fadH3 protein (Bifidobacterium dentium) - STRING interaction network

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

fadH3

fadD3 Long-chain-fatty-acid--CoA ligase. (664 aa)

Predicted Functional Partners:

fas

0.905

BDP_1047

0.823

fadD1

0.816

BDP_0300

0.815

fadD

0.808

def

0.807

BDP_1205

0.538

pyrH

0.520

rrf

0.503

rplE

0.478

Your Current Organism:

Bifidobacterium dentium

NCBI taxonomy Id: 401473
Other names: B. dentium Bd1, Bifidobacterium dentium Bd1, Bifidobacterium dentium str. Bd1, Bifidobacterium dentium strain Bd1

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
BDP_0300	BDP_1047	BDP_0300	BDP_1047	Alpha/beta fold family hydrolase membrane associated protein.	Long-chain-fatty acid CoA ligase.	0.815
BDP_0300	fadD	BDP_0300	BDP_1917	Alpha/beta fold family hydrolase membrane associated protein.	long-chain-fatty-acid--CoA ligase.	0.815
BDP_0300	fadD1	BDP_0300	BDP_1209	Alpha/beta fold family hydrolase membrane associated protein.	fadD1 Long-chain-fatty-acid--CoA ligase.	0.815
BDP_0300	fadH3	BDP_0300	BDP_1204	Alpha/beta fold family hydrolase membrane associated protein.	fadD3 Long-chain-fatty-acid--CoA ligase.	0.815
BDP_1047	BDP_0300	BDP_1047	BDP_0300	Long-chain-fatty acid CoA ligase.	Alpha/beta fold family hydrolase membrane associated protein.	0.815
BDP_1047	fadD	BDP_1047	BDP_1917	Long-chain-fatty acid CoA ligase.	long-chain-fatty-acid--CoA ligase.	0.815
BDP_1047	fadD1	BDP_1047	BDP_1209	Long-chain-fatty acid CoA ligase.	fadD1 Long-chain-fatty-acid--CoA ligase.	0.815
BDP_1047	fadH3	BDP_1047	BDP_1204	Long-chain-fatty acid CoA ligase.	fadD3 Long-chain-fatty-acid--CoA ligase.	0.823
BDP_1047	fas	BDP_1047	BDP_0362	Long-chain-fatty acid CoA ligase.	Fatty acid synthase Fas.	0.905
BDP_1047	rplE	BDP_1047	BDP_0443	Long-chain-fatty acid CoA ligase.	rplE 50S ribosomal protein L5; This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.	0.478
BDP_1205	def	BDP_1205	BDP_1203	Conserved hypothetical protein.	Def Peptide deformylase; Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.	0.493
BDP_1205	fadH3	BDP_1205	BDP_1204	Conserved hypothetical protein.	fadD3 Long-chain-fatty-acid--CoA ligase.	0.538
BDP_1205	pyrH	BDP_1205	BDP_1199	Conserved hypothetical protein.	PyrH Uridylate kinase; Catalyzes the reversible phosphorylation of UMP to UDP.	0.455
def	BDP_1205	BDP_1203	BDP_1205	Def Peptide deformylase; Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.	Conserved hypothetical protein.	0.493
def	fadH3	BDP_1203	BDP_1204	Def Peptide deformylase; Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.	fadD3 Long-chain-fatty-acid--CoA ligase.	0.807
def	pyrH	BDP_1203	BDP_1199	Def Peptide deformylase; Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.	PyrH Uridylate kinase; Catalyzes the reversible phosphorylation of UMP to UDP.	0.545
def	rplE	BDP_1203	BDP_0443	Def Peptide deformylase; Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.	rplE 50S ribosomal protein L5; This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.	0.645
def	rrf	BDP_1203	BDP_1198	Def Peptide deformylase; Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.	Ribosome Recycling Factor (RRF); Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another; Belongs to the RRF family.	0.595
fadD	BDP_0300	BDP_1917	BDP_0300	long-chain-fatty-acid--CoA ligase.	Alpha/beta fold family hydrolase membrane associated protein.	0.815
fadD	BDP_1047	BDP_1917	BDP_1047	long-chain-fatty-acid--CoA ligase.	Long-chain-fatty acid CoA ligase.	0.815