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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