(10 nodes) Base excision repair network (Thioploca ingrica)

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:
	ung	uracil-DNA glycosylase; Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. (221 aa)
	THII_1245	single-stranded-DNA-specific exonuclease RecJ. (584 aa)
	polA	DNA-directed DNA polymerase; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family. (910 aa)
	THII_1458	Endonuclease/exonuclease/phosphatase. (258 aa)
	nth	Endonuclease III; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate. (218 aa)
	mutM	formamidopyrimidine-DNA glycosylase; Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. (271 aa)
	THII_2966	Endonuclease/exonuclease/phosphatase. (257 aa)
	ligA	NAD-dependent DNA ligase; DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double- stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA; Belongs to the NAD-dependent DNA ligase family. LigA subfamily. (671 aa)
	THII_3866	A/G-specific adenine glycosylase; Adenine glycosylase active on G-A mispairs. (355 aa)
	THII_3896	Phage SPO1 DNA polymerase-related protein. (255 aa)

Your Current Organism:

Thioploca ingrica

NCBI taxonomy Id: 40754
Other names: T. ingrica

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
THII_1245	polA	THII_1245	THII_1270	single-stranded-DNA-specific exonuclease RecJ.	DNA-directed DNA polymerase; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.461
THII_1458	THII_2966	THII_1458	THII_2966	Endonuclease/exonuclease/phosphatase.	Endonuclease/exonuclease/phosphatase.	0.923
THII_1458	THII_3866	THII_1458	THII_3866	Endonuclease/exonuclease/phosphatase.	A/G-specific adenine glycosylase; Adenine glycosylase active on G-A mispairs.	0.732
THII_1458	nth	THII_1458	THII_2415	Endonuclease/exonuclease/phosphatase.	Endonuclease III; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.925
THII_1458	polA	THII_1458	THII_1270	Endonuclease/exonuclease/phosphatase.	DNA-directed DNA polymerase; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.920
THII_1458	ung	THII_1458	THII_0101	Endonuclease/exonuclease/phosphatase.	uracil-DNA glycosylase; Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.	0.654
THII_2966	THII_1458	THII_2966	THII_1458	Endonuclease/exonuclease/phosphatase.	Endonuclease/exonuclease/phosphatase.	0.923
THII_2966	THII_3866	THII_2966	THII_3866	Endonuclease/exonuclease/phosphatase.	A/G-specific adenine glycosylase; Adenine glycosylase active on G-A mispairs.	0.732
THII_2966	nth	THII_2966	THII_2415	Endonuclease/exonuclease/phosphatase.	Endonuclease III; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.983
THII_2966	polA	THII_2966	THII_1270	Endonuclease/exonuclease/phosphatase.	DNA-directed DNA polymerase; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.920
THII_2966	ung	THII_2966	THII_0101	Endonuclease/exonuclease/phosphatase.	uracil-DNA glycosylase; Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.	0.654
THII_3866	THII_1458	THII_3866	THII_1458	A/G-specific adenine glycosylase; Adenine glycosylase active on G-A mispairs.	Endonuclease/exonuclease/phosphatase.	0.732
THII_3866	THII_2966	THII_3866	THII_2966	A/G-specific adenine glycosylase; Adenine glycosylase active on G-A mispairs.	Endonuclease/exonuclease/phosphatase.	0.732
THII_3866	mutM	THII_3866	THII_2806	A/G-specific adenine glycosylase; Adenine glycosylase active on G-A mispairs.	formamidopyrimidine-DNA glycosylase; Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.	0.474
THII_3866	polA	THII_3866	THII_1270	A/G-specific adenine glycosylase; Adenine glycosylase active on G-A mispairs.	DNA-directed DNA polymerase; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.402
ligA	polA	THII_3208	THII_1270	NAD-dependent DNA ligase; DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double- stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA; Belongs to the NAD-dependent DNA ligase family. LigA subfamily.	DNA-directed DNA polymerase; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.676
mutM	THII_3866	THII_2806	THII_3866	formamidopyrimidine-DNA glycosylase; Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.	A/G-specific adenine glycosylase; Adenine glycosylase active on G-A mispairs.	0.474
mutM	nth	THII_2806	THII_2415	formamidopyrimidine-DNA glycosylase; Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.	Endonuclease III; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.645
mutM	polA	THII_2806	THII_1270	formamidopyrimidine-DNA glycosylase; Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.	DNA-directed DNA polymerase; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.977
nth	THII_1458	THII_2415	THII_1458	Endonuclease III; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	Endonuclease/exonuclease/phosphatase.	0.925