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

View: Disulfideome of E.coli K-12 (MG1655) proteome Export to Excel Export to HTML Export to XML Export to CSV

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

(mouse over and click on the one letter topology symbols to see which proteins of this specific subproteome are localized in each location)

Bacterial cell cartoon of sub-cellular locations

show distribution

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

86

# Proteins
	K-12
N	5
A	77
r	3
F1	28
B	8
F2	1
E	1
G	86
I	13
F3	1
H	15
F4	4
X	3

Manual Curation in STEP

Comments

UniProt Name:
50S ribosomal protein L31 (Large ribosomal subunit protein bL31-A)
Localization:
Cytoplasmic, Ribosomal (Probable)
Notes:
Identified in nucleoids collected by sucrose gradient centrifugation and analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). PMID: 21541338 Disulfide bond-containing protein PMID: 25664544
References:
PMID: 21541338
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

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

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
637 ppm

show distribution

#7cb5ec

red

#7cb5ec

EcoCyc

Protein:
EG10889
Gene Locus:
rpmE

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
L28p-like SCOP: 143799
Super Family:
L28p-like
SCOP: 143800

Protein Family Domains

Pfam domains

PFAM: P0A7M9

SMART database

SMART: rpmE

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
66 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
31
Cleavage Score (Cmax):
0.105

LipoP 1.0

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

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Cytoplasmic
Score:
9

LocTree3

Localization:
secreted
Score:
35

ClubSub-P

Localization:
-

sosuiGramN

Localization:
C (cytoplasmic)

PRED-TAT

Localization:
No signal peptide predicted
Score:
0.991

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
30S ribosomal protein S12 (Small ribosomal subunit protein uS12)
Localization:
Cytoplasmic, Ribosomal (Probable)
Notes:
Identified in nucleoids collected by sucrose gradient centrifugation and analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). PMID: 21541338 Disulfide bond-containing protein PMID: 25664544
References:
PMID: 21541338
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: 20803007 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
PMID: 17309111

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
857 ppm

show distribution

#7cb5ec

red

#7cb5ec

EcoCyc

Protein:
EG10911
Gene Locus:
rpsL

Structural Annotation

SCOP

Class:
All beta proteins
SCOP: 48724
Fold:
OB-fold SCOP: 50198
Super Family:
Nucleic acid-binding proteins
SCOP: 50249

Protein Family Domains

Pfam domains

PFAM: P0A7S3

SMART database

SMART: rpsL

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
84 % 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:
27
Cleavage Score (Cmax):
0.105

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:
45

ClubSub-P

Localization:
-

sosuiGramN

Localization:
unknown

PRED-TAT

Localization:
No signal peptide predicted
Score:
0.997

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
50S ribosomal protein L36 2 (Large ribosomal subunit protein bL36-B)
Localization:
-
Notes:
Translation, Ribosomal. Expressed during stationary phase in minimal medium (at protein level). Disulfide bond-containing protein PMID: 25664544
References:
-
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
-
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
104 ppm

show distribution

#7cb5ec

red

#7cb5ec

EcoCyc

Protein:
EG14432
Gene Locus:
ykgO

Structural Annotation

SCOP

Class:
Small proteins
SCOP: 56992
Fold:
Ribosomal protein L36 SCOP: 57839
Super Family:
Ribosomal protein L36
SCOP: 57840

Protein Family Domains

Pfam domains

PFAM: Q2EEQ2

SMART database

SMART: ykgO

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
136 % 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):
0.12

LipoP 1.0

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

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Unknown
Score:
2

LocTree3

Localization:
secreted
Score:
42

ClubSub-P

Localization:
-

sosuiGramN

Localization:
unknown

PRED-TAT

Localization:
No signal peptide predicted
Score:
1

TatP

Prediction:
No signal peptide predicted.

Predict Now

Protein ID (Uniprot)

Accession (Uniprot)

Gene Name (Uniprot)

Order Locus Name

Protein Name (STEPdb)

Full Name

Symbol

Bernsel et al

Uniprot

EchoLOCATION

Extracellular Appendage

First Level Targeting Chaperoning

First Level Secretion System

Second Level Targeting Chaperoning

Second Level Secretion System

K-12 Core Proteome (yes/no)

K-12 Basic Proteome (yes/no)

RL31_ECOLI

P0A7M9

rpmE

b3936 JW3907

ribosomal protein, 50S L31 RpmE

Cytoplasmic, Ribosomal

A, r

N/A

Cytoplasmic

ribosome

yes

RS12_ECOLI

P0A7S3

rpsL

strA

b3342 JW3304

ribosomal protein, 30S S12 RpsL

Cytoplasmic, Ribosomal

A, r

Soluble IM Fraction

Cytoplasmic

ribosome

yes

RL362_ECOLI

Q2EEQ2

ykgO

rpmJ2

b4506 JW5034

ribosomal protein, 50S L36 2 YkgO

Cytoplasmic, Ribosomal

A, r

N/A

ribosome

yes

Records 1 to 3 of 3

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