speA_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

Cooccurrence

Coexpression

Experiments

Databases

Textmining

[Homology]

Score

speA_1

Arginine decarboxylase. (462 aa)

Predicted Functional Partners:

speB

0.923

speA_2

0.867

tmk

0.863

argH

0.856

rocF

0.801

OPJ55042.1

0.775

dnaX_1

0.771

arcA

0.683

speE

0.677

OPJ57166.1

0.645

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
OPJ55042.1	dnaX_1	CLOTH_17070	CLOTH_17060	Hypothetical protein; PSP1 C-terminal conserved region.	DNA polymerase III subunit tau.	0.868
OPJ55042.1	speA_1	CLOTH_17070	CLOTH_17040	Hypothetical protein; PSP1 C-terminal conserved region.	Arginine decarboxylase.	0.775
OPJ55042.1	tmk	CLOTH_17070	CLOTH_17050	Hypothetical protein; PSP1 C-terminal conserved region.	Thymidylate kinase; Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis; Belongs to the thymidylate kinase family.	0.845
OPJ57166.1	speA_1	CLOTH_04490	CLOTH_17040	Methionine gamma-lyase.	Arginine decarboxylase.	0.645
OPJ57166.1	speA_2	CLOTH_04490	CLOTH_17390	Methionine gamma-lyase.	Arginine decarboxylase.	0.496
arcA	argH	CLOTH_19140	CLOTH_07980	Arginine deiminase.	Argininosuccinate lyase.	0.724
arcA	rocF	CLOTH_19140	CLOTH_11750	Arginine deiminase.	Arginase; Belongs to the arginase family.	0.506
arcA	speA_1	CLOTH_19140	CLOTH_17040	Arginine deiminase.	Arginine decarboxylase.	0.683
arcA	speA_2	CLOTH_19140	CLOTH_17390	Arginine deiminase.	Arginine decarboxylase.	0.677
arcA	speB	CLOTH_19140	CLOTH_05430	Arginine deiminase.	Agmatinase; Belongs to the arginase family.	0.506
argH	arcA	CLOTH_07980	CLOTH_19140	Argininosuccinate lyase.	Arginine deiminase.	0.724
argH	rocF	CLOTH_07980	CLOTH_11750	Argininosuccinate lyase.	Arginase; Belongs to the arginase family.	0.759
argH	speA_1	CLOTH_07980	CLOTH_17040	Argininosuccinate lyase.	Arginine decarboxylase.	0.856
argH	speA_2	CLOTH_07980	CLOTH_17390	Argininosuccinate lyase.	Arginine decarboxylase.	0.844
argH	speB	CLOTH_07980	CLOTH_05430	Argininosuccinate lyase.	Agmatinase; Belongs to the arginase family.	0.538
argH	speE	CLOTH_07980	CLOTH_05420	Argininosuccinate lyase.	Spermidine synthase; Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy-AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine.	0.453
dnaX_1	OPJ55042.1	CLOTH_17060	CLOTH_17070	DNA polymerase III subunit tau.	Hypothetical protein; PSP1 C-terminal conserved region.	0.868
dnaX_1	speA_1	CLOTH_17060	CLOTH_17040	DNA polymerase III subunit tau.	Arginine decarboxylase.	0.771
dnaX_1	tmk	CLOTH_17060	CLOTH_17050	DNA polymerase III subunit tau.	Thymidylate kinase; Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis; Belongs to the thymidylate kinase family.	0.855
rocF	arcA	CLOTH_11750	CLOTH_19140	Arginase; Belongs to the arginase family.	Arginine deiminase.	0.506