PDDEXK family nucleases; Superfamily of PDDEXK nucleases including very short patch repair ...
465-626
4.35e-17
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 cd22343:
Pssm-ID: 477358 [Multi-domain] Cd Length: 182 Bit Score: 80.46 E-value: 4.35e-17
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
465-626
4.35e-17
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a diverse set of nucleases such as alkaline exonuclease from Laribacter hongkongensis, lambda phage exonuclease, or a Cas4-like protein from the Mimivirus virophage resistance element system. They belong 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: 411747 [Multi-domain] Cd Length: 182 Bit Score: 80.46 E-value: 4.35e-17
putative phage-type endonuclease; Members of this protein family are found often in phage ...
465-603
3.37e-11
putative phage-type endonuclease; Members of this protein family are found often in phage genomes and in prokaryotic genomes in uncharacterized regions that resemble integrated prophage regions.
Pssm-ID: 200235 [Multi-domain] Cd Length: 153 Bit Score: 62.83 E-value: 3.37e-11
Membrane-bound lytic murein transglycosylase D and similar proteins; Lytic transglycosylases ...
1099-1208
9.60e-10
Membrane-bound lytic murein transglycosylase D and similar proteins; Lytic transglycosylases (LT) catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc). Membrane-bound lytic murein transglycosylase D protein (MltD) family members may have one or more small LysM domains, which may contribute to peptidoglycan binding. Unlike the similar "goose-type" lysozymes, LTs also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as the eukaryotic "goose-type" lysozymes (goose egg-white lysozyme; GEWL).
Pssm-ID: 381615 [Multi-domain] Cd Length: 129 Bit Score: 57.91 E-value: 9.60e-10
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial ...
470-599
4.08e-09
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.
Pssm-ID: 430702 [Multi-domain] Cd Length: 142 Bit Score: 56.22 E-value: 4.08e-09
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found ...
1099-1193
3.20e-08
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found in phages, type II, type III and type IV secretion systems.
Pssm-ID: 396169 [Multi-domain] Cd Length: 114 Bit Score: 53.08 E-value: 3.20e-08
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
465-626
4.35e-17
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a diverse set of nucleases such as alkaline exonuclease from Laribacter hongkongensis, lambda phage exonuclease, or a Cas4-like protein from the Mimivirus virophage resistance element system. They belong 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: 411747 [Multi-domain] Cd Length: 182 Bit Score: 80.46 E-value: 4.35e-17
putative phage-type endonuclease; Members of this protein family are found often in phage ...
465-603
3.37e-11
putative phage-type endonuclease; Members of this protein family are found often in phage genomes and in prokaryotic genomes in uncharacterized regions that resemble integrated prophage regions.
Pssm-ID: 200235 [Multi-domain] Cd Length: 153 Bit Score: 62.83 E-value: 3.37e-11
Membrane-bound lytic murein transglycosylase D and similar proteins; Lytic transglycosylases ...
1099-1208
9.60e-10
Membrane-bound lytic murein transglycosylase D and similar proteins; Lytic transglycosylases (LT) catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc). Membrane-bound lytic murein transglycosylase D protein (MltD) family members may have one or more small LysM domains, which may contribute to peptidoglycan binding. Unlike the similar "goose-type" lysozymes, LTs also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as the eukaryotic "goose-type" lysozymes (goose egg-white lysozyme; GEWL).
Pssm-ID: 381615 [Multi-domain] Cd Length: 129 Bit Score: 57.91 E-value: 9.60e-10
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial ...
470-599
4.08e-09
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.
Pssm-ID: 430702 [Multi-domain] Cd Length: 142 Bit Score: 56.22 E-value: 4.08e-09
70kDa soluble lytic transglycosylase (Slt70) and similar proteins; Catalytic domain of the ...
1116-1200
1.99e-08
70kDa soluble lytic transglycosylase (Slt70) and similar proteins; Catalytic domain of the 70kda soluble lytic transglycosylase (LT)-like proteins, which also have an N-terminal U-shaped U-domain and a linker L-domain. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do "goose-type" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda.
Pssm-ID: 381604 [Multi-domain] Cd Length: 152 Bit Score: 54.79 E-value: 1.99e-08
lytic transglycosylase(LT)-like domain; Members include the soluble and insoluble ...
1118-1191
2.66e-08
lytic transglycosylase(LT)-like domain; Members include the soluble and insoluble membrane-bound LTs in bacteria and LTs in bacteriophage lambda. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do "goose-type" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue.
Pssm-ID: 381594 [Multi-domain] Cd Length: 111 Bit Score: 52.99 E-value: 2.66e-08
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found ...
1099-1193
3.20e-08
Transglycosylase SLT domain; This family is distantly related to pfam00062. Members are found in phages, type II, type III and type IV secretion systems.
Pssm-ID: 396169 [Multi-domain] Cd Length: 114 Bit Score: 53.08 E-value: 3.20e-08
membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily ...
1098-1199
6.45e-03
membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins; This subfamily includes membrane-bound lytic murein transglycosylase F (MltF, murein lyase F) that degrades murein glycan strands. It is responsible for catalyzing the release of 1,6-anhydromuropeptides from peptidoglycan. Lytic transglycosylase catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc) as do goose-type lysozymes. However, in addition, it also makes a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue.
Pssm-ID: 381606 [Multi-domain] Cd Length: 161 Bit Score: 38.67 E-value: 6.45e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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