(27 nodes) Base excision repair, and DNA ligase (ATP) activity network (Gordonia neofelifaecis)

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Known Interactions

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Predicted Interactions

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Your Input:
	EGD56924.1	DNA polymerase LigD; COG3285 Predicted eukaryotic-type DNA primase. (323 aa)
	ligA	NAD-dependent DNA ligase LigA; 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. (692 aa)
	EGD56990.1	Hypothetical protein. (201 aa)
	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. (225 aa)
	EGD56546.1	COG0708 Exonuclease III. (281 aa)
	EGD56587.1	Formamidopyrimidine-DNA glycosylase catalytic domain-containing protein; COG0266 Formamidopyrimidine-DNA glycosylase. (261 aa)
	EGD56588.1	DEAD/H associated domain-containing protein; COG1201 Lhr-like helicases. (1534 aa)
	EGD55593.1	DNA-(apurinic or apyrimidinic site) lyase; COG0266 Formamidopyrimidine-DNA glycosylase; Belongs to the FPG family. (231 aa)
	mutM	Formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil 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. (295 aa)
	EGD55629.1	COG0266 Formamidopyrimidine-DNA glycosylase. (53 aa)
	EGD55407.1	HhH-GPD family protein; COG1194 A/G-specific DNA glycosylase. (288 aa)
	EGD55470.1	3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase-like protein; COG0366 Glycosidases. (291 aa)
	EGD55076.1	Colicin V production protein; COG0265 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain. (400 aa)
	EGD55077.1	NUDIX hydrolase; COG0494 NTP pyrophosphohydrolases including oxidative damage repair enzymes. (268 aa)
	EGD55078.1	Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen; COG0526 Thiol-disulfide isomerase and thioredoxins. (230 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. (250 aa)
	EGD55080.1	Hypothetical protein. (84 aa)
	EGD54812.1	COG3285 Predicted eukaryotic-type DNA primase. (346 aa)
	ligC	COG1793 ATP-dependent DNA ligase. (358 aa)
	ku	Ku protein; 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. (290 aa)
	EGD54862.1	ATP-dependent DNA ligase; COG3285 Predicted eukaryotic-type DNA primase. (649 aa)
	EGD54645.1	COG0266 Formamidopyrimidine-DNA glycosylase; Belongs to the FPG family. (294 aa)
	EGD54247.1	Hypothetical protein; COG1055 Na+/H+ antiporter NhaD and related arsenite permeases. (390 aa)
	EGD54275.1	Exodeoxyribonuclease III Xth; COG0708 Exonuclease III. (294 aa)
	EGD53776.1	COG0648 Endonuclease IV. (255 aa)
	EGD53823.1	COG0708 Exonuclease III. (291 aa)
	ligB	COG1793 ATP-dependent DNA ligase. (514 aa)

Your Current Organism:

Gordonia neofelifaecis

NCBI taxonomy Id: 644548
Other names: G. neofelifaecis NRRL B-59395, Gordonia neofelifaecis AD-6, Gordonia neofelifaecis NRRL B-59395, Gordonia neofelifaecis str. NRRL B-59395, Gordonia neofelifaecis strain NRRL B-59395, Gordonia sp. AD-6

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
EGD53776.1	EGD53823.1	SCNU_16808	SCNU_17053	COG0648 Endonuclease IV.	COG0708 Exonuclease III.	0.881
EGD53776.1	EGD54275.1	SCNU_16808	SCNU_14841	COG0648 Endonuclease IV.	Exodeoxyribonuclease III Xth; COG0708 Exonuclease III.	0.885
EGD53776.1	EGD55470.1	SCNU_16808	SCNU_09431	COG0648 Endonuclease IV.	3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase-like protein; COG0366 Glycosidases.	0.531
EGD53776.1	EGD56546.1	SCNU_16808	SCNU_03307	COG0648 Endonuclease IV.	COG0708 Exonuclease III.	0.881
EGD53776.1	nth	SCNU_16808	SCNU_11136	COG0648 Endonuclease IV.	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.	0.870
EGD53776.1	ung	SCNU_16808	SCNU_01405	COG0648 Endonuclease IV.	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.	0.612
EGD53823.1	EGD53776.1	SCNU_17053	SCNU_16808	COG0708 Exonuclease III.	COG0648 Endonuclease IV.	0.881
EGD53823.1	EGD54275.1	SCNU_17053	SCNU_14841	COG0708 Exonuclease III.	Exodeoxyribonuclease III Xth; COG0708 Exonuclease III.	0.767
EGD53823.1	EGD54862.1	SCNU_17053	SCNU_11665	COG0708 Exonuclease III.	ATP-dependent DNA ligase; COG3285 Predicted eukaryotic-type DNA primase.	0.652
EGD53823.1	EGD55407.1	SCNU_17053	SCNU_09116	COG0708 Exonuclease III.	HhH-GPD family protein; COG1194 A/G-specific DNA glycosylase.	0.854
EGD53823.1	EGD55470.1	SCNU_17053	SCNU_09431	COG0708 Exonuclease III.	3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase-like protein; COG0366 Glycosidases.	0.730
EGD53823.1	EGD56546.1	SCNU_17053	SCNU_03307	COG0708 Exonuclease III.	COG0708 Exonuclease III.	0.821
EGD53823.1	ligB	SCNU_17053	SCNU_17430	COG0708 Exonuclease III.	COG1793 ATP-dependent DNA ligase.	0.626
EGD53823.1	ligC	SCNU_17053	SCNU_11410	COG0708 Exonuclease III.	COG1793 ATP-dependent DNA ligase.	0.626
EGD53823.1	nth	SCNU_17053	SCNU_11136	COG0708 Exonuclease III.	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.	0.910
EGD53823.1	ung	SCNU_17053	SCNU_01405	COG0708 Exonuclease III.	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.	0.778
EGD54275.1	EGD53776.1	SCNU_14841	SCNU_16808	Exodeoxyribonuclease III Xth; COG0708 Exonuclease III.	COG0648 Endonuclease IV.	0.885
EGD54275.1	EGD53823.1	SCNU_14841	SCNU_17053	Exodeoxyribonuclease III Xth; COG0708 Exonuclease III.	COG0708 Exonuclease III.	0.767
EGD54275.1	EGD54862.1	SCNU_14841	SCNU_11665	Exodeoxyribonuclease III Xth; COG0708 Exonuclease III.	ATP-dependent DNA ligase; COG3285 Predicted eukaryotic-type DNA primase.	0.652
EGD54275.1	EGD55407.1	SCNU_14841	SCNU_09116	Exodeoxyribonuclease III Xth; COG0708 Exonuclease III.	HhH-GPD family protein; COG1194 A/G-specific DNA glycosylase.	0.833

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