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dnaN dnaN recF recF polA polA PFL_0289 PFL_0289 PFL_0379 PFL_0379 priA priA PFL_0481 PFL_0481 mutL mutL dnaB_2 dnaB_2 recN recN holC holC recJ recJ rnhB rnhB dnaE dnaE mutS mutS recA recA recX recX recQ recQ PFL_1674 PFL_1674 holB holB ligA ligA dnaX dnaX PFL_1905 PFL_1905 PFL_1906 PFL_1906 recR recR topA_1 topA_1 sulA sulA lexA lexA PFL_1952 PFL_1952 PFL_1953 PFL_1953 mfd mfd PFL_2022 PFL_2022 uvrB uvrB polB polB mag1 mag1 sbcC sbcC sbcD sbcD PFL_3042 PFL_3042 dnaQ dnaQ rnhA rnhA uvrC uvrC uvrA_1 uvrA_1 dnaE2 dnaE2 PFL_3698 PFL_3698 PFL_3699 PFL_3699 lexA2 lexA2 ftsK ftsK xth xth deaD deaD hda hda alkA alkA dnaB_1 dnaB_1 topA_2 topA_2 rulA rulA rulB rulB ruvB ruvB ruvA ruvA ruvC ruvC PFL_4766 PFL_4766 ogt ogt radA radA PFL_5412 PFL_5412 holA holA ssb ssb uvrA_2 uvrA_2 dnaG dnaG ligA-2 ligA-2 mutM mutM rep rep PFL_6057 PFL_6057 uvrD uvrD parB parB parA parA PFL_6260 PFL_6260 PFL_6269 PFL_6269
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query proteins and first shell of interactors
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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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Known Interactions
from curated databases
experimentally determined
Predicted Interactions
gene neighborhood
gene fusions
gene co-occurrence
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textmining
co-expression
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dnaNDNA 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 [...] (367 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. (367 aa)
polADNA-directed DNA polymerase; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family. (929 aa)
PFL_0289ATP-dependent DNA helicase, RecQ family; Identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM TIGR00614. (644 aa)
PFL_0379methylated-DNA-[protein]-cysteine S-methyltransferase, ADA family; Identified by similarity to SP:P06134; match to protein family HMM PF01035; match to protein family HMM PF02805; match to protein family HMM TIGR00589. (364 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. (739 aa)
PFL_0481CobQ/CobB/MinD/ParA nucleotide binding domain protein; Identified by match to protein family HMM PF01656. (256 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. (636 aa)
dnaB_2Replicative 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. (465 aa)
recNDNA repair protein RecN; May be involved in recombinational repair of damaged DNA. (557 aa)
holCDNA polymerase III, chi subunit; Identified by similarity to SP:P28905; match to protein family HMM PF04364. (142 aa)
recJsingle-stranded-DNA-specific exonuclease RecJ; Identified by match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644. (569 aa)
rnhBRibonuclease HII; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids; Belongs to the RNase HII family. (208 aa)
dnaEDNA polymerase III, alpha subunit; Identified by similarity to SP:P10443; match to protein family HMM PF01336; match to protein family HMM PF02811; match to protein family HMM PF07733; match to protein family HMM TIGR00594. (1173 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. (859 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. (350 aa)
recXRegulatory protein RecX; Modulates RecA activity; Belongs to the RecX family. (155 aa)
recQATP-dependent DNA helicase RecQ; Identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF00570; match to protein family HMM PF09382; match to protein family HMM TIGR00614; match to protein family HMM TIGR01389. (708 aa)
PFL_1674CobQ/CobB/MinD/ParA nucleotide binding domain protein; Identified by match to protein family HMM PF01656. (262 aa)
holBDNA polymerase III, delta' subunit; Identified by match to protein family HMM TIGR00678. (328 aa)
ligADNA ligase (NAD+); 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. (788 aa)
dnaXDNA polymerase III, gamma and tau subunit; 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. (692 aa)
PFL_1905TIGR00103 family protein; Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. (111 aa)
PFL_1906Oxidoreductase, zinc-binding dehydrogenase family; Identified by similarity to SP:P76113; match to protein family HMM PF00107. (347 aa)
recRRecombination protein RecR; 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. (200 aa)
topA_1DNA 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 [...] (870 aa)
sulACell division inhibitor SulA; Component of the SOS system and an inhibitor of cell division. Accumulation of SulA causes rapid cessation of cell division and the appearance of long, non-septate filaments. In the presence of GTP, binds a polymerization-competent form of FtsZ in a 1:1 ratio, thus inhibiting FtsZ polymerization and therefore preventing it from participating in the assembly of the Z ring. This mechanism prevents the premature segregation of damaged DNA to daughter cells during cell division. (157 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. (201 aa)
PFL_1952SNF2 family domain/helicase domain protein; Identified by match to protein family HMM PF00176; match to protein family HMM PF00271; match to protein family HMM PF04434. (896 aa)
PFL_1953Conserved hypothetical protein. (188 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. (1149 aa)
PFL_2022Identified by match to protein family HMM PF00817. (426 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 [...] (671 aa)
polBDNA polymerase II; Identified by similarity to SP:P21189; match to protein family HMM PF00136; match to protein family HMM PF03104. (786 aa)
mag1DNA-3-methyladenine glycosylase; Identified by similarity to SP:Q92383; match to protein family HMM PF00730. (203 aa)
sbcCExonuclease SbcCD, C subunit; Identified by similarity to SP:P13458; match to protein family HMM PF02463. (1214 aa)
sbcDExonuclease SbcCD, D subunit; 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. (414 aa)
PFL_3042Site-specific recombinase, phage integrase family; Identified by match to protein family HMM PF00589; Belongs to the 'phage' integrase family. (313 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. (249 aa)
rnhARibonuclease HI; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (150 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. (607 aa)
uvrA_1Excinuclease ABC, A subunit; Identified by similarity to SP:O34863; match to protein family HMM PF00005; match to protein family HMM TIGR00630. (888 aa)
dnaE2DNA polymerase III, alpha subunit; DNA polymerase involved in damage-induced mutagenesis and translesion synthesis (TLS). It is not the major replicative DNA polymerase. (1034 aa)
PFL_3698Conserved hypothetical protein. (471 aa)
PFL_3699Conserved hypothetical protein. (205 aa)
lexA2Putative LexA 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. (202 aa)
ftsKDNA translocase FtsK; Identified by similarity to SP:P46889; match to protein family HMM PF01580; match to protein family HMM PF09397. (802 aa)
xthExodeoxyribonuclease III; Identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633. (270 aa)
deaDCold-shock DEAD box protein A; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. (557 aa)
hdaDnaA regulatory inactivator Hda; Identified by match to protein family HMM PF00308; match to protein family HMM TIGR03420; Belongs to the DnaA family. HdA subfamily. (234 aa)
alkADNA-3-methyladenine glycosylase II; Identified by similarity to SP:P04395; match to protein family HMM PF00730; match to protein family HMM PF06029. (289 aa)
dnaB_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. (449 aa)
topA_2DNA 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 [...] (638 aa)
rulAUltraviolet light resistance protein RulA; Identified by similarity to SP:P0AG13; similarity to GB:AAG39343.1; match to protein family HMM PF00717; Belongs to the peptidase S24 family. (141 aa)
rulBUltraviolet light resistance protein RulB; Identified by similarity to SP:P04152; similarity to GB:AAR02142.1; match to protein family HMM PF00817. (423 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. (352 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)
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. (174 aa)
PFL_4766DNA-binding regulatory protein, YebC/PmpR family; Identified by match to protein family HMM PF01709; match to protein family HMM TIGR01033. (248 aa)
ogtmethylated-DNA--[protein]-cysteine S-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. (166 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. (455 aa)
PFL_5412Identified by match to protein family HMM PF00929. (203 aa)
holADNA polymerase III, delta subunit; Identified by similarity to SP:P28630; match to protein family HMM PF06144; match to protein family HMM TIGR01128. (345 aa)
ssbSingle-strand DNA-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. (169 aa)
uvrA_2Excinuclease 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. (944 aa)
dnaGDNA primase; RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. (657 aa)
ligA-2NAD-dependent DNA ligase adenylation domain protein; 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. Belongs to the NAD-dependent DNA ligase family. LigB subfamily. (556 aa)
mutMDNA-formamidopyrimidine glycosylase; 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. (270 aa)
repATP-dependent DNA helicase Rep; Rep helicase is a single-stranded DNA-dependent ATPase involved in DNA replication; 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. (669 aa)
PFL_6057Putative exodeoxyribonuclease III; Identified by match to protein family HMM PF03372; match to protein family HMM TIGR00633. (259 aa)
uvrDDNA helicase II; Identified by similarity to SP:P03018; match to protein family HMM PF00580. (727 aa)
parBChromosome partitioning protein ParB; Identified by similarity to SP:O05190; match to protein family HMM PF02195; match to protein family HMM TIGR00180; Belongs to the ParB family. (290 aa)
parAChromosome partitioning protein ParA; Identified by similarity to SP:O05189; match to protein family HMM PF01656. (265 aa)
PFL_6260Conserved hypothetical protein. (231 aa)
PFL_6269Hypothetical protein. (186 aa)
Your Current Organism:
Pseudomonas protegens
NCBI taxonomy Id: 220664
Other names: P. protegens Pf-5, Pseudomonas fluorescens Pf-5, Pseudomonas protegens Pf-5, Pseudomonas protegens str. Pf-5, Pseudomonas protegens strain Pf-5, Pseudomonas sp. Pf-5
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