(22 nodes) Homologous recombination network (Actinoplanes sp. SE50110)

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:
	dnaN	DNA polymerase III subunit beta; 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 [...] (377 aa)
	recF	DNA replication and repair protein recF; The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP; Belongs to the RecF family. (376 aa)
	ssb	Single-stranded DNA-binding protein. (215 aa)
	ACPL_1392	DNA polymerase III, delta subunit. (327 aa)
	recO	DNA repair protein recO; Involved in DNA repair and RecF pathway recombination. (240 aa)
	ACPL_1659	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex. (603 aa)
	dnaE-2	DNA polymerase III, alpha subunit. (1176 aa)
	polA	DNA polymerase I; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family. (899 aa)
	ACPL_1946	DNA polymerase I - 3'-5' exonuclease and polymerase domains. (546 aa)
	holB	DNA polymerase III subunit delta; ATPase involved in DNA replication. (394 aa)
	recD	Exodeoxyribonuclease V alpha subunit; DNA-dependent ATPase and ATP-dependent 5'-3' DNA helicase. Has no activity on blunt DNA or DNA with 3'-overhangs, requires at least 10 bases of 5'-ssDNA for helicase activity; Belongs to the RecD family. RecD-like subfamily. (732 aa)
	ssb-2	Single-stranded DNA-binding protein. (164 aa)
	priA	Primosomal protein N' (replication factor Y) (superfamily II helicase); Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA; Belongs to the helicase family. PriA subfamily. (734 aa)
	ruvB	Holliday junction DNA helicase RuvB; The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. (348 aa)
	ruvA	Holliday junction ATP-dependent DNA helicase ruvA; The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB. (200 aa)
	ruvC	Holliday junction resolvase; Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group. (175 aa)
	dnaQ	DNA polymerase III, alpha subunit (gram-positive type). (401 aa)
	recA	Recombinase A; Can catalyze the hydrolysis of ATP in the presence of single- stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage; Belongs to the RecA family. (361 aa)
	recG	RecG-like helicase. (726 aa)
	recR	Recombination protein recR; May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO. (197 aa)
	dnaZ	DNA polymerase III, gamma/tau subunits. (1175 aa)
	ssb-3	Single-stranded DNA-binding protein. (190 aa)

Your Current Organism:

Actinoplanes sp. SE50110

NCBI taxonomy Id: 134676
Other names: A. sp. SE50/110, Actinoplanes sp. (strain 50/110), Actinoplanes sp. 50/110, Actinoplanes sp. SE50/110

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
ACPL_1392	ACPL_1659	ACPL_1392	ACPL_1659	DNA polymerase III, delta subunit.	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	0.958
ACPL_1392	dnaE-2	ACPL_1392	ACPL_1776	DNA polymerase III, delta subunit.	DNA polymerase III, alpha subunit.	0.993
ACPL_1392	dnaN	ACPL_1392	ACPL_117	DNA polymerase III, delta subunit.	DNA polymerase III subunit beta; 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 [...]	0.993
ACPL_1392	dnaQ	ACPL_1392	ACPL_6692	DNA polymerase III, delta subunit.	DNA polymerase III, alpha subunit (gram-positive type).	0.960
ACPL_1392	dnaZ	ACPL_1392	ACPL_8134	DNA polymerase III, delta subunit.	DNA polymerase III, gamma/tau subunits.	0.993
ACPL_1392	holB	ACPL_1392	ACPL_496	DNA polymerase III, delta subunit.	DNA polymerase III subunit delta; ATPase involved in DNA replication.	0.995
ACPL_1392	polA	ACPL_1392	ACPL_1827	DNA polymerase III, delta subunit.	DNA polymerase I; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.590
ACPL_1392	priA	ACPL_1392	ACPL_6465	DNA polymerase III, delta subunit.	Primosomal protein N' (replication factor Y) (superfamily II helicase); Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA; Belongs to the helicase family. PriA subfamily.	0.449
ACPL_1392	recO	ACPL_1392	ACPL_1420	DNA polymerase III, delta subunit.	DNA repair protein recO; Involved in DNA repair and RecF pathway recombination.	0.592
ACPL_1392	ssb	ACPL_1392	ACPL_1290	DNA polymerase III, delta subunit.	Single-stranded DNA-binding protein.	0.495
ACPL_1659	ACPL_1392	ACPL_1659	ACPL_1392	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	DNA polymerase III, delta subunit.	0.958
ACPL_1659	ACPL_1946	ACPL_1659	ACPL_1946	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	DNA polymerase I - 3'-5' exonuclease and polymerase domains.	0.506
ACPL_1659	dnaE-2	ACPL_1659	ACPL_1776	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	DNA polymerase III, alpha subunit.	0.954
ACPL_1659	dnaN	ACPL_1659	ACPL_117	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	DNA polymerase III subunit beta; 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 [...]	0.945
ACPL_1659	dnaQ	ACPL_1659	ACPL_6692	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	DNA polymerase III, alpha subunit (gram-positive type).	0.955
ACPL_1659	dnaZ	ACPL_1659	ACPL_8134	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	DNA polymerase III, gamma/tau subunits.	0.953
ACPL_1659	holB	ACPL_1659	ACPL_496	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	DNA polymerase III subunit delta; ATPase involved in DNA replication.	0.961
ACPL_1659	polA	ACPL_1659	ACPL_1827	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	DNA polymerase I; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.928
ACPL_1659	priA	ACPL_1659	ACPL_6465	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	Primosomal protein N' (replication factor Y) (superfamily II helicase); Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA; Belongs to the helicase family. PriA subfamily.	0.426
ACPL_1659	recA	ACPL_1659	ACPL_7172	DNA polymerase III subunit epsilon; Nuclease subunit of the excinuclease complex.	Recombinase A; Can catalyze the hydrolysis of ATP in the presence of single- stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage; Belongs to the RecA family.	0.601