E.coli K-12 (MG1655) Non-classical secretome

UniProt Name:
Uncharacterized protein YmgJ
Localization:
-
Notes:
Weak signal peptide prediction. Function Unkown.
References:
-
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
-
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
0 ppm

Class:
-
Fold:
-
Super Family:
-

Go to Complexes

UniProt Name:
Superoxide dismutase [Mn] (EC 1.15.1.1) (MnSOD)
Localization:
Periplasmic
Notes:
The superoxide dismutase SodA is targeted to the periplasm in a SecA-dependent manner by a novel mechanism in Rhizobium leguminosarum. SodM and SodF are <i>E.coli</i> proteins that are close homoloques of the RISodA. SodA does not possess a hydrophobic cleaved N-terminal signal peptide typically present in soluble proteins exported by the Sec-dependent (Sec) pathway or the twin-arginine translocation (TAT) pathway. TatC or SecB mutants in Rhizobium leguminosarum do not affect export of SodA to the periplasm. Inhibition of SecA ATPase activity by azide blocks SodA export to the periplasm.
References:
PMID: 21854464
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

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

Protein molec/cell:
-
PaxDb:
4185 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Long alpha-hairpin
SCOP: 46556
Fe,Mn superoxide dismutase (SOD), C-terminal domain
SCOP: 54718
Super Family:
Fe,Mn superoxide dismutase (SOD), N-terminal domain
SCOP: 46609
Fe,Mn superoxide dismutase (SOD), C-terminal domain
SCOP: 54719

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UniProt Name:
Enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (2-phosphoglycerate dehydratase)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm, Peripheral outer membrane protein facing the extra-cellular space
Notes:
When modified at Lys342 possibly secreted by an unknown mechanism, no evidence of signal peptide) Homodimer, stabilized by Mg2+; Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. Essential for the degradation of carbohydrates via glycolysis. Also a component of the RNA degradosome. The covalent binding to the substrate at Lys-342 causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Interacts with the C-terminal region of the endoribonuclease RNase EIn the RNA degradosome. Fractions of enolase are present in both the cytoplasm and on the cell surface. As part of the bacterial cytoskeleton in the cytoplasm,Is organized as extended coiled structures that wind around the cell, from one cell pole to the other. When covalently bound to the substrate at Lys-342, the inactive enolase is secreted, and remains attached to the bacterial cell surface. PMID: 8610017 PMID: 9600841 PMID: 9740056 PMID: 9732527 PMID: 12035760 Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 12035760 PMID: 15003462 PMID: 17242352 PMID: 18337249 PMID: 23230279 PMID: 8610017 PMID: 9600841 PMID: 9732527 PMID: 9740056
Pseudogene/Mobile Element:
-

mRNA molec/cell:
21

Proteomics:
PMID: 12624733 PMID: 12488465 PMID: 17137328 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 20521846 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18425732
Proteomics / Inner Membrane fraction:
PMID: 17309111

Protein molec/cell:
567
PaxDb:
3361 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Enolase N-terminal domain-like SCOP: 54825
Super Family:
Enolase C-terminal domain-like
SCOP: 51604
Enolase N-terminal domain-like
SCOP: 54826

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UniProt Name:
tRNA-modifying protein YgfZ
Localization:
Cytoplasmic, Periplasmic
Notes:
Subcellular localization analysis of cytotoxic necrotizing factor 1 <a href="http://www.uniprot.org/uniprot/Q1R2U0">(CNF1)</a> demonstrated that YgfZ, a periplasmic protein, contributes to secretion of CNF1 (a normally cytoplasmic protein) into outer-membrane vesicles (OMVs) in pathogenic E.coli strain RS218 O18:K1:H7 PMID: 22174383. PMID: 9298646
References:
PMID: 22174383 PMID: 9298646
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 12488465 PMID: 17137328 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
372 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Elongation factor/aminomethyltransferase common domain
SCOP: 50464
Folate-binding domain
SCOP: 103024
Super Family:
Aminomethyltransferase beta-barrel domain
SCOP: 101790
Folate-binding domain
SCOP: 103025

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UniProt Name:
Cell division protein FtsL
Localization:
Inner Membrane Lipoprotein
Notes:
Localizes to potential division sites in filamentous cells. Proven pignal peptidase II substrate. PMID: 1332942
References:
PMID: 10027987 PMID: 11703663 PMID: 11948172 PMID: 1332942 PMID: 15165235 PMID: 15174130 PMID: 21890895
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
2.55 ppm

Class:
-
Fold:
-
Super Family:
-

Go to Complexes

UniProt Name:
Superoxide dismutase [Fe] (EC 1.15.1.1)
Localization:
Periplasmic
Notes:
The superoxide dismutase SodA is targeted to the periplasm in a SecA-dependent manner by a novel mechanism in Rhizobium leguminosarum. SodM and SodF are <i>E.coli</i> proteins that are close homoloques of the RISodA. SodA does not possess a hydrophobic cleaved N-terminal signal peptide typically present in soluble proteins exported by the Sec-dependent (Sec) pathway or the twin-arginine translocation (TAT) pathway. TatC or SecB mutants in Rhizobium leguminosarum do not affect export of SodA to the periplasm. Inhibition of SecA ATPase activity by azide blocks SodA export to the periplasm.
References:
-
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 12624733 PMID: 19348461 PMID: 20222674 PMID: 16858726 PMID: 19767571 PMID: 20803007 PMID: 20521846 PMID: 15115803 PMID: 17446557 PMID: 18425732
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
706 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Long alpha-hairpin
SCOP: 46556
Fe,Mn superoxide dismutase (SOD), C-terminal domain
SCOP: 54718
Super Family:
Fe,Mn superoxide dismutase (SOD), N-terminal domain
SCOP: 46609
Fe,Mn superoxide dismutase (SOD), C-terminal domain
SCOP: 54719

Go to Complexes

UniProt Name:
Nicotinate phosphoribosyltransferase (NAPRTase) (EC 6.3.4.21)
Localization:
Periplasmic
Notes:
PncB is localized in the periplasm although it does not possess a signal peptide.
References:
PMID: 346557
Pseudogene/Mobile Element:
-

mRNA molec/cell:
7

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

Protein molec/cell:
27
PaxDb:
126 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
TIM beta/alpha-barrel
SCOP: 51350
alpha/beta-Hammerhead
SCOP: 54664
Super Family:
Nicotinate/Quinolinate PRTase C-terminal domain-like
SCOP: 51690
Nicotinate/Quinolinate PRTase N-terminal domain-like
SCOP: 54675

Go to Complexes

UniProt Name:
Biosynthetic arginine decarboxylase (ADC) (EC 4.1.1.19)
Localization:
Periplasmic
Notes:
Trigger factor-sensitive aggregation. Experimentally detected by proteomics analysis of E.coli membrane fraction PMID: 19766000. No transmembrane helix is predicted. Weak hydrophobic and non cytoplasmic regions predicted by Phobius. Potential peripherally associated protein facing the cytoplasm or integral inner membrane protein. PMID: 2198270 Selective disruption of the cell envelope and an assessment of Spea activity or immunoprecipitable SpeA in various fractions demonstrated its location between the cytoplasmic membrane and peptidoglycan layer. PMID: 3894328
References:
PMID: 15919657 PMID: 19737520 PMID: 19766000 PMID: 2198270 PMID: 3894328
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 19767571 PMID: 15919657 PMID: 15115803
Proteomics / Inner Membrane fraction:
PMID: 15919657

Protein molec/cell:
-
PaxDb:
199 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Domain of alpha and beta subunits of F1 ATP synthase-like
SCOP: 50614
TIM beta/alpha-barrel
SCOP: 51350
Super Family:
Alanine racemase C-terminal domain-like
SCOP: 50621
PLP-binding barrel
SCOP: 51419

Go to Complexes

UniProt Name:
Putative attaching and effacing protein homolog
Localization:
Periplasmic
Notes:
Uniprot gives portential signal peptide (1-25) although it is not predicted by any tool. Intimin homologue but missing the C-terminus. Intimin is in the OM. Could be periplasmic. The signal peptide could be long autotransporter-like signal peptide. Intimin does not have a classical signal peptide either.
References:
-
Pseudogene/Mobile Element:
pseudogene (Uniprot), pseudogene (Ochman & Davalos, 2006)

mRNA molec/cell:
-

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

Protein molec/cell:
-
PaxDb:
0 ppm

Class:
-
Fold:
-
Super Family:
-

Go to Complexes

UniProt Name:
Probable lipoprotein YiaD
Localization:
Outer Membrane Lipoprotein
Notes:
Proven pignal peptidase II substrate. PMID: 15174130
References:
PMID: 15174130 PMID: 15919996 PMID: 20932056
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 20803007 PMID: 15115803 PMID: 20932056 PMID: 19343722
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
40.1 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Bacillus chorismate mutase-like SCOP: 55297
Super Family:
OmpA-like
SCOP: 103088

Go to Complexes

UniProt Name:
Glucose-1-phosphate thymidylyltransferase 1 (G1P-TT 1) (EC 2.7.7.24) (dTDP-glucose pyrophosphorylase 1) (dTDP-glucose synthase 1)
Localization:
Periplasmic
Notes:
-
References:
PMID: 23138692 PMID: 7537247
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

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

Protein molec/cell:
-
PaxDb:
207 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Nucleotide-diphospho-sugar transferases SCOP: 53447
Super Family:
Nucleotide-diphospho-sugar transferases
SCOP: 53448

Go to Complexes

UniProt Name:
Putative uncharacterized protein YcgI
Localization:
-
Notes:
Contains a predicted autotransporter domain. Potential outer membrane b-barrel protein though it does not have prediction for a signal peptide. Contains autotransporter beta-domain <a href="http://www.ebi.ac.uk/interpro/entry/IPR005546/proteins-matched?species=83333">(IPR005546)</a>
References:
-
Pseudogene/Mobile Element:
pseudogene (Uniprot), pseudogene (Ochman & Davalos, 2006)

mRNA molec/cell:
-

Proteomics:
-
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
0 ppm

Class:
-
Fold:
-
Super Family:
-

Go to Complexes

UniProt Name:
Uncharacterized protein YcgV
Localization:
Outer Membrane b-barrel protein
Notes:
Ag43 homologue; known autotransporter protein. Signal peptide 1-56 (by clustalW). Contains autotransporter beta-domain <a href="http://www.ebi.ac.uk/interpro/entry/IPR005546/proteins-matched?species=83333">(IPR005546)</a>. Potential Srp-dependent autotransporter. Homologous to hemoglobin-binding protease hbp. Hbp is the only known autotransporter that is secreted through the integral membrane in a Srp-dependent manner.
References:
PMID: 12466262 PMID: 15590781
Pseudogene/Mobile Element:
-

mRNA molec/cell:
0

Proteomics:
PMID: 17446557
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
0
PaxDb:
0.228 ppm

Class:
Membrane and cell surface proteins and peptides
SCOP: 56835
Fold:
Transmembrane beta-barrels SCOP: 56924
Super Family:
Pectin lyase-like
SCOP: 51126
Autotransporter
SCOP: 103515

Go to Complexes

UniProt Name:
Multidrug resistance protein MdtA (Multidrug transporter MdtA)
Localization:
Peripheral inner membrane protein facing the periplasm
Notes:
Part of MdtABC-TolC multidrug efflux transport system = [(TolC)3][MdtC][MdtB][MdtA].
References:
PMID: 12107133 PMID: 12107134 PMID: 21890895
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
1
PaxDb:
3.05 ppm

Class:
Membrane and cell surface proteins and peptides
SCOP: 56835
Fold:
HlyD-like secretion proteins SCOP: 111368
Super Family:
HlyD-like secretion proteins
SCOP: 111369

Go to Complexes

UniProt Name:
Putative protein LomR
Localization:
-
Notes:
-
References:
-
Pseudogene/Mobile Element:
Insertion Sequence, pseudogene (Uniprot), pseudogene (Ochman & Davalos, 2006)

mRNA molec/cell:
-

Proteomics:
-
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
1
PaxDb:
0 ppm

Class:
-
Fold:
-
Super Family:
-

Go to Complexes

UniProt Name:
Uncharacterized protein YdeU
Localization:
Outer Membrane b-barrel protein
Notes:
Ag43 homologue; predicted autotransporter.
References:
PMID: 15590781
Pseudogene/Mobile Element:
pseudogene (Uniprot)

mRNA molec/cell:
-

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

Protein molec/cell:
-
PaxDb:
0 ppm

Class:
-
Fold:
-
Super Family:
-

Go to Complexes

UniProt Name:
Hemolysin E, chromosomal (Cytotoxin ClyA) (Hemolysis-inducing protein) (Latent pore-forming 34 kDa hemolysin) (Silent hemolysin SheA)
Localization:
Periplasmic, Extra-cellular
Notes:
HlyE(ClyA) forms a dodecameric transmembrane pore. The ability of ClyA to translocate to the periplasm is abolished in deletion mutants lacking the last 23 or 11 amino acid residues of the C-terminal region. Also, analysis of ClyA mutants with defined deletions and amino acid exchanges revealed that several ClyA segments which are distant of each other in the primary structure, namely, the N-terminal ??A1 region, the C-terminal region, and the hydrophobic sequence ranging from residues 89 to 101, are crucial for ClyA translocation from the E. coli cytoplasm to the periplasm. In the soluble ClyA monomer, these regions are found closely adjacent to each other in the tail domain. ClyA assembles into an oligomeric structure in solution in the absence of either bilayer membranes or detergents at physiological temperature.These oligomers can rearrange to create transmembrane pores when in contact with detergents or biological membranes. ClyA does not form transmembrane pores on E. coli lipid membranes. Recombinant E. coli overexpressing the cloned clyA gene accumulated this haemolysin in the periplasm and released only very small amounts of it into the external medium. PMID: 11902713 Disulfide bridge (87 285) PMID: 14532000
References:
PMID: 10027972 PMID: 11902713 PMID: 14532000 PMID: 19421192 PMID: 20511497 PMID: 24019520 PMCID: PMC2916382
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

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

Protein molec/cell:
-
PaxDb:
4.77 ppm

Class:
Coiled coil proteins
SCOP: 57942
Fold:
Antiparallel coiled-coil SCOP: 58086
Super Family:
Bacterial hemolysins
SCOP: 58100

Go to Complexes

UniProt Name:
Lipoprotein YafY
Localization:
Inner Membrane Lipoprotein
Notes:
-
References:
PMID: 23138451
Pseudogene/Mobile Element:
Prophage Integrase (EcoGene)

mRNA molec/cell:
-

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

Protein molec/cell:
-
PaxDb:
0 ppm

Class:
-
Fold:
-
Super Family:
-

Go to Complexes