(14 nodes) Membrane assembly, and Lipopolysaccharide biosynthesis network (Nitrosomonas europaea)

Nodes:

Network nodes represent proteins

splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.

Node Color

colored nodes:
query proteins and first shell of interactors

white nodes:
second shell of interactors

Node Content

empty nodes:
proteins of unknown 3D structure

filled nodes:
a 3D structure is known or predicted

Edges:

Edges represent protein-protein associations

associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding to each other.

Known Interactions

from curated databases

experimentally determined

Predicted Interactions

gene neighborhood

gene fusions

gene co-occurrence

Others

textmining

co-expression

protein homology

Your Input:
	NE0063	ATPase component ABC-type (unclassified) transport system. (240 aa)
	lptA	Putative signal peptide protein; Involved in the assembly of lipopolysaccharide (LPS). Required for the translocation of LPS from the inner membrane to the outer membrane. (205 aa)
	NE0065	Conserved hypothetical protein; COGs COG3117. (193 aa)
	fkpA	FKBP-type peptidyl-prolyl cis-trans isomerase (PPIase). (153 aa)
	bamD	TPR repeat; Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. (255 aa)
	omlA	Possible outer membrane lipoprotein OmlA; Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. (164 aa)
	lptD	Putative organic solvent tolerance transmembrane protein; Together with LptE, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. (723 aa)
	surA	PpiC-type peptidyl-prolyl cis-trans isomerase; Chaperone involved in the correct folding and assembly of outer membrane proteins. Recognizes specific patterns of aromatic residues and the orientation of their side chains, which are found more frequently in integral outer membrane proteins. May act in both early periplasmic and late outer membrane-associated steps of protein maturation. (448 aa)
	rlpB	Putative lipoprotein B precursor transmembrane; Together with LptD, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. Required for the proper assembly of LptD. Binds LPS and may serve as the LPS recognition site at the outer membrane; Belongs to the LptE lipoprotein family. (165 aa)
	NE1686	Cytidylyltransferase (CMP-NeuAc synthetase). (252 aa)
	bamA	Bacterial surface antigen (D15); Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. (758 aa)
	lpxK	Tetraacyldisaccharide-1-P 4'-kinase; Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA); In the C-terminal section; belongs to the UPF0434 family. (396 aa)
	ppiD	PpiC-type peptidyl-prolyl cis-trans isomerase. (630 aa)
	NE2404	Putative transmembrane protein. (385 aa)

Your Current Organism:

Nitrosomonas europaea

NCBI taxonomy Id: 228410
Other names: N. europaea ATCC 19718, Nitrosomonas europaea ATCC 19718, Nitrosomonas europaea str. ATCC 19718

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

structured XML interaction data, according to the 'PSI-MI' data standard

... protein node degrees:

download

node degree of proteins in your network (given the current score cut-off)

... network coordinates:

download

a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

download

MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

download

a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

download

a tab-delimited file containing all known functional terms of protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
NE0063	NE0065	NE0063	NE0065	ATPase component ABC-type (unclassified) transport system.	Conserved hypothetical protein; COGs COG3117.	0.998
NE0063	NE1686	NE0063	NE1686	ATPase component ABC-type (unclassified) transport system.	Cytidylyltransferase (CMP-NeuAc synthetase).	0.652
NE0063	bamA	NE0063	NE1710	ATPase component ABC-type (unclassified) transport system.	Bacterial surface antigen (D15); Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane.	0.585
NE0063	lptA	NE0063	NE0064	ATPase component ABC-type (unclassified) transport system.	Putative signal peptide protein; Involved in the assembly of lipopolysaccharide (LPS). Required for the translocation of LPS from the inner membrane to the outer membrane.	0.973
NE0063	lptD	NE0063	NE0881	ATPase component ABC-type (unclassified) transport system.	Putative organic solvent tolerance transmembrane protein; Together with LptE, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane.	0.507
NE0063	lpxK	NE0063	NE2164	ATPase component ABC-type (unclassified) transport system.	Tetraacyldisaccharide-1-P 4'-kinase; Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA); In the C-terminal section; belongs to the UPF0434 family.	0.593
NE0065	NE0063	NE0065	NE0063	Conserved hypothetical protein; COGs COG3117.	ATPase component ABC-type (unclassified) transport system.	0.998
NE0065	lptA	NE0065	NE0064	Conserved hypothetical protein; COGs COG3117.	Putative signal peptide protein; Involved in the assembly of lipopolysaccharide (LPS). Required for the translocation of LPS from the inner membrane to the outer membrane.	0.995
NE0065	lptD	NE0065	NE0881	Conserved hypothetical protein; COGs COG3117.	Putative organic solvent tolerance transmembrane protein; Together with LptE, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane.	0.434
NE0065	lpxK	NE0065	NE2164	Conserved hypothetical protein; COGs COG3117.	Tetraacyldisaccharide-1-P 4'-kinase; Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA); In the C-terminal section; belongs to the UPF0434 family.	0.504
NE0065	rlpB	NE0065	NE1138	Conserved hypothetical protein; COGs COG3117.	Putative lipoprotein B precursor transmembrane; Together with LptD, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. Required for the proper assembly of LptD. Binds LPS and may serve as the LPS recognition site at the outer membrane; Belongs to the LptE lipoprotein family.	0.553
NE1686	NE0063	NE1686	NE0063	Cytidylyltransferase (CMP-NeuAc synthetase).	ATPase component ABC-type (unclassified) transport system.	0.652
NE1686	lpxK	NE1686	NE2164	Cytidylyltransferase (CMP-NeuAc synthetase).	Tetraacyldisaccharide-1-P 4'-kinase; Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA); In the C-terminal section; belongs to the UPF0434 family.	0.912
NE2404	bamA	NE2404	NE1710	Putative transmembrane protein.	Bacterial surface antigen (D15); Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane.	0.952
NE2404	bamD	NE2404	NE0506	Putative transmembrane protein.	TPR repeat; Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane.	0.940
NE2404	lptA	NE2404	NE0064	Putative transmembrane protein.	Putative signal peptide protein; Involved in the assembly of lipopolysaccharide (LPS). Required for the translocation of LPS from the inner membrane to the outer membrane.	0.613
NE2404	omlA	NE2404	NE0615	Putative transmembrane protein.	Possible outer membrane lipoprotein OmlA; Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane.	0.909
NE2404	rlpB	NE2404	NE1138	Putative transmembrane protein.	Putative lipoprotein B precursor transmembrane; Together with LptD, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. Required for the proper assembly of LptD. Binds LPS and may serve as the LPS recognition site at the outer membrane; Belongs to the LptE lipoprotein family.	0.711
bamA	NE0063	NE1710	NE0063	Bacterial surface antigen (D15); Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane.	ATPase component ABC-type (unclassified) transport system.	0.585
bamA	NE2404	NE1710	NE2404	Bacterial surface antigen (D15); Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane.	Putative transmembrane protein.	0.952