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

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:

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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

Predict Now

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:

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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.

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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

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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:

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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

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Manual Curation in STEP

Comments

UniProt Name:
Hydrogenase-2 small chain (HYD2) (EC 1.12.99.6) (Membrane-bound hydrogenase 2 small subunit) (NiFe hydrogenase)
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
Copurifies with trigger factor in pull down assays. Exported by the Tat system. Experimentally proven signal peptide cleavage site. Under anaerobic conditions Escherichia coli synthesizes three membrane-associated [NiFe]-hydrogenases (Hyd). Hyd-1 and Hyd-2 are respiratory hydrogenases with their active sites facing the periplasm. PMID: 22769583 PMID: 9738917
References:
PMID: 17218314 PMID: 19737520 PMID: 22769583 PMID: 9738917
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 19348461 PMID: 20222674 PMID: 16858726 PMID: 19767571
Proteomics / Inner Membrane fraction:
PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG13006
Gene Locus:
hybO

Structural Annotation

SCOP

Class:
Multi-domain proteins (alpha and beta)
SCOP: 56572
Fold:
HydA/Nqo6-like SCOP: 56769
Super Family:
HydA/Nqo6-like
SCOP: 56770

Protein Family Domains

Pfam domains

PFAM: P69741

SMART database

SMART: hybO

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:
38
Cleavage Score (Cmax):
0.248

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
37
Score:
7.00921
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
Yes
Number of TMs:
1

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
10

LocTree3

Localization:
periplasm
Score:
37

ClubSub-P

Localization:
Uncertain

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 37 [AAA-EM]
Score:
0.989

TatP

Prediction:
Found RRDFM as Tat motif starting at pos. 15
Cleavage site:
Most likely cleavage site between pos. 37 and 38: AAA-EM

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Protein-methionine-sulfoxide reductase catalytic subunit MsrP (EC 1.8.5.-)
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
TAT secretion system. PMID: 15355966
References:
PMID: 15355966 PMID: 16042411 PMID: 17218314
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:
13.2 ppm

show distribution

EcoCyc

Protein:
EG14047
Gene Locus:
msrP

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Oxidoreductase molybdopterin-binding domain SCOP: 56523
Super Family:
Oxidoreductase molybdopterin-binding domain
SCOP: 56524

Protein Family Domains

Pfam domains

PFAM: P76342

SMART database

SMART: msrP

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:
No
Cleavage site amino acid:
45
Cleavage Score (Cmax):
0.526

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
44
Score:
7.04958
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:
Uncertain

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 44 [AHA-DL]
Score:
1

TatP

Prediction:
Found RRQVL as Tat motif starting at pos. 22
Cleavage site:
Most likely cleavage site between pos. 44 and 45: AHA-DL

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Manual Curation in STEP

Comments

UniProt Name:
Putative dimethyl sulfoxide reductase chain YnfE (DMSO reductase) (EC 1.8.99.-)
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
TAT secretion system. 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 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 PMID: 19767571 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0.593 ppm

show distribution

EcoCyc

Protein:
EG13843
Gene Locus:
ynfE

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: P77374

SMART database

SMART: ynfE

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
21 % 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):
0.177

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
42
Score:
4.96127
Cleavage Rule:
-

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:
periplasm
Score:
18

ClubSub-P

Localization:
-

sosuiGramN

Localization:
C (cytoplasmic)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 42 [AAA-AV]
Score:
0.998

TatP

Prediction:
Found RRTLV as Tat motif starting at pos. 12
Cleavage site:
Most likely cleavage site between pos. 42 and 43: AAA-AV

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Manual Curation in STEP

Comments

UniProt Name:
Probable dimethyl sulfoxide reductase chain YnfF (DMSO reductase) (EC 1.8.99.-)
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
Verified Tat substrate: YnfF has a Tat-only (Class II) predicted 45 aa signal peptide (Tullman-Ercek, 2007). The physiological substrate and relevance of the YnfFGH S- and N-oxide reductase is unknown.; DmsA paralog.So far, hydroxy pyridine N-oxide is the 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 PMID: 17218314 PMID: 19415239
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: 16967446 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0.552 ppm

show distribution

EcoCyc

Protein:
EG13844
Gene Locus:
ynfF

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: P77783

SMART database

SMART: ynfF

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
9 % 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:
46
Cleavage Score (Cmax):
0.406

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
45
Score:
11.1244
Cleavage Rule:
-

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:
periplasm
Score:
15

ClubSub-P

Localization:
-

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Tat signal peptide predicted. Most likely cleavage site: 1 - 45 [VRA-AE]
Score:
0.999

TatP

Prediction:
Found RRSLM as Tat motif starting at pos. 16
Cleavage site:
Most likely cleavage site between pos. 45 and 46: VRA-AE

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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