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Conserved domains on  [gi|1631926143|ref|YP_009603966|]
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hypothetical protein FDH83_gp83 [Enterococcus phage IMEEF1]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PDDEXK_nuclease-like super family cl40440
PDDEXK family nucleases; Superfamily of PDDEXK nucleases including very short patch repair ...
 65-115 2.19e-03

PDDEXK family nucleases; Superfamily of PDDEXK 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.


The actual alignment was detected with superfamily member cd22315:

Pssm-ID: 477358  Cd Length: 288  Bit Score: 36.82  E-value: 2.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1631926143  65 AESNGEDWGDEMLLDSLYTDSEVLVTKYKHLLSEDQLESINNSIKNFAESA 115
Cdd:cd22315    26 AKNPADLLNIPDIRPALLTAAGLSDKAAKHLLEQDKQEAIKELIENFLEPA 76
 
Name Accession Description Interval E-value
BsoBI-like cd22315
Type II restriction endonuclease BsoBI and similar proteins; BsoBI is a thermophilic ...
 65-115 2.19e-03

Type II restriction endonuclease BsoBI and similar proteins; BsoBI is a thermophilic PDDEXK-family restriction endonuclease exhibiting both base-specific and degenerate recognition within the sequence C-Y-C-G-R-G. (R = A or G, Y = T or C) A conserved histidine has been proposed to act as a general base in the catalysis. BsoBI belongs to a wider 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: 411719  Cd Length: 288  Bit Score: 36.82  E-value: 2.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1631926143  65 AESNGEDWGDEMLLDSLYTDSEVLVTKYKHLLSEDQLESINNSIKNFAESA 115
Cdd:cd22315    26 AKNPADLLNIPDIRPALLTAAGLSDKAAKHLLEQDKQEAIKELIENFLEPA 76
 
Name Accession Description Interval E-value
BsoBI-like cd22315
Type II restriction endonuclease BsoBI and similar proteins; BsoBI is a thermophilic ...
 65-115 2.19e-03

Type II restriction endonuclease BsoBI and similar proteins; BsoBI is a thermophilic PDDEXK-family restriction endonuclease exhibiting both base-specific and degenerate recognition within the sequence C-Y-C-G-R-G. (R = A or G, Y = T or C) A conserved histidine has been proposed to act as a general base in the catalysis. BsoBI belongs to a wider 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: 411719  Cd Length: 288  Bit Score: 36.82  E-value: 2.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1631926143  65 AESNGEDWGDEMLLDSLYTDSEVLVTKYKHLLSEDQLESINNSIKNFAESA 115
Cdd:cd22315    26 AKNPADLLNIPDIRPALLTAAGLSDKAAKHLLEQDKQEAIKELIENFLEPA 76
 
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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