STRINGSTRING
dnaA dnaA dnaN dnaN recF recF gyrB gyrB res res uvrD uvrD mutL mutL recJ recJ dinB dinB holA holA radA radA dnaG dnaG xni xni dnaE dnaE SO_1651 SO_1651 dinG dinG polB polB uvrC uvrC dnaX dnaX SO_2081 SO_2081 SO_2204 SO_2204 SO_2245 SO_2245 SO_2380 SO_2380 gyrA gyrA ruvB ruvB ruvA ruvA ruvC ruvC yebC yebC uvrB uvrB nth nth dnaQ dnaQ rnhA rnhA holB holB topA topA sbcC sbcC sbcD sbcD SO_2855 SO_2855 ligA ligA xth xth topB topB holC holC recX recX recA recA mutS mutS recN recN SO_3480 SO_3480 dnaB dnaB ssb ssb uvrA uvrA recQ recQ recG recG lexA lexA polA polA
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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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empty nodes:
proteins of unknown 3D structure
filled nodes:
a 3D structure is known or predicted
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Edges represent protein-protein associations
associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding to each other.
Known Interactions
from curated databases
experimentally determined
Predicted Interactions
gene neighborhood
gene fusions
gene co-occurrence
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textmining
co-expression
protein homology
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dnaAChromosomal replication initiator protein DnaA; Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; 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. (460 aa)
dnaNDNA polymerase III beta subunit DnaN; 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 initiatio [...] (366 aa)
recFDNA replication and repair protein RecF; The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP. (360 aa)
gyrBDNA gyrase B subunit GyrB; 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. (805 aa)
resType III restriction-modification system restriction subunit Res. (1055 aa)
uvrDDNA helicase II UvrD. (722 aa)
mutLDNA mismatch repair protein MutL; 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. (631 aa)
recJ5'-3' ssDNA exonuclease RecJ. (574 aa)
dinBDNA polymerase IV DinB; 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. (357 aa)
holADNA polymerase III delta subunit HolA. (343 aa)
radAATP-dependent protease 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. (454 aa)
dnaGDNA primase DnaG; RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. (574 aa)
xniExodeoxyribonuclease III associated protein Xni; Has flap endonuclease activity. During DNA replication, flap endonucleases cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. (261 aa)
dnaEDNA polymerase III alpha subunit DnaE. (1158 aa)
SO_1651helicase/SNF2 family domain protein. (1096 aa)
dinGATP-dependent helicase DinG; DNA-dependent ATPase and 5'-3' DNA helicase. (690 aa)
polBDNA polymerase II PolB. (808 aa)
uvrCExcinuclease ABC C subunit UvrC; 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. (609 aa)
dnaXDNA polymerase III gamma and tau subunits DnaX. (1002 aa)
SO_2081ATP-dependent helicase DinG family. (633 aa)
SO_2204DNA ligase ATP-dependent. (311 aa)
SO_2245Exonuclease family protein. (212 aa)
SO_2380ATP-dependent DNA helicase RecQ family. (654 aa)
gyrADNA gyrase subunit GyrA; 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. (919 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. (334 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)
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. (173 aa)
yebCDNA-binding regulatory protein YebC. (248 aa)
uvrBExcinuclease ABC B subunit UvrB; 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 dissoc [...] (673 aa)
nthEndonuclease III Nth; 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. (231 aa)
dnaQDNA polymerase III epsilon subunit DnaQ; 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. (242 aa)
rnhARibonuclease HI RnhA; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (158 aa)
holBDNA polymerase III delta' subunit HolB. (318 aa)
topADNA topoisomerase I TopA; 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 [...] (878 aa)
sbcCdsDNA exonuclease SbcC. (1018 aa)
sbcDdsDNA exonuclease SbcD; 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; Belongs to the SbcD family. (399 aa)
SO_2855Exonuclease. (225 aa)
ligADNA ligase NAD-dependent LigA; DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double- stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. (689 aa)
xthExodeoxyribonuclease III Xth. (270 aa)
topBDNA topoisomerase III TopB; 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 D [...] (702 aa)
holCDNA polymerase III chi subunit HolC. (154 aa)
recXRegulatory protein RecX; Modulates RecA activity; Belongs to the RecX family. (127 aa)
recARecombinase A RecA; 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. (357 aa)
mutSDNA mismatch repair protein MutS; This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity. (856 aa)
recNDNA repair protein RecN; May be involved in recombinational repair of damaged DNA. (552 aa)
SO_3480Cold-active protein-tyrosine phosphatase. (384 aa)
dnaBReplicative DNA helicase DnaB; Participates in initiation and elongation during chromosome replication; 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. Belongs to the helicase family. DnaB subfamily. (468 aa)
ssbSingle-strand binding protein Ssb; 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. (238 aa)
uvrAExcinuclease ABC A subunit UvrA; 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. (950 aa)
recQATP-dependent DNA helicase RecQ. (607 aa)
recGATP-dependent DNA helicase RecG; 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); Belongs to the helicase family. RecG subfamily. (691 aa)
lexABifunctional transcriptional repressor of SOS-response/self-cleaving protease LexA; Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair. (206 aa)
polADNA polymerase I PolA; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family. (922 aa)
Your Current Organism:
Shewanella oneidensis
NCBI taxonomy Id: 211586
Other names: S. oneidensis MR-1, Shewanella oneidensis ATCC 700550, Shewanella oneidensis MR-1, Shewanella oneidensis str. MR-1, Shewanella oneidensis strain MR-1, Shewanella sp. MR-1
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