(24 nodes) NagB/RpiA transferase-like network (Clostridium estertheticum)

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:
	APC40218.1	DNA-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (251 aa)
	APC40224.1	3-oxoacid CoA-transferase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the 3-oxoacid CoA-transferase family. (526 aa)
	APC40737.1	4-hydroxybutyrate CoA-transferase; Derived by automated computational analysis using gene prediction method: Protein Homology. (436 aa)
	APC42672.1	acetyl-CoA hydrolase; Derived by automated computational analysis using gene prediction method: Protein Homology. (507 aa)
	APC42673.1	4-hydroxybutyrate CoA-transferase; Derived by automated computational analysis using gene prediction method: Protein Homology. (432 aa)
	APC41797.1	5-formyltetrahydrofolate cyclo-ligase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the 5-formyltetrahydrofolate cyclo-ligase family. (193 aa)
	nagB	Glucosamine-6-phosphate deaminase; Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion. (241 aa)
	APC42085.1	Cro/Cl family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology. (344 aa)
	APC42247.1	DeoR family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology. (253 aa)
	APC38641.1	DeoR family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology. (253 aa)
	APC39143.1	Branched-chain amino acid dehydrogenase; Derived by automated computational analysis using gene prediction method: Protein Homology. (238 aa)
	APC38978.1	Acyl CoA:acetate/3-ketoacid CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the 3-oxoacid CoA-transferase family. (516 aa)
	APC38976.1	Acyl CoA:acetate/3-ketoacid CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the 3-oxoacid CoA-transferase family. (517 aa)
	APC38974.1	Acyl CoA:acetate/3-ketoacid CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the 3-oxoacid CoA-transferase family. (519 aa)
	APC39144.1	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology. (219 aa)
	APC39211.1	Citrate lyase subunit alpha; Derived by automated computational analysis using gene prediction method: Protein Homology. (513 aa)
	APC39330.1	Branched-chain amino acid dehydrogenase; Derived by automated computational analysis using gene prediction method: Protein Homology. (217 aa)
	APC39331.1	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology. (219 aa)
	APC39403.1	DeoR family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology. (251 aa)
	APC39437.1	DeoR family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology. (252 aa)
	APC39960.1	DeoR family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology. (253 aa)
	APC40019.1	Citrate lyase subunit alpha; Derived by automated computational analysis using gene prediction method: Protein Homology. (512 aa)
	APC40180.1	RNA polymerase subunit sigma-70; Derived by automated computational analysis using gene prediction method: Protein Homology. (311 aa)
	APC40207.1	Transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology. (327 aa)

Your Current Organism:

Clostridium estertheticum

NCBI taxonomy Id: 1552
Other names: C. estertheticum subsp. estertheticum, Clostridium estertheticum subsp. estertheticum

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
APC39143.1	APC39144.1	A7L45_03215	A7L45_03220	Branched-chain amino acid dehydrogenase; Derived by automated computational analysis using gene prediction method: Protein Homology.	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
APC39143.1	APC39331.1	A7L45_03215	A7L45_04285	Branched-chain amino acid dehydrogenase; Derived by automated computational analysis using gene prediction method: Protein Homology.	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.997
APC39144.1	APC39143.1	A7L45_03220	A7L45_03215	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Branched-chain amino acid dehydrogenase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
APC39144.1	APC39330.1	A7L45_03220	A7L45_04280	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Branched-chain amino acid dehydrogenase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
APC39144.1	APC39331.1	A7L45_03220	A7L45_04285	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.903
APC39211.1	APC40019.1	A7L45_03610	A7L45_08035	Citrate lyase subunit alpha; Derived by automated computational analysis using gene prediction method: Protein Homology.	Citrate lyase subunit alpha; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.902
APC39330.1	APC39144.1	A7L45_04280	A7L45_03220	Branched-chain amino acid dehydrogenase; Derived by automated computational analysis using gene prediction method: Protein Homology.	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
APC39330.1	APC39331.1	A7L45_04280	A7L45_04285	Branched-chain amino acid dehydrogenase; Derived by automated computational analysis using gene prediction method: Protein Homology.	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
APC39331.1	APC39143.1	A7L45_04285	A7L45_03215	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Branched-chain amino acid dehydrogenase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.997
APC39331.1	APC39144.1	A7L45_04285	A7L45_03220	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.903
APC39331.1	APC39330.1	A7L45_04285	A7L45_04280	succinyl-CoA--3-ketoacid-CoA transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Branched-chain amino acid dehydrogenase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
APC40019.1	APC39211.1	A7L45_08035	A7L45_03610	Citrate lyase subunit alpha; Derived by automated computational analysis using gene prediction method: Protein Homology.	Citrate lyase subunit alpha; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.902
APC40737.1	APC42673.1	A7L45_11930	A7L45_11975	4-hydroxybutyrate CoA-transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	4-hydroxybutyrate CoA-transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.901
APC42672.1	APC42673.1	A7L45_11965	A7L45_11975	acetyl-CoA hydrolase; Derived by automated computational analysis using gene prediction method: Protein Homology.	4-hydroxybutyrate CoA-transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.576
APC42673.1	APC40737.1	A7L45_11975	A7L45_11930	4-hydroxybutyrate CoA-transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	4-hydroxybutyrate CoA-transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.901
APC42673.1	APC42672.1	A7L45_11975	A7L45_11965	4-hydroxybutyrate CoA-transferase; Derived by automated computational analysis using gene prediction method: Protein Homology.	acetyl-CoA hydrolase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.576