CDSs classified by EGGNOG in COG category L
Acinetobacter baylyi ADP1 - chromosome ACIAD.1
L: INFORMATION STORAGE AND PROCESSING -> Replication, recombination and repair
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OG ID | OG function | Label | Gene | Product | COG | PFAM short name | KO |
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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 |