Genomic Tools

OG ID	OG function	Label	Gene	Product	COG	PFAM short name	KO
3NIMU	it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box) 5'-TTATC CA A CA A-3'. DnaA binds to ATP and to acidic phospholipids	ACIAD0001	dnaA	Chromosomal replication initiator protein dnaA	COG0593	Bac_DnaA, Bac_DnaA_C, DnaA_N	K02313
3NJI0	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	ACIAD0002	dnaN	DNA polymerase III, beta chain	COG0592	DNA_pol3_beta, DNA_pol3_beta_2, DNA_pol3_beta_3	K02338
3NKN9	it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP	ACIAD0003	recF	DNA replication, recombinaison and repair protein	COG1195	SMC_N	K03629
3NJZQ	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-dependent manner	ACIAD0004	gyrB	DNA gyrase, subunit B (type II topoisomerase)	COG0187	DNA_gyraseB, DNA_gyraseB_C, HATPase_c, Toprim	K02470
3NKHK	Transposase DDE domain	ACIAD0057		fragment of transposase (part 1)		DDE_Tnp_1_3
3NKHK	Transposase DDE domain	ACIAD0058		fragment of transposase (part 2)		DDE_Tnp_1_3
3NKHK	Transposase DDE domain	ACIAD0059		fragment of transposase (part 3)		DDE_Tnp_1_3
1RQSR	cog cog2801	ACIAD0134		fragment of transposase		HTH_21, rve
3NJFR	nucleotide-binding protein involved in DNA uptake	ACIAD0209		putative Rossmann-fold nucleotide-binding protein involved in DNA uptake (Smf)	COG0758	DNA_processg_A	K04096
3NJQG	Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII	ACIAD0225	dinP	DNA polymerase IV, devoid of proofreading, damage-inducible protein P	COG0389	IMS, IMS_C, IMS_HHH	K02346
3NIU5	Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule	ACIAD0234	parC	DNA topoisomerase IV, subunit A	COG0188	DNA_gyraseA_C, DNA_topoisoIV	K02621
3NJQR	D12 class N6 adenine-specific DNA methyltransferase	ACIAD0248		putative DNA modification methylase (Adenine-specific methyltransferase)	COG3392	MethyltransfD12	K07318
3NNGG	DNA polymerase III, chi subunit	ACIAD0252	holC	DNA polymerase III, chi subunit	COG2927	DNA_pol3_chi	K02339
3NIZW	NUDIX domain	ACIAD0275	aspP	adenosine diphosphate sugar pyrophosphatase (ADP-ribose pyrophosphatase)	COG0494	NUDIX	K01515
3NNW1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD0320		transposase of IS1236, IS3 family (ORF 1)		HTH_Tnp_1
3NKN1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD0321		transposase of IS1236, IS3 family (ORF 2)		HTH_21, rve
3NIZV	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision	ACIAD0340	uvrC	excinuclease ABC subunit C; UvrC with UvrAB is a DNA excision repair enzyme	COG0322	GIY-YIG, UVR, UvrC_HhH_N	K03703
3NKZK	2OG-Fe(II) oxygenase superfamily	ACIAD0345	alkB	DNA repair system specific for alkylated DNA		2OG-FeII_Oxy_2
3NN70	Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA	ACIAD0352	yqgF	holliday junction resolvase yqgF-like	COG0816	RuvX	K07447
3NJAU	May be involved in recombinational repair of damaged DNA	ACIAD0354	recN	DNA repair protein RecN	COG0497	SMC_N	K03631
3NJ6N	DNA helicase	ACIAD0379		putative DNA helicase		AAA_19, UvrD_C
3NM1F	A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit recognizes the wild- type Chi sequence, and when added to isolated RecB increases its ATP-dependent helicase processivity	ACIAD0397	recC	exonuclease V, gamma chain	COG1330	Exonuc_V_gamma	K03583
3NIUR	A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit contributes ATPase, 3'-5' helicase, exonuclease activity and loads RecA onto ssDNA	ACIAD0398	recB	exonuclease V, beta chain	COG1074	PDDEXK_1, UvrD-helicase, UvrD_C	K03582
3NIKV	A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD	ACIAD0399	recD	exonuclease V, alpha subunit	COG0507	AAA_30, UvrD_C_2	K03581
3NJI2	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	ACIAD0409	priA	primosomal protein N' (= factor Y) directs replication fork assembly at D-loops, ATP-dependent.	COG1198	ResIII	K04066
3NIK9	Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage	ACIAD0455	nudH	(di)nucleoside polyphosphate hydrolase (Ap5A pyrophosphatase)	COG0494	NUDIX	K08311
3NJWY	Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone	ACIAD0493	topA	DNA topoisomerase type I, omega protein	COG0550, COG0551, COG1754	Topo_Zn_Ribbon, Topoisom_bac, Toprim, zf-C4_Topoisom	K03168
3NKBE	UvrD-like helicase C-terminal domain	ACIAD0495		putative ATP-dependent DNA helicase (PcrA)	COG0210	UvrD-helicase, UvrD_C	K03657
3NIEC	NUDIX domain	ACIAD0674		putative MutT/nudix family protein		NUDIX
3NM1X	Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. Repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme. This is a suicide reaction the enzyme is irreversibly inactivated	ACIAD0692	ogt	methylated-DNA--protein-cysteine methyltransferase (6-O- methylguanine-DNA methyltransferase) (O-6-methylguanine-DNA- alkyltransferase)	COG0350	DNA_binding_1, Methyltransf_1N	K00567
3NKR9	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	ACIAD0707	mutM	formamidopyrimidine-DNA glycosylase	COG0266	Fapy_DNA_glyco, H2TH, zf-FPG_IleRS	K10563
3NNRI	NUDIX domain	ACIAD0720		putative MutT/nudix family protein		NUDIX
3NIX0	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	ACIAD0848	ligA	DNA ligase	COG0272	BRCT, DNA_ligase_OB, DNA_ligase_ZBD, DNA_ligase_aden, HHH_2, HHH_5	K01972
3NKQE	it can initiate unwinding at a nick in the DNA. It binds to the single-stranded DNA and acts in a progressive fashion along the DNA in the 3' to 5' direction	ACIAD0900	rep	ATP-dependent DNA helicase	COG0210	UvrD-helicase, UvrD_C	K03656
3NJ9P	Putative exonuclease SbcCD, C subunit	ACIAD0916	sbcC	ATP-dependent dsDNA exonuclease (Suppression of recBC)	COG0419	AAA_23, SbcCD_C	K03546
3NKS4	SbcCD cleaves DNA hairpin structures. These structures can inhibit DNA replication and are intermediates in certain DNA recombination reactions. The complex acts as a 3'- 5' double strand exonuclease that can open hairpins. It also has a 5' single-strand endonuclease activity	ACIAD0917	sbcD	ATP-dependent dsDNA exonuclease (Suppression of recBC)	COG0420	Metallophos, SbcD_C	K03547
3NKN1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD0952		transposase of IS1236, IS3 family (ORF 2)		HTH_21, rve
3NNW1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD0953		transposase of IS1236, IS3 family (ORF 1)		HTH_Tnp_1
3NKN1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD0957		transposase of IS1236, IS3 family (ORF 2)		HTH_21, rve
3NNW1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD0958		transposase of IS1236, IS3 family (ORF 1)		HTH_Tnp_1
3NKBU	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	ACIAD1108	nth	endonuclease III DNA glycosylase/apyrimidinic (AP) lyase	COG0177	EndIII_4Fe-2S, HhH-GPD	K10773
3NP49	Belongs to the UPF0102 family	ACIAD1132		conserved hypothetical protein	COG0792	UPF0102	K07460
3NJQ4	NADH pyrophosphatase zinc ribbon domain	ACIAD1135	nudC	NADH pyrophosphatase (NUDIX hydrolase family)	COG2816	NUDIX, zf-NADH-PPase	K03426
3NKVD	Endonuclease that specifically degrades the RNA of RNA- DNA hybrids	ACIAD1137	rnhA-dnaQ	bifunctional protein [Includes: ribonuclease HI; DNA polymerase III ,epsilon subunit, 3-5 exonucleolytic proofreading function]	COG0847, COG0328	RNase_H, RNase_T	K14159
3NJ5Q	Trims short 3' overhangs of a variety of RNA species, leaving a one or two nucleotide 3' overhang. Responsible for the end-turnover of tRNA specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A). Also appears to be involved in tRNA biosynthesis	ACIAD1149	rnt	ribonuclease T (degrades tRNA , has exonuclease and ssDNAse activity)	COG0847	RNase_T	K03683
3NJ70	Domain of unknown function (DUF4130	ACIAD1171		conserved hypothetical protein		DUF4130
3NJJE	DNA photolyase	ACIAD1182	phrB	deoxyribodipyrimidine photolyase (photoreactivation), FAD-binding	COG0415	DNA_photolyase, FAD_binding_7	K01669
3NJ52	Endonuclease that specifically degrades the RNA of RNA- DNA hybrids	ACIAD1248	rnhB	RNAse HII	COG0164	RNase_HII	K03470
3NKN1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD1249		transposase of IS1236, IS3 family (ORF 2)		HTH_21, rve
3NNW1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD1250		transposase of IS1236, IS3 family (ORF 1)		HTH_Tnp_1
3NIY4	DEAD-box RNA helicase involved in RNA degradation. Has RNA-dependent ATPase activity and unwinds double-stranded RNA	ACIAD1314	rhlB	ATP-dependent RNA helicase (DEAD box)	COG0513	DEAD, Helicase_C	K03732
3NNGX	Protein tyrosine kinase	ACIAD1336		putative kinase		Pkinase
3NIMT	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	ACIAD1385	recA	DNA strand exchange and recombination protein with protease and nuclease activity.	COG0468	RecA	K03553
3NJUH	Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site	ACIAD1395	mfd	transcription-repair coupling protein	COG1197	CarD_CdnL_TRCF, DEAD, Helicase_C, TRCF	K03723
3NNVG	Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions	ACIAD1408	hupB	DNA-binding protein HU-beta	COG0776	Bac_DNA_binding	K03530
3NK8D	that it carries out the mismatch recognition step. This protein has a weak ATPase activity	ACIAD1500	mutS	methyl-directed mismatch repair, recognize exocyclic adducts of guanosine	COG0249	MutS_I, MutS_II, MutS_III, MutS_IV, MutS_V	K03555
3NJHA	Arm DNA-binding domain	ACIAD1501		hypothetical protein		Arm-DNA-bind_3, Phage_integrase
3NTR4	DDE superfamily endonuclease	ACIAD1553		fragment of transposase (part 3)		DDE_Tnp_4
1XP53	overlaps another CDS with the same product name	ACIAD1563		fragment of transposase		rve
3NNYR	Homeodomain-like domain	ACIAD1564		fragment of transposase		HTH_Tnp_1
3NKN1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD1791		transposase of IS1236, IS3 family (ORF 2)		HTH_21, rve
3NNW1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD1792		transposase of IS1236, IS3 family (ORF 1)		HTH_Tnp_1
3NSUS	Evidence 3 Function proposed based on presence of conserved amino acid motif, structural feature or limited homology	ACIAD1847		putative phage replication initiation factor (RstA-like)		Rep_trans
3NSUS	Evidence 3 Function proposed based on presence of conserved amino acid motif, structural feature or limited homology	ACIAD1858		putative phage replication initiation factor (RstA-like)		Rep_trans
3NTF7	DNA glycosylase	ACIAD1882		putative G:T/U mismatch-specific DNA glycosylase
3NIRC	Helix-turn-helix domain	ACIAD2014		putative helicase		HTH_40, PIF1
3NJUP	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	ACIAD2041	ruvC	holliday junction nuclease	COG0817	RuvC	K01159
3NIGC	DNA polymerase	ACIAD2089	dnaE	DNA polymerase III, alpha chain	COG0587	DNA_pol3_alpha, HHH_6, PHP	K02337
3NJVR	Helicase associated domain (HA2) Add an annotation	ACIAD2102	hrpA	ATP-dependent helicase	COG1643	DEAD, DUF3418, HA2, Helicase_C, OB_NTP_bind	K03578
3NN19	Belongs to the 'phage' integrase family	ACIAD2131		hypothetical protein
3NN0N	DnaB-like helicase N terminal domain	ACIAD2185		putative replicative DNA helicase		DnaB, DnaB_C
3NMXN	DnaD domain protein	ACIAD2186		hypothetical protein
3NM1I	Phage integrase family	ACIAD2200		putative integrase/recombinase protein		Phage_integrase
3NK9K	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease	ACIAD2257		putative DNA exonuclease X	COG0847	QSregVF_b, RNase_T	K10857
3NKAI	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	ACIAD2312	recR	recombination protein, gap repair	COG0353	RecR, Toprim_4	K06187
3NITV	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	ACIAD2352	ung	uracil-DNA glycosylase	COG0692	UDG	K03648
3NJ9T	TatD related DNase	ACIAD2359		conserved hypothetical protein; putative deoxyribonuclease	COG0084	TatD_DNase	K03424
3NK7S	DNA polymerase III	ACIAD2361	holB	DNA polymerase III, delta prime subunit	COG0470	DNA_pol3_delta2	K02341
3NIU8	This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a molecular matchmaker , a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex	ACIAD2375	mutL	enzyme in methyl-directed mismatch repair, stimulates binding of Vsr and MutS to heteroduplex DNA	COG0323	DNA_mis_repair, HATPase_c_3, MutL_C	K03572
3NNVR	RelB antitoxin	ACIAD2378		conserved hypothetical protein		RelB
3NK54	it exhibits DNA-dependent ATPase activity and contains distinct active sites for ATP binding, DNA binding, and interaction with DnaC protein, primase, and other prepriming proteins	ACIAD2433	dnaB	replicative DNA helicase;chromosome replication, chain elongation	COG0305	DnaB, DnaB_C	K02314
3NNW8	Activates ribosomal RNA transcription. Plays a direct role in upstream activation of rRNA promoters	ACIAD2446	fis	DNA-binding protein for site-specific recombination, transcription of rRNA and tRNA operons and DNA replication	COG2901	HTH_8	K03557
3NKDP	CRISPR-associated helicase, Cas3	ACIAD2477		putative CRISPR-associated helicase Cas3	COG1203		K07012
3NKQR	CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette	ACIAD2484		putative CRISPR-associated protein Cas1	COG1518	Cas_Cas1	K15342
3NJGC	damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage	ACIAD2569	uvrB	excinuclease ABC subunit B (ATP-dependent DNA excision repair enzyme UvrAC)	COG0556	Helicase_C, ResIII, UVR, UvrB	K03702
3NJ9I	Belongs to the RecO family	ACIAD2578	recO	DNA repair protein	COG1381	RecO_C, RecO_N	K03584
3NIER	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	ACIAD2614	ruvA	holliday junction helicase subunit A	COG0632	HHH_5, RuvA_C, RuvA_N	K03550
3NIMR	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	ACIAD2615	ruvB	holliday junction helicase, subunit B	COG2255	RuvB_C, RuvB_N	K03551
3NIVI	Belongs to the DnaA family	ACIAD2632		putative chromosomal replication initiator, DnaA-homolog protein hda	COG0593	Bac_DnaA	K10763
3NJ9E	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-dependent manner	ACIAD2652	gyrA	DNA gyrase, subunit A, type II topoisomerase	COG0188	DNA_gyraseA_C, DNA_topoisoIV	K02469
3NK1C	DNA polymerase	ACIAD2718		fragment of component of DNA polymerase V (UmuC) (part 1)	COG0389	DUF4113, IMS, IMS_C, IMS_HHH	K03502
3NK1C	DNA polymerase	ACIAD2728		fragment of component of DNA polymerase V (UmuC) (part 2)		DUF4113, IMS, IMS_C, IMS_HHH
3NKN1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD2779		fragment of transposase of IS1236, IS3 family (ORF 2) (part 4)		HTH_21, rve
3NKN1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD2780		fragment of transposase of IS1236, IS3 family (ORF 2) (part 3)		HTH_21, rve
3NKN1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD2781		fragment of transposase of IS1236, IS3 family (ORF 2) (part 2)		HTH_21, rve
3NNW1	Evidence 1 Function experimentally demonstrated in the studied organism	ACIAD2782		fragment of transposase of IS1236, IS3 family (ORF 1) (part 1)		HTH_Tnp_1
3NIIT	YqaJ-like viral recombinase domain	ACIAD2799		putative phage-type endonuclease domain protein		YqaJ
3NIIT	YqaJ-like viral recombinase domain	ACIAD2800		hypothetical protein		YqaJ
3NPDQ	6-O-methylguanine DNA methyltransferase, DNA binding domain	ACIAD2864		putative methyltransferase	COG3695	DNA_binding_1	K07443
3NIVT	RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication	ACIAD2899	dnaG	DNA primase	COG0358	DnaB_bind, Toprim_4, Toprim_N, zf-CHC2	K02316
3NJ3G	Site-specific recombinase	ACIAD2941		conserved hypothetical protein; (putative site-specific recombinase)		SpecificRecomb
3NK2H	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity	ACIAD3030	polA	DNA polymerase I, 3' --> 5' polymerase, 5' --> 3' and 3'--> 5' exonuclease	COG0749, COG0258	5_3_exonuc, 5_3_exonuc_N, DNA_pol_A, DNA_pol_A_exo1	K02335
3NPCU	Helix-hairpin-helix motif	ACIAD3064		putative DNA uptake protein and/or related DNA-binding protein	COG1555	HHH_3	K02237
3NINT	3'-5' exonuclease related to the exonuclease domain of PolB	ACIAD3070		conserved hypothetical protein	COG3298	DNA_pol_B_exo2	K07501
3NK6P	TatD related DNase	ACIAD3091		putative DNase	COG0084	TatD_DNase	K03424
3NJD1	DNA polymerase III, delta subunit	ACIAD3108		putative DNA polymerase III, delta subunit (probably ATP hydrolase) (HolA)	COG1466	DNA_pol3_delta	K02340
3NJA4	Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has a DNA unwinding activity characteristic of a DNA helicase with a 3'- to 5'- polarity. Unwinds branched duplex DNA (Y-DNA)	ACIAD3235	recG	ATP-dependent DNA helicase	COG1200	DEAD, Helicase_C, RecG_wedge	K03655
3NIUV	Belongs to the DEAD box helicase family	ACIAD3245		putative ATP-dependent RNA helicase		DEAD, Helicase_C
3NSY9	Arm DNA-binding domain	ACIAD3414		putative integrase		Arm-DNA-bind_3, Phage_integrase
3NJIW	Type I restriction enzyme R protein N terminus (HSDR_N)	ACIAD3430		putative type I restriction-modification system (HsdR)	COG0610	HSDR_N, ResIII	K01153
3NM7Z	Domain of unknown function (DUF4357)	ACIAD3437		DUF4357 domain-containing protein		DUF4357
3NJSD	Plays an important role in DNA replication, recombination and repair. Binds to ssDNA and to an array of partner proteins to recruit them to their sites of action during DNA metabolism	ACIAD3449	ssb	ssDNA-binding protein controls activity of RecBCD nuclease	COG0629	SSB	K03111
3NK1U	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate	ACIAD3455	uvrA	excinuclease ABC subunit A	COG0178	ABC_tran	K03701
3NK36	single-stranded-DNA-specific exonuclease RecJ	ACIAD3500	recJ	ssDNA exonuclease, 5' --> 3' specific , Mg dependent	COG0608	DHH, DHHA1	K07462
3NJV4	Endonuclease/Exonuclease/phosphatase family	ACIAD3526	crc	catabolite repression control protein	COG0708	Exo_endo_phos	K01142
3NJCN	Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule	ACIAD3544	parE	topoisomerase IV subunit B	COG0187	DNA_gyraseB, DNA_gyraseB_C, HATPase_c, Toprim	K02622
3NJIQ	COG2256 ATPase related to the helicase subunit of the Holliday junction resolvase	ACIAD3596		putative ATPase	COG2256	AAA, AAA_assoc_2, MgsA_C	K07478
3NJ2N	A G-specific	ACIAD3606	mutY	A/G specific adenine glycosylase	COG1194	HhH-GPD, NUDIX_4	K03575
3NJYJ	Methyladenine glycosylase	ACIAD3611	tag	3-methyl-adenine DNA glycosylase I, constitutive	COG2818	Adenine_glyco	K01246

3NIMU

it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box) 5'-TTATC CA A CA A-3'. DnaA binds to ATP and to acidic phospholipids

ACIAD0001

dnaA

Chromosomal replication initiator protein dnaA

COG0593

Bac_DnaA, Bac_DnaA_C, DnaA_N

K02313

3NJI0

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

ACIAD0002

dnaN

DNA polymerase III, beta chain

COG0592

DNA_pol3_beta, DNA_pol3_beta_2, DNA_pol3_beta_3

K02338

3NKN9

it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP

ACIAD0003

recF

DNA replication, recombinaison and repair protein

COG1195

SMC_N

K03629

3NJZQ

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-dependent manner

ACIAD0004

gyrB

DNA gyrase, subunit B (type II topoisomerase)

COG0187

DNA_gyraseB, DNA_gyraseB_C, HATPase_c, Toprim

K02470

3NKHK

Transposase DDE domain

ACIAD0057

fragment of transposase (part 1)

DDE_Tnp_1_3

3NKHK

Transposase DDE domain

ACIAD0058

fragment of transposase (part 2)

DDE_Tnp_1_3

3NKHK

Transposase DDE domain

ACIAD0059

fragment of transposase (part 3)

DDE_Tnp_1_3

1RQSR

cog cog2801

ACIAD0134

fragment of transposase

HTH_21, rve

3NJFR

nucleotide-binding protein involved in DNA uptake

ACIAD0209

putative Rossmann-fold nucleotide-binding protein involved in DNA uptake (Smf)

COG0758

DNA_processg_A

K04096

3NJQG

Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII

ACIAD0225

dinP

DNA polymerase IV, devoid of proofreading, damage-inducible protein P

COG0389

IMS, IMS_C, IMS_HHH

K02346

3NIU5

Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule

ACIAD0234

parC

DNA topoisomerase IV, subunit A

COG0188

DNA_gyraseA_C, DNA_topoisoIV

K02621

3NJQR

D12 class N6 adenine-specific DNA methyltransferase

ACIAD0248

putative DNA modification methylase (Adenine-specific methyltransferase)

COG3392

MethyltransfD12

K07318

3NNGG

DNA polymerase III, chi subunit

ACIAD0252

holC

DNA polymerase III, chi subunit

DNA_pol3_chi

NUDIX domain

aspP

adenosine diphosphate sugar pyrophosphatase (ADP-ribose pyrophosphatase)

COG0494

NUDIX

K01515

3NNW1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD0320

transposase of IS1236, IS3 family (ORF 1)

HTH_Tnp_1

3NKN1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD0321

transposase of IS1236, IS3 family (ORF 2)

HTH_21, rve

3NIZV

The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision

ACIAD0340

uvrC

excinuclease ABC subunit C; UvrC with UvrAB is a DNA excision repair enzyme

COG0322

GIY-YIG, UVR, UvrC_HhH_N

K03703

3NKZK

2OG-Fe(II) oxygenase superfamily

ACIAD0345

alkB

DNA repair system specific for alkylated DNA

2OG-FeII_Oxy_2

3NN70

Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA

ACIAD0352

yqgF

holliday junction resolvase yqgF-like

COG0816

RuvX

K07447

3NJAU

May be involved in recombinational repair of damaged DNA

ACIAD0354

recN

DNA repair protein RecN

SMC_N

DNA helicase

putative DNA helicase

AAA_19, UvrD_C

3NM1F

A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit recognizes the wild- type Chi sequence, and when added to isolated RecB increases its ATP-dependent helicase processivity

ACIAD0397

recC

exonuclease V, gamma chain

COG1330

Exonuc_V_gamma

K03583

3NIUR

A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit contributes ATPase, 3'-5' helicase, exonuclease activity and loads RecA onto ssDNA

ACIAD0398

recB

exonuclease V, beta chain

COG1074

PDDEXK_1, UvrD-helicase, UvrD_C

K03582

3NIKV

A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD

ACIAD0399

recD

exonuclease V, alpha subunit

COG0507

AAA_30, UvrD_C_2

K03581

3NJI2

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

ACIAD0409

priA

primosomal protein N' (= factor Y) directs replication fork assembly at D-loops, ATP-dependent.

COG1198

ResIII

K04066

3NIK9

Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage

ACIAD0455

nudH

(di)nucleoside polyphosphate hydrolase (Ap5A pyrophosphatase)

COG0494

NUDIX

K08311

3NJWY

Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone

ACIAD0493

topA

DNA topoisomerase type I, omega protein

COG0550, COG0551, COG1754

Topo_Zn_Ribbon, Topoisom_bac, Toprim, zf-C4_Topoisom

K03168

3NKBE

UvrD-like helicase C-terminal domain

ACIAD0495

putative ATP-dependent DNA helicase (PcrA)

COG0210

UvrD-helicase, UvrD_C

K03657

3NIEC

NUDIX domain

ACIAD0674

putative MutT/nudix family protein

NUDIX

3NM1X

Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. Repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme. This is a suicide reaction the enzyme is irreversibly inactivated

ACIAD0692

ogt

methylated-DNA--protein-cysteine methyltransferase (6-O- methylguanine-DNA methyltransferase) (O-6-methylguanine-DNA- alkyltransferase)

COG0350

DNA_binding_1, Methyltransf_1N

K00567

3NKR9

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

ACIAD0707

mutM

formamidopyrimidine-DNA glycosylase

COG0266

Fapy_DNA_glyco, H2TH, zf-FPG_IleRS

K10563

3NNRI

NUDIX domain

ACIAD0720

putative MutT/nudix family protein

NUDIX

3NIX0

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

ACIAD0848

ligA

DNA ligase

COG0272

BRCT, DNA_ligase_OB, DNA_ligase_ZBD, DNA_ligase_aden, HHH_2, HHH_5

K01972

3NKQE

it can initiate unwinding at a nick in the DNA. It binds to the single-stranded DNA and acts in a progressive fashion along the DNA in the 3' to 5' direction

ACIAD0900

rep

ATP-dependent DNA helicase

COG0210

UvrD-helicase, UvrD_C

K03656

3NJ9P

Putative exonuclease SbcCD, C subunit

ACIAD0916

sbcC

ATP-dependent dsDNA exonuclease (Suppression of recBC)

COG0419

AAA_23, SbcCD_C

K03546

3NKS4

SbcCD cleaves DNA hairpin structures. These structures can inhibit DNA replication and are intermediates in certain DNA recombination reactions. The complex acts as a 3'- 5' double strand exonuclease that can open hairpins. It also has a 5' single-strand endonuclease activity

ACIAD0917

sbcD

ATP-dependent dsDNA exonuclease (Suppression of recBC)

COG0420

Metallophos, SbcD_C

K03547

3NKN1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD0952

transposase of IS1236, IS3 family (ORF 2)

HTH_21, rve

3NNW1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD0953

transposase of IS1236, IS3 family (ORF 1)

HTH_Tnp_1

3NKN1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD0957

transposase of IS1236, IS3 family (ORF 2)

HTH_21, rve

3NNW1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD0958

transposase of IS1236, IS3 family (ORF 1)

HTH_Tnp_1

3NKBU

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

ACIAD1108

nth

endonuclease III DNA glycosylase/apyrimidinic (AP) lyase

COG0177

EndIII_4Fe-2S, HhH-GPD

K10773

3NP49

Belongs to the UPF0102 family

ACIAD1132

conserved hypothetical protein

COG0792

UPF0102

K07460

3NJQ4

NADH pyrophosphatase zinc ribbon domain

ACIAD1135

nudC

NADH pyrophosphatase (NUDIX hydrolase family)

COG2816

NUDIX, zf-NADH-PPase

K03426

3NKVD

Endonuclease that specifically degrades the RNA of RNA- DNA hybrids

ACIAD1137

rnhA-dnaQ

bifunctional protein [Includes: ribonuclease HI; DNA polymerase III ,epsilon subunit, 3-5 exonucleolytic proofreading function]

COG0847, COG0328

RNase_H, RNase_T

K14159

3NJ5Q

Trims short 3' overhangs of a variety of RNA species, leaving a one or two nucleotide 3' overhang. Responsible for the end-turnover of tRNA specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A). Also appears to be involved in tRNA biosynthesis

ACIAD1149

rnt

ribonuclease T (degrades tRNA , has exonuclease and ssDNAse activity)

COG0847

RNase_T

K03683

3NJ70

Domain of unknown function (DUF4130

ACIAD1171

conserved hypothetical protein

DUF4130

3NJJE

DNA photolyase

ACIAD1182

phrB

deoxyribodipyrimidine photolyase (photoreactivation), FAD-binding

COG0415

DNA_photolyase, FAD_binding_7

K01669

3NJ52

Endonuclease that specifically degrades the RNA of RNA- DNA hybrids

ACIAD1248

rnhB

RNAse HII

COG0164

RNase_HII

K03470

3NKN1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD1249

transposase of IS1236, IS3 family (ORF 2)

HTH_21, rve

3NNW1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD1250

transposase of IS1236, IS3 family (ORF 1)

HTH_Tnp_1

3NIY4

DEAD-box RNA helicase involved in RNA degradation. Has RNA-dependent ATPase activity and unwinds double-stranded RNA

ACIAD1314

rhlB

ATP-dependent RNA helicase (DEAD box)

COG0513

DEAD, Helicase_C

K03732

3NNGX

Protein tyrosine kinase

ACIAD1336

putative kinase

Pkinase

3NIMT

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

ACIAD1385

recA

DNA strand exchange and recombination protein with protease and nuclease activity.

COG0468

RecA

K03553

3NJUH

Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site

ACIAD1395

mfd

transcription-repair coupling protein

COG1197

CarD_CdnL_TRCF, DEAD, Helicase_C, TRCF

K03723

3NNVG

Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions

ACIAD1408

hupB

DNA-binding protein HU-beta

COG0776

Bac_DNA_binding

K03530

3NK8D

that it carries out the mismatch recognition step. This protein has a weak ATPase activity

ACIAD1500

mutS

methyl-directed mismatch repair, recognize exocyclic adducts of guanosine

COG0249

MutS_I, MutS_II, MutS_III, MutS_IV, MutS_V

K03555

3NJHA

Arm DNA-binding domain

ACIAD1501

hypothetical protein

Arm-DNA-bind_3, Phage_integrase

3NTR4

DDE superfamily endonuclease

ACIAD1553

fragment of transposase (part 3)

DDE_Tnp_4

1XP53

overlaps another CDS with the same product name

ACIAD1563

fragment of transposase

rve

3NNYR

Homeodomain-like domain

ACIAD1564

fragment of transposase

HTH_Tnp_1

3NKN1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD1791

transposase of IS1236, IS3 family (ORF 2)

HTH_21, rve

3NNW1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD1792

transposase of IS1236, IS3 family (ORF 1)

HTH_Tnp_1

3NSUS

Evidence 3 Function proposed based on presence of conserved amino acid motif, structural feature or limited homology

ACIAD1847

putative phage replication initiation factor (RstA-like)

Rep_trans

3NSUS

Evidence 3 Function proposed based on presence of conserved amino acid motif, structural feature or limited homology

ACIAD1858

putative phage replication initiation factor (RstA-like)

Rep_trans

3NTF7

DNA glycosylase

ACIAD1882

putative G:T/U mismatch-specific DNA glycosylase

3NIRC

Helix-turn-helix domain

ACIAD2014

putative helicase

HTH_40, PIF1

3NJUP

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

ACIAD2041

ruvC

holliday junction nuclease

RuvC

DNA polymerase

dnaE

DNA polymerase III, alpha chain

COG0587

DNA_pol3_alpha, HHH_6, PHP

K02337

3NJVR

Helicase associated domain (HA2) Add an annotation

ACIAD2102

hrpA

ATP-dependent helicase

COG1643

DEAD, DUF3418, HA2, Helicase_C, OB_NTP_bind

K03578

3NN19

Belongs to the 'phage' integrase family

ACIAD2131

hypothetical protein

3NN0N

DnaB-like helicase N terminal domain

ACIAD2185

putative replicative DNA helicase

DnaB, DnaB_C

3NMXN

DnaD domain protein

ACIAD2186

hypothetical protein

3NM1I

Phage integrase family

ACIAD2200

putative integrase/recombinase protein

Phage_integrase

3NK9K

DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease

ACIAD2257

putative DNA exonuclease X

COG0847

QSregVF_b, RNase_T

K10857

3NKAI

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

ACIAD2312

recR

recombination protein, gap repair

COG0353

RecR, Toprim_4

K06187

3NITV

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

ACIAD2352

ung

uracil-DNA glycosylase

UDG

TatD related DNase

conserved hypothetical protein; putative deoxyribonuclease

TatD_DNase

DNA polymerase III

holB

DNA polymerase III, delta prime subunit

COG0470

DNA_pol3_delta2

K02341

3NIU8

This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a molecular matchmaker , a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex

ACIAD2375

mutL

enzyme in methyl-directed mismatch repair, stimulates binding of Vsr and MutS to heteroduplex DNA

COG0323

DNA_mis_repair, HATPase_c_3, MutL_C

K03572

3NNVR

RelB antitoxin

ACIAD2378

conserved hypothetical protein

RelB

3NK54

it exhibits DNA-dependent ATPase activity and contains distinct active sites for ATP binding, DNA binding, and interaction with DnaC protein, primase, and other prepriming proteins

ACIAD2433

dnaB

replicative DNA helicase;chromosome replication, chain elongation

COG0305

DnaB, DnaB_C

K02314

3NNW8

Activates ribosomal RNA transcription. Plays a direct role in upstream activation of rRNA promoters

ACIAD2446

fis

DNA-binding protein for site-specific recombination, transcription of rRNA and tRNA operons and DNA replication

COG2901

HTH_8

K03557

3NKDP

CRISPR-associated helicase, Cas3

ACIAD2477

putative CRISPR-associated helicase Cas3

COG1203

K07012

3NKQR

CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette

ACIAD2484

putative CRISPR-associated protein Cas1

COG1518

Cas_Cas1

K15342

3NJGC

damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage

ACIAD2569

uvrB

excinuclease ABC subunit B (ATP-dependent DNA excision repair enzyme UvrAC)

COG0556

Helicase_C, ResIII, UVR, UvrB

K03702

3NJ9I

Belongs to the RecO family

ACIAD2578

recO

DNA repair protein

COG1381

RecO_C, RecO_N

K03584

3NIER

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

ACIAD2614

ruvA

holliday junction helicase subunit A

COG0632

HHH_5, RuvA_C, RuvA_N

K03550

3NIMR

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

ACIAD2615

ruvB

holliday junction helicase, subunit B

COG2255

RuvB_C, RuvB_N

K03551

3NIVI

Belongs to the DnaA family

ACIAD2632

putative chromosomal replication initiator, DnaA-homolog protein hda

COG0593

Bac_DnaA

K10763

3NJ9E

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-dependent manner

ACIAD2652

gyrA

DNA gyrase, subunit A, type II topoisomerase

COG0188

DNA_gyraseA_C, DNA_topoisoIV

K02469

3NK1C

DNA polymerase

ACIAD2718

fragment of component of DNA polymerase V (UmuC) (part 1)

COG0389

DUF4113, IMS, IMS_C, IMS_HHH

K03502

3NK1C

DNA polymerase

ACIAD2728

fragment of component of DNA polymerase V (UmuC) (part 2)

DUF4113, IMS, IMS_C, IMS_HHH

3NKN1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD2779

fragment of transposase of IS1236, IS3 family (ORF 2) (part 4)

HTH_21, rve

3NKN1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD2780

fragment of transposase of IS1236, IS3 family (ORF 2) (part 3)

HTH_21, rve

3NKN1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD2781

fragment of transposase of IS1236, IS3 family (ORF 2) (part 2)

HTH_21, rve

3NNW1

Evidence 1 Function experimentally demonstrated in the studied organism

ACIAD2782

fragment of transposase of IS1236, IS3 family (ORF 1) (part 1)

HTH_Tnp_1

3NIIT

YqaJ-like viral recombinase domain

ACIAD2799

putative phage-type endonuclease domain protein

YqaJ

3NIIT

YqaJ-like viral recombinase domain

ACIAD2800

hypothetical protein

YqaJ

3NPDQ

6-O-methylguanine DNA methyltransferase, DNA binding domain

ACIAD2864

putative methyltransferase

COG3695

DNA_binding_1

K07443

3NIVT

RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication

ACIAD2899

dnaG

DNA primase

COG0358

DnaB_bind, Toprim_4, Toprim_N, zf-CHC2

K02316

3NJ3G

Site-specific recombinase

ACIAD2941

conserved hypothetical protein; (putative site-specific recombinase)

SpecificRecomb

3NK2H

In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity

ACIAD3030

polA

DNA polymerase I, 3' --> 5' polymerase, 5' --> 3' and 3'--> 5' exonuclease

COG0749, COG0258

5_3_exonuc, 5_3_exonuc_N, DNA_pol_A, DNA_pol_A_exo1

K02335

3NPCU

Helix-hairpin-helix motif

ACIAD3064

putative DNA uptake protein and/or related DNA-binding protein

COG1555

HHH_3

K02237

3NINT

3'-5' exonuclease related to the exonuclease domain of PolB

ACIAD3070

conserved hypothetical protein

DNA_pol_B_exo2

TatD related DNase

putative DNase

TatD_DNase

DNA polymerase III, delta subunit

ACIAD3108

putative DNA polymerase III, delta subunit (probably ATP hydrolase) (HolA)

COG1466

DNA_pol3_delta

K02340

3NJA4

Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has a DNA unwinding activity characteristic of a DNA helicase with a 3'- to 5'- polarity. Unwinds branched duplex DNA (Y-DNA)

ACIAD3235

recG

ATP-dependent DNA helicase

COG1200

DEAD, Helicase_C, RecG_wedge

K03655

3NIUV

Belongs to the DEAD box helicase family

ACIAD3245

putative ATP-dependent RNA helicase

DEAD, Helicase_C

3NSY9

Arm DNA-binding domain

ACIAD3414

putative integrase

Arm-DNA-bind_3, Phage_integrase

3NJIW

Type I restriction enzyme R protein N terminus (HSDR_N)

ACIAD3430

putative type I restriction-modification system (HsdR)

COG0610

HSDR_N, ResIII

K01153

3NM7Z

Domain of unknown function (DUF4357)

ACIAD3437

DUF4357 domain-containing protein

DUF4357

3NJSD

Plays an important role in DNA replication, recombination and repair. Binds to ssDNA and to an array of partner proteins to recruit them to their sites of action during DNA metabolism

ACIAD3449

ssb

ssDNA-binding protein controls activity of RecBCD nuclease

COG0629

SSB

K03111

3NK1U

The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate

ACIAD3455

uvrA

excinuclease ABC subunit A

COG0178

ABC_tran

K03701

3NK36

single-stranded-DNA-specific exonuclease RecJ

ACIAD3500

recJ

ssDNA exonuclease, 5' --> 3' specific , Mg dependent

COG0608

DHH, DHHA1

K07462

3NJV4

Endonuclease/Exonuclease/phosphatase family

ACIAD3526

crc

catabolite repression control protein

COG0708

Exo_endo_phos

K01142

3NJCN

Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule

ACIAD3544

parE

topoisomerase IV subunit B

COG0187

DNA_gyraseB, DNA_gyraseB_C, HATPase_c, Toprim

K02622

3NJIQ

COG2256 ATPase related to the helicase subunit of the Holliday junction resolvase

ACIAD3596

putative ATPase

COG2256

AAA, AAA_assoc_2, MgsA_C