ycgR 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

ycgR

Flagellar brake protein YcgR. (215 aa)

Predicted Functional Partners:

flhF

0.945

cheB

0.932

fliN

0.930

cheA

0.929

cheW_1

0.917

motB

0.910

OPJ56055.1

0.906

fliM

0.897

OPJ57090.1

0.896

pomA

0.895

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
OPJ56055.1	OPJ57090.1	CLOTH_12330	CLOTH_03730	FlgN protein.	Flagellar hook-length control protein FliK.	0.921
OPJ56055.1	cheA	CLOTH_12330	CLOTH_03930	FlgN protein.	Chemotaxis protein CheA.	0.645
OPJ56055.1	cheW_1	CLOTH_12330	CLOTH_03940	FlgN protein.	Chemotaxis protein CheW.	0.643
OPJ56055.1	flhF	CLOTH_12330	CLOTH_03890	FlgN protein.	Flagellar biosynthesis protein FlhF.	0.459
OPJ56055.1	fliM	CLOTH_12330	CLOTH_03800	FlgN protein.	Flagellar motor switch protein FliM.	0.851
OPJ56055.1	fliN	CLOTH_12330	CLOTH_03810	FlgN protein.	Flagellar motor switch protein FliN.	0.890
OPJ56055.1	motB	CLOTH_12330	CLOTH_03780	FlgN protein.	Motility protein B.	0.754
OPJ56055.1	pomA	CLOTH_12330	CLOTH_03770	FlgN protein.	Chemotaxis protein PomA.	0.737
OPJ56055.1	ycgR	CLOTH_12330	CLOTH_03910	FlgN protein.	Flagellar brake protein YcgR.	0.906
OPJ57090.1	OPJ56055.1	CLOTH_03730	CLOTH_12330	Flagellar hook-length control protein FliK.	FlgN protein.	0.921
OPJ57090.1	cheA	CLOTH_03730	CLOTH_03930	Flagellar hook-length control protein FliK.	Chemotaxis protein CheA.	0.847
OPJ57090.1	cheB	CLOTH_03730	CLOTH_03920	Flagellar hook-length control protein FliK.	Chemotaxis response regulator protein-glutamate methylesterase; Involved in chemotaxis. Part of a chemotaxis signal transduction system that modulates chemotaxis in response to various stimuli. Catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins or MCP) by CheR. Also mediates the irreversible deamidation of specific glutamine residues to glutamic acid. Belongs to the CheB family.	0.810
OPJ57090.1	cheW_1	CLOTH_03730	CLOTH_03940	Flagellar hook-length control protein FliK.	Chemotaxis protein CheW.	0.769
OPJ57090.1	flhF	CLOTH_03730	CLOTH_03890	Flagellar hook-length control protein FliK.	Flagellar biosynthesis protein FlhF.	0.928
OPJ57090.1	fliM	CLOTH_03730	CLOTH_03800	Flagellar hook-length control protein FliK.	Flagellar motor switch protein FliM.	0.988
OPJ57090.1	fliN	CLOTH_03730	CLOTH_03810	Flagellar hook-length control protein FliK.	Flagellar motor switch protein FliN.	0.996
OPJ57090.1	motB	CLOTH_03730	CLOTH_03780	Flagellar hook-length control protein FliK.	Motility protein B.	0.931
OPJ57090.1	pomA	CLOTH_03730	CLOTH_03770	Flagellar hook-length control protein FliK.	Chemotaxis protein PomA.	0.917
OPJ57090.1	ycgR	CLOTH_03730	CLOTH_03910	Flagellar hook-length control protein FliK.	Flagellar brake protein YcgR.	0.896
cheA	OPJ56055.1	CLOTH_03930	CLOTH_12330	Chemotaxis protein CheA.	FlgN protein.	0.645