CAZyme Information: MGYG000001299_00557

Basic Information

• Species: Amedibacillus dolichus
• Lineage: Bacteria; Firmicutes; Bacilli; Erysipelotrichales; Erysipelotrichaceae; Amedibacillus; Amedibacillus dolichus
• CAZyme ID: MGYG000001299_00557
• CAZy Family: CE4
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
436		50637.32	6.2049

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001299	2190453	Isolate	not provided	not provided

• Gene Location: Start: 283452; End: 284762 Strand: +

Full Sequence      

MSKRCKIIVNSIIVFVLLLIVGIIVKFVFFSGSFTPLLKLNGDKQMVIDVHQEFEDPFVK
ARYHLKDISDEVEVLGQVDCEKIGTYQLVYRLKEHDKEVVREVKVVDRTAPKLMLKGASH
VRVFLGGKYQESGYAASDDVDGDLSDEVRVESHVNMNKKGIYKIHYYVKDHSGNGSKRTR
SVEVCEDPTSLKLHYNYDTYDNTMEEWWFHKSEKHERNKGAKSAAYLKKFDTYYQGPDEK
VIYLTFDEGGNEVTYSKEIAEILKKHDVQATYFFTLNYLRDEAEFVRELVANGNLIGNHT
WHHYDMTTLANAHSVDKFVKEITETEKMYMEITGEEMPKIFRFPRGGGSERAMKMVQDLG
YRNYYWSHAFYDYGDDVSKEEALRTMMEHYHNGAIYLLHPSNRGNYEAIESFIVAMKDLG
YRFETLDAIGKDSQEP

Enzyme Prediction     

No EC number prediction in MGYG000001299_00557.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	235	363	1.2e-25	0.9230769230769231

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10948	CE4_BsPdaA_like	1.29e-96	203	426	1	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.
TIGR02884	spore_pdaA	1.96e-64	206	427	1	221	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]
cd10917	CE4_NodB_like_6s_7s	7.95e-41	240	413	1	167	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.
cd10950	CE4_BsYlxY_like	2.63e-32	237	429	3	187	Putative catalytic NodB homology domain of uncharacterized protein YlxY from Bacillus subtilis 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 putative polysaccharide deacetylase BsYlxY, encoded by the ylxY gene, which is a member of the carbohydrate esterase 4 (CE4) superfamily. Although its biological function still remains unknown, BsYlxY shows high sequence homology to the catalytic domain of Bacillus subtilis pdaB gene encoding a putative polysaccharide deacetylase (BsPdaB), which is essential for the maintenance of spores after the late stage of sporulation and is highly conserved in spore-forming bacteria. However, disruption of the ylxY gene in B. subtilis did not cause any sporulation defect. Moreover, the Asp residue in the classical His-His-Asp zinc-binding motif of CE4 esterases is mutated to a Val residue in this family. Other catalytically relevant residues of CE4 esterases are also not conserved, which suggest that members of this family may be inactive.
COG0726	CDA1	1.40e-28	215	429	39	256	Peptidoglycan/xylan/chitin deacetylase, PgdA/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis].

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QJA03535.1	6.32e-200	1	435	1	435
QQR25816.1	6.32e-200	1	435	1	435
ANU70313.1	6.32e-200	1	435	1	435
ASU17265.1	6.32e-200	1	435	1	435
QIX09940.1	8.97e-200	1	435	1	435

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1W1A_1	4.78e-39	207	427	25	244	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	5.59e-39	207	427	31	250	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	6.11e-38	207	427	8	227	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]
2J13_A	1.08e-33	227	434	41	246	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
6HM9_A	1.36e-20	234	422	78	259	Crystalstructure of a BA3943 mutant,a CE4 family pseudoenzyme with restored enzymatic activity. [Bacillus anthracis]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q04729	1.03e-42	207	427	32	251	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928	3.06e-38	207	427	31	250	Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
Q8DP63	5.76e-17	230	426	258	444	Peptidoglycan-N-acetylglucosamine deacetylase OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) OX=171101 GN=pgdA PE=1 SV=1
Q81EK9	3.28e-15	225	435	65	273	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
P50850	4.17e-15	233	426	123	308	Uncharacterized protein YlxY OS=Bacillus subtilis (strain 168) OX=224308 GN=ylxY PE=3 SV=2

SignalP and Lipop Annotations

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.988562	0.007564	0.000826	0.000063	0.000031	0.002982

TMHMM  Annotations     

start	end
7	29