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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Metabolic Modeling Tutorial
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Escherichia coli K-12 substr. MG1655 Gene-Ontology-Terms Class: GO:0006281 - DNA repair

Definition: The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

Parent Classes:
GO:0006259 - DNA metabolic process ,
GO:0006974 - cellular response to DNA damage stimulus ,
GO:0044710 - single-organism metabolic process ,
GO:0044763 - single-organism cellular process

Child Classes:
GO:0000012 - single strand break repair (1) ,
GO:0000725 - recombinational repair (8) ,
GO:0000726 - non-recombinational repair (1) ,
GO:0006284 - base-excision repair (10) ,
GO:0006289 - nucleotide-excision repair (6) ,
GO:0006298 - mismatch repair (10) ,
GO:0006301 - postreplication repair (2) ,
GO:0006302 - double-strand break repair (6) ,
GO:0045004 - DNA replication proofreading (2)

Parts:
GO:0051103 - DNA ligation involved in DNA repair (2) ,
GO:0000731 - DNA synthesis involved in DNA repair (4) ,
GO:0006282 - regulation of DNA repair (1)

Term Members:
RNA ligase (rtcB) ,
30S ribosomal subunit protein S3 (rpsC) ,
DNA polymerase IV (Y-family DNA polymerase; translesion DNA synthesis) (dinB) ,
endonuclease VIII (nei) ,
regulatory protein RecX; inhibitor of RecA ,
DNA recombination protein (radA) ,
MutS ,
MutL ,
DNA polymerase II (polB) ,
adenine glycosylase; G.C --> T.A transversions (mutY) ,
ATP-dependent dsDNA exonuclease (sbcC) ,
exonuclease X (exoX) ,
stationary phase mismatch/uracil DNA glycosylase (mug) ,
Holliday junction nuclease; resolution of structures; repair (ruvC) ,
branch migration of Holliday structures; repair helicase (ruvB) ,
branch migration of Holliday structures; repair (ruvA) ,
recombination and repair (recR) ,
ssDNA and dsDNA binding, ATP binding (recF) ,
endonuclease IV (nfo) ,
DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway (vsr) ,
RecB ,
RecC ,
MutH ,
protein used in recombination and DNA repair (recN) ,
formamidopyrimidine DNA glycosylase (mutM) ,
RecD ,
3-methyl-adenine DNA glycosylase II, inducible (alkA) ,
SOS mutagenesis and repair (umuC) ,
ssDNA-binding protein (ssb) ,
5-hydroxy-CTP diphosphatase (nudG) ,
conserved protein (yegI) ,
RecJ ,
transcription termination/antitermination L factor (nusA) ,
dihydroneopterin triphosphate pyrophosphohydrolase (nudB) ,
periplasmic protein associated with repression of competance (ybaV) ,
multifunctional nuclease (cas1) ,
predicted acyltransferase with acyl-CoA N-acyltransferase domain (yafP) ,
ribosome-dependent mRNA interferase, toxin of the YafO-YafN toxin-antitoxin system ,
antitoxin of the YafO-YafN toxin-antitoxin system ,
endonuclease V (deoxyinosine 3'-endonuclease) (nfi) ,
ModF ,
transcription-repair coupling factor (mfd) ,
DNA ligase (ligB) ,
RecG DNA helicase ,
O6-alkylguanine-DNA-alkyltransferase (ogt) ,
endonuclease III; specific for apurinic and/or apyrimidinic sites (nth) ,
predicted transcription antitermination factor (yqgF) ,
exonuclease III (xthA) ,
8-oxo-dGTP diphosphatase (mutT) ,
exonuclease I, 3' --> 5' specific; deoxyribophosphodiesterase (sbcB) ,
DNA polymerase I, 5' --> 3' polymerase, 5' --> 3' and 3' --> 5' exonuclease (polA) ,
DNA base-flipping protein (atl) ,
DNA repair; excision nuclease subunit B (uvrB) ,
UvrD ,
excinuclease ABC, subunit C; repair of UV damage to DNA (uvrC) ,
deoxyribodipyrimidine photolyase (photoreactivation) (phr) ,
Ada DNA-binding transcriptional dual regulator ,
LexA ,
phosphoglycolate phosphatase (gph) ,
endonuclease of nucleotide excision repair (cho) ,
DNA damage-inducible protein I (dinI) ,
endodeoxyribonuclease RUS (Holliday junction resolvase) (rusA) ,
conserved protein regulated by LexA (yebG) ,
ATP-dependent helicase (dinG) ,
excision nuclease subunit A (uvrA) ,
uracil-DNA glycosylase (ung) ,
SOS mutagenesis; error-prone repair; processed to UmuD'; forms complex with UmuC ,
3-methyl-adenine DNA glycosylase I, constitutive (tag) ,
SOS cell division inhibitor (sulA) ,
ATP-dependent DNA helicase (recQ) ,
protein interacts with RecR and possibly RecF proteins (recO) ,
DNA strand exchange and recombination protein with protease and nuclease activity (recA) ,
DNA ligase ,
AlkB repair system for alkylated DNA and RNA

Unification Links: GO:0006281


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, BIOCYC13B.