(9 nodes) Bacterial extracellular solute-binding protein 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:
	A361_25560	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+. (409 aa)
	A361_06335	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (428 aa)
	A361_07280	Cyclodextrin-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (430 aa)
	A361_08165	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (431 aa)
	A361_11210	Sugar ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (416 aa)
	A361_11510	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (437 aa)
	A361_13220	Hypothetical protein; Frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology. (357 aa)
	A361_14725	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (361 aa)
	A361_25395	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (492 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 annotation	node2 annotation	score
A361_06335	A361_11510	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.913
A361_06335	A361_25395	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.541
A361_11210	A361_25395	Sugar ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.554
A361_11510	A361_06335	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.913
A361_25395	A361_06335	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.541
A361_25395	A361_11210	ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Sugar ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.554