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Shew_0002 Shew_0002 recF recF Shew_0126 Shew_0126 lexA lexA rep rep priA priA rapA rapA uvrA uvrA Shew_0535 Shew_0535 mutL mutL Shew_0772 Shew_0772 Shew_0924 Shew_0924 dnaG dnaG nfo nfo Shew_1142 Shew_1142 Shew_1182 Shew_1182 Shew_1196 Shew_1196 mutS mutS recA recA recX recX Shew_1264 Shew_1264 Shew_1452 Shew_1452 Shew_1453 Shew_1453 Shew_1454 Shew_1454 Shew_1532 Shew_1532 Shew_1580 Shew_1580 Shew_1587 Shew_1587 Shew_1682 Shew_1682 Shew_1799 Shew_1799 uvrC uvrC Shew_1838 Shew_1838 Shew_1871 Shew_1871 Shew_1892 Shew_1892 Shew_2024 Shew_2024 uvrB uvrB nth nth ruvB ruvB ruvA ruvA ruvC ruvC Shew_2078 Shew_2078 dnaE2 dnaE2 Shew_2101 Shew_2101 Shew_2102 Shew_2102 dnaQ dnaQ rnhA rnhA Shew_2196 Shew_2196 topA topA recR recR Shew_2234 Shew_2234 Shew_2235 Shew_2235 Shew_2262 Shew_2262 ligA ligA Shew_2456 Shew_2456 sbcD sbcD Shew_2482 Shew_2482 dinG dinG Shew_2487 Shew_2487 Shew_2620 Shew_2620 rnhB rnhB xni xni Shew_2807 Shew_2807 dinB dinB Shew_2931 Shew_2931 ung ung Shew_3278 Shew_3278 Shew_3385 Shew_3385 Shew_3474 Shew_3474 recG recG Shew_3508 Shew_3508 polA polA Shew_3853 Shew_3853 Shew_3854 Shew_3854 rsmG rsmG mnmG mnmG mnmE mnmE
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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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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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from curated databases
experimentally determined
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Shew_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 [...] (366 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. (360 aa)
Shew_0126Conserved hypothetical protein; 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. (169 aa)
lexASOS-response transcriptional repressor, LexA; 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. (205 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. (670 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. (731 aa)
rapASNF2-related 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. (968 aa)
uvrAExcinuclease ABC subunit A; 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)
Shew_0535Single-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. (220 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. (631 aa)
Shew_0772TIGRFAM: single-stranded-DNA-specific exonuclease RecJ; PFAM: phosphoesterase, RecJ domain protein; phosphoesterase, DHHA1; KEGG: shm:Shewmr7_3226 single-stranded-DNA-specific exonuclease RecJ. (574 aa)
Shew_0924PFAM: DNA polymerase III chi subunit, HolC; KEGG: shm:Shewmr7_1202 DNA polymerase III chi subunit, HolC. (153 aa)
dnaGDNA primase; RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. (601 aa)
nfoEndonuclease IV; Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin. (283 aa)
Shew_1142Putative transcriptional regulator; PFAM: AAA-4 family protein; KEGG: tbd:Tbd_1077 predicted transcriptional regulator. (462 aa)
Shew_1182PFAM: metallophosphoesterase; KEGG: she:Shewmr4_1086 metallophosphoesterase. (372 aa)
Shew_1196DNA repair protein RecN; May be involved in recombinational repair of damaged DNA. (553 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)
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. (150 aa)
Shew_1264PFAM: UvrD/REP helicase; KEGG: sty:HCM1.103 putative DNA helicase. (678 aa)
Shew_1452DNA-3-methyladenine glycosylase II / DNA-O6-methylguanine--protein-cysteine S-methyltransferase; PFAM: helix-turn-helix- domain containing protein, AraC type; Ada, metal-binding domain protein; AlkA domain protein; SMART: HhH-GPD family protein; KEGG: she:Shewmr4_1367 transcriptional regulator, AraC family. (503 aa)
Shew_1453methylated-DNA--protein-cysteine 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. (195 aa)
Shew_1454PFAM: helicase domain protein; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases-like; KEGG: son:SO3125 ATP-dependent RNA helicase, DEAD box family; Belongs to the DEAD box helicase family. (441 aa)
Shew_1532PFAM: helicase domain protein; type III restriction enzyme, res subunit; DEAD/DEAH box helicase domain protein; SMART: DEAD-like helicases-like; KEGG: shm:Shewmr7_2435 type III restriction enzyme, res subunit. (579 aa)
Shew_1580TIGRFAM: DNA polymerase III, delta prime subunit; KEGG: son:SO2612 DNA polymerase III, delta prime subunit. (304 aa)
Shew_1587PFAM: ATP dependent DNA ligase; KEGG: sfr:Sfri_1484 ATP dependent DNA ligase. (270 aa)
Shew_1682Ribonuclease H; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (254 aa)
Shew_1799PFAM: YebG family protein; KEGG: sdn:Sden_1719 YebG. (98 aa)
uvrCExcinuclease ABC subunit C; 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. (609 aa)
Shew_1838Regulatory inactivation of DnaA Hda protein; PFAM: Chromosomal replication initiator, DnaA; KEGG: shm:Shewmr7_1651 chromosomal replication initiator, DnaA; Belongs to the DnaA family. HdA subfamily. (236 aa)
Shew_1871KEGG: vfi:VFA0016 DNA polymerase III epsilon subunit (3'-5' exonuclease); TIGRFAM: DNA polymerase III, epsilon subunit; PFAM: Exonuclease, RNase T and DNA polymerase III; SMART: Exonuclease. (204 aa)
Shew_1892PFAM: SNF2-related protein; helicase domain protein; SMART: DEAD-like helicases-like; KEGG: pae:PA0799 probable helicase. (1161 aa)
Shew_2024DNA translocase FtsK; PFAM: cell divisionFtsK/SpoIIIE; KEGG: she:Shewmr4_1963 cell divisionFtsK/SpoIIIE. (841 aa)
uvrBExcinuclease ABC subunit B; 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 [...] (672 aa)
nthEndonuclease III / DNA-(apurinic or apyrimidinic site) lyase; 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. (213 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. (337 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. (205 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. (173 aa)
Shew_2078PFAM: protein of unknown function DUF28; KEGG: sdn:Sden_1886 protein of unknown function DUF28. (248 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. (1078 aa)
Shew_2101KEGG: bxe:Bxe_A3165 hypothetical protein. (684 aa)
Shew_2102KEGG: tbd:Tbd_0830 hypothetical protein. (276 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. (242 aa)
rnhARibonuclease H; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (158 aa)
Shew_2196SMART: helicase c2; DEAD-like helicases-like; KEGG: shm:Shewmr7_2172 helicase C2. (641 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 [...] (898 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. (199 aa)
Shew_2234Conserved hypothetical protein 103; Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. (109 aa)
Shew_2235KEGG: shm:Shewmr7_2326 DNA polymerase III, subunits gamma and tau; TIGRFAM: DNA polymerase III, subunits gamma and tau; PFAM: AAA ATPase, central domain protein; SMART: AAA ATPase. (1113 aa)
Shew_2262TIGRFAM: exodeoxyribonuclease III; exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase; KEGG: shm:Shewmr7_1513 exodeoxyribonuclease III. (269 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. (669 aa)
Shew_2456PFAM: SMC domain protein; KEGG: son:SO2843 exonuclease SbcC, putative. (1018 aa)
sbcDExodeoxyribonuclease I subunit D; 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. (380 aa)
Shew_2482PFAM: DNA polymerase B, exonuclease; DNA polymerase B region; SMART: DNA-directed DNA polymerase B; KEGG: she:Shewmr4_2469 DNA polymerase B region. (795 aa)
dinGHelicase c2; DNA-dependent ATPase and 5'-3' DNA helicase. (690 aa)
Shew_2487PFAM: histone deacetylase superfamily; KEGG: she:Shewmr4_2474 histone deacetylase superfamily. (300 aa)
Shew_2620KEGG: shm:Shewmr7_2693 DNA polymerase III, alpha subunit; TIGRFAM: DNA polymerase III, alpha subunit; PFAM: PHP C-terminal domain protein; nucleic acid binding, OB-fold, tRNA/helicase-type; SMART: phosphoesterase PHP domain protein. (1157 aa)
rnhBRNase HII; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids; Belongs to the RNase HII family. (208 aa)
xni5'-3' exonuclease; Has flap endonuclease activity. During DNA replication, flap endonucleases cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. (256 aa)
Shew_2807TIGRFAM: DNA repair protein RadA; KEGG: sfr:Sfri_1010 DNA repair protein RadA. (457 aa)
dinBDNA-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. (359 aa)
Shew_2931KEGG: son:SO1172 DNA polymerase III delta subunit; TIGRFAM: DNA polymerase III, delta subunit; PFAM: DNA polymerase III, delta. (343 aa)
ungUracil-DNA glycosylase; Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. (222 aa)
Shew_3278Primary replicative 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. (468 aa)
Shew_3385TIGRFAM: DNA helicase II; PFAM: UvrD/REP helicase; KEGG: she:Shewmr4_0473 DNA helicase II. (726 aa)
Shew_3474KEGG: son:SO4241 ATP-dependent DNA helicase RecQ; TIGRFAM: 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. (610 aa)
recGATP-dependent DNA helicase RecG; Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has a DNA unwinding activity characteristic of a DNA helicase with a 3'- to 5'- polarity. Unwinds branched duplex DNA (Y- DNA); Belongs to the helicase family. RecG subfamily. (691 aa)
Shew_3508KEGG: sfr:Sfri_0355 hypothetical protein. (290 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. (930 aa)
Shew_3853Chromosome segregation DNA-binding protein; TIGRFAM: parB-like partition proteins; PFAM: ParB domain protein nuclease; KEGG: shm:Shewmr7_4025 ParB-like partition proteins; Belongs to the ParB family. (292 aa)
Shew_3854Chromosome segregation ATPase; PFAM: Cobyrinic acid a,c-diamide synthase; KEGG: son:SO4756 ParA family protein. (262 aa)
rsmGMethyltransferase GidB; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. (234 aa)
mnmGGlucose inhibited division protein A; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family. (629 aa)
mnmEtRNA modification GTPase trmE; Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34; Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family. (453 aa)
Your Current Organism:
Shewanella loihica
NCBI taxonomy Id: 323850
Other names: S. loihica PV-4, Shewanella loihica PV-4, Shewanella loihica str. PV-4, Shewanella loihica strain PV-4, Shewanella sp. PV-4
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