(18 nodes) Glyoxylate and dicarboxylate metabolism network (Aquifex aeolicus)

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:
	fdoG	Formate dehydrogenase alpha subunit. (1015 aa)
	fdoH	Formate dehydrogenase beta subunit. (303 aa)
	fdoI	Formate dehydrogenase gamma subunit. (211 aa)
	gcsH1	Glycine cleavage system protein H; The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. (143 aa)
	gcsH4	Glycine cleavage system protein H; The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. (171 aa)
	gcsP2	Glycine dehydrogenase (decarboxylating); The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. (439 aa)
	glnA	Glutamine synthetase; Catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia; Belongs to the glutamine synthetase family. (469 aa)
	gph	Phosphoglycolate phosphatase; Specifically catalyzes the dephosphorylation of 2- phosphoglycolate. (213 aa)
	gcsH2	Glycine cleavage system protein H; The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. (161 aa)
	mdh2	Malate dehydrogenase; Catalyzes the reversible oxidation of malate to oxaloacetate. Belongs to the LDH/MDH superfamily. (334 aa)
	mdh1	Malate dehydrogenase; Catalyzes the reversible oxidation of malate to oxaloacetate. Belongs to the LDH/MDH superfamily. MDH type 3 family. (335 aa)
	aco	Aconitase. (659 aa)
	purU	Formyltetrahydrofolate deformylase; Catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to formate and tetrahydrofolate (FH4). (283 aa)
	gcsP1	Glycine dehydrogenase (decarboxylating); The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein; Belongs to the GcvP family. C-terminal subunit subfamily. (482 aa)
	gcvH5	Putative protein; The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. (148 aa)
	glyA	Serine hydroxymethyl transferase; Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. (428 aa)
	lpdA	Dihydrolipoamide dehydrogenase. (465 aa)
	gcsH3	Glycine cleavage system protein H; The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. (161 aa)

Your Current Organism:

Aquifex aeolicus

NCBI taxonomy Id: 224324
Other names: A. aeolicus VF5, Aquifex aeolicus VF5, Aquifex aeolicus str. VF5

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
aco	mdh1	aq_1784	aq_1782	Aconitase.	Malate dehydrogenase; Catalyzes the reversible oxidation of malate to oxaloacetate. Belongs to the LDH/MDH superfamily. MDH type 3 family.	0.868
aco	mdh2	aq_1784	aq_1665	Aconitase.	Malate dehydrogenase; Catalyzes the reversible oxidation of malate to oxaloacetate. Belongs to the LDH/MDH superfamily.	0.442
fdoG	fdoH	aq_1039	aq_1046	Formate dehydrogenase alpha subunit.	Formate dehydrogenase beta subunit.	0.998
fdoG	fdoI	aq_1039	aq_1049	Formate dehydrogenase alpha subunit.	Formate dehydrogenase gamma subunit.	0.996
fdoG	gcsH1	aq_1039	aq_1052	Formate dehydrogenase alpha subunit.	Glycine cleavage system protein H; The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein.	0.480
fdoG	mdh1	aq_1039	aq_1782	Formate dehydrogenase alpha subunit.	Malate dehydrogenase; Catalyzes the reversible oxidation of malate to oxaloacetate. Belongs to the LDH/MDH superfamily. MDH type 3 family.	0.800
fdoG	mdh2	aq_1039	aq_1665	Formate dehydrogenase alpha subunit.	Malate dehydrogenase; Catalyzes the reversible oxidation of malate to oxaloacetate. Belongs to the LDH/MDH superfamily.	0.800
fdoG	purU	aq_1039	aq_1818	Formate dehydrogenase alpha subunit.	Formyltetrahydrofolate deformylase; Catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to formate and tetrahydrofolate (FH4).	0.900
fdoH	fdoG	aq_1046	aq_1039	Formate dehydrogenase beta subunit.	Formate dehydrogenase alpha subunit.	0.998
fdoH	fdoI	aq_1046	aq_1049	Formate dehydrogenase beta subunit.	Formate dehydrogenase gamma subunit.	0.999
fdoH	gcsH1	aq_1046	aq_1052	Formate dehydrogenase beta subunit.	Glycine cleavage system protein H; The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein.	0.506
fdoH	mdh1	aq_1046	aq_1782	Formate dehydrogenase beta subunit.	Malate dehydrogenase; Catalyzes the reversible oxidation of malate to oxaloacetate. Belongs to the LDH/MDH superfamily. MDH type 3 family.	0.800
fdoH	mdh2	aq_1046	aq_1665	Formate dehydrogenase beta subunit.	Malate dehydrogenase; Catalyzes the reversible oxidation of malate to oxaloacetate. Belongs to the LDH/MDH superfamily.	0.800
fdoH	purU	aq_1046	aq_1818	Formate dehydrogenase beta subunit.	Formyltetrahydrofolate deformylase; Catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to formate and tetrahydrofolate (FH4).	0.900
fdoI	fdoG	aq_1049	aq_1039	Formate dehydrogenase gamma subunit.	Formate dehydrogenase alpha subunit.	0.996
fdoI	fdoH	aq_1049	aq_1046	Formate dehydrogenase gamma subunit.	Formate dehydrogenase beta subunit.	0.999
fdoI	gcsH1	aq_1049	aq_1052	Formate dehydrogenase gamma subunit.	Glycine cleavage system protein H; The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein.	0.574
fdoI	mdh1	aq_1049	aq_1782	Formate dehydrogenase gamma subunit.	Malate dehydrogenase; Catalyzes the reversible oxidation of malate to oxaloacetate. Belongs to the LDH/MDH superfamily. MDH type 3 family.	0.800
fdoI	mdh2	aq_1049	aq_1665	Formate dehydrogenase gamma subunit.	Malate dehydrogenase; Catalyzes the reversible oxidation of malate to oxaloacetate. Belongs to the LDH/MDH superfamily.	0.800
fdoI	purU	aq_1049	aq_1818	Formate dehydrogenase gamma subunit.	Formyltetrahydrofolate deformylase; Catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to formate and tetrahydrofolate (FH4).	0.900