Lrub_0484 protein (Legionella rubrilucens) - STRING interaction network

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

Lrub_0484

Eukaryotic DNA topoisomerase I, catalytic core. (348 aa)

Predicted Functional Partners:

ykoU

0.856

rnhB

0.835

recQ

0.827

parE

0.783

gyrB

0.783

dnaN

0.740

ykoV

0.719

phaB_1

0.672

Lrub_0488

0.622

Lrub_0129

0.620

Your Current Organism:

Legionella rubrilucens

NCBI taxonomy Id: 458
Other names: ATCC 35304, CCUG 29671, CIP 103848, DSM 11884, JCM 7565, L. rubrilucens, NCTC 11987, strain WA-270A-C2

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
Lrub_0129	Lrub_0484	Lrub_0129	Lrub_0484	Peptide chain release factor.	Eukaryotic DNA topoisomerase I, catalytic core.	0.620
Lrub_0484	Lrub_0129	Lrub_0484	Lrub_0129	Eukaryotic DNA topoisomerase I, catalytic core.	Peptide chain release factor.	0.620
Lrub_0484	Lrub_0488	Lrub_0484	Lrub_0488	Eukaryotic DNA topoisomerase I, catalytic core.	Hypothetical protein.	0.622
Lrub_0484	dnaN	Lrub_0484	Lrub_2673	Eukaryotic DNA topoisomerase I, catalytic core.	DNA polymerase III, beta chain; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of r [...]	0.740
Lrub_0484	gyrB	Lrub_0484	Lrub_2675	Eukaryotic DNA topoisomerase I, catalytic core.	DNA gyrase, subunit B (type II topoisomerase); A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP [...]	0.783
Lrub_0484	parE	Lrub_0484	Lrub_1097	Eukaryotic DNA topoisomerase I, catalytic core.	DNA topoisomerase IV subunit B; Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule; Belongs to the type II topoisomerase family. ParE type 1 subfamily.	0.783
Lrub_0484	phaB_1	Lrub_0484	Lrub_0487	Eukaryotic DNA topoisomerase I, catalytic core.	Acetyoacetyl CoA reductase.	0.672
Lrub_0484	recQ	Lrub_0484	Lrub_2290	Eukaryotic DNA topoisomerase I, catalytic core.	ATP-dependent DNA helicase RecQ.	0.827
Lrub_0484	rnhB	Lrub_0484	Lrub_0441	Eukaryotic DNA topoisomerase I, catalytic core.	Ribonuclease HII; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.	0.835
Lrub_0484	ykoU	Lrub_0484	Lrub_1889	Eukaryotic DNA topoisomerase I, catalytic core.	Putative ATP-dependent DNA ligase YkoU.	0.856
Lrub_0484	ykoV	Lrub_0484	Lrub_1888	Eukaryotic DNA topoisomerase I, catalytic core.	Putative DNA repair protein YkoV; With LigD forms a non-homologous end joining (NHEJ) DNA repair enzyme, which repairs dsDNA breaks with reduced fidelity. Binds linear dsDNA with 5'- and 3'- overhangs but not closed circular dsDNA nor ssDNA. Recruits and stimulates the ligase activity of LigD. Belongs to the prokaryotic Ku family.	0.719
Lrub_0488	Lrub_0484	Lrub_0488	Lrub_0484	Hypothetical protein.	Eukaryotic DNA topoisomerase I, catalytic core.	0.622
Lrub_0488	phaB_1	Lrub_0488	Lrub_0487	Hypothetical protein.	Acetyoacetyl CoA reductase.	0.758
dnaN	Lrub_0484	Lrub_2673	Lrub_0484	DNA polymerase III, beta chain; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of r [...]	Eukaryotic DNA topoisomerase I, catalytic core.	0.740
dnaN	gyrB	Lrub_2673	Lrub_2675	DNA polymerase III, beta chain; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of r [...]	DNA gyrase, subunit B (type II topoisomerase); A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP [...]	0.850
dnaN	parE	Lrub_2673	Lrub_1097	DNA polymerase III, beta chain; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of r [...]	DNA topoisomerase IV subunit B; Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule; Belongs to the type II topoisomerase family. ParE type 1 subfamily.	0.595
dnaN	recQ	Lrub_2673	Lrub_2290	DNA polymerase III, beta chain; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of r [...]	ATP-dependent DNA helicase RecQ.	0.842
dnaN	rnhB	Lrub_2673	Lrub_0441	DNA polymerase III, beta chain; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of r [...]	Ribonuclease HII; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.	0.891
dnaN	ykoU	Lrub_2673	Lrub_1889	DNA polymerase III, beta chain; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of r [...]	Putative ATP-dependent DNA ligase YkoU.	0.914
gyrB	Lrub_0484	Lrub_2675	Lrub_0484	DNA gyrase, subunit B (type II topoisomerase); A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP [...]	Eukaryotic DNA topoisomerase I, catalytic core.	0.783