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

Manual Curation in STEP

Comments

UniProt Name:
Aspartate--tRNA ligase (EC 6.1.1.12) (Aspartyl-tRNA synthetase) (AspRS)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental) Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Probable)
Notes:
SecY-interacting protein. Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 19139097 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
5

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16858726 PMID: 19767571 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
182
PaxDb:
509 ppm

show distribution

EcoCyc

Protein:
EG10097
Gene Locus:
aspS

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
OB-fold
SCOP: 50198
DCoH-like
SCOP: 55247
Class II aaRS and biotin synthetases
SCOP: 55680
Super Family:
Nucleic acid-binding proteins
SCOP: 50249
GAD domain-like
SCOP: 55261
Class II aaRS and biotin synthetases
SCOP: 55681

Protein Family Domains

Pfam domains

PFAM: P21889

SMART database

SMART: aspS

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
81 % 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:
27
Cleavage Score (Cmax):
0.104

LipoP 1.0

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

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Cytoplasmic
Score:
10

LocTree3

Localization:
cytoplasm
Score:
100

ClubSub-P

Localization:
Cytoplasmic

sosuiGramN

Localization:
C (cytoplasmic)

PRED-TAT

Localization:
No signal peptide predicted
Score:
1

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Cell division protein FtsQ
Localization:
Integral Inner Membrane (Experimental) Integral Inner Membrane (Probable)
Notes:
FtsQ could be localized to the division site in constricting cells. FtsQ insertion requires SecYEG, the transmembrane electrical potential, SecA, and the SRP pathway. PMID: 15546656 YidC plays a role in the membrane integration of the FtsQ protein as the hydrophobic region of FtsQ can be cross-linked to YidC. PMID: 15546656
References:
PMID: 11415986 PMID: 11703663 PMID: 11948172 PMID: 15165235 PMID: 15546656 PMID: 17693520 PMID: 2007547 PMID: 9829918 PMID: 9882666
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: 16967446 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
4.27 ppm

show distribution

EcoCyc

Protein:
EG10342
Gene Locus:
ftsQ

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P06136

SMART database

SMART: ftsQ

Topology on the inner membrane

Orientation on the IM:
in/out (N-terminus/C-terminus)

Go to topology

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
24 % 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:
41
Cleavage Score (Cmax):
0.115

LipoP 1.0

Prediction:
TMH
Cleavage site amino acid:
0
Score:
1.18618
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
No
Number of TMs:
1

PSORTB (v3.0.2)

Localization:
Unknown
Score:
2

LocTree3

Localization:
inner membrane
Score:
100

ClubSub-P

Localization:
Cytoplasmic membrane

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
TM segment predicted: 26 - 46
Score:
0.978

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Cytochrome bo(3) ubiquinol oxidase subunit 2 (Cytochrome b562-o complex subunit II) (Cytochrome o ubiquinol oxidase subunit 2) (Cytochrome o subunit 2) (Oxidase bo(3) subunit 2) (Ubiquinol oxidase chain B) (Ubiquinol oxidase polypeptide II) (Ubiquinol oxidase subunit 2)
Localization:
Integral Inner Membrane (Experimental) Integral Inner Membrane (Probable)
Notes:
Proven signal peptidase II substrate PMID: 15174130. Identified in nucleoids collected by sucrose gradient centrifugation and analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). PMID: 21541338 The SRP interacts with the first TM of CyoA (rather than with its signal sequence) to mediate targeting of CyoA to the Sec/YidC insertion site in the inner membrane. PMID: 16481320 Efficient insertion of in vitro synthesized pre-CyoA into proteoliposomes requires YidC, SecYEG, and SecA and occurs independently of the proton motive force. PMID: 16513637
References:
PMID: 11017202 PMID: 11266632 PMID: 15174130 PMID: 15919657 PMID: 15919996 PMID: 16079137 PMID: 16481320 PMID: 16513637 PMID: 6365921
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 19767571 PMID: 15919657 PMID: 16079137 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18796603 PMID: 20923772
Proteomics / Inner Membrane fraction:
PMID: 15919657 PMID: 16079137 PMID: 17446557 PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
166 ppm

show distribution

EcoCyc

Protein:
EG10178
Gene Locus:
cyoA

Structural Annotation

SCOP

Class:
Membrane and cell surface proteins and peptides
SCOP: 56835
Fold:
Cupredoxin-like
SCOP: 49502
Transmembrane helix hairpin
SCOP: 81334
Super Family:
Cupredoxins
SCOP: 49503
Cytochrome c oxidase subunit II-like, transmembrane region
SCOP: 81464

Protein Family Domains

Pfam domains

PFAM: P0ABJ1

SMART database

SMART: cyoA

Topology on the inner membrane

Orientation on the IM:
out/out (N-terminus/C-terminus)

Go to topology

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
19 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
31
Cleavage Score (Cmax):
0.189

LipoP 1.0

Prediction:
TMH
Cleavage site amino acid:
0
Score:
11.3494
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
3

Phobius

Signal Peptide:
Yes
Number of TMs:
2

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
10

LocTree3

Localization:
inner membrane
Score:
100

ClubSub-P

Localization:
Cytoplasmic membrane

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 28 [NSA-LL]
Score:
0.985

TatP

Prediction:
No signal peptide predicted.
Cleavage site:
Most likely cleavage site between pos. 17 and 18: LFA-GT

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Manual Curation in STEP

Comments

UniProt Name:
Membrane protein insertase YidC (Foldase YidC) (Inner membrane protein YidC) (Membrane integrase YidC) (Oxa1Ec)
Localization:
Integral Inner Membrane (Experimental) Integral Inner Membrane (Probable)
Notes:
YidC, the Escherichia coli homologue of mitochondrial Oxa1p, is a component of the Sec translocase. The first periplasmic region of YidC include residues 24???346. Residues 215???265 of YidC are sufficient for SecF binding. The interaction of YidC with SecF is though not critical for cell viability as YidC, lacking residues 24-264, was fully functional to support the growth of <i>E. coli</i>. The integration of YidC into the cytoplasmic membrane requires the signal recognition particle, SecA and SecYEG.
References:
PMID: 11821429 PMID: 15919657 PMID: 16079137
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 15919657 PMID: 16079137 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18796603
Proteomics / Inner Membrane fraction:
PMID: 15919657 PMID: 16079137 PMID: 17446557 PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
70 ppm

show distribution

EcoCyc

Protein:
EG11197
Gene Locus:
yidC

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P25714

SMART database

SMART: yidC

Topology on the inner membrane

Orientation on the IM:
in/in (N-terminus/C-terminus)

Go to topology

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
26 % 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:
25
Cleavage Score (Cmax):
0.321

LipoP 1.0

Prediction:
SpI
Cleavage site amino acid:
24
Score:
12.0898
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
4

Phobius

Signal Peptide:
Yes
Number of TMs:
4

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
10

LocTree3

Localization:
inner membrane
Score:
100

ClubSub-P

Localization:
-

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 24 [AWE-QD]
Score:
0.981

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Modulator of FtsH protease HflC
Localization:
Integral Inner Membrane (Experimental) Integral Inner Membrane (Probable)
Notes:
N-terminally located transmembrane segment. PMID: 9792691 Translocation of the C-terminal domains of HflKC was retarded markedly when sodium azide was added to inhibit SecA ATPase and blocked almost completely in secY- or secD-defective mutant cells. PMID: 9792691
References:
PMID: 16834335 PMID: 8947034 PMID: 9792691
Pseudogene/Mobile Element:
Prophage Transposase (by homology to BL21)

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
2

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 15115803 PMID: 17446557 PMID: 18796603
Proteomics / Inner Membrane fraction:
PMID: 17446557 PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
2
PaxDb:
172 ppm

show distribution

EcoCyc

Protein:
EG10435
Gene Locus:
hflC

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
EF-Ts domain-like
SCOP: 54712
Super Family:
Band 7/SPFH domain
SCOP: 117892

Protein Family Domains

Pfam domains

PFAM: P0ABC3

SMART database

SMART: hflC

Topology on the inner membrane

Orientation on the IM:
out/in (N-terminus/C-terminus)

Go to topology

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:
No
Cleavage site amino acid:
25
Cleavage Score (Cmax):
0.135

LipoP 1.0

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

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
No
Number of TMs:
1

PSORTB (v3.0.2)

Localization:
Cytoplasmic
Score:
8

LocTree3

Localization:
inner membrane
Score:
100

ClubSub-P

Localization:
Uncertain

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 22 [VFV-VK]
Score:
0.872

TatP

Prediction:
No signal peptide predicted.

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Manual Curation in STEP

Comments

UniProt Name:
Modulator of FtsH protease HflK
Localization:
Integral Inner Membrane (Experimental) Integral Inner Membrane (Probable)
Notes:
Identified in nucleoids collected by sucrose gradient centrifugation and analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). PMID: 21541338 N-terminally located transmembrane segment. PMID: 9792691 Translocation of the C-terminal domains of HflKC was retarded markedly when sodium azide was added to inhibit SecA ATPase and blocked almost completely in secY- or secD-defective mutant cells. PMID: 9792691
References:
PMID: 8947034 PMID: 9792691
Pseudogene/Mobile Element:
Prophage Transposase

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: 19767571 PMID: 15115803 PMID: 20932056 PMID: 17446557
Proteomics / Inner Membrane fraction:
PMID: 17446557

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
67
PaxDb:
277 ppm

show distribution

EcoCyc

Protein:
EG10436
Gene Locus:
hflK

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
EF-Ts domain-like
SCOP: 54712
Super Family:
Band 7/SPFH domain
SCOP: 117892

Protein Family Domains

Pfam domains

PFAM: P0ABC7

SMART database

SMART: hflK

Topology on the inner membrane

Orientation on the IM:
in/out (N-terminus/C-terminus)

Go to topology

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:
3
Cleavage Score (Cmax):
0.101

LipoP 1.0

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

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
No
Number of TMs:
1

PSORTB (v3.0.2)

Localization:
Unknown
Score:
5

LocTree3

Localization:
inner membrane
Score:
100

ClubSub-P

Localization:
Cytoplasmic membrane

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
TM segment predicted: 76 - 96
Score:
0.963

TatP

Prediction:
No signal peptide predicted.
Cleavage site:
Most likely cleavage site between pos. 23 and 24: PGG-NS

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Manual Curation in STEP

Comments

UniProt Name:
Peptidyl-prolyl cis-trans isomerase D (PPIase D) (EC 5.2.1.8) (Rotamase D)
Localization:
Integral Inner Membrane (Experimental) Integral Inner Membrane (Probable)
Notes:
By in vivo and in vitro site-directed cross-linking, it has been demostrated that the periplasmic chaperone PpiD is located in front of the lateral gate of SecY, through which transmembrane domains exit the SecY channel. Blue native PAGE analyses verify the presence of a SecYEG-PpiD complex in native Escherichia coli membranes. PMID: 24951590 Consistent with a coupling between translocation across the SecYEG translocon and folding by periplasmic chaperones, a lack of PpiD retards the release of a translocating outer membrane protein into the periplasm. PMID: 18439025
References:
PMID: 16079137 PMID: 18439025 PMID: 24951590 PMID: 9670013
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: 19767571 PMID: 20521846 PMID: 16079137 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18796603
Proteomics / Inner Membrane fraction:
PMID: 16079137 PMID: 17446557 PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
249 ppm

show distribution

EcoCyc

Protein:
EG13249
Gene Locus:
ppiD

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
FKBP-like
SCOP: 54533
Triger factor/SurA peptide-binding domain-like
SCOP: 109997
Super Family:
FKBP-like
SCOP: 54534
Triger factor/SurA peptide-binding domain-like
SCOP: 109998

Protein Family Domains

Pfam domains

PFAM: P0ADY1

SMART database

SMART: ppiD

Topology on the inner membrane

Orientation on the IM:
in/out (N-terminus/C-terminus)

Go to topology

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
52 % 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:
43
Cleavage Score (Cmax):
0.199

LipoP 1.0

Prediction:
TMH
Cleavage site amino acid:
0
Score:
3.55242
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
No
Number of TMs:
1

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
10

LocTree3

Localization:
inner membrane
Score:
100

ClubSub-P

Localization:
Uncertain

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
TM segment predicted: 11 - 31
Score:
0.964

TatP

Prediction:
No signal peptide predicted.

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Manual Curation in STEP

Comments

UniProt Name:
Protein-export membrane protein SecG (P12) (Preprotein translocase band 1 subunit)
Localization:
Integral Inner Membrane (Experimental)
Notes:
-
References:
PMID: 15919657 PMID: 15919996
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 19348461 PMID: 20222674 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:
183 ppm

show distribution

EcoCyc

Protein:
EG12095
Gene Locus:
secG

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P0AG99

SMART database

SMART: secG

Topology on the inner membrane

Orientation on the IM:
in/out (N-terminus/C-terminus)

Go to topology

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
49 % 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:
29
Cleavage Score (Cmax):
0.153

LipoP 1.0

Prediction:
TMH
Cleavage site amino acid:
0
Score:
11.5638
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
2

Phobius

Signal Peptide:
Yes
Number of TMs:
1

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
10

LocTree3

Localization:
inner membrane
Score:
100

ClubSub-P

Localization:
Cytoplasmic membrane

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
TM segment predicted: 5 - 22
Score:
0.672

TatP

Prediction:
No signal peptide predicted.
Cleavage site:
Most likely cleavage site between pos. 40 and 41: ASA-TL

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Manual Curation in STEP

Comments

UniProt Name:
PTS system mannitol-specific EIICBA component (EIICBA-Mtl) (EII-Mtl) [Includes: Mannitol permease IIC component (PTS system mannitol-specific EIIC component); Mannitol-specific phosphotransferase enzyme IIB component (EC 2.7.1.197) (PTS system mannitol-specific EIIB component); Mannitol-specific pho
Localization:
Integral Inner Membrane (Experimental) Integral Inner Membrane (Probable)
Notes:
Signal recognition particle is required for insertion in the bacterial inner membrane. SRP pathway inhibition blocks membrane insertion. The signal anchor sequence of MtlA confers novel properties onto nascent chains of OmpA of being co-translationally recognized and targeted to SecY by SRP. PMCID: PMC305875 The signal anchor sequence of MtlA confers novel properties onto nascent chains of OmpA of being co-translationally recognized and targeted to SecY by SRP. Once targeted to SecY, ribosome-associated nascent chains of the hybrid protein, however, remain untranslocated unless SecA is present. These results indicate that SRP and SecA cooperate in a sequential, non-overlapping manner. PMCID: PMC305875
References:
PMID: 15919657 PMID: 15919996 PMID: 9260961 PMCID: PMC305875
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 19767571 PMID: 15919657 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18796603 PMID: 20923772
Proteomics / Inner Membrane fraction:
PMID: 15919657 PMID: 17446557 PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
165 ppm

show distribution

EcoCyc

Protein:
EG10615
Gene Locus:
mtlA

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Phosphotyrosine protein phosphatases I-like
SCOP: 52787
Phoshotransferase/anion transport protein
SCOP: 55803
Super Family:
PTS system IIB component-like
SCOP: 52794
Phoshotransferase/anion transport protein
SCOP: 55804

Protein Family Domains

Pfam domains

PFAM: P00550

SMART database

SMART: mtlA

Topology on the inner membrane

Orientation on the IM:
in/in (N-terminus/C-terminus)

Go to topology

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
26 % 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:
23
Cleavage Score (Cmax):
0.115

LipoP 1.0

Prediction:
TMH
Cleavage site amino acid:
0
Score:
11.9934
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
8

Phobius

Signal Peptide:
No
Number of TMs:
8

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
10

LocTree3

Localization:
inner membrane
Score:
100

ClubSub-P

Localization:
Cytoplasmic membrane

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
TM segment predicted: 24 - 43
Score:
0.933

TatP

Prediction:
No signal peptide predicted.

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Manual Curation in STEP

Comments

UniProt Name:
Protein translocase subunit SecE
Localization:
Integral Inner Membrane (Probable)
Notes:
Signal recognition particle is required for insertion in the bacterial inner membrane. SRP pathway inhibition blocks membrane insertion.
References:
PMID: 15919996
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

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

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
35.1 ppm

show distribution

EcoCyc

Protein:
EG10939
Gene Locus:
secE

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P0AG96

SMART database

SMART: secE

Topology on the inner membrane

Orientation on the IM:
in/out (N-terminus/C-terminus)

Go to topology

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:

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Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
48
Cleavage Score (Cmax):
0.137

LipoP 1.0

Prediction:
TMH
Cleavage site amino acid:
0
Score:
7.80526
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
3

Phobius

Signal Peptide:
No
Number of TMs:
3

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
10

LocTree3

Localization:
inner membrane
Score:
100

ClubSub-P

Localization:
Cytoplasmic membrane

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
TM segment predicted: 16 - 36
Score:
0.816

TatP

Prediction:
No signal peptide predicted.

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Manual Curation in STEP

Comments

UniProt Name:
Protein translocase subunit SecY
Localization:
Integral Inner Membrane (Experimental)
Notes:
-
References:
PMID: 15919996 PMID: 3004955
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 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
PMID: 17446557 PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
97.1 ppm

show distribution

EcoCyc

Protein:
EG10766
Gene Locus:
secY

Structural Annotation

SCOP

Class:
Membrane and cell surface proteins and peptides
SCOP: 56835
Fold:
Preprotein translocase SecY subunit
SCOP: 103490
Super Family:
Preprotein translocase SecY subunit
SCOP: 103491

Protein Family Domains

Pfam domains

PFAM: P0AGA2

SMART database

SMART: secY

Topology on the inner membrane

Orientation on the IM:
in/in (N-terminus/C-terminus)

Go to topology

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:
47
Cleavage Score (Cmax):
0.104

LipoP 1.0

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

TMHMM v2.0

Number of TMs:
10

Phobius

Signal Peptide:
No
Number of TMs:
10

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
10

LocTree3

Localization:
inner membrane
Score:
100

ClubSub-P

Localization:
Cytoplasmic membrane

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
TM segment predicted: 77 - 97
Score:
0.866

TatP

Prediction:
No signal peptide predicted.
Cleavage site:
Most likely cleavage site between pos. 29 and 30: IGA-LI

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Manual Curation in STEP

Comments

UniProt Name:
UPF0070 protein YfgM
Localization:
Integral Inner Membrane (Experimental)
Notes:
Periplasmic chaperone. Periplasmic chaperone which associates with PpiD and the SecYEG translocon and operates in a network that contains Skp and SurA. Potential substrates identified are nine inner membrane proteins (CusS, EvgS, MalF, OsmC, TdcB, TdcC, WrbA, YfhB, and YtfH) and seven periplasmic proteins (HdeA, HdeB, AnsB, Ggt, MalE, YcgK, and YnjE). PMID: 25403562 Periplasmic chaperone YfgM associates with PpiD and the SecYEG translocon and operates in a network that contains Skp and SurA. PMID: 25403562
References:
PMID: 21210718 PMID: 24855643 PMID: 25403562
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: 16967446 PMID: 16858726 PMID: 19767571 PMID: 20803007 PMID: 15115803 PMID: 17446557 PMID: 18796603
Proteomics / Inner Membrane fraction:
PMID: 17446557 PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
275 ppm

show distribution

EcoCyc

Protein:
EG14209
Gene Locus:
yfgM

Structural Annotation

SCOP

Class:
All alpha proteins
SCOP: 46456
Fold:
alpha-alpha superhelix SCOP: 48370
Super Family:
TPR-like
SCOP: 48452

Protein Family Domains

Pfam domains

PFAM: P76576

SMART database

SMART: yfgM

Topology on the inner membrane

Orientation on the IM:
in/out (N-terminus/C-terminus)

Go to topology

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
50 % 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:
27
Cleavage Score (Cmax):
0.142

LipoP 1.0

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

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
No
Number of TMs:
1

PSORTB (v3.0.2)

Localization:
Periplasmic
Score:
9

LocTree3

Localization:
inner membrane
Score:
63

ClubSub-P

Localization:
-

sosuiGramN

Localization:
IM (inner membrane)

PRED-TAT

Localization:
TM segment predicted: 22 - 42
Score:
0.97

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:
Membrane-bound lytic murein transglycosylase A (EC 4.2.2.n1) (Mlt38) (Murein hydrolase A)
Localization:
Outer Membrane Lipoprotein (Experimental)
Notes:
The formation of a complex between a murein polymerase (PBP1B) and a murein hydrolase (MltA). In the presence of MipA represents a first step in a reconstitution of the hypothetical murein-synthesizing holoenzyme. Postulated to be responsible for controlled growth of the stress-bearing sacculus of <i>E.coli</i>. Proven pignal peptidase II substrate. Outer membrane protein determined by 2D gel electrophoresis (Lopez-Campistrous et al 2005, Fountoulakis et al 2003) PMID: 15174130 SRP recognizes the first signal anchor sequence of a polytopic membrane protein (MtlA) resulting in cotranslational targeting of MtlA to SecY and phospholipids of the plasma membrane. PMID: 10619852 Possible interaction of SRP with the secretory protein pOmpA is prevented by the association of trigger factor with nascent pOmpA. PMID: 10619852
References:
PMID: 10619852 PMID: 15174130 PMID: 20932056
Pseudogene/Mobile Element:
pseudogene (Ochman & Davalos, 2006)

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
4

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 12624733 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 19767571 PMID: 15115803 PMID: 20932056 PMID: 19343722
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
1
PaxDb:
8.05 ppm

show distribution

EcoCyc

Protein:
EG13085
Gene Locus:
mltA

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
Double psi beta-barrel SCOP: 50684
Super Family:
Barwin-like endoglucanases
SCOP: 50685

Protein Family Domains

Pfam domains

PFAM: P0A935

SMART database

SMART: mltA

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
35 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
Yes
Cleavage site amino acid:
20
Cleavage Score (Cmax):
0.191

LipoP 1.0

Prediction:
SpII
Cleavage site amino acid:
20
Score:
22.7365
Cleavage Rule:
Pos+2=S

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
Yes
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
OuterMembrane
Score:
10

LocTree3

Localization:
periplasm
Score:
37

ClubSub-P

Localization:
Inner/Outer-membrane lipoprotein

sosuiGramN

Localization:
P (Periplasm)

PRED-TAT

Localization:
Sec signal peptide predicted. Most likely cleavage site: 1 - 23 [CSS-KP]
Score:
0.987

TatP

Prediction:
No signal peptide predicted.

Predict Now

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

Sub-cellular topologies of E.coli K-12(MG1655) proteins

2800

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