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

Manual Curation in STEP

Comments

UniProt Name:
Iron(3+)-hydroxamate-binding protein FhuD (Ferric hydroxamate uptake protein D) (Ferrichrome-binding periplasmic protein) (Iron(III)-hydroxamate-binding protein FhuD)
Localization:
Periplasmic
Notes:
TAT secretion system. PMID: 8522527
References:
PMID: 17218314 PMID: 8522527
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

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

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0.469 ppm

show distribution

EcoCyc

Protein:
EG10305
Gene Locus:
fhuD

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Chelatase-like SCOP: 53799
Super Family:
Helical backbone metal receptor
SCOP: 53807

Protein Family Domains

Pfam domains

PFAM: P07822

SMART database

SMART: fhuD

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:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
31
Cleavage Score (Cmax):
0.749

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
30
Score:
8.81274
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 30 [AHA-AA]
Score:
0.999

TatP

Prediction:
No signal peptide predicted.

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Manual Curation in STEP

Comments

UniProt Name:
Probable anaerobic dimethyl sulfoxide reductase chain YnfG (DMSO reductase iron-sulfur subunit YnfG)
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
The physiological substrate and relevance of the YnfFGH S- and N-oxide reductase is unknown. DmsB paralog. So far, hydroxy pyridine N-oxide is the best substrate for YnfFGH. ynfFGH are expressed anaerobically. YnfG can function with DmsAC, replacing DmsB a as the electron transfer subunit. The ynfEFGHI operon is a paralogue of the Escherichia coli dmsABC operon. ynfE and ynfF are paralogues of dmsA. ynfG and ynfH are paralogues of dmsB and dmsC, respectively. PMID: 14522592
References:
PMID: 14522592
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

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

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
7.71 ppm

show distribution

EcoCyc

Protein:
EG13845
Gene Locus:
ynfG

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Ferredoxin-like SCOP: 54861
Super Family:
4Fe-4S ferredoxins
SCOP: 54862

Protein Family Domains

Pfam domains

PFAM: P0AAJ1

SMART database

SMART: ynfG

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
38 % 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:
44
Cleavage Score (Cmax):
0.106

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:
Unknown
Score:
5

LocTree3

Localization:
periplasm
Score:
28

ClubSub-P

Localization:
-

sosuiGramN

Localization:
C (cytoplasmic)

PRED-TAT

Localization:
No signal peptide predicted
Score:
0.995

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Hydrogenase-2 operon protein HybA
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
TAT secretion system. Part of membrane-associated hydrogenase 4 complex. PMID: 9738917
References:
PMID: 15911532 PMID: 21890895 PMID: 22313414 PMID: 9738917
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 19348461 PMID: 20222674 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
12.4 ppm

show distribution

EcoCyc

Protein:
EG11799
Gene Locus:
hybA

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Ferredoxin-like SCOP: 54861
Super Family:
4Fe-4S ferredoxins
SCOP: 54862

Protein Family Domains

Pfam domains

PFAM: P0AAJ8

SMART database

SMART: hybA

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
39 % 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:
27
Cleavage Score (Cmax):
0.442

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
26
Score:
19.7463
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
1

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
9

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 28 [AAA-EN]
Score:
0.995

TatP

Prediction:
Found RRNFI as Tat motif starting at pos. 3
Cleavage site:
Most likely cleavage site between pos. 26 and 27: SHA-AA

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Manual Curation in STEP

Comments

UniProt Name:
Protein NrfC
Localization:
Periplasmic
Notes:
TAT secretion system. PMID: 15280383
References:
PMID: 15280383 PMID: 17218314
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

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

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG11946
Gene Locus:
nrfC

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Ferredoxin-like SCOP: 54861
Super Family:
4Fe-4S ferredoxins
SCOP: 54862

Protein Family Domains

Pfam domains

PFAM: P0AAK7

SMART database

SMART: nrfC

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
23 % 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:
28
Cleavage Score (Cmax):
0.447

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
27
Score:
7.45987
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Cytoplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
20

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 27 [VVA-KT]
Score:
1

TatP

Prediction:
Found RRQFL as Tat motif starting at pos. 5
Cleavage site:
Most likely cleavage site between pos. 27 and 28: VVA-KT

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Manual Curation in STEP

Comments

UniProt Name:
Ferredoxin-type protein NapG (Ubiquinol--[NapC cytochrome c] reductase NapG subunit)
Localization:
Periplasmic
Notes:
TAT secretion system. PMID: 11967083
References:
PMID: 11967083 PMID: 17218314
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:
0.067 ppm

show distribution

EcoCyc

Protein:
EG12064
Gene Locus:
napG

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Ferredoxin-like SCOP: 54861
Super Family:
4Fe-4S ferredoxins
SCOP: 54862

Protein Family Domains

Pfam domains

PFAM: P0AAL3

SMART database

SMART: napG

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
20 % 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:
42
Cleavage Score (Cmax):
0.316

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
41
Score:
0.19393
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Cytoplasmic
Score:
8

LocTree3

Localization:
cytoplasm
Score:
12

ClubSub-P

Localization:
-

sosuiGramN

Localization:
C (cytoplasmic)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 41 [ARA-SG]
Score:
0.999

TatP

Prediction:
No signal peptide predicted.
Cleavage site:
Most likely cleavage site between pos. 41 and 42: ARA-SG

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Manual Curation in STEP

Comments

UniProt Name:
Uncharacterized protein YcbK
Localization:
Periplasmic
Notes:
TAT secretion system.
References:
PMID: 17218314
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:
EG13703
Gene Locus:
ycbK

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Hedgehog/DD-peptidase SCOP: 55165
Super Family:
Hedgehog/DD-peptidase
SCOP: 55166

Protein Family Domains

Pfam domains

PFAM: P0AB06

SMART database

SMART: ycbK

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:
No
Cleavage site amino acid:
31
Cleavage Score (Cmax):
0.559

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
30
Score:
8.29508
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Unknown
Score:
2

LocTree3

Localization:
secreted
Score:
44

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 30 [AFA-TL]
Score:
1

TatP

Prediction:
Found RRKLL as Tat motif starting at pos. 8
Cleavage site:
Most likely cleavage site between pos. 30 and 31: AFA-TL

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Manual Curation in STEP

Comments

UniProt Name:
Hydrogenase-2 large chain (HYD2) (EC 1.12.99.6) (Membrane-bound hydrogenase 2 large subunit) (NiFe hydrogenase)
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
The protein is attached to this location through a 5kDa segment of its small subunit hybO that is has a TAT signal peptide. Secreted using the TAT system (piggyback). PMID: 10224080 An active tryptic fragment of membrane-bound hydrogenase isoenzyme 2 from anaerobically grown Escherichia coli has been purified. This indicates that HYD2 is attached to the periplasmic side of the cytoplasmic membrane.PMID: 3516690 The intracellular availability of nickel is essential for the processing of the large subunit and for the transmembrane translocation of HYD2. PMID: 8772179 PMID: 9738917 Disulfide bond-containing protein PMID: 25664544
References:
PMID: 10224080 PMID: 25664544 PMID: 3516690 PMID: 8772179 PMID: 9738917
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: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 15919657 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
PMID: 15919657 PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
60.5 ppm

show distribution

EcoCyc

Protein:
EG11801
Gene Locus:
hybC

Structural Annotation

SCOP

Class:
Multi-domain proteins (alpha and beta)
SCOP: 56572
Fold:
HydB/Nqo4-like
SCOP: 56761
Super Family:
HydB/Nqo4-like
SCOP: 56762

Protein Family Domains

Pfam domains

PFAM: P0ACE0

SMART database

SMART: hybC

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
28 % 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:
34
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:
CytoplasmicMembrane
Score:
10

LocTree3

Localization:
periplasm
Score:
31

ClubSub-P

Localization:
Cytoplasmic

sosuiGramN

Localization:
C (cytoplasmic)

PRED-TAT

Localization:
No signal peptide predicted
Score:
0.911

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Uncharacterized protein YfhG
Localization:
Outer Membrane Lipoprotein
Notes:
TAT secretion system.
References:
PMID: 17218314
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
2.46 ppm

show distribution

EcoCyc

Protein:
EG12139
Gene Locus:
yfhG

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P0AD44

SMART database

SMART: yfhG

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
55 % 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):
0.159

LipoP 1.0

Prediction:
SpII
Cleavage site amino acid:
25
Score:
6.96106
Cleavage Rule:
Pos+2=V

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Unknown
Score:
2

LocTree3

Localization:
periplasm
Score:
61

ClubSub-P

Localization:
-

sosuiGramN

Localization:
OM (Outer Membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 39 [TPA-EE]
Score:
0.98

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Dimethyl sulfoxide reductase DmsA (DMSO reductase) (DMSOR) (Me2SO reductase) (EC 1.8.5.3)
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
TAT signal peptide, dmsABC complex. Part of the anaerobic dimethylsulphoxide (DMSO) reductase DmsABC. The DmsC polypeptide is composed of eight segments of hydrophobic amino acids of appropriate length to cross the cytoplasmic membrane, suggesting that this subunit functions to anchor the DMSO enzyme to the membrane. PMID: 3062312 There are contradictory experiments although it seems that the senario of the DmsABC complex facing the cytoplasm is more favoured. PMID: 11389150 The hydrophobic region of the DmsA twin-arginine leader peptide determines specificity with chaperone DmsD. PMID: 24093457 Fluorescence analysis of these YFP chimeras revealed a wide range of interactions such as the one between the Tat substrate dimethyl sulfoxide reductase (DmsA) and its dedicated proofreading chaperone DmsD. PMID: 20169075 The localization of DmsAB was compared in a strain expressing a partial DmsC subunit (pDMSC59X) with full-length DmsC originating from the chromosomal copy of the dms operon. In those experiments some DmsAB was reported in the periplasm in the absence of full-length DmsC, leading us to suggest that DmsC might serve a stop-transfer role. PMID: 9546395 TTnphoA fusions, and electron paramagnetic resonance monitoring the effects of the probe dysprosium(III) on an engineered 3Fe4S cluster in DmsB indicated that DmsAB faces the cytoplasm PMID: 2170332 PMID: 3280546 PMID: 3062312 Interacts with DmsD, a redox enzyme maturation protein (REMP). PMID: 20153451
References:
PMID: 11389150 PMID: 17218314 PMID: 20153451 PMID: 20169075 PMID: 2170332 PMID: 24093457 PMID: 3062312 PMID: 3280546 PMID: 9546395
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: 19348461 PMID: 20222674 PMID: 16967446 PMID: 19767571 PMID: 15115803
Proteomics / Inner Membrane fraction:
PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
10.3 ppm

show distribution

EcoCyc

Protein:
EG10232
Gene Locus:
dmsA

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Double psi beta-barrel
SCOP: 50684
Formate dehydrogenase/DMSO reductase, domains 1-3
SCOP: 53705
Super Family:
ADC-like
SCOP: 50692
Formate dehydrogenase/DMSO reductase, domains 1-3
SCOP: 53706

Protein Family Domains

Pfam domains

PFAM: P18775

SMART database

SMART: dmsA

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
22 % 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:
46
Cleavage Score (Cmax):
0.537

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
45
Score:
5.24058
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
10

LocTree3

Localization:
periplasm
Score:
18

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 45 [AHA-VD]
Score:
1

TatP

Prediction:
Found RRGLV as Tat motif starting at pos. 16
Cleavage site:
Most likely cleavage site between pos. 45 and 46: AHA-VD

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Anaerobic dimethyl sulfoxide reductase chain B (DMSO reductase iron-sulfur subunit)
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
TAT (piggyback); DmsB is co-exported bound to Tat substrate DmsA. Part of the anaerobic dimethylsulphoxide (DMSO) reductase DmsABC. The DmsC polypeptide is composed of eight segments of hydrophobic amino acids of appropriate length to cross the cytoplasmic membrane, suggesting that this subunit functions to anchor the DMSO enzyme to the membrane. PMID: 3062312 There are contradictory experiments although it seems that the senario of the DmsABC complex facing the cytoplasm is more favoured. PMID: 11389150 The localization of DmsAB was compared in a strain expressing a partial DmsC subunit (pDMSC59X) with full-length DmsC originating from the chromosomal copy of the dms operon. In those experiments some DmsAB was reported in the periplasm in the absence of full-length DmsC, leading us to suggest that DmsC might serve a stop-transfer role. PMID: 9546395 TTnphoA fusions, and electron paramagnetic resonance monitoring the effects of the probe dysprosium(III) on an engineered 3Fe4S cluster in DmsB indicated that DmsAB faces the cytoplasm PMID: 2170332
References:
PMID: 11389150 PMID: 2170332 PMID: 3062312 PMID: 9546395
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 12624733 PMID: 20222674 PMID: 19767571 PMID: 20803007 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
5.84 ppm

show distribution

EcoCyc

Protein:
EG10233
Gene Locus:
dmsB

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Ferredoxin-like
SCOP: 54861
Super Family:
4Fe-4S ferredoxins
SCOP: 54862

Protein Family Domains

Pfam domains

PFAM: P18776

SMART database

SMART: dmsB

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
27 % 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:
44
Cleavage Score (Cmax):
0.107

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:
Unknown
Score:
5

LocTree3

Localization:
periplasm
Score:
26

ClubSub-P

Localization:
Cytoplasmic

sosuiGramN

Localization:
C (cytoplasmic)

PRED-TAT

Localization:
No signal peptide predicted
Score:
0.998

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Formate dehydrogenase, nitrate-inducible, major subunit (EC 1.17.5.3) (Anaerobic formate dehydrogenase major subunit) (Formate dehydrogenase-N subunit alpha) (FDH-N subunit alpha)
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
TAT secretion system; Formate dehydrogenase allows E.coli to use formate as major electron donor during anaerobic respiration, when nitrate is used as electron acceptor. The alpha subunit forms the active site. FdnG is the catalytic subunit of formate dehydrogenase-N (FdnGHI). FdnG was found in the periplasmic fraction of a mutant lacking the membrane anchor subunit FdnI, confirming that FdnG is located at the periplasmic face of the cytoplasmic membrane. PMID: 11929547 PMID: 11884747 PMID: 12923080 PMID: 11884747 PMID: 16858726
References:
PMID: 11884747 PMID: 11929547 PMID: 12923080 PMID: 15342602 PMID: 16858726 PMID: 17218314
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: 16858726 PMID: 19767571 PMID: 20521846 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
0
PaxDb:
2.59 ppm

show distribution

EcoCyc

Protein:
EG11227
Gene Locus:
fdnG

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Double psi beta-barrel
SCOP: 50684
Formate dehydrogenase/DMSO reductase, domains 1-3
SCOP: 53705
Super Family:
ADC-like
SCOP: 50692
Formate dehydrogenase/DMSO reductase, domains 1-3
SCOP: 53706

Protein Family Domains

Pfam domains

PFAM: P24183

SMART database

SMART: fdnG

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:
34
Cleavage Score (Cmax):
0.342

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
33
Score:
6.74593
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 33 [ALA-QA]
Score:
0.997

TatP

Prediction:
Found RRQFF as Tat motif starting at pos. 5
Cleavage site:
Most likely cleavage site between pos. 33 and 34: ALA-QA

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Cell division protein FtsP
Localization:
Periplasmic
Notes:
TAT secretion system. PMID: 9298646
References:
PMID: 10593889 PMID: 17218314 PMID: 19135451 PMID: 9298646
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 12488465 PMID: 20222674 PMID: 19003857 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
3.23 ppm

show distribution

EcoCyc

Protein:
EG11376
Gene Locus:
ftsP

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Cupredoxin-like SCOP: 49502
Super Family:
Cupredoxins
SCOP: 49503

Protein Family Domains

Pfam domains

PFAM: P26648

SMART database

SMART: ftsP

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:
28
Cleavage Score (Cmax):
0.494

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
27
Score:
10.6124
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 27 [ASA-AG]
Score:
0.999

TatP

Prediction:
Found RRQFI as Tat motif starting at pos. 5
Cleavage site:
Most likely cleavage site between pos. 27 and 28: ASA-AG

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Deferrochelatase/peroxidase EfeB (EC 1.11.1.-)
Localization:
Periplasmic
Notes:
TAT secretion system.
References:
PMID: 16551627 PMID: 17218314
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:
0.435 ppm

show distribution

EcoCyc

Protein:
EG11735
Gene Locus:
efeB

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Ferredoxin-like SCOP: 54861
Super Family:
Dimeric alpha+beta barrel
SCOP: 54909

Protein Family Domains

Pfam domains

PFAM: P31545

SMART database

SMART: efeB

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
33 % 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:
36
Cleavage Score (Cmax):
0.748

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
35
Score:
5.64598
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 35 [AHA-QK]
Score:
1

TatP

Prediction:
Found RRRLL as Tat motif starting at pos. 14
Cleavage site:
Most likely cleavage site between pos. 35 and 36: AHA-QK

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Formate dehydrogenase-O major subunit (EC 1.17.1.9) (Aerobic formate dehydrogenase major subunit) (FDH-Z subunit alpha) (Formate dehydrogenase-O subunit alpha)
Localization:
Periplasmic
Notes:
TAT secretion system. PMID: 12923080
References:
PMID: 12923080 PMID: 17218314
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: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 20521846 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18796603 PMID: 20923772
Proteomics / Inner Membrane fraction:
PMID: 17446557

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
33 ppm

show distribution

EcoCyc

Protein:
EG11858
Gene Locus:
fdoG

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Formate dehydrogenase/DMSO reductase, domains 1-3 SCOP: 53705
Super Family:
ADC-like
SCOP: 50692
Formate dehydrogenase/DMSO reductase, domains 1-3
SCOP: 53706

Protein Family Domains

Pfam domains

PFAM: P32176

SMART database

SMART: fdoG

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:
34
Cleavage Score (Cmax):
0.487

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
33
Score:
14.6779
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
71

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 33 [ALA-ET]
Score:
1

TatP

Prediction:
Found RRQFF as Tat motif starting at pos. 5
Cleavage site:
Most likely cleavage site between pos. 33 and 34: ALA-ET

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Trimethylamine-N-oxide reductase 1 (TMAO reductase 1) (Trimethylamine oxidase 1) (EC 1.7.2.3)
Localization:
Periplasmic
Notes:
TAT secretion system. Trimethylamine N-oxide (TMAO) respiration system is encoded by the torCAD operon and comprises a periplasmic TMAO reductase (TorA) and a c-type cytochrome (TorC), which shuttles electrons to TorA. Interaction studies showed that, when immature, TorC can no longer bind TorA efficiently but can bind the periplasmic detector region of sensor TorS. Electron transfer and binding of the c-type cytochrome TorC to the trimethylamine N-oxide reductase TorD, a cytoplasmic chaperone that interacts with the unfolded trimethylamine N-oxide reductase enzyme (TorA). The absence of TorD protein leads to a two times decrease of the final amount of TorA enzyme. PMID: 15073303
References:
PMID: 11056172 PMID: 15073303 PMID: 17218314 PMID: 2512991 PMID: 9632735
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
0

Protein Existence

Mass spectrometry experiments

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

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
0
PaxDb:
0.588 ppm

show distribution

EcoCyc

Protein:
EG11814
Gene Locus:
torA

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Formate dehydrogenase/DMSO reductase, domains 1-3 SCOP: 53705
Super Family:
ADC-like
SCOP: 50692
Formate dehydrogenase/DMSO reductase, domains 1-3
SCOP: 53706

Protein Family Domains

Pfam domains

PFAM: P33225

SMART database

SMART: torA

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:
No
Cleavage site amino acid:
40
Cleavage Score (Cmax):
0.294

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
39
Score:
1.32729
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 42 [AQA-AT]
Score:
0.996

TatP

Prediction:
Found RRRFL as Tat motif starting at pos. 11
Cleavage site:
Most likely cleavage site between pos. 39 and 40: ATA-AQ

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Periplasmic nitrate reductase (EC 1.9.6.1)
Localization:
Periplasmic
Notes:
TAT secretion system. Nitrate reductase, napFDAGHBC, is located in the periplasm. E. coli also expresses two membrane-bound proton-translocating nitrate reductases, encoded by the narGHJI and narZYWV operons. PMID: 11844760 PMID: 10234835 Disulfide bond-containing protein PMID: 25664544
References:
PMID: 10234835 PMID: 11844760 PMID: 17218314 PMID: 25664544
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
4.85 ppm

show distribution

EcoCyc

Protein:
EG12067
Gene Locus:
napA

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Formate dehydrogenase/DMSO reductase, domains 1-3 SCOP: 53705
Super Family:
ADC-like
SCOP: 50692
Formate dehydrogenase/DMSO reductase, domains 1-3
SCOP: 53706

Protein Family Domains

Pfam domains

PFAM: P33937

SMART database

SMART: napA

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:
32
Cleavage Score (Cmax):
0.617

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
31
Score:
20.6365
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
-

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 31 [ARA-VV]
Score:
0.999

TatP

Prediction:
Found RRSFM as Tat motif starting at pos. 5
Cleavage site:
Most likely cleavage site between pos. 31 and 32: ARA-VV

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
N-acetylmuramoyl-L-alanine amidase AmiA (EC 3.5.1.28)
Localization:
Periplasmic
Notes:
The Escherichia coli amidase AmiC is a periplasmic septal ring component exported via the twin-arginine transport pathwayPMID: 17218314 PMID: 12787347. PMID: 12787347
References:
PMID: 12787347 PMID: 17218314
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 20222674
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
2.88 ppm

show distribution

EcoCyc

Protein:
EG11823
Gene Locus:
amiA

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Phosphorylase/hydrolase-like SCOP: 53162
Super Family:
Zn-dependent exopeptidases
SCOP: 53187

Protein Family Domains

Pfam domains

PFAM: P36548

SMART database

SMART: amiA

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
36 % 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:
35
Cleavage Score (Cmax):
0.684

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
34
Score:
15.9519
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Unknown
Score:
2

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 34 [AIA-KD]
Score:
0.999

TatP

Prediction:
Found RRQVL as Tat motif starting at pos. 13
Cleavage site:
Most likely cleavage site between pos. 34 and 35: AIA-KD

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Blue copper oxidase CueO (Copper efflux oxidase)
Localization:
Periplasmic
Notes:
TAT secretion system. PMID: 9298646
References:
PMID: 17218314 PMID: 9298646
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 20222674 PMID: 19767571 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
0
PaxDb:
75.3 ppm

show distribution

EcoCyc

Protein:
EG12318
Gene Locus:
cueO

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Cupredoxin-like SCOP: 49502
Super Family:
Cupredoxins
SCOP: 49503

Protein Family Domains

Pfam domains

PFAM: P36649

SMART database

SMART: cueO

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:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
29
Cleavage Score (Cmax):
0.821

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
28
Score:
16.1248
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
unknown

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 28 [VFA-AE]
Score:
1

TatP

Prediction:
Found RRDFL as Tat motif starting at pos. 3
Cleavage site:
Most likely cleavage site between pos. 28 and 29: VFA-AE

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Glucans biosynthesis protein D
Localization:
Periplasmic
Notes:
TAT secretion system. PMID: 9298646 Disulfide bond-containing protein PMID: 25664544
References:
PMID: 17218314 PMID: 25664544 PMID: 9298646
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 20222674 PMID: 19767571 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
21 ppm

show distribution

EcoCyc

Protein:
EG12859
Gene Locus:
mdoD

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Supersandwich SCOP: 49993
Super Family:
Galactose mutarotase-like
SCOP: 74650
E set domains
SCOP: 81296

Protein Family Domains

Pfam domains

PFAM: P40120

SMART database

SMART: mdoD

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
61 % 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:
33
Cleavage Score (Cmax):
0.683

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
32
Score:
18.7932
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 32 [AFA-AD]
Score:
1

TatP

Prediction:
Found RRRFI as Tat motif starting at pos. 3
Cleavage site:
Most likely cleavage site between pos. 32 and 33: AFA-AD

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Trimethylamine-N-oxide reductase 2 (TMAO reductase 2) (Trimethylamine oxidase 2) (EC 1.7.2.3)
Localization:
Periplasmic
Notes:
TAT secretion system. PMID: 11004177
References:
PMID: 11004177 PMID: 17218314
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 17137328 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
2.7 ppm

show distribution

EcoCyc

Protein:
EG13276
Gene Locus:
torZ

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Formate dehydrogenase/DMSO reductase, domains 1-3 SCOP: 53705
Super Family:
ADC-like
SCOP: 50692
Formate dehydrogenase/DMSO reductase, domains 1-3
SCOP: 53706

Protein Family Domains

Pfam domains

PFAM: P46923

SMART database

SMART: torZ

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
33 % 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:
32
Cleavage Score (Cmax):
0.688

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
31
Score:
17.7989
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
10

LocTree3

Localization:
periplasm
Score:
100

ClubSub-P

Localization:
Periplasmic

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 31 [AWA-EE]
Score:
1

TatP

Prediction:
Found RREFI as Tat motif starting at pos. 5
Cleavage site:
Most likely cleavage site between pos. 31 and 32: AWA-EE

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E.coli K-12 (MG1655) Tat secretome

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

20

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