STRINGSTRING
Bphy_0057 Bphy_0057 Bphy_2071 Bphy_2071 Bphy_1980 Bphy_1980 dnaE2 dnaE2 uvrB uvrB Bphy_1929 Bphy_1929 Bphy_1901 Bphy_1901 Bphy_1889 Bphy_1889 Bphy_1856 Bphy_1856 Bphy_1855 Bphy_1855 Bphy_1854 Bphy_1854 recC recC recB recB recD recD rnr rnr Bphy_1640 Bphy_1640 Bphy_1549 Bphy_1549 Bphy_1478 Bphy_1478 Bphy_1448 Bphy_1448 Bphy_1444 Bphy_1444 rnhB rnhB Bphy_1246 Bphy_1246 Bphy_1105 Bphy_1105 Bphy_1045 Bphy_1045 Bphy_0981 Bphy_0981 Bphy_0964 Bphy_0964 Bphy_0963 Bphy_0963 rnhA rnhA dnaQ dnaQ uvrC uvrC rnc rnc rne rne orn orn Bphy_0734 Bphy_0734 Bphy_0677 Bphy_0677 Bphy_0668 Bphy_0668 rph rph Bphy_0633 Bphy_0633 Bphy_0623 Bphy_0623 Bphy_0541 Bphy_0541 xseA xseA ybeY ybeY uvrA uvrA Bphy_0123 Bphy_0123 Bphy_0119 Bphy_0119 Bphy_0102 Bphy_0102 Bphy_0002 Bphy_0002 Bphy_5537 Bphy_5537 Bphy_5411 Bphy_5411 Bphy_5308 Bphy_5308 Bphy_5216 Bphy_5216 Bphy_5199 Bphy_5199 Bphy_5070 Bphy_5070 Bphy_4772 Bphy_4772 Bphy_4681 Bphy_4681 Bphy_4582 Bphy_4582 polA polA Bphy_4196 Bphy_4196 Bphy_4118 Bphy_4118 xseB xseB Bphy_3641 Bphy_3641 Bphy_3555 Bphy_3555 Bphy_3551 Bphy_3551 Bphy_3414 Bphy_3414 Bphy_3405 Bphy_3405 Bphy_3341 Bphy_3341 Bphy_3106 Bphy_3106 rnpA rnpA Bphy_3002 Bphy_3002 Bphy_2626 Bphy_2626 Bphy_2623 Bphy_2623 Bphy_2603 Bphy_2603 ruvC ruvC Bphy_2326 Bphy_2326 Bphy_2171 Bphy_2171 Bphy_2141 Bphy_2141 Bphy_2134 Bphy_2134 Bphy_2079 Bphy_2079
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
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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:
Bphy_0057KEGG: bxe:Bxe_A4393 exodeoxyribonucleaseIII xth; TIGRFAM: exodeoxyribonuclease III; exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase. (259 aa)
Bphy_2071TIGRFAM: ribonuclease, Rne/Rng family; PFAM: RNA binding S1 domain protein; KEGG: bxe:Bxe_A3267 ribonuclease E and G. (489 aa)
Bphy_1980KEGG: bxe:Bxe_A3181 protein of unknown function DUF132. (171 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. (1049 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 [...] (697 aa)
Bphy_1929KEGG: bvi:Bcep1808_2388 hypothetical protein. (120 aa)
Bphy_1901KEGG: aav:Aave_1600 hypothetical protein. (120 aa)
Bphy_1889PFAM: terminase GpA; KEGG: ecx:EcHS_A2094 phage terminase large subunit (GpA). (675 aa)
Bphy_1856PFAM: YcfA family protein; KEGG: reh:H16_B2374 hypothetical protein. (71 aa)
Bphy_1855PFAM: ATP dependent DNA ligase; KEGG: afw:Anae109_0939 DNA ligase D. (205 aa)
Bphy_1854KEGG: bvi:Bcep1808_4079 hypothetical protein. (101 aa)
recCExodeoxyribonuclease V, gamma subunit; A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and r [...] (1121 aa)
recBExodeoxyribonuclease V, beta subunit; A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and re [...] (1241 aa)
recDExodeoxyribonuclease V, alpha subunit; A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and r [...] (672 aa)
rnrRibonuclease R; 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs. (817 aa)
Bphy_1640KEGG: bxe:Bxe_A2479 putative cytoplasmic protein. (70 aa)
Bphy_1549Excinuclease 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. (1997 aa)
Bphy_1478TIGRFAM: exodeoxyribonuclease III; exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase; KEGG: bxe:Bxe_A1526 exodeoxyribonucleaseIII xth. (258 aa)
Bphy_1448TIGRFAM: single-stranded-DNA-specific exonuclease RecJ; PFAM: phosphoesterase RecJ domain protein; phosphoesterase DHHA1; KEGG: bxe:Bxe_A1564 RecJ exonuclease. (577 aa)
Bphy_1444PFAM: TatD-related deoxyribonuclease; KEGG: bxe:Bxe_A1568 putative TatD-related deoxyribonuclease. (262 aa)
rnhBRibonuclease H; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (249 aa)
Bphy_1246KEGG: bxe:Bxe_A1989 hypothetical protein. (171 aa)
Bphy_1105PFAM: beta-lactamase domain protein; RNA-metabolising metallo-beta-lactamase; KEGG: bvi:Bcep1808_6325 beta-lactamase domain protein. (454 aa)
Bphy_1045TIGRFAM: hydrolase, TatD family; PFAM: TatD-related deoxyribonuclease; KEGG: bxe:Bxe_A2260 TatD-related deoxyribonuclease. (263 aa)
Bphy_0981TIGRFAM: DNA ligase D; DNA ligase D, 3'-phosphoesterase domain protein; DNA polymerase LigD, polymerase domain protein; DNA polymerase LigD, ligase domain protein; PFAM: DNA primase small subunit; ATP dependent DNA ligase domain protein; ATP dependent DNA ligase; KEGG: bxe:Bxe_A2328 putative ATP-dependent DNA ligase. (954 aa)
Bphy_0964PFAM: Endonuclease/exonuclease/phosphatase; KEGG: bvi:Bcep1808_1745 endonuclease/exonuclease/phosphatase. (287 aa)
Bphy_0963KEGG: bur:Bcep18194_A5120 3'-5' exonuclease related to the exonuclease domain of PolB. (258 aa)
rnhARibonuclease H; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (148 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)
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. (740 aa)
rncRibonuclease III; Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. (441 aa)
rneRibonuclease, Rne/Rng family; Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs. Belongs to the RNase E/G family. RNase E subfamily. (1092 aa)
ornExonuclease RNase T and DNA polymerase III; 3'-to-5' exoribonuclease specific for small oligoribonucleotides; Belongs to the oligoribonuclease family. (207 aa)
Bphy_0734GP29; KEGG: bam:Bamb_5365 GP29. (86 aa)
Bphy_0677KEGG: bxe:Bxe_A0914 DNA polymerase III, epsilon subunit; TIGRFAM: DNA polymerase III, epsilon subunit; PFAM: Excinuclease ABC C subunit domain protein; Exonuclease RNase T and DNA polymerase III; SMART: Exonuclease. (392 aa)
Bphy_0668PFAM: YicC domain protein; domain of unknown function DUF1732; KEGG: bxe:Bxe_A0904 conserved hypothetical protein 255. (319 aa)
rphRibonuclease PH; Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. (246 aa)
Bphy_0633PFAM: Smr protein/MutS2; KEGG: bxe:Bxe_A3443 hypothetical protein. (266 aa)
Bphy_0623KEGG: bxe:Bxe_A0897 hypothetical protein. (216 aa)
Bphy_0541PFAM: protein of unknown function DUF88; KEGG: bxe:Bxe_A0775 hypothetical protein. (440 aa)
xseAExodeoxyribonuclease 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. (459 aa)
ybeYProtein of unknown function UPF0054; Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. (153 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. (1032 aa)
Bphy_0123PFAM: protein of unknown function UPF0102; KEGG: bxe:Bxe_A4313 protein of unknown function UPF0102; Belongs to the UPF0102 family. (156 aa)
Bphy_0119KEGG: bxe:Bxe_A4318 hypothetical protein. (204 aa)
Bphy_0102PFAM: Endonuclease/exonuclease/phosphatase; KEGG: bxe:Bxe_A4337 putative metal-dependent hydrolase. (265 aa)
Bphy_0002DNA 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)
Bphy_5537TIGRFAM: exodeoxyribonuclease III; exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase; KEGG: rme:Rmet_4910 exodeoxyribonuclease III (xth). (308 aa)
Bphy_5411PFAM: Endonuclease/exonuclease/phosphatase; KEGG: bam:Bamb_5588 endonuclease/exonuclease/phosphatase. (250 aa)
Bphy_5308VRR-NUC domain protein; Nuclease required for the repair of DNA interstrand cross- links (ICL). Acts as a 5'-3' exonuclease that anchors at a cut end of DNA and cleaves DNA successively at every third nucleotide, allowing to excise an ICL from one strand through flanking incisions. Belongs to the FAN1 family. (571 aa)
Bphy_5216PFAM: metallophosphoesterase; KEGG: bxe:Bxe_B1235 putative exonuclease. (370 aa)
Bphy_5199KEGG: bvi:Bcep1808_2388 hypothetical protein. (90 aa)
Bphy_5070TIGRFAM: phosphonoacetate hydrolase; PFAM: type I phosphodiesterase/nucleotide pyrophosphatase; KEGG: bxe:Bxe_B1870 putative phosphonoacetate hydrolase. (423 aa)
Bphy_4772TIGRFAM: DNA ligase D; DNA polymerase LigD, polymerase domain protein; DNA polymerase LigD, ligase domain protein; PFAM: DNA primase small subunit; ATP dependent DNA ligase; KEGG: bvi:Bcep1808_6891 ATP dependent DNA ligase. (651 aa)
Bphy_4681KEGG: bxe:Bxe_B1314 putative exonuclease involved in mRNA processing. (350 aa)
Bphy_4582KEGG: rso:RSc2263 probable lipoprotein. (391 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. (915 aa)
Bphy_4196PFAM: metal-dependent phosphohydrolase HD sub domain; KEGG: bxe:Bxe_B3003 metal dependent phosphohydrolase, HD region. (229 aa)
Bphy_4118PFAM: DNA/RNA non-specific endonuclease; KEGG: pol:Bpro_5415 DNA/RNA non-specific endonuclease. (249 aa)
xseBExodeoxyribonuclease VII, 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. (105 aa)
Bphy_3641GP29; KEGG: bam:Bamb_5365 GP29. (83 aa)
Bphy_3555KEGG: reu:Reut_C6131 metal-dependent phosphohydrolase, HD subdomain; TIGRFAM: metal dependent phophohydrolase; PFAM: metal-dependent phosphohydrolase HD sub domain; SMART: metal-dependent phosphohydrolase HD region. (257 aa)
Bphy_3551PFAM: metal-dependent phosphohydrolase HD sub domain; KEGG: reu:Reut_C6136 metal-dependent phosphohydrolase, HD subdomain. (219 aa)
Bphy_3414Phage-related protein predicted endonuclease-like protein; KEGG: bld:BLi01440 YqaJ. (303 aa)
Bphy_3405PFAM: HNH endonuclease; SMART: HNH nuclease; KEGG: shw:Sputw3181_2485 HNH endonuclease. (107 aa)
Bphy_3341PFAM: protein of unknown function DUF796; KEGG: bxe:Bxe_A2091 putative cytoplasmic protein. (160 aa)
Bphy_3106KEGG: pnu:Pnuc_1610 hypothetical protein. (106 aa)
rnpARibonuclease P protein component; RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. (169 aa)
Bphy_3002KEGG: bml:BMA10299_A1540 putative lipoprotein. (119 aa)
Bphy_2626KEGG: bxe:Bxe_A0535 hypothetical protein. (217 aa)
Bphy_2623PFAM: ribonuclease II; KEGG: bxe:Bxe_A0538 putative ribonuclease II. (701 aa)
Bphy_2603PFAM: guanine-specific ribonuclease N1 and T1; KEGG: bxe:Bxe_A0559 putative guanyl-specific ribonuclease signal peptide protein. (133 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. (180 aa)
Bphy_2326Holliday junction resolvase YqgF; Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA; Belongs to the YqgF nuclease family. (151 aa)
Bphy_2171PFAM: Excinuclease ABC C subunit domain protein; KEGG: bxe:Bxe_A3398 hypothetical protein. (110 aa)
Bphy_2141DNA mismatch endonuclease Vsr; May nick specific sequences that contain T:G mispairs resulting from m5C-deamination. (148 aa)
Bphy_2134Restriction endonuclease-like protein; KEGG: bat:BAS3519 putative restriction endonuclease. (431 aa)
Bphy_2079KEGG: bxe:Bxe_A3292 DNA polymerase III alpha subunit; TIGRFAM: DNA polymerase III, alpha subunit; PFAM: PHP domain protein; nucleic acid binding OB-fold tRNA/helicase-type; DNA polymerase III alpha subunit; SMART: phosphoesterase PHP domain protein. (1187 aa)
Your Current Organism:
Paraburkholderia phymatum
NCBI taxonomy Id: 391038
Other names: Burkholderia phymatum STM815, Burkholderia sp. STM815, P. phymatum STM815, Paraburkholderia phymatum STM815
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