(9 nodes) Pre-ATP-grasp domain superfamily network (Bacillus oceanisediminis)

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:
	purD	Phosphoribosylamine--glycine ligase; Catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the GARS family. (422 aa)
	A361_23095	Glutathionylspermidine synthase; Derived by automated computational analysis using gene prediction method: Protein Homology. (414 aa)
	A361_20200	acetyl-CoA carboxylase biotin carboxylase subunit; This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA. (450 aa)
	carB-2	Carbamoyl phosphate synthase large subunit; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the CarB family. (1070 aa)
	A361_09125	Biotin carboxylase; Derived by automated computational analysis using gene prediction method: Protein Homology. (447 aa)
	A361_08940	Pyruvate carboxylase; Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second. (1146 aa)
	carB	Carbamoyl phosphate synthase large subunit; Derived by automated computational analysis using gene prediction method: Protein Homology. (1041 aa)
	ddl	D-alanine--D-alanine ligase A; Cell wall formation; Belongs to the D-alanine--D-alanine ligase family. (358 aa)
	purK	5-(carboxyamino)imidazole ribonucleotide synthase; Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR). (382 aa)

Your Current Organism:

Bacillus oceanisediminis

NCBI taxonomy Id: 1196031
Other names: B. oceanisediminis 2691, Bacillus oceanisediminis 2691

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
A361_08940	A361_09125	A361_08940	A361_09125	Pyruvate carboxylase; Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second.	Biotin carboxylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.491
A361_08940	A361_20200	A361_08940	A361_20200	Pyruvate carboxylase; Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second.	acetyl-CoA carboxylase biotin carboxylase subunit; This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA.	0.483
A361_09125	A361_08940	A361_09125	A361_08940	Biotin carboxylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Pyruvate carboxylase; Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second.	0.491
A361_09125	A361_20200	A361_09125	A361_20200	Biotin carboxylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	acetyl-CoA carboxylase biotin carboxylase subunit; This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA.	0.905
A361_20200	A361_08940	A361_20200	A361_08940	acetyl-CoA carboxylase biotin carboxylase subunit; This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA.	Pyruvate carboxylase; Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second.	0.483
A361_20200	A361_09125	A361_20200	A361_09125	acetyl-CoA carboxylase biotin carboxylase subunit; This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA.	Biotin carboxylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.905
carB	carB-2	A361_07420	A361_09350	Carbamoyl phosphate synthase large subunit; Derived by automated computational analysis using gene prediction method: Protein Homology.	Carbamoyl phosphate synthase large subunit; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the CarB family.	0.904
carB	purD	A361_07420	A361_01905	Carbamoyl phosphate synthase large subunit; Derived by automated computational analysis using gene prediction method: Protein Homology.	Phosphoribosylamine--glycine ligase; Catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the GARS family.	0.562
carB-2	carB	A361_09350	A361_07420	Carbamoyl phosphate synthase large subunit; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the CarB family.	Carbamoyl phosphate synthase large subunit; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.904
carB-2	purD	A361_09350	A361_01905	Carbamoyl phosphate synthase large subunit; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the CarB family.	Phosphoribosylamine--glycine ligase; Catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the GARS family.	0.565
purD	carB	A361_01905	A361_07420	Phosphoribosylamine--glycine ligase; Catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the GARS family.	Carbamoyl phosphate synthase large subunit; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.562
purD	carB-2	A361_01905	A361_09350	Phosphoribosylamine--glycine ligase; Catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the GARS family.	Carbamoyl phosphate synthase large subunit; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the CarB family.	0.565
purD	purK	A361_01905	A361_01855	Phosphoribosylamine--glycine ligase; Catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the GARS family.	5-(carboxyamino)imidazole ribonucleotide synthase; Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR).	0.981
purK	purD	A361_01855	A361_01905	5-(carboxyamino)imidazole ribonucleotide synthase; Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR).	Phosphoribosylamine--glycine ligase; Catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the GARS family.	0.981