STRINGSTRING
dnaA dnaA Fjoh_0041 Fjoh_0041 mutL mutL recF recF Fjoh_0281 Fjoh_0281 Fjoh_0284 Fjoh_0284 recR recR recO recO uvrC uvrC Fjoh_0807 Fjoh_0807 radA radA Fjoh_0877 Fjoh_0877 Fjoh_0985 Fjoh_0985 recA recA Fjoh_1135 Fjoh_1135 Fjoh_1310 Fjoh_1310 ruvC ruvC polA polA ruvB ruvB ruvA ruvA mutS mutS Fjoh_1760 Fjoh_1760 dnaG dnaG rnhB rnhB uvrB uvrB gyrB gyrB Fjoh_2289 Fjoh_2289 Fjoh_2429 Fjoh_2429 gyrA gyrA Fjoh_2709 Fjoh_2709 Fjoh_2720 Fjoh_2720 Fjoh_2808 Fjoh_2808 Fjoh_2849 Fjoh_2849 Fjoh_2913 Fjoh_2913 Fjoh_2918 Fjoh_2918 Fjoh_2924 Fjoh_2924 Fjoh_3465 Fjoh_3465 ligA ligA Fjoh_3662 Fjoh_3662 Fjoh_3765 Fjoh_3765 Fjoh_3773 Fjoh_3773 Fjoh_4509 Fjoh_4509 dnaX dnaX Fjoh_4531 Fjoh_4531 Fjoh_4635 Fjoh_4635 Fjoh_4743 Fjoh_4743
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:
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. (475 aa)
Fjoh_0041Replicative DNA helicase; Participates in initiation and elongation during chromosome replication; it exhibits DNA-dependent ATPase activity. Belongs to the helicase family. DnaB subfamily. (514 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. (644 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. (359 aa)
Fjoh_0281TIGRFAM: ATP-dependent DNA helicase, RecQ family; PFAM: helicase domain protein; HRDC domain protein; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases-like. (731 aa)
Fjoh_0284Alkylhydroperoxidase like protein, AhpD family; Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity. Belongs to the AhpD family. (116 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. (206 aa)
recODNA repair protein RecO; Involved in DNA repair and RecF pathway recombination. (237 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. (597 aa)
Fjoh_0807Regulatory protein RecX; Modulates RecA activity; Belongs to the RecX family. (156 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. (453 aa)
Fjoh_0877Hypothetical protein. (237 aa)
Fjoh_0985DNA polymerase III gamma/tau subunits-like protein. (382 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. (335 aa)
Fjoh_1135Ribonuclease H; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (158 aa)
Fjoh_1310TIGRFAM: DNA polymerase III, alpha subunit; PFAM: PHP C-terminal domain protein; Exonuclease, RNase T and DNA polymerase III; SMART: phosphoesterase PHP domain protein; Exonuclease. (1510 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. (184 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. (949 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)
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. (193 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. (855 aa)
Fjoh_1760Non-specific serine/threonine protein kinase; PFAM: SNF2-related protein; helicase domain protein; SMART: DEAD-like helicases-like. (966 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. (704 aa)
rnhBRibonuclease H; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids; Belongs to the RNase HII family. (221 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 [...] (663 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. (646 aa)
Fjoh_2289TIGRFAM: DNA topoisomerase III; PFAM: TOPRIM domain protein; DNA topoisomerase, type IA, central domain protein; SMART: DNA topoisomerase I, ATP-binding; DNA topoisomerase I, DNA-binding; Toprim sub domain protein. (768 aa)
Fjoh_2429Excinuclease 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. (931 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. (879 aa)
Fjoh_2709PFAM: DNA mismatch repair protein MutS domain protein. (590 aa)
Fjoh_2720DNA 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 [...] (372 aa)
Fjoh_2808TIGRFAM: 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-like. (705 aa)
Fjoh_2849PFAM: helicase domain protein; type III restriction enzyme, res subunit; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases-like. (512 aa)
Fjoh_2913DNA mismatch repair protein MutS domain protein; Endonuclease that is involved in the suppression of homologous recombination and may therefore have a key role in the control of bacterial genetic diversity. Belongs to the DNA mismatch repair MutS family. MutS2 subfamily. (721 aa)
Fjoh_2918TIGRFAM: DNA polymerase III, delta subunit; PFAM: DNA polymerase III, delta. (334 aa)
Fjoh_2924PFAM: UvrD/REP helicase. (778 aa)
Fjoh_3465DNA repair protein RecN; May be involved in recombinational repair of damaged DNA. (550 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. (668 aa)
Fjoh_3662PFAM: DNA repair protein RadC. (154 aa)
Fjoh_3765PFAM: DNA repair protein RadC. (155 aa)
Fjoh_3773ATP-dependent DNA helicase, Rep family; PFAM: UvrD/REP helicase. (787 aa)
Fjoh_4509Excinuclease 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. (943 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. (361 aa)
Fjoh_4531Hypothetical protein. (138 aa)
Fjoh_4635Hypothetical protein. (206 aa)
Fjoh_4743Putative prophage repressor; PFAM: peptidase S24, S26A and S26B. (106 aa)
Your Current Organism:
Flavobacterium johnsoniae
NCBI taxonomy Id: 376686
Other names: F. johnsoniae UW101, Flavobacterium johnsoniae ATCC 17061, Flavobacterium johnsoniae DSM 2064, Flavobacterium johnsoniae IAM 14304, Flavobacterium johnsoniae IFO 14942, Flavobacterium johnsoniae MYX.1.1.1, Flavobacterium johnsoniae NBRC 14942, Flavobacterium johnsoniae NCIB 11054, Flavobacterium johnsoniae UW101, Flavobacterium johnsoniae str. UW101, Flavobacterium johnsoniae strain UW101
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