Table 2

Domains that Identify Secretins and Ushers in Shewanella

Domain

Short Model Descriptor

Secretion System

Proteins Detected

Predicted Localization in Shewanella


pfam02321

Outer membrane efflux protein

T1SS1

AggA

OM

TIGR01844

type I secretion outer membrane protein, TolC family

T1SS

TolC, AggA

OM

TIGR02519

pilus (MSHA type) biogenesis protein MshL

T2bSS

MshL

OM lipoprotein

pfam07655

Secretin N-terminal domain

T2bSS

MshL

OM lipoprotein

TIGR02515

type IV pilus secretin (or competence protein) PilQ

T2bSS

PilQ

OM lipoprotein

pfam00263

Bacterial type II and III secretion system protein

T2a-cSS, T3aSS

GspD, PilQ, MshL, YscC, RcpA, SspD

mixed

pfam03958

Bacterial type II/III secretion system short domain

T2a-bSS, T3aSS

GspD, PilQ, YscC

mixed

pfam02107

Flagellar L-ring protein

T3bSS

FlgH

OM lipoprotein

pfam03524

Conjugal transfer protein

T4bSS

TrbG

OM

pfam03895

YadA-like C-terminal region

T5cSS

OM | extra

pfam03797

Autotransporter beta-domain

T5aSS

OM | extra

pfam06586

TraK protein

T4bSS

TraK, TrhK

OM

pfam07660

Secretin and TonB N terminus short domain

T2bSS2

PilQ, MshL

OM lipoprotein

TIGR02516

type III secretion outer membrane pore, YscC/HrcC family

T3aSS

YscC

OM

TIGR02756

type-F conjugative transfer system secretin TraK

T4bSS

TraK

OM

TIGR03352

type VI secretion lipoprotein, VC_A0113 family

T6SS

SciN

OM lipoprotein

pfam00577

Fimbrial Usher protein

T7SS

PapC/FimD

OM

pfam03783

Curli production assembly/transport component CsgG

T8SS

CsgG

OM lipoprotein


1 Also detects OM component of drug and metal efflux pumps

2 also detects some TonB receptor proteins

Romine BMC Genomics 2011 12(Suppl 1):S1   doi:10.1186/1471-2164-12-S1-S1

Open Data