cpu_04720 protein (Carboxydothermus pertinax)

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

cpu_04720

Radical SAM domain-containing protein. (432 aa)

Predicted Functional Partners:

cpu_04710

0.569

ribBA

0.567

cpu_04730

0.545

cpu_06470

0.538

cpu_04740

0.530

cpu_22140

0.488

cpu_07570

0.486

cpu_01990

0.485

cpu_11040

0.472

cpu_13660

0.424

Your Current Organism:

Carboxydothermus pertinax

NCBI taxonomy Id: 870242
Other names: C. pertinax, Carboxydothermus pertinax Yoneda et al. 2012, Carboxydothermus sp. Ug1, DSM 23698, NBRC 107576, strain Ug1

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
cpu_01990	cpu_04720	cpu_01990	cpu_04720	Hypothetical protein.	Radical SAM domain-containing protein.	0.485
cpu_01990	cpu_06470	cpu_01990	cpu_06470	Hypothetical protein.	Hypothetical protein.	0.698
cpu_01990	cpu_11040	cpu_01990	cpu_11040	Hypothetical protein.	Hypothetical protein.	0.438
cpu_01990	cpu_22140	cpu_01990	cpu_22140	Hypothetical protein.	Zinc/iron-chelating domain-containing protein.	0.613
cpu_04710	cpu_04720	cpu_04710	cpu_04720	Hydrolase.	Radical SAM domain-containing protein.	0.569
cpu_04720	cpu_01990	cpu_04720	cpu_01990	Radical SAM domain-containing protein.	Hypothetical protein.	0.485
cpu_04720	cpu_04710	cpu_04720	cpu_04710	Radical SAM domain-containing protein.	Hydrolase.	0.569
cpu_04720	cpu_04730	cpu_04720	cpu_04730	Radical SAM domain-containing protein.	phenylacetate--CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	0.545
cpu_04720	cpu_04740	cpu_04720	cpu_04740	Radical SAM domain-containing protein.	Amino acid-binding protein.	0.530
cpu_04720	cpu_06470	cpu_04720	cpu_06470	Radical SAM domain-containing protein.	Hypothetical protein.	0.538
cpu_04720	cpu_07570	cpu_04720	cpu_07570	Radical SAM domain-containing protein.	Sensor domain-containing diguanylate cyclase.	0.486
cpu_04720	cpu_11040	cpu_04720	cpu_11040	Radical SAM domain-containing protein.	Hypothetical protein.	0.472
cpu_04720	cpu_13660	cpu_04720	cpu_13660	Radical SAM domain-containing protein.	Hypothetical protein.	0.424
cpu_04720	cpu_22140	cpu_04720	cpu_22140	Radical SAM domain-containing protein.	Zinc/iron-chelating domain-containing protein.	0.488
cpu_04720	ribBA	cpu_04720	cpu_22250	Radical SAM domain-containing protein.	3,4-dihydroxy-2-butanone-4-phosphate synthase; 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.	0.567
cpu_04730	cpu_04720	cpu_04730	cpu_04720	phenylacetate--CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	Radical SAM domain-containing protein.	0.545
cpu_04730	cpu_04740	cpu_04730	cpu_04740	phenylacetate--CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	Amino acid-binding protein.	0.966
cpu_04740	cpu_04720	cpu_04740	cpu_04720	Amino acid-binding protein.	Radical SAM domain-containing protein.	0.530
cpu_04740	cpu_04730	cpu_04740	cpu_04730	Amino acid-binding protein.	phenylacetate--CoA ligase; Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).	0.966
cpu_06470	cpu_01990	cpu_06470	cpu_01990	Hypothetical protein.	Hypothetical protein.	0.698