(14 nodes) Cyclic nucleotide-binding domain network (Dechloromonas aromatica)

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:
	Daro_1036	Cyclic nucleotide-binding protein. (245 aa)
	Daro_3546	Cyclic nucleotide-binding protein. (124 aa)
	Daro_3322	Cyclic nucleotide-binding protein. (495 aa)
	Daro_3649	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp. (222 aa)
	Daro_3904	Sulfate permease, SulP family; Cyclic nucleotide-binding:Sulfate transporter/antisigma-factor antagonist STAS:Xanthine/uracil/vitamin C permease:Sulphate transporter. (736 aa)
	Daro_3198	Transcriptional regulator, Crp/Fnr family. (231 aa)
	ackA-3	Acetate kinase; Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction; Belongs to the acetokinase family. (772 aa)
	Daro_1669	Transcriptional regulator, Crp/Fnr family. (233 aa)
	Daro_1635	Cyclic nucleotide-binding:CBS:Protein of unknown function DUF294, nucleotidyltransferase putative. (646 aa)
	Daro_1294	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp. (220 aa)
	Daro_1089	Transcriptional regulator, Crp/Fnr family. (218 aa)
	Daro_1047	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp. (247 aa)
	Daro_0925	Cyclic nucleotide-binding:Protein kinase. (454 aa)
	Daro_0248	Cyclic nucleotide-binding protein. (224 aa)

Your Current Organism:

Dechloromonas aromatica

NCBI taxonomy Id: 159087
Other names: D. aromatica RCB, Dechloromonas aromatica RCB, Dechloromonas aromatica str. RCB, Dechloromonas sp. RCB

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
Daro_0248	Daro_1036	Cyclic nucleotide-binding protein.	Cyclic nucleotide-binding protein.	0.464
Daro_0248	Daro_1089	Cyclic nucleotide-binding protein.	Transcriptional regulator, Crp/Fnr family.	0.537
Daro_0248	Daro_1294	Cyclic nucleotide-binding protein.	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	0.927
Daro_0248	Daro_3546	Cyclic nucleotide-binding protein.	Cyclic nucleotide-binding protein.	0.926
Daro_1036	Daro_0248	Cyclic nucleotide-binding protein.	Cyclic nucleotide-binding protein.	0.464
Daro_1036	Daro_1047	Cyclic nucleotide-binding protein.	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	0.525
Daro_1036	Daro_1089	Cyclic nucleotide-binding protein.	Transcriptional regulator, Crp/Fnr family.	0.638
Daro_1036	Daro_3649	Cyclic nucleotide-binding protein.	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	0.484
Daro_1047	Daro_1036	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	Cyclic nucleotide-binding protein.	0.525
Daro_1047	Daro_1669	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	Transcriptional regulator, Crp/Fnr family.	0.450
Daro_1047	Daro_3198	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	Transcriptional regulator, Crp/Fnr family.	0.492
Daro_1089	Daro_0248	Transcriptional regulator, Crp/Fnr family.	Cyclic nucleotide-binding protein.	0.537
Daro_1089	Daro_1036	Transcriptional regulator, Crp/Fnr family.	Cyclic nucleotide-binding protein.	0.638
Daro_1089	Daro_1294	Transcriptional regulator, Crp/Fnr family.	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	0.741
Daro_1089	Daro_1669	Transcriptional regulator, Crp/Fnr family.	Transcriptional regulator, Crp/Fnr family.	0.538
Daro_1089	Daro_3198	Transcriptional regulator, Crp/Fnr family.	Transcriptional regulator, Crp/Fnr family.	0.673
Daro_1089	Daro_3649	Transcriptional regulator, Crp/Fnr family.	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	0.415
Daro_1294	Daro_0248	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	Cyclic nucleotide-binding protein.	0.927
Daro_1294	Daro_1089	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	Transcriptional regulator, Crp/Fnr family.	0.741
Daro_1294	Daro_3546	Cyclic nucleotide-binding:Bacterial regulatory protein, Crp.	Cyclic nucleotide-binding protein.	0.960