STRINGSTRING
Swit_0197 Swit_0197 nth nth polA polA mutL mutL recA recA Swit_0547 Swit_0547 Swit_0549 Swit_0549 Swit_0551 Swit_0551 Swit_0614 Swit_0614 Swit_0874 Swit_0874 Swit_1120 Swit_1120 Swit_1121 Swit_1121 Swit_1127 Swit_1127 apaG apaG Swit_1220 Swit_1220 Swit_1248 Swit_1248 mfd mfd Swit_1914 Swit_1914 Swit_1938 Swit_1938 ruvB ruvB ruvA ruvA ruvC ruvC Swit_2198 Swit_2198 Swit_2247 Swit_2247 Swit_2427 Swit_2427 Swit_2524 Swit_2524 Swit_2536 Swit_2536 Swit_2681 Swit_2681 mutS mutS recF recF Swit_2843 Swit_2843 uvrA uvrA ung ung lexA lexA dinB dinB Swit_3788 Swit_3788 Swit_3911 Swit_3911 Swit_3959 Swit_3959 Swit_3979 Swit_3979 ku ku Swit_3982 Swit_3982 recR recR Swit_4063 Swit_4063 radA radA Swit_4095 Swit_4095 uvrC uvrC recO recO uvrB uvrB Swit_4680 Swit_4680 Swit_4690 Swit_4690 ligA ligA Swit_4729 Swit_4729 Swit_4733 Swit_4733 mutM mutM
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:
Swit_0197Hypothetical protein. (1414 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. (218 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. (941 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. (594 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. (357 aa)
Swit_0547DNA-3-methyladenine glycosylase II; PFAM: HhH-GPD family protein. (212 aa)
Swit_0549DNA-N1-methyladenine dioxygenase; PFAM: 2OG-Fe(II) oxygenase. (214 aa)
Swit_0551TIGRFAM: methylated-DNA--protein-cysteine methyltransferase; PFAM: Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding. (169 aa)
Swit_0614PFAM: NUDIX hydrolase; Belongs to the Nudix hydrolase family. (135 aa)
Swit_0874PFAM: protein of unknown function DUF1006. (494 aa)
Swit_1120Nucleotidyltransferase/DNA polymerase involved in DNA repair-like protein. (515 aa)
Swit_1121Conserved hypothetical protein. (268 aa)
Swit_1127DNA-O6-methylguanine--protein-cysteine S-methyltransferase / Transcriptional regulator Ada; TIGRFAM: methylated-DNA--protein-cysteine methyltransferase; PFAM: helix-turn-helix- domain containing protein, AraC type; Ada, metal-binding domain protein; Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding. (351 aa)
apaGPFAM: ApaG domain protein. (134 aa)
Swit_1220PFAM: Uracil-DNA glycosylase superfamily. (232 aa)
Swit_1248methylated-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. (163 aa)
mfdTranscription-repair coupling factor; 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. (1195 aa)
Swit_1914TIGRFAM: 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. (588 aa)
Swit_1938Hypothetical protein. (288 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. (342 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. (199 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. (165 aa)
Swit_2198TIGRFAM: single-strand binding protein; PFAM: single-strand binding protein/Primosomal replication protein n. (151 aa)
Swit_2247PFAM: ThiJ/PfpI domain protein. (227 aa)
Swit_2427PFAM: HhH-GPD family protein. (368 aa)
Swit_2524PFAM: ThiJ/PfpI domain protein. (234 aa)
Swit_2536T/G mismatch-specific endonuclease; May nick specific sequences that contain T:G mispairs resulting from m5C-deamination. (141 aa)
Swit_2681TIGRFAM: Double-strand break repair helicase AddA; PFAM: UvrD/REP helicase; Belongs to the helicase family. UvrD subfamily. (1142 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. (904 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. (356 aa)
Swit_2843TIGRFAM: methylated-DNA--protein-cysteine methyltransferase; PFAM: Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding. (162 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. (988 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. (261 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. (224 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. (380 aa)
Swit_3788TIGRFAM: exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase. (285 aa)
Swit_3911TIGRFAM: exodeoxyribonuclease III; exodeoxyribonuclease III Xth; PFAM: Endonuclease/exonuclease/phosphatase. (271 aa)
Swit_3959PFAM: Uracil-DNA glycosylase superfamily. (190 aa)
Swit_3979PFAM: ATP dependent DNA ligase domain protein; ATP dependent DNA ligase. (532 aa)
kuKu family containing 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. (285 aa)
Swit_3982TIGRFAM: DNA ligase D; DNA ligase D, 3'-phosphoesterase domain; DNA polymerase LigD, polymerase domain; DNA polymerase LigD, ligase region; PFAM: DNA primase, small subunit; ATP dependent DNA ligase domain protein; ATP dependent DNA ligase. (837 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. (198 aa)
Swit_4063Hypothetical protein. (233 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. (455 aa)
Swit_4095PFAM: Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB. (362 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. (642 aa)
recODNA repair protein RecO; Involved in DNA repair and RecF pathway recombination. (243 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 [...] (815 aa)
Swit_4680TIGRFAM: DNA-3-methyladenine glycosylase I; PFAM: methyladenine glycosylase. (185 aa)
Swit_4690A/G-specific DNA-adenine glycosylase; Adenine glycosylase active on G-A mispairs. (344 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. (708 aa)
Swit_4729DNA repair protein RecN; May be involved in recombinational repair of damaged DNA. (553 aa)
Swit_4733TIGRFAM: single-stranded-DNA-specific exonuclease RecJ; PFAM: phosphoesterase, RecJ domain protein; phosphoesterase, DHHA1. (588 aa)
mutMFormamidopyrimidine-DNA glycosylase / DNA-(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. (270 aa)
Your Current Organism:
Sphingomonas wittichii
NCBI taxonomy Id: 392499
Other names: S. wittichii RW1, Sphingomonas sp. RW1, Sphingomonas wittichii DSM 6014, Sphingomonas wittichii RW1, Sphingomonas wittichii str. RW1, Sphingomonas wittichii strain RW1
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