(6 nodes) (2009) HlyU acts as an H-NS antirepressor in the regulation of the RTX toxin gene essential for the virulence of the human pathogen Vibrio vulnificus CMCP6. network (Shigella flexneri)

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:
	gapA	Glyceraldehyde-3-phosphate dehydrogenase A; Catalyzes the oxidative phosphorylation of glyceraldehyde 3- phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG. (331 aa)
	slyA	Transcriptional regulator; Transcription regulator that can specifically activate or repress expression of target genes; Belongs to the SlyA family. (146 aa)
	leuO	Probable transcriptional activator for leuABCD operon; Code: K; COG: COG0583; Belongs to the LysR transcriptional regulatory family. (373 aa)
	fadR	Negative regulator for fad regulon, and positive activator of fabA; Multifunctional regulator of fatty acid metabolism. (239 aa)
	gapC	Glyceraldehyde-3-phosphate dehydrogenase. (83 aa)
	gapC-2	Putative glyceraldehyde-3-phosphate dehydrogenase A; Code: G; COG: COG0057; Belongs to the glyceraldehyde-3-phosphate dehydrogenase family. (250 aa)

Your Current Organism:

Shigella flexneri

NCBI taxonomy Id: 198214
Other names: S. flexneri 2a str. 301, Shigella flexneri 2a str. 301, Shigella flexneri serotype 2a str. 301

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 proteins in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
gapA	gapC	SF1444	SF1796	Glyceraldehyde-3-phosphate dehydrogenase A; Catalyzes the oxidative phosphorylation of glyceraldehyde 3- phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG.	Glyceraldehyde-3-phosphate dehydrogenase.	0.929
gapA	gapC-2	SF1444	SF1795	Glyceraldehyde-3-phosphate dehydrogenase A; Catalyzes the oxidative phosphorylation of glyceraldehyde 3- phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG.	Putative glyceraldehyde-3-phosphate dehydrogenase A; Code: G; COG: COG0057; Belongs to the glyceraldehyde-3-phosphate dehydrogenase family.	0.906
gapC	gapA	SF1796	SF1444	Glyceraldehyde-3-phosphate dehydrogenase.	Glyceraldehyde-3-phosphate dehydrogenase A; Catalyzes the oxidative phosphorylation of glyceraldehyde 3- phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG.	0.929
gapC	gapC-2	SF1796	SF1795	Glyceraldehyde-3-phosphate dehydrogenase.	Putative glyceraldehyde-3-phosphate dehydrogenase A; Code: G; COG: COG0057; Belongs to the glyceraldehyde-3-phosphate dehydrogenase family.	0.999
gapC-2	gapA	SF1795	SF1444	Putative glyceraldehyde-3-phosphate dehydrogenase A; Code: G; COG: COG0057; Belongs to the glyceraldehyde-3-phosphate dehydrogenase family.	Glyceraldehyde-3-phosphate dehydrogenase A; Catalyzes the oxidative phosphorylation of glyceraldehyde 3- phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG.	0.906
gapC-2	gapC	SF1795	SF1796	Putative glyceraldehyde-3-phosphate dehydrogenase A; Code: G; COG: COG0057; Belongs to the glyceraldehyde-3-phosphate dehydrogenase family.	Glyceraldehyde-3-phosphate dehydrogenase.	0.999
leuO	slyA	SF0071	SF1669	Probable transcriptional activator for leuABCD operon; Code: K; COG: COG0583; Belongs to the LysR transcriptional regulatory family.	Transcriptional regulator; Transcription regulator that can specifically activate or repress expression of target genes; Belongs to the SlyA family.	0.802
slyA	leuO	SF1669	SF0071	Transcriptional regulator; Transcription regulator that can specifically activate or repress expression of target genes; Belongs to the SlyA family.	Probable transcriptional activator for leuABCD operon; Code: K; COG: COG0583; Belongs to the LysR transcriptional regulatory family.	0.802