Pden_1069 protein (Paracoccus denitrificans)

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:

Neighborhood

Gene Fusion

Cooccurrence

Coexpression

Experiments

Databases

Textmining

[Homology]

Score

Pden_1069

KEGG: aba:Acid345_1171 hypothetical protein. (140 aa)

Predicted Functional Partners:

Pden_1070

0.697

Pden_1068

0.504

Pden_0836

0.476

Pden_1071

0.449

Your Current Organism:

Paracoccus denitrificans

NCBI taxonomy Id: 318586
Other names: P. denitrificans PD1222, Paracoccus denitrificans PD1222

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
Pden_0836	Pden_1069	PFAM: beta-ketoacyl synthase; Thioesterase; acyl transferase domain protein; NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; phosphopantetheine-binding; KR; KEGG: sil:SPO0849 non-ribosomal peptide synthase.	KEGG: aba:Acid345_1171 hypothetical protein.	0.476
Pden_0836	Pden_1071	PFAM: beta-ketoacyl synthase; Thioesterase; acyl transferase domain protein; NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; phosphopantetheine-binding; KR; KEGG: sil:SPO0849 non-ribosomal peptide synthase.	PFAM: aminotransferase, class V; KEGG: bja:blr3095 probable aminotransferase.	0.503
Pden_1068	Pden_1069	PFAM: regulatory protein, MarR; KEGG: mlo:mlr2690 probable transcriptional regulator.	KEGG: aba:Acid345_1171 hypothetical protein.	0.504
Pden_1068	Pden_1070	PFAM: regulatory protein, MarR; KEGG: mlo:mlr2690 probable transcriptional regulator.	PFAM: regulatory proteins, IclR; KEGG: bja:bll3094 transcriptional regulatory protein.	0.469
Pden_1069	Pden_0836	KEGG: aba:Acid345_1171 hypothetical protein.	PFAM: beta-ketoacyl synthase; Thioesterase; acyl transferase domain protein; NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; phosphopantetheine-binding; KR; KEGG: sil:SPO0849 non-ribosomal peptide synthase.	0.476
Pden_1069	Pden_1068	KEGG: aba:Acid345_1171 hypothetical protein.	PFAM: regulatory protein, MarR; KEGG: mlo:mlr2690 probable transcriptional regulator.	0.504
Pden_1069	Pden_1070	KEGG: aba:Acid345_1171 hypothetical protein.	PFAM: regulatory proteins, IclR; KEGG: bja:bll3094 transcriptional regulatory protein.	0.697
Pden_1069	Pden_1071	KEGG: aba:Acid345_1171 hypothetical protein.	PFAM: aminotransferase, class V; KEGG: bja:blr3095 probable aminotransferase.	0.449
Pden_1070	Pden_1068	PFAM: regulatory proteins, IclR; KEGG: bja:bll3094 transcriptional regulatory protein.	PFAM: regulatory protein, MarR; KEGG: mlo:mlr2690 probable transcriptional regulator.	0.469
Pden_1070	Pden_1069	PFAM: regulatory proteins, IclR; KEGG: bja:bll3094 transcriptional regulatory protein.	KEGG: aba:Acid345_1171 hypothetical protein.	0.697
Pden_1070	Pden_1071	PFAM: regulatory proteins, IclR; KEGG: bja:bll3094 transcriptional regulatory protein.	PFAM: aminotransferase, class V; KEGG: bja:blr3095 probable aminotransferase.	0.432
Pden_1071	Pden_0836	PFAM: aminotransferase, class V; KEGG: bja:blr3095 probable aminotransferase.	PFAM: beta-ketoacyl synthase; Thioesterase; acyl transferase domain protein; NAD-dependent epimerase/dehydratase; short-chain dehydrogenase/reductase SDR; 3-beta hydroxysteroid dehydrogenase/isomerase; phosphopantetheine-binding; KR; KEGG: sil:SPO0849 non-ribosomal peptide synthase.	0.503
Pden_1071	Pden_1069	PFAM: aminotransferase, class V; KEGG: bja:blr3095 probable aminotransferase.	KEGG: aba:Acid345_1171 hypothetical protein.	0.449
Pden_1071	Pden_1070	PFAM: aminotransferase, class V; KEGG: bja:blr3095 probable aminotransferase.	PFAM: regulatory proteins, IclR; KEGG: bja:bll3094 transcriptional regulatory protein.	0.432