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Conserved domains on  [gi|2747583665|ref|WP_350669771|]
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DpnI domain-containing protein, partial [Pseudoalteromonas sp. 43-MNA-CIBAN-0464]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DpnI super family cl05536
Dam-replacing family; Dam-replacing protein (DRP) is an restriction endonuclease that is ...
 1-50 1.29e-21

Dam-replacing family; Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis.


The actual alignment was detected with superfamily member pfam06044:

Pssm-ID: 428737  Cd Length: 182  Bit Score: 81.24  E-value: 1.29e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2747583665   1 MNLNFNKNLAANYKSPSQIIRVLSEDWVSNQSYCPNCNAQPLAEFTNNQP 50
Cdd:pfam06044   1 MNLFFDTSLAEEYKSASQKARVLTEDWVAKNSYCPNCGNKPLSQFENNRP 50
 
Name Accession Description Interval E-value
DpnI pfam06044
Dam-replacing family; Dam-replacing protein (DRP) is an restriction endonuclease that is ...
 1-50 1.29e-21

Dam-replacing family; Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis.


Pssm-ID: 428737  Cd Length: 182  Bit Score: 81.24  E-value: 1.29e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2747583665   1 MNLNFNKNLAANYKSPSQIIRVLSEDWVSNQSYCPNCNAQPLAEFTNNQP 50
Cdd:pfam06044   1 MNLFFDTSLAEEYKSASQKARVLTEDWVAKNSYCPNCGNKPLSQFENNRP 50
DpnI-like cd22319
type II restriction endonuclease DpnI and similar proteins; This catalytic PD-(D/E)XK domain ...
 6-50 6.37e-19

type II restriction endonuclease DpnI and similar proteins; This catalytic PD-(D/E)XK domain co-occurs with a C-terminal winged-helix DNA binding domain that is not included in the model. Both domains of R.DpnI bind DNA and are separately specific for the Gm6ATC sequences in Dam-methylated DNA. DpnI or Dam-replacing protein (DRP) is a restriction endonuclease flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis. Type II restriction endonuclease DpnI belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411723  Cd Length: 174  Bit Score: 74.16  E-value: 6.37e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2747583665   6 NKNLAANYKSPSQIIRVLSEDWVSNQSYCPNCNAQPLAEFTNNQP 50
Cdd:cd22319     1 DLELAEGYKSNSQKARVLTEAWVSRNLYCPACGSNKLKHFPNNKP 45
 
Name Accession Description Interval E-value
DpnI pfam06044
Dam-replacing family; Dam-replacing protein (DRP) is an restriction endonuclease that is ...
 1-50 1.29e-21

Dam-replacing family; Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis.


Pssm-ID: 428737  Cd Length: 182  Bit Score: 81.24  E-value: 1.29e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2747583665   1 MNLNFNKNLAANYKSPSQIIRVLSEDWVSNQSYCPNCNAQPLAEFTNNQP 50
Cdd:pfam06044   1 MNLFFDTSLAEEYKSASQKARVLTEDWVAKNSYCPNCGNKPLSQFENNRP 50
DpnI-like cd22319
type II restriction endonuclease DpnI and similar proteins; This catalytic PD-(D/E)XK domain ...
 6-50 6.37e-19

type II restriction endonuclease DpnI and similar proteins; This catalytic PD-(D/E)XK domain co-occurs with a C-terminal winged-helix DNA binding domain that is not included in the model. Both domains of R.DpnI bind DNA and are separately specific for the Gm6ATC sequences in Dam-methylated DNA. DpnI or Dam-replacing protein (DRP) is a restriction endonuclease flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis. Type II restriction endonuclease DpnI belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411723  Cd Length: 174  Bit Score: 74.16  E-value: 6.37e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2747583665   6 NKNLAANYKSPSQIIRVLSEDWVSNQSYCPNCNAQPLAEFTNNQP 50
Cdd:cd22319     1 DLELAEGYKSNSQKARVLTEAWVSRNLYCPACGSNKLKHFPNNKP 45
 
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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