cobD_1 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

cobD_1

Threonine-phosphate decarboxylase. (360 aa)

Predicted Functional Partners:

cobQ

0.968

cbiB

0.955

pduX

0.891

cobD_2

0.884

OPJ57056.1

0.735

yvqK

0.700

nasF

0.689

aroC

0.656

aroA1

0.651

cobT

0.629

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
OPJ57056.1	cobD_1	CLOTH_03380	CLOTH_01100	Putative GTP cyclohydrolase 1 type 2; Belongs to the GTP cyclohydrolase I type 2/NIF3 family.	Threonine-phosphate decarboxylase.	0.735
OPJ57056.1	cobD_2	CLOTH_03380	CLOTH_11520	Putative GTP cyclohydrolase 1 type 2; Belongs to the GTP cyclohydrolase I type 2/NIF3 family.	Threonine-phosphate decarboxylase.	0.735
aroA1	aroC	CLOTH_01220	CLOTH_01200	3-phosphoshikimate 1-carboxyvinyltransferase 1; Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate.	Chorismate synthase; Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system.	0.999
aroA1	cobD_1	CLOTH_01220	CLOTH_01100	3-phosphoshikimate 1-carboxyvinyltransferase 1; Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate.	Threonine-phosphate decarboxylase.	0.651
aroA1	cobD_2	CLOTH_01220	CLOTH_11520	3-phosphoshikimate 1-carboxyvinyltransferase 1; Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate.	Threonine-phosphate decarboxylase.	0.600
aroC	aroA1	CLOTH_01200	CLOTH_01220	Chorismate synthase; Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system.	3-phosphoshikimate 1-carboxyvinyltransferase 1; Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate.	0.999
aroC	cobD_1	CLOTH_01200	CLOTH_01100	Chorismate synthase; Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system.	Threonine-phosphate decarboxylase.	0.656
aroC	cobD_2	CLOTH_01200	CLOTH_11520	Chorismate synthase; Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system.	Threonine-phosphate decarboxylase.	0.606
cbiB	cobD_1	CLOTH_11540	CLOTH_01100	Cobalamin biosynthesis protein CbiB; Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group.	Threonine-phosphate decarboxylase.	0.955
cbiB	cobD_2	CLOTH_11540	CLOTH_11520	Cobalamin biosynthesis protein CbiB; Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group.	Threonine-phosphate decarboxylase.	0.992
cbiB	cobQ	CLOTH_11540	CLOTH_20350	Cobalamin biosynthesis protein CbiB; Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group.	Cobyric acid synthase; Catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation. Belongs to the CobB/CobQ family. CobQ subfamily.	0.991
cbiB	cobT	CLOTH_11540	CLOTH_11800	Cobalamin biosynthesis protein CbiB; Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group.	Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase; Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB).	0.885
cbiB	nasF	CLOTH_11540	CLOTH_11460	Cobalamin biosynthesis protein CbiB; Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group.	uroporphyrinogen-III C-methyltransferase.	0.875
cbiB	pduX	CLOTH_11540	CLOTH_11510	Cobalamin biosynthesis protein CbiB; Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group.	L-threonine kinase.	0.862
cbiB	yvqK	CLOTH_11540	CLOTH_01110	Cobalamin biosynthesis protein CbiB; Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group.	Cob(I)yrinic acid a,c-diamide adenosyltransferase; Belongs to the Cob(I)alamin adenosyltransferase family.	0.874
cobD_1	OPJ57056.1	CLOTH_01100	CLOTH_03380	Threonine-phosphate decarboxylase.	Putative GTP cyclohydrolase 1 type 2; Belongs to the GTP cyclohydrolase I type 2/NIF3 family.	0.735
cobD_1	aroA1	CLOTH_01100	CLOTH_01220	Threonine-phosphate decarboxylase.	3-phosphoshikimate 1-carboxyvinyltransferase 1; Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate.	0.651
cobD_1	aroC	CLOTH_01100	CLOTH_01200	Threonine-phosphate decarboxylase.	Chorismate synthase; Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system.	0.656
cobD_1	cbiB	CLOTH_01100	CLOTH_11540	Threonine-phosphate decarboxylase.	Cobalamin biosynthesis protein CbiB; Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group.	0.955
cobD_1	cobD_2	CLOTH_01100	CLOTH_11520	Threonine-phosphate decarboxylase.	Threonine-phosphate decarboxylase.	0.884