STEPdb: Sub-cellular Topologies of E.coli Polypeptides.

Manual Curation in STEP

Comments

UniProt Name:
Maltoporin (Lambda receptor protein) (Maltose-inducible porin)
Localization:
Outer Membrane b-barrel protein (Experimental) Outer Membrane b-barrel protein (Probable)
Notes:
Potential pubstrate of periplasmic chaperones Skp. Substrate of periplasmic peptidyl prolyl cis???trans isomerase SurA. Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005, Fountoulakis et al 2003, Molloy 2000). Experimentally verified trimeric beta-barrel. N-terminal region is in periplasm. Potential Skp substrate PMID: 19953543 Identified SurA substrates PMID: 19953543 PMID: 346375 Disulfide bridges between 47 and 63 PMID: 1988451 Disulfide bond-containing protein PMID: 25664544
References:
PMID: 10806384 PMID: 15911532 PMID: 16079137 PMID: 16372265 PMID: 1988451 PMID: 20932056 PMID: 346375
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 17595003 PMID: 12624733 PMID: 17137328 PMID: 19348461 PMID: 20222674 PMID: 19003857 PMID: 16967446 PMID: 19767571 PMID: 15919657 PMID: 16079137 PMID: 15115803 PMID: 20932056 PMID: 19343722 PMID: 17446557
Proteomics / Inner Membrane fraction:
PMID: 15919657 PMID: 16079137

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
102 ppm

show distribution

EcoCyc

Protein:
EG10528
Gene Locus:
lamB

Structural Annotation

SCOP

Class:
Membrane and cell surface proteins and peptides
SCOP: 56835
Fold:
Transmembrane beta-barrels SCOP: 56924
Super Family:
Porins
SCOP: 56935

Protein Family Domains

Pfam domains

PFAM: P02943

SMART database

SMART: lamB

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
54 % 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):
0.795

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
25
Score:
20.7922
Cleavage Rule:
-

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:
outer membrane
Score:
100

ClubSub-P

Localization:
Outer membrane beta-barrel

sosuiGramN

Localization:
EC (Extracellular)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 25 [AMA-VD]
Score:
1

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Ferrienterobactin receptor (Enterobactin outer-membrane receptor)
Localization:
Outer Membrane b-barrel protein (Experimental) Outer Membrane b-barrel protein (Probable)
Notes:
Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005, Fountoulakis et al 2003, Molloy et al 2000) Potential Skp substrate PMID: 19953543 PMID: 10529396 Disulfide bond-containing protein PMID: 25664544
References:
PMID: 10529396 PMID: 10806384 PMID: 11266632 PMID: 20932056 PMID: 9886293
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 12624733 PMID: 19348461 PMID: 20222674 PMID: 19003857 PMID: 16967446 PMID: 19767571 PMID: 20932056 PMID: 19343722 PMID: 18425732
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
168 ppm

show distribution

EcoCyc

Protein:
EG10293
Gene Locus:
fepA

Structural Annotation

SCOP

Class:
Membrane and cell surface proteins and peptides
SCOP: 56835
Fold:
Transmembrane beta-barrels SCOP: 56924
Super Family:
Porins
SCOP: 56935

Protein Family Domains

Pfam domains

PFAM: P05825

SMART database

SMART: fepA

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
11 % 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):
0.836

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
22
Score:
11.5401
Cleavage Rule:
-

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:
outer membrane
Score:
100

ClubSub-P

Localization:
Outer membrane beta-barrel

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

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

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Ferrichrome outer membrane transporter/phage receptor (Ferric hydroxamate receptor) (Ferric hydroxamate uptake) (Ferrichrome-iron receptor)
Localization:
Outer Membrane b-barrel protein (Experimental) Outer Membrane b-barrel protein (Probable)
Notes:
SecB substrate; Substrate of periplasmic peptidyl prolyl cis???trans isomerase SurA. Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005, Fountoulakis et al 2003, Molloy et al 2000) Potential Skp substrate PMID: 19953543 Identified SurA substrates PMID: 19953543 PMID: 3079747 Disulfide bridge (351 362;725 731) Disulfide bond-containing protein PMID: 25664544
References:
PMID: 10806384 PMID: 11266632 PMID: 15911532 PMID: 3079747 PMID: 9856937
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
2

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 19348461 PMID: 20222674 PMID: 19003857 PMID: 16967446 PMID: 19767571 PMID: 15115803 PMID: 19343722
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
3
PaxDb:
62.9 ppm

show distribution

EcoCyc

Protein:
EG10302
Gene Locus:
fhuA

Structural Annotation

SCOP

Class:
Membrane and cell surface proteins and peptides
SCOP: 56835
Fold:
Transmembrane beta-barrels SCOP: 56924
Super Family:
Porins
SCOP: 56935

Protein Family Domains

Pfam domains

PFAM: P06971

SMART database

SMART: fhuA

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
7 % 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:
34
Cleavage Score (Cmax):
0.805

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
33
Score:
20.4987
Cleavage Rule:
-

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:
outer membrane
Score:
100

ClubSub-P

Localization:
Outer membrane beta-barrel

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 33 [AQA-AV]
Score:
0.999

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Outer membrane protein A (Outer membrane protein II*)
Localization:
Outer Membrane b-barrel protein (Experimental) Outer Membrane b-barrel protein (Potential) Outer Membrane b-barrel protein (Probable)
Notes:
Substrate of periplasmic peptidyl prolyl cis???trans isomerase SurA. Potential pubstrate of periplasmic chaperones Skp. Trigger factor-sensitive aggregation. Trigger factor-sensitive aggregation. Copurifies with trigger factor in pull down assays. The Lipid Bilayer-Inserted Membrane Protein BamA of Escherichia coli Facilitates Insertion and Folding of Outer Membrane Protein A from Its Complex with Skp. Outer membrane protein determined by LC-MS (Gevaert et al 2002). Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005, Fountoulakis et al 2003, Molloy et al 2000) Identified in nucleoids collected by sucrose gradient centrifugation and analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). PMID: 21541338 Potential Skp substrate PMID: 19953543 Identified SurA substrates PMID: 19953543 Identified DsbA substrate PMID: 19953543 PMID: 9298646 SecA is sufficient to transport a secretory protein with hydrophobic signal sequence across SecYEG, but efficient translocation requires SRP in Addition PMID: 24717922 Disulfide bridge (311 323) Disulfide bond-containing protein PMID: 25664544
References:
PMID: 10806384 PMID: 16079137 PMID: 19953543 PMID: 20932056 PMID: 21778229 PMID: 24717922 PMID: 7813480 PMID: 9298646 PMID: 9808047
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 12488465 PMID: 17137328 PMID: 19348461 PMID: 20222674 PMID: 19003857 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 18727129 PMID: 16079137 PMID: 15115803 PMID: 20932056 PMID: 19343722 PMID: 17446557 PMID: 18796603 PMID: 20923772 PMID: 18425732
Proteomics / Inner Membrane fraction:
PMID: 16079137 PMID: 17446557 PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
2767 ppm

show distribution

EcoCyc

Protein:
EG10669
Gene Locus:
ompA

Structural Annotation

SCOP

Class:
Membrane and cell surface proteins and peptides
SCOP: 56835
Fold:
Transmembrane beta-barrels SCOP: 56924
Super Family:
OMPA-like
SCOP: 56925
OmpA-like
SCOP: 103088

Protein Family Domains

Pfam domains

PFAM: P0A910

SMART database

SMART: ompA

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
10 % 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:
22
Cleavage Score (Cmax):
0.872

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
21
Score:
28.1613
Cleavage Rule:
-

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:
outer membrane
Score:
100

ClubSub-P

Localization:
Outer membrane beta-barrel

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 21 [AQA-AP]
Score:
1

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Colicin I receptor
Localization:
Outer Membrane b-barrel protein (Experimental) Outer Membrane b-barrel protein (Potential)
Notes:
Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005, Fountoulakis et al 2003, Molloy et al 2000) Potential Skp substrate PMID: 19953543 Identified DsbA substrate PMID: 19953543 PMID: 10430870 Disulfide bond-containing protein PMID: 25664544
References:
PMID: 10430870 PMID: 10806384 PMID: 15911532 PMID: 19953543 PMID: 20932056
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
0

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 19348461 PMID: 20222674 PMID: 19003857 PMID: 16967446 PMID: 19767571 PMID: 20932056 PMID: 19343722
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
0
PaxDb:
259 ppm

show distribution

EcoCyc

Protein:
EG10155
Gene Locus:
cirA

Structural Annotation

SCOP

Class:
Membrane and cell surface proteins and peptides
SCOP: 56835
Fold:
Transmembrane beta-barrels
SCOP: 56924
Super Family:
Porins
SCOP: 56935

Protein Family Domains

Pfam domains

PFAM: P17315

SMART database

SMART: cirA

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
46 % 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):
0.695

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
25
Score:
11.8271
Cleavage Rule:
-

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:
outer membrane
Score:
24

ClubSub-P

Localization:
Outer membrane beta-barrel

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 25 [VLA-VD]
Score:
1

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Outer membrane usher protein FimD
Localization:
Outer Membrane b-barrel protein (Experimental) Outer Membrane b-barrel protein (Probable)
Notes:
Fim operon (class ??1); Usher. ??uter membrane protein related to resistance to ampicillin and tetracycline. Outer membrane protein determined by LC-MS (Gevaert et al 2002) Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005, Fountoulakis et al 2003) Identified in the outer membrane by biochemical fractionation followed by two-dimensional gel electrophoresis and tandem mass spectrometry. PMID: 15911532 PMID: 12842468 Disulfide bridge (855 877)
References:
PMID: 12488465 PMID: 12842468 PMID: 15911532
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
0

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 17595003 PMID: 12624733 PMID: 12488465 PMID: 19348461 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
0
PaxDb:
0.99 ppm

show distribution

EcoCyc

Protein:
EG10311
Gene Locus:
fimD

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
FimD N-terminal domain-like SCOP: 141728
Super Family:
FimD N-terminal domain-like
SCOP: 141729

Protein Family Domains

Pfam domains

PFAM: P30130

SMART database

SMART: fimD

Protein Complexes

Go to 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:
38
Cleavage Score (Cmax):
0.415

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
37
Score:
1.20154
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
OuterMembrane
Score:
10

LocTree3

Localization:
outer membrane
Score:
22

ClubSub-P

Localization:
Uncertain

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 37 [AFA-AQ]
Score:
0.977

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
LPS-assembly protein LptD (Organic solvent tolerance protein)
Localization:
Outer Membrane b-barrel protein (Experimental) Outer Membrane b-barrel protein (Probable)
Notes:
The Protein-disulfide Isomerase DsbC Cooperates with SurA and DsbA in the Assembly of LptD. Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005) Potential Skp substrate PMID: 19953543 Identified SurA substrates PMID: 19953543 Identified DsbA substrate PMID: 19953543 PMID: 9298646 Disulfide bridge (31 724;173 725)
References:
PMID: 12724388 PMID: 15911532 PMID: 16079137 PMID: 20932056 PMID: 9298646
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 12488465 PMID: 17137328 PMID: 19348461 PMID: 20222674 PMID: 19003857 PMID: 16967446 PMID: 19767571 PMID: 16079137 PMID: 15115803 PMID: 20932056 PMID: 19343722 PMID: 17446557
Proteomics / Inner Membrane fraction:
PMID: 16079137

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
64.9 ppm

show distribution

EcoCyc

Protein:
EG11569
Gene Locus:
lptD

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P31554

SMART database

SMART: lptD

Protein Complexes

Go to 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:
25
Cleavage Score (Cmax):
0.626

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
24
Score:
18.6702
Cleavage Rule:
-

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:
outer membrane
Score:
77

ClubSub-P

Localization:
Outer membrane beta-barrel

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 24 [GLA-AD]
Score:
0.999

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Outer membrane usher protein HtrE (Heat shock protein E)
Localization:
-
Notes:
Putative chaperone???usher fimbrial operon (class ??4); Usher. Disulfide bridge (838 862)
References:
-
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 17595003
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
1
PaxDb:
1.88 ppm

show distribution

EcoCyc

Protein:
EG11972
Gene Locus:
htrE

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
FimD N-terminal domain-like SCOP: 141728
Super Family:
FimD N-terminal domain-like
SCOP: 141729

Protein Family Domains

Pfam domains

PFAM: P33129

SMART database

SMART: htrE

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
8 % 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:
30
Cleavage Score (Cmax):
0.677

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
29
Score:
6.72527
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
OuterMembrane
Score:
10

LocTree3

Localization:
outer membrane
Score:
16

ClubSub-P

Localization:
Uncertain

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 29 [AFS-AE]
Score:
0.999

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Outer membrane usher protein YehB
Localization:
-
Notes:
Putative chaperone???usher fimbrial operon yeh (class ??4); Usher. Disulfide bridge (809 825)
References:
-
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 19348461 PMID: 20222674
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0.011 ppm

show distribution

EcoCyc

Protein:
EG11988
Gene Locus:
yehB

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
FimD N-terminal domain-like SCOP: 141728
Super Family:
FimD N-terminal domain-like
SCOP: 141729

Protein Family Domains

Pfam domains

PFAM: P33341

SMART database

SMART: yehB

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
5 % 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):
0.679

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
22
Score:
11.7505
Cleavage Rule:
-

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:
outer membrane
Score:
12

ClubSub-P

Localization:
Outer membrane beta-barrel

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

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

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Outer membrane usher protein YraJ
Localization:
-
Notes:
Potential fimbrial yra operon (class ??1); Usher. Disulfide bridge (815 837)
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:
0.033 ppm

show distribution

EcoCyc

Protein:
EG12775
Gene Locus:
yraJ

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
FimD N-terminal domain-like SCOP: 141728
Super Family:
FimD N-terminal domain-like
SCOP: 141729

Protein Family Domains

Pfam domains

PFAM: P42915

SMART database

SMART: yraJ

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
6 % 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:
41
Cleavage Score (Cmax):
0.51

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
40
Score:
9.33083
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
OuterMembrane
Score:
10

LocTree3

Localization:
outer membrane
Score:
19

ClubSub-P

Localization:
-

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 40 [ANA-EE]
Score:
0.998

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Uncharacterized outer membrane usher protein YhcD
Localization:
-
Notes:
Potential fimbrial yhc operon (class ??); Uknown function. Disulfide bridge (769 792)
References:
-
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

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

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0.017 ppm

show distribution

EcoCyc

Protein:
EG12810
Gene Locus:
yhcD

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
FimD N-terminal domain-like SCOP: 141728
Super Family:
FimD N-terminal domain-like
SCOP: 141729

Protein Family Domains

Pfam domains

PFAM: P45420

SMART database

SMART: yhcD

Protein Complexes

Go to 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:
22
Cleavage Score (Cmax):
0.809

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
21
Score:
10.0887
Cleavage Rule:
-

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:
outer membrane
Score:
11

ClubSub-P

Localization:
-

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 21 [ANA-DG]
Score:
1

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Uncharacterized outer membrane usher protein YbgQ
Localization:
-
Notes:
Putative chaperone???usher fimbrial operon yeh (class ??); Usher. Disulfide bridge (795 814)
References:
-
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 17595003 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG13313
Gene Locus:
ybgQ

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
FimD N-terminal domain-like SCOP: 141728
Super Family:
FimD N-terminal domain-like
SCOP: 141729

Protein Family Domains

Pfam domains

PFAM: P75750

SMART database

SMART: ybgQ

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
10 % 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:
22
Cleavage Score (Cmax):
0.84

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
21
Score:
8.29107
Cleavage Rule:
-

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:
outer membrane
Score:
23

ClubSub-P

Localization:
Outer membrane beta-barrel

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 21 [AMA-VE]
Score:
1

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Catecholate siderophore receptor Fiu (Ferric iron uptake protein) (TonB-dependent receptor Fiu)
Localization:
Outer Membrane b-barrel protein (Experimental)
Notes:
Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005, Fountoulakis et al 2003)','Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005, Fountoulakis et al 2003, Molloy et al 2000) Potential Skp substrate PMID: 19953543 PMID: 10806384 Disulfide bond-containing protein PMID: 25664544
References:
PMID: 10806384 PMID: 20932056
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 19348461 PMID: 19003857 PMID: 19767571 PMID: 20932056 PMID: 19343722
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
75.6 ppm

show distribution

EcoCyc

Protein:
EG13317
Gene Locus:
fiu

Structural Annotation

SCOP

Class:
Membrane and cell surface proteins and peptides
SCOP: 56835
Fold:
Transmembrane beta-barrels SCOP: 56924
Super Family:
Porins
SCOP: 56935

Protein Family Domains

Pfam domains

PFAM: P75780

SMART database

SMART: fiu

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
10 % 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:
34
Cleavage Score (Cmax):
0.525

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
33
Score:
11.8291
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
OuterMembrane
Score:
10

LocTree3

Localization:
outer membrane
Score:
11

ClubSub-P

Localization:
Outer membrane beta-barrel

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 33 [ALA-AE]
Score:
0.998

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Putative outer membrane usher protein YqiG
Localization:
-
Notes:
Putative chaperone???usher fimbrial operon (class ??); Usher. Disulfide bridge (798 817)
References:
-
Pseudogene/Mobile Element:
pseudogene (Uniprot)

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 20222674 PMID: 16967446
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG14228
Gene Locus:
yqiG

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P76655

SMART database

SMART: yqiG

Protein Complexes

Go to 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:
No
Cleavage site amino acid:
21
Cleavage Score (Cmax):
0.333

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:
OuterMembrane
Score:
10

LocTree3

Localization:
outer membrane
Score:
24

ClubSub-P

Localization:
-

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 20 [AYA-VE]
Score:
0.996

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Outer membrane usher protein SfmD
Localization:
-
Notes:
Potential fimbrial sfm operon (class ??1); Usher. Disulfide bridge (840 862)
References:
-
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

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

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG13883
Gene Locus:
sfmD

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
FimD N-terminal domain-like SCOP: 141728
Super Family:
FimD N-terminal domain-like
SCOP: 141729

Protein Family Domains

Pfam domains

PFAM: P77468

SMART database

SMART: sfmD

Protein Complexes

Go to 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:
No
Cleavage site amino acid:
36
Cleavage Score (Cmax):
0.404

LipoP 1.0

Prediction:
TMH
Cleavage site amino acid:
0
Score:
3.9822
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
No
Number of TMs:
1

PSORTB (v3.0.2)

Localization:
OuterMembrane
Score:
10

LocTree3

Localization:
outer membrane
Score:
17

ClubSub-P

Localization:
Uncertain

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 35 [SYA-ES]
Score:
0.993

TatP

Prediction:
No signal peptide predicted.

Predict Now

Disulfideome of E.coli K-12 (MG1655) proteome

Distribution of sub-cellular topologies of this subproteome in K-12

86

Manual Curation in STEP

mRNA Expression

Protein Existence

Protein abundance/solubility

Structural Annotation

Protein Family Domains

Protein Hydrodynamics

Bioinformatic tools and predictions

Manual Curation in STEP

mRNA Expression

Protein Existence

Protein abundance/solubility

Structural Annotation

Protein Family Domains

Protein Hydrodynamics

Bioinformatic tools and predictions

Manual Curation in STEP

mRNA Expression

Protein Existence

Protein abundance/solubility

Structural Annotation

Protein Family Domains

Protein Hydrodynamics

Bioinformatic tools and predictions

Manual Curation in STEP

mRNA Expression

Protein Existence

Protein abundance/solubility

Structural Annotation

Protein Family Domains

Protein Hydrodynamics

Bioinformatic tools and predictions

Manual Curation in STEP

mRNA Expression

Protein Existence

Protein abundance/solubility

Structural Annotation

Protein Family Domains

Protein Hydrodynamics

Bioinformatic tools and predictions

Manual Curation in STEP

mRNA Expression

Protein Existence

Protein abundance/solubility

Structural Annotation

Protein Family Domains

Protein Hydrodynamics

Bioinformatic tools and predictions

Manual Curation in STEP

mRNA Expression

Protein Existence

Protein abundance/solubility

Structural Annotation

Protein Family Domains

Protein Hydrodynamics

Bioinformatic tools and predictions

Manual Curation in STEP

mRNA Expression

Protein Existence

Protein abundance/solubility

Structural Annotation

Protein Family Domains

Protein Hydrodynamics

Bioinformatic tools and predictions

Manual Curation in STEP

mRNA Expression

Protein Existence

Protein abundance/solubility

Structural Annotation

Protein Family Domains

Protein Hydrodynamics

Bioinformatic tools and predictions

Manual Curation in STEP

mRNA Expression

Protein Existence

Protein abundance/solubility

Structural Annotation