STRINGSTRING
argR argR fis_2 fis_2 qseF_1 qseF_1 ftsK ftsK basR basR ruvA ruvA pmpR pmpR parB_2 parB_2 uvrY uvrY GCA_000236165_02433 GCA_000236165_02433 GCA_000236165_02466 GCA_000236165_02466 smc smc GCA_000236165_02524 GCA_000236165_02524 oxyR oxyR ompR_3 ompR_3 GCA_000236165_02583 GCA_000236165_02583 uvrA uvrA fur fur ssb ssb nsrR_1 nsrR_1 greA greA mutM_1 mutM_1 fis_1 fis_1 rpoH rpoH ihfA ihfA cynR cynR zur zur greB greB Int-Tn Int-Tn polA polA traR traR rapA rapA parC parC xerC_4 xerC_4 dinB_2 dinB_2 rstA rstA aroK_4 aroK_4 GCA_000236165_03500 GCA_000236165_03500 rpoS rpoS fliA fliA recA recA mutS mutS addA addA uvrD uvrD mutM_2 mutM_2 ku ku intS intS mraZ mraZ dnaB dnaB nrdR nrdR parE parE araC araC fixJ_1 fixJ_1 topA topA radA radA GCA_000236165_01874 GCA_000236165_01874 dnaG dnaG rpoD rpoD GCA_000236165_01902 GCA_000236165_01902 GCA_000236165_01915 GCA_000236165_01915 GCA_000236165_01929 GCA_000236165_01929 gltC gltC gltR gltR dinB_1 dinB_1 fixJ_2 fixJ_2 luxR luxR dmlR dmlR aroK_3 aroK_3 dnaA dnaA dnaN dnaN recF recF gyrB gyrB ihfB ihfB cysL cysL parB_1 parB_1 priA priA nth nth rep rep ompR_1 ompR_1 ybaB ybaB cmpR cmpR nodD2 nodD2 GCA_000236165_00326 GCA_000236165_00326 nreC nreC aroK_2 aroK_2 vjbR vjbR GCA_000236165_00414 GCA_000236165_00414 cbpA cbpA birA birA qseF_2 qseF_2 mfd mfd hupB hupB fis_3 fis_3 gyrA gyrA ompR_2 ompR_2 putA putA rpoE rpoE GCA_000236165_01096 GCA_000236165_01096
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.
Node Color
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:
argRUnannotated protein; Regulates arginine biosynthesis genes. (151 aa)
fis_2Unannotated protein; Belongs to the transcriptional regulatory Fis family. (93 aa)
qseF_1Unannotated protein. (437 aa)
ftsKUnannotated protein. (790 aa)
basRUnannotated protein. (225 aa)
ruvAUnannotated protein; 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. (199 aa)
pmpRUnannotated protein. (247 aa)
parB_2Unannotated protein; Belongs to the ParB family. (263 aa)
uvrYUnannotated protein. (219 aa)
GCA_000236165_02433Unannotated protein. (290 aa)
GCA_000236165_02466Unannotated protein; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. (465 aa)
smcUnannotated protein; Required for chromosome condensation and partitioning. Belongs to the SMC family. (1164 aa)
GCA_000236165_02524Unannotated protein. (70 aa)
oxyRUnannotated protein; Belongs to the LysR transcriptional regulatory family. (306 aa)
ompR_3Unannotated protein. (242 aa)
GCA_000236165_02583Unannotated protein. (286 aa)
uvrAUnannotated protein; 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. (941 aa)
furUnannotated protein; Belongs to the Fur family. (137 aa)
ssbUnannotated protein. (156 aa)
nsrR_1Unannotated protein. (153 aa)
greAUnannotated protein; Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreA releases sequences of 2 to 3 nucleotides. (158 aa)
mutM_1Unannotated protein; 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. (271 aa)
fis_1Unannotated protein; Belongs to the transcriptional regulatory Fis family. (93 aa)
rpoHUnannotated protein; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is involved in regulation of expression of heat shock genes. (285 aa)
ihfAUnannotated protein; This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Belongs to the bacterial histone-like protein family. (97 aa)
cynRUnannotated protein; Belongs to the LysR transcriptional regulatory family. (293 aa)
zurUnannotated protein; Belongs to the Fur family. (148 aa)
greBUnannotated protein; Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreB releases sequences of up to 9 nucleotides in length. (181 aa)
Int-TnUnannotated protein; Belongs to the 'phage' integrase family. (397 aa)
polAUnannotated protein; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family. (892 aa)
traRUnannotated protein. (249 aa)
rapAUnannotated protein; Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair; Belongs to the SNF2/RAD54 helicase family. RapA subfamily. (951 aa)
parCUnannotated protein; 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. (750 aa)
xerC_4Unannotated protein; Belongs to the 'phage' integrase family. (291 aa)
dinB_2Unannotated protein; 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. (383 aa)
rstAUnannotated protein. (230 aa)
aroK_4Unannotated protein; Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate; Belongs to the shikimate kinase family. (259 aa)
GCA_000236165_03500Unannotated protein. (187 aa)
rpoSUnannotated protein; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response. (339 aa)
fliAUnannotated protein; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor controls the expression of flagella-related genes; Belongs to the sigma-70 factor family. FliA subfamily. (236 aa)
recAUnannotated 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. (348 aa)
mutSUnannotated 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. (840 aa)
addAUnannotated protein; Belongs to the helicase family. UvrD subfamily. (1080 aa)
uvrDUnannotated protein. (721 aa)
mutM_2Unannotated protein. (268 aa)
kuUnannotated protein; With LigD forms a non-homologous end joining (NHEJ) DNA repair enzyme, which repairs dsDNA breaks with reduced fidelity. Binds linear dsDNA with 5'- and 3'- overhangs but not closed circular dsDNA nor ssDNA. Recruits and stimulates the ligase activity of LigD. Belongs to the prokaryotic Ku family. (276 aa)
intSUnannotated protein; Belongs to the 'phage' integrase family. (409 aa)
mraZUnannotated protein; Belongs to the MraZ family. (152 aa)
dnaBUnannotated protein; 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. (460 aa)
nrdRUnannotated protein; Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes; Belongs to the NrdR family. (150 aa)
parEUnannotated protein; 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. (627 aa)
araCUnannotated protein. (248 aa)
fixJ_1Unannotated protein. (212 aa)
topAUnannotated protein; 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 [...] (761 aa)
radAUnannotated protein; 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. (449 aa)
GCA_000236165_01874Unannotated protein. (270 aa)
dnaGUnannotated protein; RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. (574 aa)
rpoDUnannotated protein; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth. (621 aa)
GCA_000236165_01902Unannotated protein; Belongs to the 'phage' integrase family. (214 aa)
GCA_000236165_01915Unannotated protein. (312 aa)
GCA_000236165_01929Unannotated protein. (158 aa)
gltCUnannotated protein; Belongs to the LysR transcriptional regulatory family. (294 aa)
gltRUnannotated protein; Belongs to the LysR transcriptional regulatory family. (283 aa)
dinB_1Unannotated protein; 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. (355 aa)
fixJ_2Unannotated protein. (213 aa)
luxRUnannotated protein. (246 aa)
dmlRUnannotated protein; Belongs to the LysR transcriptional regulatory family. (302 aa)
aroK_3Unannotated protein; Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate; Belongs to the shikimate kinase family. (252 aa)
dnaAUnannotated protein; 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. (460 aa)
dnaNUnannotated protein; 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 replication [...] (367 aa)
recFUnannotated protein; 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. (355 aa)
gyrBUnannotated protein; 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)
ihfBUnannotated protein; This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control. Belongs to the bacterial histone-like protein family. (103 aa)
cysLUnannotated protein; Belongs to the LysR transcriptional regulatory family. (295 aa)
parB_1Unannotated protein; Belongs to the ParB family. (291 aa)
priAUnannotated protein; 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. (758 aa)
nthUnannotated protein; 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. (210 aa)
repUnannotated protein; 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. (667 aa)
ompR_1Unannotated protein. (240 aa)
ybaBUnannotated protein; Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. (111 aa)
cmpRUnannotated protein; Belongs to the LysR transcriptional regulatory family. (301 aa)
nodD2Unannotated protein; Belongs to the LysR transcriptional regulatory family. (287 aa)
GCA_000236165_00326Unannotated protein; Belongs to the 'phage' integrase family. (324 aa)
nreCUnannotated protein. (191 aa)
aroK_2Unannotated protein; Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate; Belongs to the shikimate kinase family. (259 aa)
vjbRUnannotated protein. (267 aa)
GCA_000236165_00414Unannotated protein; Belongs to the 'phage' integrase family. (386 aa)
cbpAUnannotated protein. (294 aa)
birAUnannotated protein; Acts both as a biotin--[acetyl-CoA-carboxylase] ligase and a biotin-operon repressor. In the presence of ATP, BirA activates biotin to form the BirA-biotinyl-5'-adenylate (BirA-bio-5'-AMP or holoBirA) complex. HoloBirA can either transfer the biotinyl moiety to the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase, or bind to the biotin operator site and inhibit transcription of the operon. (328 aa)
qseF_2Unannotated protein. (471 aa)
mfdUnannotated protein; 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. (1151 aa)
hupBUnannotated protein; Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions. (92 aa)
fis_3Unannotated protein; Belongs to the transcriptional regulatory Fis family. (115 aa)
gyrAUnannotated protein; 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. (865 aa)
ompR_2Unannotated protein. (226 aa)
putAUnannotated protein; Oxidizes proline to glutamate for use as a carbon and nitrogen source; In the C-terminal section; belongs to the aldehyde dehydrogenase family. (1048 aa)
rpoEUnannotated protein; Belongs to the sigma-70 factor family. ECF subfamily. (207 aa)
GCA_000236165_01096Unannotated protein. (259 aa)
Your Current Organism:
Fluoribacter dumoffii
NCBI taxonomy Id: 1094715
Other names: F. dumoffii NY 23, Fluoribacter dumoffii ATCC 33279, Fluoribacter dumoffii NY 23, Fluoribacter dumoffii str. NY 23, Fluoribacter dumoffii strain NY 23
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