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Xaut_0002 Xaut_0002 Xaut_0331 Xaut_0331 rnhA rnhA rnhB rnhB xseA xseA Xaut_1426 Xaut_1426 Xaut_1448 Xaut_1448 Xaut_1459 Xaut_1459 ligA ligA dnaQ dnaQ gyrB gyrB priA priA dnaX dnaX Xaut_2302 Xaut_2302 Xaut_2303 Xaut_2303 uvrC uvrC rnhA-2 rnhA-2 polA polA radA radA Xaut_2426 Xaut_2426 uvrB uvrB Xaut_3049 Xaut_3049 ruvC ruvC Xaut_3066 Xaut_3066 ruvA ruvA ruvB ruvB Xaut_3602 Xaut_3602 Xaut_3622 Xaut_3622 Xaut_3681 Xaut_3681 parC parC topA topA recA recA Xaut_4284 Xaut_4284 Xaut_4306 Xaut_4306 uvrA uvrA Xaut_4316 Xaut_4316 gyrA gyrA Xaut_4326 Xaut_4326 xseB xseB parE parE
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splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.
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query proteins and first shell of interactors
white nodes:
second shell of interactors
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proteins of unknown 3D structure
filled nodes:
a 3D structure is known or predicted
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experimentally determined
Predicted Interactions
gene neighborhood
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textmining
co-expression
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Xaut_0002DNA polymerase III, beta subunit; 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; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...] (373 aa)
Xaut_0331DNA repair protein RecN; May be involved in recombinational repair of damaged DNA. (565 aa)
rnhARibonuclease H; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (245 aa)
rnhBRibonuclease H; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids; Belongs to the RNase HII family. (249 aa)
xseAExodeoxyribonuclease VII, large subunit; Bidirectionally degrades single-stranded DNA into large acid- insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides; Belongs to the XseA family. (496 aa)
Xaut_1426PFAM: UvrD/REP helicase; KEGG: nwi:Nwi_2360 UvrD/REP helicase. (817 aa)
Xaut_1448TIGRFAM: DNA polymerase III, delta subunit; PFAM: DNA polymerase III delta; KEGG: nha:Nham_0100 DNA polymerase III, delta subunit. (342 aa)
Xaut_1459PFAM: DNA polymerase III chi subunit HolC; KEGG: rpa:RPA3059 DNA polymerase III chi subunit. (153 aa)
ligADNA ligase, NAD-dependent; 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. (720 aa)
dnaQDNA polymerase III, epsilon subunit; 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. (240 aa)
gyrBDNA gyrase, B subunit; 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. (813 aa)
priAPrimosomal protein N; 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; Belongs to the helicase family. PriA subfamily. (727 aa)
dnaXDNA polymerase III, subunits gamma and tau; DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. (622 aa)
Xaut_2302PFAM: SMC domain protein; KEGG: swi:Swit_4996 hypothetical protein. (880 aa)
Xaut_2303PFAM: metallophosphoesterase; KEGG: swi:Swit_4995 metallophosphoesterase. (373 aa)
uvrCExcinuclease ABC, C subunit; 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. (779 aa)
rnhA-2Ribonuclease H; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (151 aa)
polADNA polymerase I; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family. (1000 aa)
radADNA repair protein RadA; DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function. (489 aa)
Xaut_2426KEGG: pde:Pden_5114 DNA polymerase III, epsilon subunit; TIGRFAM: DNA polymerase III, epsilon subunit; PFAM: Exonuclease RNase T and DNA polymerase III; SMART: Exonuclease. (719 aa)
uvrBExcinuclease ABC, B subunit; The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative 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 [...] (866 aa)
Xaut_3049PFAM: Exonuclease RNase T and DNA polymerase III; SMART: Exonuclease; KEGG: mag:amb2073 DNA polymerase III epsilon subunit and related 3'-5' exonuclease. (298 aa)
ruvCCrossover junction endodeoxyribonuclease RuvC; 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. (169 aa)
Xaut_3066PFAM: Protein of unknown function DUF1772; KEGG: sme:SMc01456 hypothetical protein. (141 aa)
ruvAHolliday junction DNA helicase RuvA; 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. (205 aa)
ruvBHolliday junction DNA helicase RuvB; 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. (343 aa)
Xaut_3602PFAM: 5'-3' exonuclease; SMART: Helix-hairpin-helix domain protein class 2; KEGG: mmr:Mmar10_0016 DNA polymerase I. (299 aa)
Xaut_3622TIGRFAM: single-strand binding protein; PFAM: single-strand binding protein/Primosomal replication protein n; KEGG: rsq:Rsph17025_0451 single-strand binding protein. (158 aa)
Xaut_3681PFAM: Exonuclease RNase T and DNA polymerase III; SMART: Exonuclease; KEGG: mhu:Mhun_0639 exonuclease. (200 aa)
parCDNA topoisomerase IV, A subunit; Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule; Belongs to the type II topoisomerase GyrA/ParC subunit family. ParC type 1 subfamily. (745 aa)
topADNA topoisomerase I; 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 supe [...] (901 aa)
recArecA protein; 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; Belongs to the RecA family. (361 aa)
Xaut_4284KEGG: bbt:BBta_4522 DNA polymerase III, alpha subunit; TIGRFAM: DNA polymerase III, alpha subunit; PFAM: PHP domain protein; nucleic acid binding OB-fold tRNA/helicase-type; DNA polymerase III alpha subunit; SMART: phosphoesterase PHP domain protein. (1150 aa)
Xaut_4306TIGRFAM: ATP-dependent DNA helicase, RecQ family; ATP-dependent DNA helicase RecQ; PFAM: helicase domain protein; HRDC domain protein; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases; KEGG: mag:amb4254 superfamily II DNA helicase. (607 aa)
uvrAExcinuclease ABC, A subunit; 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. (1039 aa)
Xaut_4316Single-strand binding protein; 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. (180 aa)
gyrADNA gyrase, A subunit; 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. (914 aa)
Xaut_4326KEGG: nha:Nham_2009 DNA-directed DNA polymerase. (347 aa)
xseBExodeoxyribonuclease VII, small subunit; Bidirectionally degrades single-stranded DNA into large acid- insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides; Belongs to the XseB family. (97 aa)
parEDNA topoisomerase IV, B subunit; Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule; Belongs to the type II topoisomerase family. ParE type 1 subfamily. (678 aa)
Your Current Organism:
Xanthobacter autotrophicus
NCBI taxonomy Id: 78245
Other names: X. autotrophicus Py2, Xanthobacter autotrophicus Py2, Xanthobacter autotrophicus str. Py2, Xanthobacter autotrophicus strain Py2, Xanthobacter sp. Py2
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