(6 nodes) Xylose metabolism, and Monosaccharide binding network (Betaproteobacteria bacterium GR1643)

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:
	xylB	Xylulokinase; Derived by automated computational analysis using gene prediction method: Protein Homology. (487 aa)
	xylA	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family. (431 aa)
	xylA-2	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family. (430 aa)
	APV48671.1	D-xylose ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (354 aa)
	APV48672.1	Sugar ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the binding-protein-dependent transport system permease family. (401 aa)
	APV48673.1	ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (257 aa)

Your Current Organism:

Betaproteobacteria bacterium GR1643

NCBI taxonomy Id: 1904640
Other names: B. bacterium GR16-43, Betaproteobacteria bacterium GR16-43, Nnibrrimonas geomnyongensis

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
APV48671.1	APV48672.1	BWI17_02615	BWI17_02620	D-xylose ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Sugar ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the binding-protein-dependent transport system permease family.	0.997
APV48671.1	APV48673.1	BWI17_02615	BWI17_02625	D-xylose ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.996
APV48671.1	xylA	BWI17_02615	BWI17_02605	D-xylose ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	0.854
APV48671.1	xylA-2	BWI17_02615	BWI17_02610	D-xylose ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	0.884
APV48671.1	xylB	BWI17_02615	BWI17_02600	D-xylose ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Xylulokinase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.859
APV48672.1	APV48671.1	BWI17_02620	BWI17_02615	Sugar ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the binding-protein-dependent transport system permease family.	D-xylose ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.997
APV48672.1	APV48673.1	BWI17_02620	BWI17_02625	Sugar ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the binding-protein-dependent transport system permease family.	ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.996
APV48672.1	xylA	BWI17_02620	BWI17_02605	Sugar ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the binding-protein-dependent transport system permease family.	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	0.786
APV48672.1	xylA-2	BWI17_02620	BWI17_02610	Sugar ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the binding-protein-dependent transport system permease family.	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	0.822
APV48672.1	xylB	BWI17_02620	BWI17_02600	Sugar ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the binding-protein-dependent transport system permease family.	Xylulokinase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.845
APV48673.1	APV48671.1	BWI17_02625	BWI17_02615	ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	D-xylose ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.996
APV48673.1	APV48672.1	BWI17_02625	BWI17_02620	ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Sugar ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the binding-protein-dependent transport system permease family.	0.996
APV48673.1	xylA	BWI17_02625	BWI17_02605	ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	0.724
APV48673.1	xylA-2	BWI17_02625	BWI17_02610	ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	0.770
APV48673.1	xylB	BWI17_02625	BWI17_02600	ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Xylulokinase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.812
xylA	APV48671.1	BWI17_02605	BWI17_02615	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	D-xylose ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.854
xylA	APV48672.1	BWI17_02605	BWI17_02620	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	Sugar ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the binding-protein-dependent transport system permease family.	0.786
xylA	APV48673.1	BWI17_02605	BWI17_02625	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.724
xylA	xylA-2	BWI17_02605	BWI17_02610	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	0.966
xylA	xylB	BWI17_02605	BWI17_02600	Xylose isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the xylose isomerase family.	Xylulokinase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.996