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Conserved domains on  [gi|2507793406|ref|WP_283140028|]
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restriction endonuclease subunit S [Bacteroides congonensis]

Protein Classification

restriction endonuclease subunit S( domain architecture ID 11432594)

type I restriction-modification system specificity (S) subunit (HsdS) dictates DNA sequence specificity; it consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs; each TRD binds to different specific sequences in the DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
303-370 2.17e-06

Restriction endonuclease S subunit [Defense mechanisms];


:

Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 45.43  E-value: 2.17e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2507793406 303 SEFDRYSRFNSWGSARETFDWSELCRAKIPLPPIEAQQSIVNLYHCMEEAKGVAAIAREKLKTICPAL 370
Cdd:COG0732     9 PSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDAL 76
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
117-184 2.63e-03

Restriction endonuclease S subunit [Defense mechanisms];


:

Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 36.58  E-value: 2.63e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2507793406 117 PEFDRYSRFNSWGSARETFDWEEFCRVDIPLPSIEVQRELVETYNGLKVLAEQNEVLVASLSKMCEAL 184
Cdd:COG0732     9 PSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDAL 76
 
Name Accession Description Interval E-value
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
303-370 2.17e-06

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 45.43  E-value: 2.17e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2507793406 303 SEFDRYSRFNSWGSARETFDWSELCRAKIPLPPIEAQQSIVNLYHCMEEAKGVAAIAREKLKTICPAL 370
Cdd:COG0732     9 PSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDAL 76
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
117-184 2.63e-03

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 36.58  E-value: 2.63e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2507793406 117 PEFDRYSRFNSWGSARETFDWEEFCRVDIPLPSIEVQRELVETYNGLKVLAEQNEVLVASLSKMCEAL 184
Cdd:COG0732     9 PSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDAL 76
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 138-184 6.43e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR),similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Salmonella enterica subsp. enterica serovar Potsdam S sub; Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3' and Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 both recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2.It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.


Pssm-ID: 341198 [Multi-domain]  Cd Length: 192  Bit Score: 37.52  E-value: 6.43e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2507793406 138 EEFCRVDIPLPSIEVQRELVETYNGLKVLAEQNEVLVASLSKMCEAL 184
Cdd:cd17517   142 KDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSL 188
RMtype1_S_Asp27244ORF1181P-TRD1-CR1_like cd17518
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 315-364 7.96e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter sp. S subunit (S.Asp27244ORF1181P) TRD1-CR1; The recognition sequence of Acinetobacter sp. S subunit (S.Asp27244ORF1181P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341199 [Multi-domain]  Cd Length: 180  Bit Score: 36.96  E-value: 7.96e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2507793406 315 GSARETFDWSELCRAKIPLPPIEAQQSIVNLYHCMEEAKGVAAIAREKLK 364
Cdd:cd17518   128 GGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIEAALEALRKKK 177
 
Name Accession Description Interval E-value
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
303-370 2.17e-06

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 45.43  E-value: 2.17e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2507793406 303 SEFDRYSRFNSWGSARETFDWSELCRAKIPLPPIEAQQSIVNLYHCMEEAKGVAAIAREKLKTICPAL 370
Cdd:COG0732     9 PSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDAL 76
HsdS COG0732
Restriction endonuclease S subunit [Defense mechanisms];
117-184 2.63e-03

Restriction endonuclease S subunit [Defense mechanisms];


Pssm-ID: 440496 [Multi-domain]  Cd Length: 88  Bit Score: 36.58  E-value: 2.63e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2507793406 117 PEFDRYSRFNSWGSARETFDWEEFCRVDIPLPSIEVQRELVETYNGLKVLAEQNEVLVASLSKMCEAL 184
Cdd:COG0732     9 PSFREYLRSLATGSTQPNLNKKDLKKLPIPLPPLEEQKRIVEILDSLFDKIAALEKEIEKLKELRDAL 76
RMtype1_S_EcoKI_StySPI-TRD2-CR2_like cd17517
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 138-184 6.43e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR),similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Salmonella enterica subsp. enterica serovar Potsdam S sub; Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3' and Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 both recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2.It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'.


Pssm-ID: 341198 [Multi-domain]  Cd Length: 192  Bit Score: 37.52  E-value: 6.43e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2507793406 138 EEFCRVDIPLPSIEVQRELVETYNGLKVLAEQNEVLVASLSKMCEAL 184
Cdd:cd17517   142 KDLKKLPIPLPPLEEQKEIVEILESLDSKIDLLEKKLEKLEQLFKSL 188
RMtype1_S_Asp27244ORF1181P-TRD1-CR1_like cd17518
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 315-364 7.96e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter sp. S subunit (S.Asp27244ORF1181P) TRD1-CR1; The recognition sequence of Acinetobacter sp. S subunit (S.Asp27244ORF1181P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341199 [Multi-domain]  Cd Length: 180  Bit Score: 36.96  E-value: 7.96e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2507793406 315 GSARETFDWSELCRAKIPLPPIEAQQSIVNLYHCMEEAKGVAAIAREKLK 364
Cdd:cd17518   128 GGAQPNFGPSHLKKIKIPLPPLEEQKRIAEILDDADDAIEAALEALRKKK 177
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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