paaD protein (Rhodopseudomonas palustris CGA009)

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.

Knowledge-based Evidence

from curated databases

textmining

Assay-based Predictions

experimentally determined

co-expression

Genomic Predictions

gene neighborhood

gene co-occurrence

gene fusions

Your Input:

Neighborhood

Gene Fusion

Cooccurrence

Coexpression

Experiments

Databases

Textmining

[Homology]

Score

paaD

Putative phenylacetic acid degradation protein PaaD. (167 aa)

Predicted Functional Partners:

RPA3764

0.999

paaC

0.999

paaB

0.999

paaA

0.999

paaI

0.992

paaK

0.971

RPA1758

0.967

paaG1

0.953

RPA1229

0.934

RPA1725

0.932

Your Current Organism:

Rhodopseudomonas palustris CGA009

NCBI taxonomy Id: 258594
Other names: R. palustris CGA009, Rhodopseudomonas palustris str. CGA009, Rhodopseudomonas palustris strain CGA009

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
RPA1229	RPA1725	RPA1229	RPA1725	Probable aerobic phenylacetate-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.455
RPA1229	RPA3764	RPA1229	RPA3764	Probable aerobic phenylacetate-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	Putative 2Fe:2S ferredoxin; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.931
RPA1229	paaA	RPA1229	RPA3768	Probable aerobic phenylacetate-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	Phenylacetic acid degradation protein paaA; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.943
RPA1229	paaB	RPA1229	RPA3767	Probable aerobic phenylacetate-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	Phenylacetic acid degradation protein paaB; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.931
RPA1229	paaC	RPA1229	RPA3766	Probable aerobic phenylacetate-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	Phenylacetic acid degradation protein paaC; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.934
RPA1229	paaD	RPA1229	RPA3765	Probable aerobic phenylacetate-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	Putative phenylacetic acid degradation protein PaaD.	0.934
RPA1229	paaI	RPA1229	RPA1724	Probable aerobic phenylacetate-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	Putative phenylacetic acid degredation protein.	0.960
RPA1229	paaK	RPA1229	RPA1723	Probable aerobic phenylacetate-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	phenylacetyl-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	0.904
RPA1725	RPA1229	RPA1725	RPA1229	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Probable aerobic phenylacetate-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	0.455
RPA1725	RPA1758	RPA1725	RPA1758	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Putative enoyl-CoA hydratase paaG; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.963
RPA1725	RPA3764	RPA1725	RPA3764	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Putative 2Fe:2S ferredoxin; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.915
RPA1725	paaA	RPA1725	RPA3768	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Phenylacetic acid degradation protein paaA; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.934
RPA1725	paaB	RPA1725	RPA3767	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Phenylacetic acid degradation protein paaB; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.906
RPA1725	paaC	RPA1725	RPA3766	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Phenylacetic acid degradation protein paaC; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.921
RPA1725	paaD	RPA1725	RPA3765	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Putative phenylacetic acid degradation protein PaaD.	0.932
RPA1725	paaG1	RPA1725	RPA0484	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Putative enoyl-CoA hydratase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished; Belongs to the enoyl-CoA hydratase/isomerase family.	0.963
RPA1725	paaI	RPA1725	RPA1724	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Putative phenylacetic acid degredation protein.	0.936
RPA1725	paaK	RPA1725	RPA1723	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	phenylacetyl-CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	0.748
RPA1758	RPA1725	RPA1758	RPA1725	Putative enoyl-CoA hydratase paaG; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Putative aldehyde dehydrogenase; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.963
RPA1758	RPA3764	RPA1758	RPA3764	Putative enoyl-CoA hydratase paaG; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	Putative 2Fe:2S ferredoxin; Observed by proteomics; Citation: Proteomics from VerBerkmoes et al. (2003) unpublished.	0.941