2 - + - Proteolysis
Subt-PA-DUF1034 NP_693854.1 2 - + + Proteolysis
Subt-PKD-PKD YP_326498.1 2 + + + Carbohydrate metabolism, signalling
Subt-P_proprotein-PKD NP_716498.1 2 - + - Carbohydrate metabolism, signalling
GRP-Subt NP_435320.1 1 - + - Stress response
(Hemolys)2-Subt-P_proprotein NP_747027.1 1 - + - Cell surface binding
(Hemolys)3-Subt-P_proprot-Hemolys NP_927988.1 1 - + - Cell surface binding
PPC-Subt YP_436813.1 1 - + - Carbohydrate metabolism, signalling
Subt-BNR NP_824495.1 1 - + - Proteolysis
Subt-(CARDB)9 NP_954260.1 1 - + - Cell adhesion, pathogenesis
Subt-Cleaved_Adhesin-fn3-PKD-PKD YP_074547.1 1 - + - Virulence, signalling, metabolism
Subt-CUB NP_967057.1 1 - + + Signalling
Subt-(Dockerin_1)2 NP_280653.1 1 - + - Cellulose degradation, metabolism
Subt-DUF11 NP_951948.1 1 - + - Cellular transport
Subt-fn3 YP_446403.1 1 - + - Cell surface binding
Subt-(fn3)3-(PKD)3 YP_565583.1 1 - + - Cell surface binding, signalling, metabolism
Subt-Gram_pos_anchor NP_241562.1 1 - + - Cell invasion, pathogenesis
Subt-NosD NP_616940.1 1 + - - Respiratory metabolism
Subt-PA-DUF1034-(Big_2)2-(SLH)2 NP_624131.1 1 - + - Cell adhesion, pathogenesis
Subt-PilZ NP_969350.1 1 - + - Signalling
Subt-(P_proprotein)2 YP_434175.1 1 - + - Proteolysis
Sub_N-Subt-Cleaved_Adhesin NP_693252.1 1 - + - Virulence
Sub_N-Subt-PA-Dockerin NP_691157.1 1 - + - Cellulose degradation, metabolism
Sub_N-Subt-PA-DUF1034-Gram_pos_anchor NP_345151.1 1 - + - Cell invasion, pathogenesis
Sub_N-Subt-PA-DUF1034-(FIVAR)5-Gram_pos_anchor NP_965819.1 1 - + - Cell recognition and invasion, Sugar binding
Sub_N-Subt-PA-PPC NP_717522.1 1 - + - Carbohydrate metabolism, signalling
Sub_N-Subt-PA-PPC- P_proprotein NP_718668.1 1 - + - Carbohydrate metabolism, signalling
Thermopsin-Subt NP_394205.1 1 + - - Thermostability
(W_rich_C)2-(PPC)2-Subt YP_382882.1 1 - + - Cell surface signalling
YSIRK_signal-Subt-PA-DUF1034-(FIVAR)3- Gram_pos_anchor NP_689039.1 1 - + - Cell recognition and invasion, Sugar binding
DD-peptidase family (S12; DD-Pept(idase) -PF00144)
DDPept NP_811352.1 249 + + + Cell wall biosynthesis
DDPept -ABC_tran YP_434618.1 1 - + - Biological transport
DDPept -DUF1343 YP_439122.1 1 - + - Cell wall biosynthesis
(Cond-AMP-PPbind)3- DDPept NP_824819.1 1 - + - Metabolism of Antibiotic compounds
Glyco_hydr_3- DDPept NP_811352.1 1 - + - Carbohydrate hydrolysis
Glyc_hyd_3_Glyc_hyd_3_C- DDPept YP_444518.1 1 - + - Carbohydrate hydrolysis, metabolism
Clp protease family (S14; Clp(_protease)- PF00574)
Clp NP_811352.1 118 + + + Proteolysis
Clp-Nfed NP_126341.1 3 + + - Proteolysis
Lon protease family (S16; Lon_C- PF05362)
Lon_C NP_623361.1 39 + + + Proteolysis
LON-AAA-Lon_C NP_743601.1 58 + + + Signalling, metabolism
Sigma54_activat-AAA-Lon_C YP_183677.1 8 + + - Transcription regulation, metabolism
Sigma54_activat-Lon_C NP_127256.1 5 + - - Transcription regulation
Mg_chelatase-Lon_C NP_248420.1 4 + - - Bacteriochlorophyll metabolism
Mg_chelat-Sigma54_activat-Lon_C NP_578196.1 1 + - - Transcription regulation
DnaB_C-Tryp YP_160730.1 1 - + - DNA metabolism
PDZ-Lon_C NP_389388.1 1 - + - Signalling
  1. # Co-exisiting domains: Tryp-Trypsin; Subt-Subtilisin; DDPept- DD-peptidase; Clp- Clp protease; Lon _C- Lon protease; AAA- ATPase family associated with various cellular activities (PF00004); ABC_tran- ABC transporter (PF00005); AMP-binding- AMP-binding enzyme (PF00501); ANF_receptor- Receptor family ligand binding region (PF01094); Autotransporter- Autotransporter beta-domain (PF03797); Big_2- Bacterial Ig-like domain (group 2) (PF02368); BNR- BNR/Asp-box repeat (PF02012); CARDB- Cell adhesion related domain found in bacteria (PF07705); Colicin_V- Colicin V production protein (PF02674); CBM_5_12- Carbohydrate binding domain (PF02839); Cleaved_Adhesin- Cleaved Adhesin Domain (PF07675); Cond(ensation)- Condensation domain (PF00668); CUB- CUB domain (PF00431); CW_binding_1- Putative cell wall binding repeat (PF01473); DnaB_C- DnaB-like helicase C terminal domain (PF03796); Dockerin_1- Dockerin type I repeat (PF00404); DUF1034- Domain of unknown function (PF06280); DUF11- Domain of unknown function (PF01345); DUF1343- Protein of unknown function (PF07075); FG-GAP- FG-GAP repeat (PF01839); Endonuclease_NS- DNA/RNA non-specific endonuclease (PF01233); FHA- FHA (Forkhead-associated) domain (PF00498); FIVAR- Uncharacterised Sugar-binding Domain (PF07554); fn3- Fibronectin type III domain (PF00041); Glyc _ hyd _ 3- Glycosyl hydrolase family 3 N terminal domain (PF00933); Glyc_hydr _ 3 _ C- Glycosyl hydrolase family 3 C terminal domain (PF01915); Gram_pos_anchor- Gram positive anchor (PF00746); GRP- Glycine rich protein family (PF07172); Hemolys- Hemolysin-type calcium-binding repeat (2 copies) (PF00353); LON- ATP-dependent protease La (LON) domain (PF02190); Mg_chelat- Magnesium chelatase, subunit ChlI (PF01078); Nfed- Nfed-like (PF01957); NosD- Periplasmic copper-binding protein (NosD) (PF05048); P_proprotein- Proprotein convertase P-domain (PF01483); PA- Protease associated domain (PF02225); PDZ- PDZ domain (PF00595); PKD- PKD domain (PF00801); PP-binding- Phosphopantetheine attachment site (PF00550); PPC- Bacterial pre-peptidase C-terminal domain (PF04151); Pro_Al_prot- Alpha-lytic protease prodomain (PF02983); Sel 1- Sel1 repeat (PF08238); SCP- SCP-like extracellular protein (PF00188); Sigma54_activat- Sigma-54 interaction domain (PF00158); SLH- S-layer homology domain (PF00395); Sub(tilisin) _ N- Subtilisin N-terminal region (PF005922); TerD- Bacterial stress protein (PF02342); Thermopsin- Thermopsin (PF05317); W_rich_C- Tryptophan-rich Synechocystis species C-terminal domain (PF07483) * Lineage: A- Archaea; B- Bacteria; E- Eukaryotes