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dnaA dnaA Sps_00035 Sps_00035 recF recF Sps_00071 Sps_00071 polA polA mutM mutM Sps_00240 Sps_00240 Sps_00264 Sps_00264 lexA lexA Sps_00496 Sps_00496 Sps_00522 Sps_00522 Sps_00586 Sps_00586 uvrC uvrC Sps_00626 Sps_00626 Sps_00663 Sps_00663 Sps_00798 Sps_00798 Sps_00863 Sps_00863 Sps_01021 Sps_01021 Sps_01022 Sps_01022 Sps_01072 Sps_01072 uvrB uvrB nth nth ruvB ruvB ruvA ruvA ruvC ruvC Sps_01166 Sps_01166 dnaQ dnaQ rnhA rnhA Sps_01251 Sps_01251 Sps_01307 Sps_01307 Sps_01356 Sps_01356 Sps_01379 Sps_01379 Sps_01387 Sps_01387 Sps_01645 Sps_01645 topA topA recR recR Sps_01670 Sps_01670 Sps_01671 Sps_01671 Sps_01702 Sps_01702 topB topB Sps_01833 Sps_01833 sbcD sbcD Sps_01855 Sps_01855 dinG dinG Sps_02003 Sps_02003 Sps_02117 Sps_02117 rnhB rnhB Sps_02227 Sps_02227 Sps_02352 Sps_02352 nfo nfo Sps_02579 Sps_02579 Sps_02604 Sps_02604 Sps_02624 Sps_02624 xerD xerD Sps_02935 Sps_02935 uvrA uvrA rep rep Sps_03138 Sps_03138 Sps_03223 Sps_03223 Sps_03292 Sps_03292 recG recG Sps_03327 Sps_03327 Sps_03431 Sps_03431 Sps_03444 Sps_03444 ligA ligA Sps_03635 Sps_03635 Sps_03636 Sps_03636 Sps_03637 Sps_03637 Sps_03638 Sps_03638 Sps_03661 Sps_03661 Sps_03698 Sps_03698 recA recA mutS mutS Sps_04116 Sps_04116 Sps_04138 Sps_04138 Sps_04227 Sps_04227 dinB dinB Sps_04371 Sps_04371 Sps_04600 Sps_04600 ung ung sfsA sfsA mutL mutL Sps_05174 Sps_05174 rapA rapA priA priA coaE coaE Sps_05391 Sps_05391 Sps_05668 Sps_05668 Sps_05669 Sps_05669
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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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experimentally determined
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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. (462 aa)
Sps_00035DNA 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; Belongs to the RecF family. (365 aa)
Sps_00071PFAM: DNA recombination-mediator protein A; TIGRFAM: DNA protecting protein DprA. (331 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. (917 aa)
mutMDNA-(apurinic or apyrimidinic site) lyase; 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)
Sps_00240Putative amidophosphoribosyltransferase; PFAM: Phosphoribosyl transferase domain; TIGRFAM: comF family protein. (258 aa)
Sps_00264Cell division inhibitor SulA; 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. (170 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)
Sps_00496Hypothetical protein; PFAM: RecX family. (270 aa)
Sps_00522DNA/RNA helicase, superfamily II; 'PFAM: Helicase conserved C-terminal domain; Type III restriction enzyme, res subunit'. (592 aa)
Sps_00586PFAM: YebG protein. (101 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)
Sps_00626PFAM: Bacterial dnaA protein; TIGRFAM: DnaA regulatory inactivator Hda; Belongs to the DnaA family. (236 aa)
Sps_00663PFAM: Exonuclease; 'TIGRFAM: exonuclease, DNA polymerase III, epsilon subunit family'. (206 aa)
Sps_00798ATP-dependent DNA helicase, RecQ-like; PFAM: Helicase conserved C-terminal domain; DEAD/DEAH box helicase; 'TIGRFAM: ATP-dependent DNA helicase, RecQ family'. (654 aa)
Sps_00863PFAM: UvrD/REP helicase N-terminal domain. (989 aa)
Sps_01021PFAM: Peptidase S24-like; Belongs to the peptidase S24 family. (144 aa)
Sps_01022nucleotidyltransferase/DNA polymerase involved in DNA repair; PFAM: Domain of unknown function (DUF4113); impB/mucB/samB family C-terminal domain; impB/mucB/samB family. (417 aa)
Sps_01072DNA translocase FtsK; PFAM: Ftsk gamma domain; FtsK/SpoIIIE family; Domain of unknown function (DUF4117). (843 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 [...] (671 aa)
nthEndonuclease III; 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. (227 aa)
ruvBHolliday junction DNA helicase subunit 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. (339 aa)
ruvAHolliday junction DNA helicase subunit 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)
ruvCHolliday junction endonuclease 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)
Sps_01166PFAM: Transcriptional regulator; 'TIGRFAM: DNA-binding regulatory protein, YebC/PmpR family'. (248 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 HI; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (154 aa)
Sps_01251PFAM: Phage integrase family. (170 aa)
Sps_01307DNA helicase, Rad3; PFAM: Helicase C-terminal domain; DEAD/DEAH box helicase. (644 aa)
Sps_01356PFAM: Exonuclease; Exonuclease C-terminal. (470 aa)
Sps_01379PFAM: DNA ligase OB-like domain; ATP dependent DNA ligase domain. (285 aa)
Sps_01387'PFAM: DNA polymerase III, delta subunit'; 'TIGRFAM: DNA polymerase III, delta' subunit'. (304 aa)
Sps_01645DNA internalization-related competence protein ComEC/Rec2; PFAM: Competence protein; Domain of unknown function (DUF4131); Metallo-beta-lactamase superfamily; TIGRFAM: ComEC/Rec2-related protein; DNA internalization-related competence protein ComEC/Rec2. (763 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 [...] (919 aa)
recRDNA replication and repair 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)
Sps_01670DNA-binding protein, YbaB/EbfC family; Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. (109 aa)
Sps_01671'PFAM: DNA polymerase III tau subunit V interacting with alpha; DNA polymerase III subunits gamma and tau domain III; DNA polymerase III, delta subunit'; 'TIGRFAM: DNA polymerase III, delta' subunit; DNA polymerase III, subunit gamma and tau'. (940 aa)
Sps_01702Exodeoxyribonuclease III; PFAM: Endonuclease/Exonuclease/phosphatase family; TIGRFAM: exodeoxyribonuclease III; exodeoxyribonuclease III (xth). (268 aa)
topBDNA topoisomerase III; 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 su [...] (649 aa)
Sps_01833ATPase involved in DNA repair; 'PFAM: AAA domain; Putative exonuclease SbcCD, C subunit'; TIGRFAM: exonuclease SbcC. (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. (381 aa)
Sps_01855'PFAM: DNA polymerase family B; DNA polymerase family B, exonuclease domain'. (811 aa)
dinGDNA helicase, Rad3; DNA-dependent ATPase and 5'-3' DNA helicase. (701 aa)
Sps_02003Ribonuclease HI; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (255 aa)
Sps_02117PFAM: Bacterial DNA polymerase III alpha subunit; PHP domain; OB-fold nucleic acid binding domain; Helix-hairpin-helix motif; TIGRFAM: DNA-directed DNA polymerase III (polc). (1157 aa)
rnhBRNase HII; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (218 aa)
Sps_02227'PFAM: 5'-3' exonuclease, C-terminal SAM fold; 5'-3' exonuclease, N-terminal resolvase-like domain'. (252 aa)
Sps_02352A/G-specific DNA-adenine glycosylase; Adenine glycosylase active on G-A mispairs. (364 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. (284 aa)
Sps_02579PFAM: FKBP-type peptidyl-prolyl cis-trans isomerase; Domain amino terminal to FKBP-type peptidyl-prolyl isomerase. (156 aa)
Sps_02604PFAM: FKBP-type peptidyl-prolyl cis-trans isomerase; Domain amino terminal to FKBP-type peptidyl-prolyl isomerase. (263 aa)
Sps_02624Exonuclease RecJ; PFAM: DHHA1 domain; DHH family; TIGRFAM: single-stranded-DNA-specific exonuclease RecJ. (574 aa)
xerDTyrosine recombinase XerD; Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC- XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids. (305 aa)
Sps_02935Single-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. (238 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. (944 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)
Sps_03138PFAM: UvrD-like helicase C-terminal domain; UvrD/REP helicase N-terminal domain; TIGRFAM: DNA helicase II. (721 aa)
Sps_03223Mg chelatase-related protein; 'PFAM: Magnesium chelatase, subunit ChlI; Subunit ChlI of Mg-chelatase'; TIGRFAM: Mg chelatase-related protein. (507 aa)
Sps_03292ATP-dependent DNA helicase RecQ; PFAM: Helicase conserved C-terminal domain; RQC domain; HRDC domain; DEAD/DEAH box helicase; 'TIGRFAM: ATP-dependent DNA helicase RecQ; ATP-dependent DNA helicase, RecQ family'. (608 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. (706 aa)
Sps_03327PFAM: Protein of unknown function (DUF3014). (284 aa)
Sps_03431PFAM: Exonuclease; 'TIGRFAM: exonuclease, DNA polymerase III, epsilon subunit family'. (227 aa)
Sps_03444TIGRFAM: tape measure domain. (970 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. (682 aa)
Sps_03635DNA/RNA helicase, superfamily II; PFAM: Helicase conserved C-terminal domain; DEAD/DEAH box helicase; Belongs to the DEAD box helicase family. (431 aa)
Sps_03636O-6-methylguanine DNA 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. (187 aa)
Sps_03637DNA-3-methyladenine glycosylase II; PFAM: Helix-turn-helix domain; Metal binding domain of Ada; AlkA N-terminal domain; HhH-GPD superfamily base excision DNA repair protein. (510 aa)
Sps_03638ABC-type multidrug transport system, ATPase and permease component; PFAM: ABC transporter; ABC transporter transmembrane region. (609 aa)
Sps_03661PFAM: FKBP-type peptidyl-prolyl cis-trans isomerase. (113 aa)
Sps_03698PFAM: DHHA1 domain. (318 aa)
recAProtein RecA; 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. (352 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)
Sps_04116DNA replication and repair protein RecN; May be involved in recombinational repair of damaged DNA. (553 aa)
Sps_04138PFAM: Calcineurin-like phosphoesterase. (371 aa)
Sps_04227DNA repair protein RadA; PFAM: Subunit ChlI of Mg-chelatase; AAA domain; TIGRFAM: DNA repair protein RadA. (457 aa)
dinBnucleotidyltransferase/DNA polymerase involved in DNA repair; 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. (353 aa)
Sps_04371DNA polymerase III, delta subunit; 'PFAM: Processivity clamp loader gamma complex DNA pol III C-term; DNA polymerase III, delta subunit'; 'TIGRFAM: DNA polymerase III, delta subunit'. (346 aa)
Sps_04600'PFAM: DNA polymerase III chi subunit, HolC'. (156 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)
sfsAPFAM: Sugar fermentation stimulation protein; TIGRFAM: sugar fermentation stimulation protein; Belongs to the SfsA family. (238 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. (621 aa)
Sps_05174Primary 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)
rapADNA/RNA helicase, superfamily II, SNF2 family; 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)
priAReplication restart DNA helicase PriA; 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)
coaEdephospho-CoA kinase; Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; Belongs to the CoaE family. (201 aa)
Sps_053918-oxo-dGTPase; PFAM: NUDIX domain; TIGRFAM: mutator mutT protein; Belongs to the Nudix hydrolase family. (136 aa)
Sps_05668Chromosome segregation DNA-binding protein; PFAM: ParB-like nuclease domain; TIGRFAM: ParB/RepB/Spo0J family partition protein; Belongs to the ParB family. (295 aa)
Sps_05669Chromosome segregation ATPase; PFAM: CobQ/CobB/MinD/ParA nucleotide binding domain. (262 aa)
Your Current Organism:
Shewanella psychrophila
NCBI taxonomy Id: 225848
Other names: CGMCC 1.6159, JCM 13876, S. psychrophila, Shewanella psychrophila Xiao et al. 2007 emend. Thorell et al. 2019, Shewanella sp. WP2, strain WP2
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