(13 nodes) Arginine biosynthesis network (Salinibacter ruber)

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:
	glnA	Glutamine synthetase, type I; Identified by match to protein family HMM PF00120; match to protein family HMM PF03951; match to protein family HMM TIGR00653. (465 aa)
	gdhA	Glutamate dehydrogenase; Identified by similarity to SP:P96110; match to protein family HMM PF00208; match to protein family HMM PF02812; Belongs to the Glu/Leu/Phe/Val dehydrogenases family. (434 aa)
	purQ	Phosphoribosylformylglycinamidine synthase I; Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP- dependent manner. PurS interacts with PurQ and PurL and is thought to assist i [...] (235 aa)
	SRU_0666	Amidinotransferase superfamily; Identified by match to protein family HMM PF02274. (435 aa)
	SRU_0938	Aspartate aminotransferase; Identified by match to protein family HMM PF00155; match to protein family HMM PF01212. (404 aa)
	argB	Acetylglutamate kinase. (247 aa)
	argG	Argininosuccinate synthase; Identified by match to protein family HMM PF00764; match to protein family HMM TIGR00032; Belongs to the argininosuccinate synthase family. Type 1 subfamily. (413 aa)
	SRU_2217	Aminotransferase, class III superfamily; Identified by match to protein family HMM PF00202; Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. (395 aa)
	SRU_2218	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain family; Identified by match to protein family HMM PF00185; match to protein family HMM PF02729; Belongs to the aspartate/ornithine carbamoyltransferase superfamily. (352 aa)
	argB-2	Acetylglutamate kinase; Catalyzes the ATP-dependent phosphorylation of N-acetyl-L- glutamate; Belongs to the acetylglutamate kinase family. ArgB subfamily. (267 aa)
	SRU_2220	Peptidase, M20A family; Identified by match to protein family HMM PF01546; match to protein family HMM PF07687. (361 aa)
	argH	Argininosuccinate lyase; Identified by match to protein family HMM PF00206; match to protein family HMM TIGR00838. (437 aa)
	SRU_2255	Glutamate dehydrogenase, short peptide; Identified by match to protein family HMM PF00208; match to protein family HMM PF02812; Belongs to the Glu/Leu/Phe/Val dehydrogenases family. (553 aa)

Your Current Organism:

Salinibacter ruber

NCBI taxonomy Id: 309807
Other names: S. ruber DSM 13855, Salinibacter ruber DSM 13855, Salinibacter ruber str. DSM 13855, Salinibacter ruber strain DSM 13855

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
SRU_0666	SRU_2218	SRU_0666	SRU_2218	Amidinotransferase superfamily; Identified by match to protein family HMM PF02274.	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain family; Identified by match to protein family HMM PF00185; match to protein family HMM PF02729; Belongs to the aspartate/ornithine carbamoyltransferase superfamily.	0.896
SRU_0666	SRU_2220	SRU_0666	SRU_2220	Amidinotransferase superfamily; Identified by match to protein family HMM PF02274.	Peptidase, M20A family; Identified by match to protein family HMM PF01546; match to protein family HMM PF07687.	0.918
SRU_0666	argG	SRU_0666	SRU_2214	Amidinotransferase superfamily; Identified by match to protein family HMM PF02274.	Argininosuccinate synthase; Identified by match to protein family HMM PF00764; match to protein family HMM TIGR00032; Belongs to the argininosuccinate synthase family. Type 1 subfamily.	0.915
SRU_0666	argH	SRU_0666	SRU_2221	Amidinotransferase superfamily; Identified by match to protein family HMM PF02274.	Argininosuccinate lyase; Identified by match to protein family HMM PF00206; match to protein family HMM TIGR00838.	0.915
SRU_0938	SRU_2255	SRU_0938	SRU_2255	Aspartate aminotransferase; Identified by match to protein family HMM PF00155; match to protein family HMM PF01212.	Glutamate dehydrogenase, short peptide; Identified by match to protein family HMM PF00208; match to protein family HMM PF02812; Belongs to the Glu/Leu/Phe/Val dehydrogenases family.	0.908
SRU_0938	argG	SRU_0938	SRU_2214	Aspartate aminotransferase; Identified by match to protein family HMM PF00155; match to protein family HMM PF01212.	Argininosuccinate synthase; Identified by match to protein family HMM PF00764; match to protein family HMM TIGR00032; Belongs to the argininosuccinate synthase family. Type 1 subfamily.	0.925
SRU_0938	gdhA	SRU_0938	SRU_0505	Aspartate aminotransferase; Identified by match to protein family HMM PF00155; match to protein family HMM PF01212.	Glutamate dehydrogenase; Identified by similarity to SP:P96110; match to protein family HMM PF00208; match to protein family HMM PF02812; Belongs to the Glu/Leu/Phe/Val dehydrogenases family.	0.908
SRU_2217	SRU_2218	SRU_2217	SRU_2218	Aminotransferase, class III superfamily; Identified by match to protein family HMM PF00202; Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain family; Identified by match to protein family HMM PF00185; match to protein family HMM PF02729; Belongs to the aspartate/ornithine carbamoyltransferase superfamily.	0.997
SRU_2217	SRU_2220	SRU_2217	SRU_2220	Aminotransferase, class III superfamily; Identified by match to protein family HMM PF00202; Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.	Peptidase, M20A family; Identified by match to protein family HMM PF01546; match to protein family HMM PF07687.	0.951
SRU_2217	argB	SRU_2217	SRU_1732	Aminotransferase, class III superfamily; Identified by match to protein family HMM PF00202; Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.	Acetylglutamate kinase.	0.800
SRU_2217	argB-2	SRU_2217	SRU_2219	Aminotransferase, class III superfamily; Identified by match to protein family HMM PF00202; Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.	Acetylglutamate kinase; Catalyzes the ATP-dependent phosphorylation of N-acetyl-L- glutamate; Belongs to the acetylglutamate kinase family. ArgB subfamily.	0.991
SRU_2217	argG	SRU_2217	SRU_2214	Aminotransferase, class III superfamily; Identified by match to protein family HMM PF00202; Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.	Argininosuccinate synthase; Identified by match to protein family HMM PF00764; match to protein family HMM TIGR00032; Belongs to the argininosuccinate synthase family. Type 1 subfamily.	0.968
SRU_2217	argH	SRU_2217	SRU_2221	Aminotransferase, class III superfamily; Identified by match to protein family HMM PF00202; Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.	Argininosuccinate lyase; Identified by match to protein family HMM PF00206; match to protein family HMM TIGR00838.	0.953
SRU_2217	glnA	SRU_2217	SRU_0385	Aminotransferase, class III superfamily; Identified by match to protein family HMM PF00202; Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.	Glutamine synthetase, type I; Identified by match to protein family HMM PF00120; match to protein family HMM PF03951; match to protein family HMM TIGR00653.	0.518
SRU_2218	SRU_0666	SRU_2218	SRU_0666	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain family; Identified by match to protein family HMM PF00185; match to protein family HMM PF02729; Belongs to the aspartate/ornithine carbamoyltransferase superfamily.	Amidinotransferase superfamily; Identified by match to protein family HMM PF02274.	0.896
SRU_2218	SRU_2217	SRU_2218	SRU_2217	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain family; Identified by match to protein family HMM PF00185; match to protein family HMM PF02729; Belongs to the aspartate/ornithine carbamoyltransferase superfamily.	Aminotransferase, class III superfamily; Identified by match to protein family HMM PF00202; Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.	0.997
SRU_2218	SRU_2220	SRU_2218	SRU_2220	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain family; Identified by match to protein family HMM PF00185; match to protein family HMM PF02729; Belongs to the aspartate/ornithine carbamoyltransferase superfamily.	Peptidase, M20A family; Identified by match to protein family HMM PF01546; match to protein family HMM PF07687.	0.981
SRU_2218	argB	SRU_2218	SRU_1732	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain family; Identified by match to protein family HMM PF00185; match to protein family HMM PF02729; Belongs to the aspartate/ornithine carbamoyltransferase superfamily.	Acetylglutamate kinase.	0.807
SRU_2218	argB-2	SRU_2218	SRU_2219	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain family; Identified by match to protein family HMM PF00185; match to protein family HMM PF02729; Belongs to the aspartate/ornithine carbamoyltransferase superfamily.	Acetylglutamate kinase; Catalyzes the ATP-dependent phosphorylation of N-acetyl-L- glutamate; Belongs to the acetylglutamate kinase family. ArgB subfamily.	0.974
SRU_2218	argG	SRU_2218	SRU_2214	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain family; Identified by match to protein family HMM PF00185; match to protein family HMM PF02729; Belongs to the aspartate/ornithine carbamoyltransferase superfamily.	Argininosuccinate synthase; Identified by match to protein family HMM PF00764; match to protein family HMM TIGR00032; Belongs to the argininosuccinate synthase family. Type 1 subfamily.	0.995