E. coli K-12 / MG1655/ ATCC 47076 proteome

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
30 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
20
Cleavage Score (Cmax):
0.853

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
19
Score:
13.9164
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
9

LocTree3

Localization:
secreted
Score:
34

ClubSub-P

Localization:
Extracellular AND signal peptide

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 19 [SWA-GT]
Score:
0.853

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Major curlin subunit
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental) Peripheral outer membrane protein facing the extra-cellular space (Probable)
Notes:
Curli component. CsgA, is secreted from the cell in an unpolymerized form PMID: 11823641 The secretion and stability of CsgA and CsgB are dependent on the outer membrane lipoprotein CsgG. PMID: 21645131 Curli are a functional amyloid whose in vivo polymerization requires a dedicated nucleator protein, CsgB, and an assembly protein, CsgF. Without CsgF, curli subunits are released from the cell into the media and are inefficiently polymerized, resulting in fewer and mislocalized curli fibers. PMID: 19131513 PMID: 9383186 PMID: 9312041 During a process called interbacterial complementation, a csgB mutant cell secretes soluble CsgA that can be assembled on the surface of a cell expressing only csgB PMID: 8817489 High levels of both IbsC and ShoB lead to changes in membrane potential suggesting that both act at the membrane, consistent with the hydrophobic nature of the proteins.
References:
PMID: 11823641 PMID: 18710431 PMID: 21645131 PMID: 8817489 PMID: 9312041 PMID: 9383186
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
-
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG11489
Gene Locus:
csgA

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P28307

SMART database

SMART: csgA

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
66 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
21
Cleavage Score (Cmax):
0.854

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
20
Score:
20.7833
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
9

LocTree3

Localization:
fimbrium
Score:
100

ClubSub-P

Localization:
Extracellular AND signal peptide

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 20 [ALA-GV]
Score:
0.999

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Minor curlin subunit
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental) Peripheral outer membrane protein facing the extra-cellular space (Probable)
Notes:
Curli component. CsgB localization requires at least one component of the curli secretion apparatus, CsgF. Curli are a functional amyloid whose in vivo polymerization requires a dedicated nucleator protein, CsgB, and an assembly protein, CsgF. Without CsgF, curli subunits are released from the cell into the media and are inefficiently polymerized, resulting in fewer and mislocalized curli fibers. PMID: 19131513 PMID: 9383186 PMID: 9312041
References:
PMID: 19131513 PMID: 9312041 PMID: 9383186
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 19348461
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0.693 ppm

EcoCyc

Protein:
EG12621
Gene Locus:
csgB

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P0ABK7

SMART database

SMART: csgB

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
% PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
22
Cleavage Score (Cmax):
0.53

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
21
Score:
16.29
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
9

LocTree3

Localization:
fimbrium
Score:
100

ClubSub-P

Localization:
Extracellular AND signal peptide

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 21 [AAA-AG]
Score:
0.998

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Curli production assembly/transport component CsgG
Localization:
Outer Membrane Lipoprotein, Peripheral outer membrane protein facing the extra-cellular space (Experimental) Outer Membrane Lipoprotein, Peripheral outer membrane protein facing the extra-cellular space (Probable)
Notes:
Curli component. Proven signal peptidase II substrate. CsgG is an outer membrane protein required for the secretion of the two curli structural subunits CsgA and CsgB. CsgG is a lipoprotein that spans the outermembrane and assembles into an oligomeric annular-shaped structure with an inner diameter of approximately 2 nm (Margery L. Evans and Matthew R. Chapman in press). Overexpression of CsgG results in increased sensitivity to the small antibiotic erythromycin (740Da) but not the larger vancomycin (1440Da) suggesting that CsgG has a pore-like activity (Robinson et al 2006). PMID: 15174130
References:
PMID: 15174130 PMID: 21645131
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
1

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 17595003
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
2
PaxDb:
22.4 ppm

EcoCyc

Protein:
EG13413
Gene Locus:
csgG

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P0AEA2

SMART database

SMART: csgG

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
44 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
20
Cleavage Score (Cmax):
0.544

LipoP 1.0

Prediction:
SpII
Cleavage site amino acid:
15
Score:
12.9163
Cleavage Rule:
Pos+2=L

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
9

LocTree3

Localization:
secreted
Score:
33

ClubSub-P

Localization:
Inner/Outer-membrane lipoprotein

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 25 [EAA-RP]
Score:
0.993

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (2-phosphoglycerate dehydratase)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm, Peripheral outer membrane protein facing the extra-cellular space (Experimental) Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm, Peripheral outer membrane protein facing the extra-cellular space (Potential) Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm, Peripheral outer membrane protein facing the extra-cellular space (Probable)
Notes:
When modified at Lys342 possibly secreted by an unknown mechanism, no evidence of signal peptide) Homodimer, stabilized by Mg2+; Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. Essential for the degradation of carbohydrates via glycolysis. Also a component of the RNA degradosome. The covalent binding to the substrate at Lys-342 causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Interacts with the C-terminal region of the endoribonuclease RNase EIn the RNA degradosome. Fractions of enolase are present in both the cytoplasm and on the cell surface. As part of the bacterial cytoskeleton in the cytoplasm,Is organized as extended coiled structures that wind around the cell, from one cell pole to the other. When covalently bound to the substrate at Lys-342, the inactive enolase is secreted, and remains attached to the bacterial cell surface. PMID: 8610017 PMID: 9600841 PMID: 9740056 PMID: 9732527 PMID: 12035760 Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 12035760 PMID: 15003462 PMID: 17242352 PMID: 18337249 PMID: 23230279 PMID: 8610017 PMID: 9600841 PMID: 9732527 PMID: 9740056
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
21

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 12624733 PMID: 12488465 PMID: 17137328 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 20521846 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18425732
Proteomics / Inner Membrane fraction:
PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
567
PaxDb:
3361 ppm

EcoCyc

Protein:
EG10258
Gene Locus:
eno

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Enolase N-terminal domain-like SCOP: 54825
Super Family:
Enolase C-terminal domain-like
SCOP: 51604
Enolase N-terminal domain-like
SCOP: 54826

Protein Family Domains

Pfam domains

PFAM: P0A6P9

SMART database

SMART: eno

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
100 % PMID: 19251648

Heat-stability

Heat stable (85oC):
yes PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
42
Cleavage Score (Cmax):
0.139

LipoP 1.0

Prediction:
CYT
Cleavage site amino acid:
0
Score:
-0.200913
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Cytoplasmic
Score:
9

LocTree3

Localization:
cytoplasm
Score:
91

ClubSub-P

Localization:
Cytoplasmic

sosuiGramN

Localization:
C (cytoplasmic)

PRED-TAT

Localization:
No signal peptide predicted
Score:
0.975

TatP

Prediction:
No signal peptide predicted.
Cleavage site:
Most likely cleavage site between pos. 48 and 49: REA-LE

Manual Curation in STEP

Comments

UniProt Name:
Protein FimF
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental)
Notes:
Fim operon (class ??1); Fimbrial Subunit. Required for the regulation of length and mediation of adhesion of Escherichia coli type 1 fimbriae. PMID: 15372038 Disulfide bridge (38 78) Disulfide bond-containing protein PMID: 25664544
References:
PMID: 15372038
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 19767571 PMID: 18425732
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG10313
Gene Locus:
fimF

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Common fold of diphtheria toxin/transcription factors/cytochrome f SCOP: 49379
Super Family:
Bacterial adhesins
SCOP: 49401

Protein Family Domains

Pfam domains

PFAM: P08189

SMART database

SMART: fimF

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
% PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
23
Cleavage Score (Cmax):
0.871

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
22
Score:
17.2366
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
9

LocTree3

Localization:
fimbrium
Score:
100

ClubSub-P

Localization:
Extracellular AND signal peptide

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 22 [ALA-AD]
Score:
1

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Protein FimG
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental)
Notes:
Fim operon (class ??1); Fimbrial Subunit. Required for the regulation of length and mediation of adhesion of Escherichia coli type 1 fimbriae. PMID: 15372038 Disulfide bridge (39 77) Disulfide bond-containing protein PMID: 25664544
References:
PMID: 15372038
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
-
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG10314
Gene Locus:
fimG

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Common fold of diphtheria toxin/transcription factors/cytochrome f SCOP: 49379
Super Family:
Bacterial adhesins
SCOP: 49401

Protein Family Domains

Pfam domains

PFAM: P08190

SMART database

SMART: fimG

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
73 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
24
Cleavage Score (Cmax):
0.773

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
23
Score:
18.1281
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
9

LocTree3

Localization:
fimbrium
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 23 [IQA-AD]
Score:
1

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Type 1 fimbrin D-mannose specific adhesin (Protein FimH)
Localization:
Peripheral outer membrane protein facing the extra-cellular space ( Experimental) Peripheral outer membrane protein facing the extra-cellular space (Experimental)
Notes:
Fim operon (class ??1); Potential tip-adhesin. Required for the regulation of length and mediation of adhesion of Escherichia coli type 1 fimbriae. PMID: 1971261 PMID: 2900235 PMID: 2890081
References:
PMID: 1971261 PMID: 20345943 PMID: 2890081 PMID: 2900235
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG10315
Gene Locus:
fimH

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Common fold of diphtheria toxin/transcription factors/cytochrome f SCOP: 49379
Super Family:
Bacterial adhesins
SCOP: 49401

Protein Family Domains

Pfam domains

PFAM: P08191

SMART database

SMART: fimH

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
19 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
20
Cleavage Score (Cmax):
0.539

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
21
Score:
14.3197
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Unknown
Score:
4

LocTree3

Localization:
fimbrium
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 19 [VNA-WS]
Score:
0.984

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Type-1 fimbrial protein, A chain (Type-1A pilin)
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental)
Notes:
Fim operon (class ??1); Fimbrial Subunit. Experimentally verified signal peptide PMID: 2858471 Disulfide bridge (44 84) Disulfide bond-containing protein PMID: 25664544
References:
PMID: 2858471
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 19348461 PMID: 19767571 PMID: 20803007 PMID: 18425732
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
21.4 ppm

EcoCyc

Protein:
EG10308
Gene Locus:
fimA

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Common fold of diphtheria toxin/transcription factors/cytochrome f SCOP: 49379
Super Family:
Bacterial adhesins
SCOP: 49401

Protein Family Domains

Pfam domains

PFAM: P04128

SMART database

SMART: fimA

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
% PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
24
Cleavage Score (Cmax):
0.78

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
23
Score:
25.7568
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
10

LocTree3

Localization:
fimbrium
Score:
100

ClubSub-P

Localization:
Extracellular AND signal peptide

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 23 [ALA-AA]
Score:
0.998

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Uncharacterized fimbrial-like protein YadC
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Potential)
Notes:
Potential fimbrial yad operon (class ??4); Potential tip-adhesin.
References:
PMID: 20345943
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
-
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0.016 ppm

EcoCyc

Protein:
EG11678
Gene Locus:
yadC

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Common fold of diphtheria toxin/transcription factors/cytochrome f SCOP: 49379
Super Family:
Bacterial adhesins
SCOP: 49401

Protein Family Domains

Pfam domains

PFAM: P31058

SMART database

SMART: yadC

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
14 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
23
Cleavage Score (Cmax):
0.677

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
22
Score:
12.8917
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
9

LocTree3

Localization:
fimbrium
Score:
22

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 22 [VSA-YT]
Score:
0.999

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Uncharacterized fimbrial-like protein YdeS
Localization:
-
Notes:
Potential fimbrial yde operon (class ??1); Fimbrial Subunit. Disulfide bridge (38 78)
References:
-
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
-
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0.032 ppm

EcoCyc

Protein:
EG13801
Gene Locus:
ydeS

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Common fold of diphtheria toxin/transcription factors/cytochrome f SCOP: 49379
Super Family:
Bacterial adhesins
SCOP: 49401

Protein Family Domains

Pfam domains

PFAM: P77789

SMART database

SMART: ydeS

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
79 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
23
Cleavage Score (Cmax):
0.426

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
22
Score:
11.5353
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
10

LocTree3

Localization:
fimbrium
Score:
31

ClubSub-P

Localization:
Extracellular AND signal peptide

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 22 [ALS-AD]
Score:
0.997

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Basal-body rod modification protein FlgD
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental)
Notes:
Hook-capping protein. The hook cap FlgD is displaced by FlgK, allowing filament growth PMID: 12631703 Using the hook scaffolding protein FlgD of Escherichia coli as a model substrate, it is demonstrated that the export signal is contained within the N-terminal 71 amino acids of FlgD. PMID: 16897036 PMID: 16897036
References:
PMID: 12631703
Pseudogene/Mobile Element:
pseudogene (Ochman & Davalos, 2006)

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
-
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG14268
Gene Locus:
flgD

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P75936

SMART database

SMART: flgD

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
106 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
29
Cleavage Score (Cmax):
0.171

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
28
Score:
2.5996
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
10

LocTree3

Localization:
secreted
Score:
77

ClubSub-P

Localization:
Extracellular

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 28 [SNA-AD]
Score:
0.998

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Flagellin
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental) Peripheral outer membrane protein facing the extra-cellular space (Probable)
Notes:
Flameint protein, flagellin. Flagella proteins contribute to the production of outer membrane vesicles. Analysis of E. coli W3110 OMVs revealed that they contain abundant levels of FliC. Compared to the parental strain expressing wild-type fliC, an E. coli strain with a fliC-null mutation produced reduced amounts of OMVs based on both protein and phosphate levels. Identified in nucleoids collected by sucrose gradient centrifugation and analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). PMID: 21541338 PMID: 12730325
References:
PMID: 12730325 PMID: 24134841
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 17595003 PMID: 17137328 PMID: 20222674 PMID: 19767571
Proteomics / Inner Membrane fraction:
PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
1212 ppm

EcoCyc

Protein:
EG10321
Gene Locus:
fliC

Structural Annotation

SCOP

Class:
Multi-domain proteins (alpha and beta)
SCOP: 56572
Fold:
Phase 1 flagellin SCOP: 64517
Super Family:
Phase 1 flagellin
SCOP: 64518

Protein Family Domains

Pfam domains

PFAM: P04949

SMART database

SMART: fliC

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
80 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
52
Cleavage Score (Cmax):
0.13

LipoP 1.0

Prediction:
CYT
Cleavage site amino acid:
0
Score:
-0.200913
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
10

LocTree3

Localization:
periplasm
Score:
27

ClubSub-P

Localization:
Extracellular

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
No signal peptide predicted
Score:
0.745

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Flagellar hook protein FlgE
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental)
Notes:
Hook protein. PMID: 12730325
References:
PMID: 12730325
Pseudogene/Mobile Element:
pseudogene (Ochman & Davalos, 2006)

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 19767571 PMID: 18796603
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
17.2 ppm

EcoCyc

Protein:
EG14269
Gene Locus:
flgE

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Flagellar hook protein flgE SCOP: 117142
Super Family:
Flagellar hook protein flgE
SCOP: 117143

Protein Family Domains

Pfam domains

PFAM: P75937

SMART database

SMART: flgE

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
106 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
28
Cleavage Score (Cmax):
0.186

LipoP 1.0

Prediction:
CYT
Cleavage site amino acid:
0
Score:
-0.200913
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
10

LocTree3

Localization:
secreted
Score:
75

ClubSub-P

Localization:
Extracellular

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 21 [VIG-NN]
Score:
0.902

TatP

Prediction:
No signal peptide predicted.
Cleavage site:
Most likely cleavage site between pos. 42 and 43: ADM-FA

Manual Curation in STEP

Comments

UniProt Name:
Flagellar hook-associated protein 1 (HAP1)
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental) Peripheral outer membrane protein facing the extra-cellular space (Probable)
Notes:
Part of FlgN-FlgK-FliJ-FlhA complex. First hook-filament junction protein. Flagella proteins contribute to the production of outer membrane vesicles. Analysis of E. coli W3110 OMVs revealed that they contain abundant levels of FliC. Compared to the parental strain expressing wild-type flgK, an E. coli strain with a flgK-null mutation produced reduced amounts of OMVs. PMID: 12730325
References:
PMID: 12730325 PMID: 24134841
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 19767571 PMID: 17446557
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
56.2 ppm

EcoCyc

Protein:
EG11967
Gene Locus:
flgK

Structural Annotation

SCOP

Class:
Multi-domain proteins (alpha and beta)
SCOP: 56572
Fold:
Phase 1 flagellin SCOP: 64517
Super Family:
Phase 1 flagellin
SCOP: 64518

Protein Family Domains

Pfam domains

PFAM: P33235

SMART database

SMART: flgK

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
43 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
18
Cleavage Score (Cmax):
0.238

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
17
Score:
2.83622
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
9

LocTree3

Localization:
secreted
Score:
67

ClubSub-P

Localization:
Extracellular

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 17 [AQA-AL]
Score:
0.976

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Flagellar hook-associated protein 2 (HAP2) (Filament cap protein) (Flagellar cap protein)
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental)
Notes:
Filament capping protein. PMID: 7551038 PMID: 1527488 PMID: 6305924
References:
PMID: 1527488 PMID: 6305924 PMID: 7551038
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
45.4 ppm

EcoCyc

Protein:
EG10841
Gene Locus:
fliD

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P24216

SMART database

SMART: fliD

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
93 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
25
Cleavage Score (Cmax):
0.12

LipoP 1.0

Prediction:
CYT
Cleavage site amino acid:
0
Score:
-0.200913
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
10

LocTree3

Localization:
periplasm
Score:
10

ClubSub-P

Localization:
Extracellular

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 24 [LTA-AQ]
Score:
0.977

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Flagellar hook-associated protein 3 (HAP3) (Hook-filament junction protein)
Localization:
Peripheral outer membrane protein facing the extra-cellular space (Experimental)
Notes:
Second hook-filament junction protein. PMID: 12730325
References:
PMID: 12730325
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 19767571 PMID: 17446557
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
67.6 ppm

EcoCyc

Protein:
EG11545
Gene Locus:
flgL

Structural Annotation

SCOP

Class:
Multi-domain proteins (alpha and beta)
SCOP: 56572
Fold:
Phase 1 flagellin SCOP: 64517
Super Family:
Phase 1 flagellin
SCOP: 64518

Protein Family Domains

Pfam domains

PFAM: P29744

SMART database

SMART: flgL

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
35 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
58
Cleavage Score (Cmax):
0.149

LipoP 1.0

Prediction:
CYT
Cleavage site amino acid:
0
Score:
-0.200913
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Extracellular
Score:
10

LocTree3

Localization:
periplasm
Score:
16

ClubSub-P

Localization:
Extracellular

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
No signal peptide predicted
Score:
0.971

TatP

Prediction:
No signal peptide predicted.
Cleavage site:
Most likely cleavage site between pos. 45 and 46: PIA-AS

Manual Curation in STEP

Comments

UniProt Name:
Putative polysaccharide export protein Wza
Localization:
Outer Membrane Lipoprotein, Peripheral outer membrane protein facing the extra-cellular space (Experimental) Outer Membrane Lipoprotein, Peripheral outer membrane protein facing the extra-cellular space (Probable)
Notes:
Has a helical structure that crosses membrane. The transmembrane region of Wza is an alpha-helical barrel. Proven pignal peptidase II substrate. It has been demostrated that it can be also secreted and be surface exposed. PMID: 15174130
References:
PMID: 10619844 PMID: 15174130 PMCID: PMC3315050
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 20222674 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0.366 ppm

EcoCyc

Protein:
EG13566
Gene Locus:
wza

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P0A930

SMART database

SMART: wza

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
44 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
26
Cleavage Score (Cmax):
0.13

LipoP 1.0

Prediction:
SpII
Cleavage site amino acid:
20
Score:
12.3938
Cleavage Rule:
Pos+2=T

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
OuterMembrane
Score:
9

LocTree3

Localization:
outer membrane
Score:
14

ClubSub-P

Localization:
Outer membrane beta-barrel AND lipid-anchor

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 30 [NMS-TM]
Score:
0.972

TatP

Prediction:
No signal peptide predicted.

Manual Curation in STEP

Comments

UniProt Name:
Major outer membrane prolipoprotein Lpp [Cleaved into: Major outer membrane lipoprotein Lpp (Braun lipoprotein) (Murein-lipoprotein)]
Localization:
Outer Membrane Lipoprotein, Peripheral outer membrane protein facing the extra-cellular space (Experimental) Outer Membrane Lipoprotein, Peripheral outer membrane protein facing the extra-cellular space (Probable)
Notes:
Trigger factor-sensitive aggregation. Proven pignal peptidase II substrate. Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005). Covalently attached to the peptidoglycan cell wall by the ??-amino group of its C-terminal Lys residue; stabilizes the bacterial envelope. Identified in nucleoids collected by sucrose gradient centrifugation and analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). PMID: 21541338 PMID: 4575979
References:
PMID: 15174130 PMID: 15911532 PMID: 16079137 PMID: 3013869 PMID: 4575979
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 16079137 PMID: 15115803 PMID: 20932056 PMID: 19343722 PMID: 20923772
Proteomics / Inner Membrane fraction:
PMID: 16079137 PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
6110 ppm

EcoCyc

Protein:
EG10544
Gene Locus:
lpp

Structural Annotation

SCOP

Class:
Coiled coil proteins
SCOP: 57942
Fold:
Parallel coiled-coil SCOP: 57943
Super Family:
Outer membrane lipoprotein
SCOP: 58042

Protein Family Domains

Pfam domains

PFAM: P69776

SMART database

SMART: lpp

Protein Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
58 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
26
Cleavage Score (Cmax):
0.325

LipoP 1.0

Prediction:
SpII
Cleavage site amino acid:
20
Score:
26.7873
Cleavage Rule:
Pos+2=S

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
OuterMembrane
Score:
10

LocTree3

Localization:
secreted
Score:
59

ClubSub-P

Localization:
Inner/Outer-membrane lipoprotein

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 25 [SNA-KI]
Score:
0.999

TatP

Prediction:
No signal peptide predicted.