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Conserved domains on  [gi|818624528|gb|KKS72529|]
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50S ribosomal protein L7/L12 [candidate division WWE3 bacterium GW2011_GWD1_42_70]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11633 super family cl25866
cell division protein DedD; Provisional
 203-249 4.22e-04

cell division protein DedD; Provisional


The actual alignment was detected with superfamily member PRK11633:

Pssm-ID: 236940 [Multi-domain]  Cd Length: 226  Bit Score: 40.37  E-value: 4.22e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 818624528 203 ETKKSEARSVQKPVERKIVSPVKPKPTVKPEVKPESKSAPEPPKTQK 249
Cdd:PRK11633  86 DPATVAPPNTPVEPEPAPVEPPKPKPVEKPKPKPKPQQKVEAPPAPK 132
RMtype1_S_TRD-CR_like super family cl38903
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 27-68 4.75e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR) and similar domains; The restriction-modification (RM) system S subunit generally 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 superfamily represents a single TRD-CR unit; in addition to type I TRD-CR units, it includes RMtype1_S_TRD-CR_like domains of various putative Helicobacter type II restriction enzymes and methyltransferases, such as Hci611ORFHP and HfeORF12890P, as well as TRD-CR-like sequence-recognition domains of the M subunit of putative type I DNA methyltransferase such as M2.CinURNWORF2828P and M.Mae7806ORF3969P.


The actual alignment was detected with superfamily member cd17262:

Pssm-ID: 365779 [Multi-domain]  Cd Length: 172  Bit Score: 37.03  E-value: 4.75e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 818624528  27 NLEKISRILDN----IDKEKRKEMYKEMP-----GVSGY-----FDGTY-LIGEDGS 68
Cdd:cd17262    5 KLGEVVENLDSkripLSSEERERRQGNYPyygasGIVDYvddyiFDGEYvLIGEDGA 61
 
Name Accession Description Interval E-value
PRK11633 PRK11633
cell division protein DedD; Provisional
 203-249 4.22e-04

cell division protein DedD; Provisional


Pssm-ID: 236940 [Multi-domain]  Cd Length: 226  Bit Score: 40.37  E-value: 4.22e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 818624528 203 ETKKSEARSVQKPVERKIVSPVKPKPTVKPEVKPESKSAPEPPKTQK 249
Cdd:PRK11633  86 DPATVAPPNTPVEPEPAPVEPPKPKPVEKPKPKPKPQQKVEAPPAPK 132
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 27-68 4.75e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) TRD2-CR2 and Moraxella catarrhalis S subunit (S.Mca353ORF290P) TRD2; Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) recognizes 5'... GCANNNNNNTGT ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 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. 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341151 [Multi-domain]  Cd Length: 172  Bit Score: 37.03  E-value: 4.75e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 818624528  27 NLEKISRILDN----IDKEKRKEMYKEMP-----GVSGY-----FDGTY-LIGEDGS 68
Cdd:cd17262    5 KLGEVVENLDSkripLSSEERERRQGNYPyygasGIVDYvddyiFDGEYvLIGEDGA 61
 
Name Accession Description Interval E-value
PRK11633 PRK11633
cell division protein DedD; Provisional
 203-249 4.22e-04

cell division protein DedD; Provisional


Pssm-ID: 236940 [Multi-domain]  Cd Length: 226  Bit Score: 40.37  E-value: 4.22e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 818624528 203 ETKKSEARSVQKPVERKIVSPVKPKPTVKPEVKPESKSAPEPPKTQK 249
Cdd:PRK11633  86 DPATVAPPNTPVEPEPAPVEPPKPKPVEKPKPKPKPQQKVEAPPAPK 132
RMtype1_S_Aco12261I-TRD2-CR2 cd17262
Type I restriction-modification system specificity (S) subunit Target Recognition ...
 27-68 4.75e-03

Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) TRD2-CR2 and Moraxella catarrhalis S subunit (S.Mca353ORF290P) TRD2; Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) recognizes 5'... GCANNNNNNTGT ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 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. 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 may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.


Pssm-ID: 341151 [Multi-domain]  Cd Length: 172  Bit Score: 37.03  E-value: 4.75e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 818624528  27 NLEKISRILDN----IDKEKRKEMYKEMP-----GVSGY-----FDGTY-LIGEDGS 68
Cdd:cd17262    5 KLGEVVENLDSkripLSSEERERRQGNYPyygasGIVDYvddyiFDGEYvLIGEDGA 61
PRK11633 PRK11633
cell division protein DedD; Provisional
 212-250 5.80e-03

cell division protein DedD; Provisional


Pssm-ID: 236940 [Multi-domain]  Cd Length: 226  Bit Score: 37.29  E-value: 5.80e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 818624528 212 VQKPVERKIVSPVKPKPTVKPEVKPESKSAPEPPKTQKE 250
Cdd:PRK11633 103 PVEPPKPKPVEKPKPKPKPQQKVEAPPAPKPEPKPVVEE 141
 
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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