STRINGSTRING
ADM08193.1 ADM08193.1 mfd mfd ADM08247.1 ADM08247.1 gyrB gyrB recF recF ADM08372.1 ADM08372.1 ADM08373.1 ADM08373.1 ADM08424.1 ADM08424.1 ADM08426.1 ADM08426.1 uvrB uvrB ADM08498.1 ADM08498.1 ADM08499.1 ADM08499.1 ruvC ruvC ruvA ruvA ruvB ruvB ADM08611.1 ADM08611.1 xseA xseA mutS mutS dnaX dnaX priA priA ADM08895.1 ADM08895.1 polA polA dnaQ dnaQ ADM09013.1 ADM09013.1 ADM09127.1 ADM09127.1 ADM09393.1 ADM09393.1 queG queG ADM09485.1 ADM09485.1 ADM09610.1 ADM09610.1 uvrC uvrC xseB xseB ADM09854.1 ADM09854.1 ADM09856.1 ADM09856.1 ADM09880.1 ADM09880.1 ligA ligA parC parC mutL mutL parE parE gyrA gyrA topA topA ADM10270.1 ADM10270.1 ADM10282.1 ADM10282.1 uvrA uvrA trmFO trmFO ADM10288.1 ADM10288.1 recA recA ADM10443.1 ADM10443.1 dnaG dnaG lexA lexA
Nodes:
Network nodes represent proteins
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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colored nodes:
query proteins and first shell of interactors
white nodes:
second shell of interactors
Node Content
empty nodes:
proteins of unknown 3D structure
filled nodes:
a 3D structure is known or predicted
Edges:
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
Others
textmining
co-expression
protein homology
Your Input:
ADM08193.1Single-stranded DNA-binding protein. (148 aa)
mfdTranscription-repair coupling factor; 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; In the C-terminal section; belongs to the helicase family. RecG subfamily. (1163 aa)
ADM08247.1Replicative DNA helicase; 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. (492 aa)
gyrBDNA gyrase subunit B; 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. (770 aa)
recFRecombination protein F; 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; Belongs to the RecF family. (375 aa)
ADM08372.1DNA polymerase III subunit beta; 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)
ADM08373.1Chromosomal 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. (503 aa)
ADM08424.1single-stranded-DNA-specific exonuclease RecJ. (610 aa)
ADM08426.1DNA helicase RecQ. (410 aa)
uvrBPutative excinuclease abc subunit b protein; 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 sub [...] (724 aa)
ADM08498.1Modification methylase; Belongs to the N(4)/N(6)-methyltransferase family. (344 aa)
ADM08499.1Putative mutY, A/G-specific adenine glycosylase; Adenine glycosylase active on G-A mispairs. (352 aa)
ruvCHolliday junction resolvase; 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. (170 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. (202 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. (340 aa)
ADM08611.1Hypothetical protein. (142 aa)
xseAExonuclease 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. (550 aa)
mutSDNA mismatch repair protein; 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. (873 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. (607 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. (738 aa)
ADM08895.1Exodeoxyribonuclease III. (264 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. (940 aa)
dnaQPutative DNA polymerase III, epsilon subunit and related 3'-5'exonuclease; 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. (245 aa)
ADM09013.1Hypothetical protein. (351 aa)
ADM09127.1Putative methylated-DNA--protein-cysteine methyltransferase; 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. Belongs to the MGMT family. (351 aa)
ADM09393.1Hypothetical protein. (143 aa)
queGIron-sulfur cluster binding protein; Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr); Belongs to the QueG family. (397 aa)
ADM09485.1Exodeoxyribonuclease III. (273 aa)
ADM09610.1Hypothetical protein. (691 aa)
uvrCExcinuclease ABC subunit C; 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. (650 aa)
xseBExodeoxyribonuclease 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. (78 aa)
ADM09854.1DNA helicase II. (775 aa)
ADM09856.1DNA polymerase III, alpha subunit. (1152 aa)
ADM09880.1Putative DNA repair protein RecN; May be involved in recombinational repair of damaged DNA. (564 aa)
ligANAD-dependent DNA ligase; 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; Belongs to the NAD-dependent DNA ligase family. LigA subfamily. (727 aa)
parCDNA topoisomerase IV subunit A; 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. (754 aa)
mutLDNA mismatch repair protein; 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. (632 aa)
parEDNA topoisomerase IV subunit B; 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. (665 aa)
gyrADNA gyrase subunit A; 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. (924 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 [...] (876 aa)
ADM10270.1DNA polymerase III, delta prime subunit. (331 aa)
ADM10282.1Single-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. (154 aa)
uvrAExcinuclease ABC subunit A; 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. (977 aa)
trmFOGlucose-inhibited division protein A; Catalyzes the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs; Belongs to the MnmG family. TrmFO subfamily. (461 aa)
ADM10288.1Endonuclease III family protein. (261 aa)
recARecombinase A; 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. (360 aa)
ADM10443.1DNA polymerase III subunit chi. (145 aa)
dnaGDNA primase; RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. Belongs to the DnaG primase family. (625 aa)
lexALexA repressor; 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. (229 aa)
Your Current Organism:
Parvularcula bermudensis
NCBI taxonomy Id: 314260
Other names: P. bermudensis HTCC2503, Parvularcula bermudensis HTCC2503, Parvularcula bermudensis str. HTCC2503, Parvularcula bermudensis strain HTCC2503
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