Species | Paenibacillus amylolyticus | |||||||||||
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Lineage | Bacteria; Firmicutes; Bacilli; Paenibacillales; Paenibacillaceae; Paenibacillus; Paenibacillus amylolyticus | |||||||||||
CAZyme ID | MGYG000003072_03610 | |||||||||||
CAZy Family | CE4 | |||||||||||
CAZyme Description | Peptidoglycan-N-acetylmuramic acid deacetylase PdaA | |||||||||||
CAZyme Property |
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Genome Property |
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Gene Location | Start: 146156; End: 146935 Strand: + |
Family | Start | End | Evalue | family coverage |
---|---|---|---|---|
CE4 | 64 | 185 | 1.2e-33 | 0.9153846153846154 |
Cdd ID | Domain | E-Value | qStart | qEnd | sStart | sEnd | Domain Description |
---|---|---|---|---|---|---|---|
TIGR02884 | spore_pdaA | 7.28e-127 | 32 | 254 | 1 | 223 | delta-lactam-biosynthetic de-N-acetylase. Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores in the peptidoglycan wall, or spore cortex. The proteins in this family are PdaA (yfjS), a member of a larger family of polysaccharide deacetylases, and are specificially involved in delta-lactam biosynthesis. PdaA acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation. PdaA may also perform the following transpeptidation for lactam ring formation, as heterologous expression in E. coli of CwlD and PdaA together is sufficient for delta-lactam production. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Cellular processes, Sporulation and germination] |
cd10948 | CE4_BsPdaA_like | 5.21e-114 | 30 | 251 | 2 | 223 | Catalytic NodB homology domain of Bacillus subtilis polysaccharide deacetylase PdaA, and its bacterial homologs. The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. This family is represented by Bacillus subtilis pdaA gene encoding polysaccharide deacetylase BsPdaA, which is a member of the carbohydrate esterase 4 (CE4) superfamily. BsPdaA deacetylates peptidoglycan N-acetylmuramic acid (MurNAc) residues to facilitate the formation of muramic delta-lactam, which is required for recognition of germination lytic enzymes. BsPdaA deficiency leads to the absence of muramic delta-lactam residues in the spore cortex. Like other CE4 esterases, BsPdaA consists of a single catalytic NodB homology domain that appears to adopt a deformed (beta/alpha)8 barrel fold with a putative substrate binding groove harboring the majority of the conserved residues. It utilizes a general acid/base catalytic mechanism involving a tetrahedral transition intermediate, where a water molecule functions as the nucleophile tightly associated to the zinc cofactor. |
cd10917 | CE4_NodB_like_6s_7s | 2.35e-64 | 69 | 242 | 1 | 171 | Catalytic NodB homology domain of rhizobial NodB-like proteins. This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes many rhizobial NodB chitooligosaccharide N-deacetylase (EC 3.5.1.-)-like proteins, mainly from bacteria and eukaryotes, such as chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan. All members of this family contain a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold with 6- or 7 strands. Their catalytic activity is dependent on the presence of a divalent cation, preferably cobalt or zinc, and they employ a conserved His-His-Asp zinc-binding triad closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. Several family members show diversity both in metal ion specificities and in the residues that coordinate the metal. |
TIGR02764 | spore_ybaN_pdaB | 8.59e-53 | 64 | 254 | 1 | 190 | polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown. [Cellular processes, Sporulation and germination] |
COG0726 | CDA1 | 1.85e-50 | 14 | 255 | 16 | 257 | Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis]. |
Hit ID | E-Value | Query Start | Query End | Hit Start | Hit End |
---|---|---|---|---|---|
APO44870.1 | 6.15e-188 | 1 | 259 | 1 | 259 |
QZN73205.1 | 2.40e-185 | 1 | 259 | 1 | 259 |
QOS77900.1 | 2.18e-172 | 1 | 259 | 1 | 259 |
QKS59259.1 | 3.10e-172 | 1 | 259 | 1 | 259 |
QLG41736.1 | 1.26e-171 | 1 | 259 | 1 | 259 |
Hit ID | E-Value | Query Start | Query End | Hit Start | Hit End | Description |
---|---|---|---|---|---|---|
2J13_A | 3.36e-93 | 31 | 254 | 18 | 241 | Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames] |
1W1A_1 | 4.75e-88 | 20 | 254 | 13 | 246 | Structureof Bacillus subtilis PdaA in complex with NAG, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W1A_2 Structure of Bacillus subtilis PdaA in complex with NAG, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W1B_1 Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W1B_2 Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase. [Bacillus subtilis] |
1W17_A | 5.79e-88 | 20 | 254 | 19 | 252 | Structureof Bacillus subtilis PdaA, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W17_B Structure of Bacillus subtilis PdaA, a family 4 Carbohydrate esterase. [Bacillus subtilis] |
1NY1_A | 7.24e-86 | 32 | 254 | 7 | 229 | CrystalStructure Of B. Subtilis Polysaccharide Deacetylase Northeast Structural Genomics Consortium Target Sr127. [Bacillus subtilis],1NY1_B Crystal Structure Of B. Subtilis Polysaccharide Deacetylase Northeast Structural Genomics Consortium Target Sr127. [Bacillus subtilis] |
5O6Y_A | 4.08e-34 | 62 | 254 | 14 | 207 | Crystalstructure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide [Bacillus cereus ATCC 14579] |
Hit ID | E-Value | Query Start | Query End | Hit Start | Hit End | Description |
---|---|---|---|---|---|---|
Q04729 | 6.74e-92 | 22 | 254 | 21 | 253 | Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1 |
O34928 | 3.17e-87 | 20 | 254 | 19 | 252 | Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1 |
Q81EK9 | 9.96e-33 | 62 | 254 | 74 | 267 | Peptidoglycan-N-acetylglucosamine deacetylase BC_1960 OS=Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711) OX=226900 GN=BC_1960 PE=1 SV=1 |
P50352 | 5.47e-32 | 69 | 244 | 21 | 192 | Chitooligosaccharide deacetylase OS=Bradyrhizobium elkanii OX=29448 GN=nodB PE=3 SV=1 |
Q52845 | 1.52e-31 | 66 | 253 | 18 | 217 | Chitooligosaccharide deacetylase OS=Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099) OX=266835 GN=nodB PE=3 SV=2 |
Other | SP_Sec_SPI | LIPO_Sec_SPII | TAT_Tat_SPI | TATLIP_Sec_SPII | PILIN_Sec_SPIII |
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0.000244 | 0.999099 | 0.000165 | 0.000162 | 0.000155 | 0.000143 |
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