STRINGSTRING
EFM12669.1 EFM12669.1 EFM12721.1 EFM12721.1 EFM12932.1 EFM12932.1 dinB-2 dinB-2 topA topA polC polC recA recA recX recX mutS mutS mutL mutL lexA lexA EFM12116.1 EFM12116.1 EFM12232.1 EFM12232.1 EFM12364.1 EFM12364.1 EFM12423.1 EFM12423.1 EFM12461.1 EFM12461.1 EFM12475.1 EFM12475.1 EFM12487.1 EFM12487.1 EFM11589.1 EFM11589.1 EFM11615.1 EFM11615.1 EFM11726.1 EFM11726.1 EFM11261.1 EFM11261.1 ligA ligA EFM11553.1 EFM11553.1 pcrB pcrB mfd mfd EFM10953.1 EFM10953.1 gyrA gyrA gyrB gyrB EFM10964.1 EFM10964.1 recF recF EFM10966.1 EFM10966.1 EFM10967.1 EFM10967.1 dnaA dnaA EFM10987.1 EFM10987.1 EFM10650.1 EFM10650.1 EFM10416.1 EFM10416.1 uvrC uvrC sbcD sbcD EFM10113.1 EFM10113.1 EFM10245.1 EFM10245.1 dinG dinG dnaX dnaX EFM09214.1 EFM09214.1 EFM09228.1 EFM09228.1 ruvC ruvC ruvA ruvA ruvB ruvB EFM09327.1 EFM09327.1 queA queA tgt tgt uvrA uvrA uvrB uvrB EFM08752.1 EFM08752.1 polA polA EFM08448.1 EFM08448.1
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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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colored nodes:
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
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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
protein homology
Your Input:
EFM12669.1SMART: Mov34/MPN/PAD-1 family protein; KEGG: pjd:Pjdr2_2144 hypothetical protein. (164 aa)
EFM12721.1KEGG: pjd:Pjdr2_2197 DNA polymerase III, delta subunit; TIGRFAM: DNA polymerase III, delta subunit; PFAM: DNA polymerase III delta. (351 aa)
EFM12932.1KEGG: pjd:Pjdr2_3778 type III restriction protein res subunit; PFAM: type III restriction protein res subunit; helicase domain protein; SMART: DEAD-like helicase; helicase domain protein. (568 aa)
dinB-2DNA-directed DNA polymerase; 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. (414 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 [...] (704 aa)
polCDNA polymerase III, alpha subunit; Required for replicative DNA synthesis. This DNA polymerase also exhibits 3' to 5' exonuclease activity. (1439 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. (353 aa)
recXRegulatory protein RecX; Modulates RecA activity; Belongs to the RecX family. (225 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. (909 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. (684 aa)
lexATranscriptional repressor, LexA family; 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. (208 aa)
EFM12116.1TIGRFAM: DNA topoisomerase III; PFAM: DNA topoisomerase type IA central domain protein; TOPRIM domain protein; KEGG: bbe:BBR47_37990 probable DNA topoisomerase III; SMART: DNA topoisomerase I DNA-binding; DNA topoisomerase I ATP-binding; Toprim sub domain protein. (769 aa)
EFM12232.1PFAM: ABC transporter related; KEGG: bbe:BBR47_28510 putative excinuclease ABC subunit A. (751 aa)
EFM12364.1PFAM: protein of unknown function DUF28; KEGG: pjd:Pjdr2_2775 hypothetical protein. (238 aa)
EFM12423.1SMART: helicase c2; KEGG: pjd:Pjdr2_2692 helicase C2. (647 aa)
EFM12461.1KEGG: hypothetical protein. (70 aa)
EFM12475.1KEGG: pjd:Pjdr2_2957 UvrD/Rep family helicase. (791 aa)
EFM12487.1KEGG: bcq:BCQ_2651 UvrD/Rep helicase family protein. (694 aa)
EFM11589.1KEGG: pjd:Pjdr2_1417 HRDC domain protein; PFAM: HRDC domain protein; SMART: HRDC domain protein. (335 aa)
EFM11615.1KEGG: pjd:Pjdr2_1409 5'-3' exonuclease; PFAM: 5'-3' exonuclease, N-terminal resolvase-like domain; 5'-3' exonuclease, SAM-fold domain; SMART: 5'-3' exonuclease; Helix-hairpin-helix domain protein class 2. (294 aa)
EFM11726.1SMART: helicase c2; Helicase-like, DEXD box c2 type; KEGG: pjd:Pjdr2_3184 DEAD_2 domain protein. (822 aa)
EFM11261.1SMART: DNA topoisomerase I DNA-binding; DNA topoisomerase I ATP-binding; Toprim sub domain protein; TIGRFAM: DNA topoisomerase III; KEGG: pjd:Pjdr2_4839 DNA topoisomerase III; PFAM: DNA topoisomerase type IA central domain protein; TOPRIM domain protein; DNA topoisomerase type IA zn finger domain protein. (739 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. (689 aa)
EFM11553.1KEGG: pjd:Pjdr2_5720 ATP-dependent DNA helicase PcrA; TIGRFAM: ATP-dependent DNA helicase PcrA; PFAM: UvrD/REP helicase. (801 aa)
pcrBGeranylgeranylglyceryl phosphate synthase family protein; Prenyltransferase that catalyzes in vivo the transfer of the heptaprenyl moiety of heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P), producing heptaprenylglyceryl phosphate (HepGP). This reaction is an ether-bond- formation step in the biosynthesis of archaea-type G1P-based membrane lipids found in Bacillales. (234 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. (1177 aa)
EFM10953.1TIGRFAM: DNA polymerase III, delta prime subunit; KEGG: pjd:Pjdr2_0016 DNA polymerase III, delta prime subunit. (325 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. (825 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. (636 aa)
EFM10964.1KEGG: pjd:Pjdr2_0005 hypothetical protein. (82 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; Belongs to the RecF family. (367 aa)
EFM10966.1TIGRFAM: S4 domain protein YaaA; KEGG: pjd:Pjdr2_0003 S4 domain protein YaaA. (71 aa)
EFM10967.1DNA 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 [...] (380 aa)
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. Belongs to the DnaA family. (448 aa)
EFM10987.1Single-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. (176 aa)
EFM10650.1KEGG: pjd:Pjdr2_0293 type III restriction protein res subunit; PFAM: type III restriction protein res subunit; helicase domain protein; SMART: DEAD-like helicase; helicase domain protein. (1052 aa)
EFM10416.1PFAM: UvrD/REP helicase; KEGG: pjd:Pjdr2_1267 UvrD/REP helicase. (772 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. (677 aa)
sbcDNuclease 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. (390 aa)
EFM10113.1KEGG: pjd:Pjdr2_4629 exonuclease, putative. (1031 aa)
EFM10245.1DNA polymerase III, alpha subunit; SMART: phosphoesterase PHP domain protein; TIGRFAM: DNA polymerase III, alpha subunit; KEGG: pjd:Pjdr2_4482 DNA polymerase III, alpha subunit; PFAM: DNA polymerase III alpha subunit; PHP domain protein; nucleic acid binding OB-fold tRNA/helicase-type. (1086 aa)
dinGDnaQ family exonuclease/DinG family helicase; 3'-5' exonuclease. (957 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. (597 aa)
EFM09214.1KEGG: pjd:Pjdr2_4482 DNA polymerase III, alpha subunit. (118 aa)
EFM09228.1TIGRFAM: ATP-dependent DNA helicase RecQ; ATP-dependent DNA helicase, RecQ family; PFAM: RQC domain; DEAD/DEAH box helicase domain protein; helicase domain protein; HRDC domain protein; KEGG: pjd:Pjdr2_4470 ATP-dependent DNA helicase RecQ; SMART: helicase domain protein; DEAD-like helicase; HRDC domain protein. (743 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. (166 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. (210 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. (336 aa)
EFM09327.1KEGG: pjd:Pjdr2_4398 SpoIID/LytB domain protein; TIGRFAM: SpoIID/LytB domain protein; PFAM: Stage II sporulation D domain protein; Sporulation domain protein. (694 aa)
queAS-adenosylmethionine/tRNA-ribosyltransferase- isomerase; Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA). (348 aa)
tgtQueuine tRNA-ribosyltransferase; Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, - Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form t [...] (377 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. (964 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 [...] (667 aa)
EFM08752.1KEGG: pjd:Pjdr2_1782 hypothetical protein. (126 aa)
polADNA polymerase I; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity. (885 aa)
EFM08448.1PFAM: Domain of unknown function DUF1877; KEGG: cpi:Cpin_2977 domain of unknown function DUF1877. (168 aa)
Your Current Organism:
Paenibacillus curdlanolyticus
NCBI taxonomy Id: 717606
Other names: P. curdlanolyticus YK9, Paenibacillus curdlanolyticus ATCC 51898, Paenibacillus curdlanolyticus DSM 10247, Paenibacillus curdlanolyticus IFO 15724, Paenibacillus curdlanolyticus NBRC 15724, Paenibacillus curdlanolyticus YK9, Paenibacillus curdlanolyticus str. YK9, Paenibacillus curdlanolyticus strain YK9
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