rpfG_3 protein (Clostridium thermoalcaliphilum)

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

Co-occurrence

Co-expression

Experiments

Databases

Textmining

[Homology]

Score

rpfG_3

Cyclic di-GMP phosphodiesterase response regulator RpfG. (827 aa)

Predicted Functional Partners:

kinE

0.981

OPJ56036.1

0.973

OPJ55297.1

0.948

cph2

0.942

ydaM_1

0.931

gmr

0.887

ribBA

0.873

OPJ55298.1

0.847

ydaM_2

0.789

guaA

0.781

Your Current Organism:

Clostridium thermoalcaliphilum

NCBI taxonomy Id: 29349
Other names: ATCC 51508, CIP 105528, DSM 7309, [. thermoalcaliphilum, [Clostridium] thermoalcaliphilum, strain JW/YL23-2

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
OPJ55297.1	OPJ55298.1	CLOTH_16000	CLOTH_16010	GH3 auxin-responsive promoter.	Hypothetical protein.	0.842
OPJ55297.1	rpfG_3	CLOTH_16000	CLOTH_15990	GH3 auxin-responsive promoter.	Cyclic di-GMP phosphodiesterase response regulator RpfG.	0.948
OPJ55298.1	OPJ55297.1	CLOTH_16010	CLOTH_16000	Hypothetical protein.	GH3 auxin-responsive promoter.	0.842
OPJ55298.1	rpfG_3	CLOTH_16010	CLOTH_15990	Hypothetical protein.	Cyclic di-GMP phosphodiesterase response regulator RpfG.	0.847
OPJ56036.1	cph2	CLOTH_12140	CLOTH_14430	Blue-light-activated protein.	Phytochrome-like protein cph2.	0.982
OPJ56036.1	gmr	CLOTH_12140	CLOTH_17900	Blue-light-activated protein.	Cyclic di-GMP phosphodiesterase Gmr.	0.995
OPJ56036.1	guaA	CLOTH_12140	CLOTH_11700	Blue-light-activated protein.	GMP synthase; Catalyzes the synthesis of GMP from XMP.	0.689
OPJ56036.1	kinE	CLOTH_12140	CLOTH_12130	Blue-light-activated protein.	Sporulation kinase E.	0.999
OPJ56036.1	ribBA	CLOTH_12140	CLOTH_14300	Blue-light-activated protein.	Riboflavin biosynthesis protein RibBA; Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate; In the C-terminal section; belongs to the GTP cyclohydrolase II family.	0.933
OPJ56036.1	rpfG_3	CLOTH_12140	CLOTH_15990	Blue-light-activated protein.	Cyclic di-GMP phosphodiesterase response regulator RpfG.	0.973
OPJ56036.1	ydaM_1	CLOTH_12140	CLOTH_10170	Blue-light-activated protein.	Putative diguanylate cyclase YdaM.	0.997
OPJ56036.1	ydaM_2	CLOTH_12140	CLOTH_14220	Blue-light-activated protein.	Putative diguanylate cyclase YdaM.	0.980
cph2	OPJ56036.1	CLOTH_14430	CLOTH_12140	Phytochrome-like protein cph2.	Blue-light-activated protein.	0.982
cph2	gmr	CLOTH_14430	CLOTH_17900	Phytochrome-like protein cph2.	Cyclic di-GMP phosphodiesterase Gmr.	0.994
cph2	kinE	CLOTH_14430	CLOTH_12130	Phytochrome-like protein cph2.	Sporulation kinase E.	0.979
cph2	ribBA	CLOTH_14430	CLOTH_14300	Phytochrome-like protein cph2.	Riboflavin biosynthesis protein RibBA; Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate; In the C-terminal section; belongs to the GTP cyclohydrolase II family.	0.731
cph2	rpfG_3	CLOTH_14430	CLOTH_15990	Phytochrome-like protein cph2.	Cyclic di-GMP phosphodiesterase response regulator RpfG.	0.942
cph2	ydaM_1	CLOTH_14430	CLOTH_10170	Phytochrome-like protein cph2.	Putative diguanylate cyclase YdaM.	0.998
cph2	ydaM_2	CLOTH_14430	CLOTH_14220	Phytochrome-like protein cph2.	Putative diguanylate cyclase YdaM.	0.984
gmr	OPJ56036.1	CLOTH_17900	CLOTH_12140	Cyclic di-GMP phosphodiesterase Gmr.	Blue-light-activated protein.	0.995