rob_4 protein (Clostridium saccharobutylicum)

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

rob_4

Right origin-binding protein. (290 aa)

Predicted Functional Partners:

AQS01739.1

0.893

rpoA

0.831

rhaS_4

0.778

rpoB

0.738

sigA

0.738

rpoC

0.730

rpoZ

0.726

rhaS_2

0.722

adaA

0.685

soxS_2

0.675

Your Current Organism:

Clostridium saccharobutylicum

NCBI taxonomy Id: 169679
Other names: ATCC BAA-117, C. saccharobutylicum, Clostridium saccharobutylicum Keis et al. 2001, DSM 13864, strain NCP 262

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
AQS01739.1	rob_4	CSACC_35700	CSACC_35690	Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase.	Right origin-binding protein.	0.893
adaA	rhaS_4	CSACC_16880	CSACC_21740	Bifunctional transcriptional activator/DNA repair enzyme AdaA.	HTH-type transcriptional activator RhaS.	0.784
adaA	rob_4	CSACC_16880	CSACC_35690	Bifunctional transcriptional activator/DNA repair enzyme AdaA.	Right origin-binding protein.	0.685
adaA	rpoA	CSACC_16880	CSACC_02300	Bifunctional transcriptional activator/DNA repair enzyme AdaA.	DNA-directed RNA polymerase subunit alpha; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.477
adaA	soxS_2	CSACC_16880	CSACC_31360	Bifunctional transcriptional activator/DNA repair enzyme AdaA.	Regulatory protein SoxS.	0.654
rhaS_2	rob_4	CSACC_18250	CSACC_35690	HTH-type transcriptional activator RhaS.	Right origin-binding protein.	0.722
rhaS_2	rpoA	CSACC_18250	CSACC_02300	HTH-type transcriptional activator RhaS.	DNA-directed RNA polymerase subunit alpha; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.477
rhaS_2	soxS_2	CSACC_18250	CSACC_31360	HTH-type transcriptional activator RhaS.	Regulatory protein SoxS.	0.455
rhaS_4	adaA	CSACC_21740	CSACC_16880	HTH-type transcriptional activator RhaS.	Bifunctional transcriptional activator/DNA repair enzyme AdaA.	0.784
rhaS_4	rob_4	CSACC_21740	CSACC_35690	HTH-type transcriptional activator RhaS.	Right origin-binding protein.	0.778
rhaS_4	rpoA	CSACC_21740	CSACC_02300	HTH-type transcriptional activator RhaS.	DNA-directed RNA polymerase subunit alpha; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.483
rhaS_4	sigA	CSACC_21740	CSACC_11010	HTH-type transcriptional activator RhaS.	RNA polymerase sigma factor SigA; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.	0.576
rhaS_4	soxS_2	CSACC_21740	CSACC_31360	HTH-type transcriptional activator RhaS.	Regulatory protein SoxS.	0.772
rob_4	AQS01739.1	CSACC_35690	CSACC_35700	Right origin-binding protein.	Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase.	0.893
rob_4	adaA	CSACC_35690	CSACC_16880	Right origin-binding protein.	Bifunctional transcriptional activator/DNA repair enzyme AdaA.	0.685
rob_4	rhaS_2	CSACC_35690	CSACC_18250	Right origin-binding protein.	HTH-type transcriptional activator RhaS.	0.722
rob_4	rhaS_4	CSACC_35690	CSACC_21740	Right origin-binding protein.	HTH-type transcriptional activator RhaS.	0.778
rob_4	rpoA	CSACC_35690	CSACC_02300	Right origin-binding protein.	DNA-directed RNA polymerase subunit alpha; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.831
rob_4	rpoB	CSACC_35690	CSACC_01940	Right origin-binding protein.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.738
rob_4	rpoC	CSACC_35690	CSACC_01950	Right origin-binding protein.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.730