dbCAN-seq: a database of CAZyme sequence and annotation

Basic Information help

Species

Ruminococcus_F champanellensis

Lineage

Bacteria; Firmicutes_A; Clostridia; Oscillospirales; Ruminococcaceae; Ruminococcus_F; Ruminococcus_F champanellensis

CAZyme ID

MGYG000001375_02254

CAZy Family

GH11

CAZyme Description

hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
883		94529.21	4.3442

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001375	2513436	Isolate	not provided	not provided

Gene Location

Start: 2462190; End: 2464841 Strand: -

Enzyme Prediction help

EC	3.2.1.8	3.1.1.72	3.2.1.73

CAZyme Signature Domains help

Family	Start	End	Evalue	family coverage
GH11	43	231	3.9e-73	0.9887005649717514
CBM22	495	622	2e-34	0.9618320610687023
CBM22	259	386	1.4e-32	0.9694656488549618
CE4	672	793	1.2e-21	0.8692307692307693

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
pfam00457	Glyco_hydro_11	2.43e-77	43	230	1	175	Glycosyl hydrolases family 11.
cd10954	CE4_CtAXE_like	3.16e-64	675	865	1	180	Catalytic NodB homology domain of Clostridium thermocellum acetylxylan esterase and its bacterial homologs. This family is represented by Clostridium thermocellum acetylxylan esterase (CtAXE, EC 3.1.1.72), a member of the carbohydrate esterase 4 (CE4) superfamily. CtAXE deacetylates O-acetylated xylan, a key component of plant cell walls. It shows no detectable activity on generic esterase substrates including para-nitrophenyl acetate. It is specific for sugar-based substrates and will precipitate acetylxylan, as a consequence of deacetylation. CtAXE is a monomeric protein containing a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold as other CE4 esterases. However, due to differences in the topography of the substrate-binding groove, the chemistry of the active center, and metal ion coordination, CtAXE has different metal ion preference and lacks activity on N-acetyl substrates. It is significantly activated by Co2+. Moreover, CtAXE displays distinctly different ligand coordination to the metal ion, utilizing an aspartate, a histidine, and four water molecules, as opposed to the conserved His-His-Asp zinc-binding triad of other CE4 esterases.
cd10917	CE4_NodB_like_6s_7s	6.96e-44	675	853	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.
cd10950	CE4_BsYlxY_like	5.52e-35	671	866	2	188	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.
cd10951	CE4_ClCDA_like	1.81e-32	673	862	5	197	Catalytic NodB homology domain of Colletotrichum lindemuthianum chitin deacetylase and similar proteins. This family is represented by the chitin deacetylase (endo-chitin de-N-acetylase, ClCDA, EC 3.5.1.41) from Colletotrichum lindemuthianum (also known as Glomerella lindemuthiana), which is a member of the carbohydrate esterase 4 (CE4) superfamily. ClCDA catalyzes the hydrolysis of N-acetamido groups of N-acetyl-D-glucosamine residues in chitin, converting it to chitosan in fungal cell walls. It consists of a single catalytic domain similar to the deformed (alpha/beta)8 barrel fold adopted by other CE4 esterases, which encompasses a mononuclear metalloenzyme employing 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. It possesses a highly conserved substrate-binding groove, with subtle alterations that influence substrate specificity and subsite affinity. Unlike its bacterial homologs, ClCDA contains two intramolecular disulfide bonds that may add stability to this secreted protein. The family also includes many uncharacterized deacetylases and hypothetical proteins mainly from eukaryotes, which show high sequence similarity to ClCDA.

CAZyme Hits help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
CBL18305.1	0.0	1	883	1	883
AEE64769.1	3.21e-209	11	879	3	753
ADU20638.1	1.70e-193	33	880	56	677
AAA85198.1	9.59e-193	33	880	56	677
AEE64770.1	2.30e-191	33	879	60	678

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
7AYL_A	2.69e-96	24	240	22	231	Crystalstructure of the GH11 domain of a multidomain xylanase from the hindgut metagenome of Trinervitermes trinervoides [uncultured bacterium],7AYL_B Crystal structure of the GH11 domain of a multidomain xylanase from the hindgut metagenome of Trinervitermes trinervoides [uncultured bacterium]
7AYP_A	9.00e-93	31	240	1	203	Structureof a GH11 domain refined from the X-ray diffraction data of a GH11-CBM36-1 crystal. [uncultured bacterium]
2F6B_A	6.54e-82	32	240	1	203	Structuraland active site modification studies implicate Glu, Trp and Arg in the activity of xylanase from alkalophilic Bacillus sp. (NCL 87-6-10). [Bacillus],2F6B_B Structural and active site modification studies implicate Glu, Trp and Arg in the activity of xylanase from alkalophilic Bacillus sp. (NCL 87-6-10). [Bacillus]
1H4G_A	1.88e-80	33	240	2	203	Oligosaccharide-bindingto family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5B conformations at the active-centre [Salipaludibacillus agaradhaerens],1H4G_B Oligosaccharide-binding to family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5B conformations at the active-centre [Salipaludibacillus agaradhaerens],1QH6_A CATALYSIS AND SPECIFICITY IN ENZYMATIC GLYCOSIDE HYDROLASES: A 2,5B CONFORMATION FOR THE GLYCOSYL-ENZYME INTERMIDIATE REVEALED BY THE STRUCTURE OF THE BACILLUS AGARADHAERENS FAMILY 11 XYLANASE [Salipaludibacillus agaradhaerens],1QH6_B CATALYSIS AND SPECIFICITY IN ENZYMATIC GLYCOSIDE HYDROLASES: A 2,5B CONFORMATION FOR THE GLYCOSYL-ENZYME INTERMIDIATE REVEALED BY THE STRUCTURE OF THE BACILLUS AGARADHAERENS FAMILY 11 XYLANASE [Salipaludibacillus agaradhaerens],1QH7_A CATALYSIS AND SPECIFICITY IN ENZYMATIC GLYCOSIDE HYDROLASES: A 2,5B CONFORMATION FOR THE GLYCOSYL-ENZYME INTERMIDIATE REVEALED BY THE STRUCTURE OF THE BACILLUS AGARADHAERENS FAMILY 11 XYLANASE [Salipaludibacillus agaradhaerens],1QH7_B CATALYSIS AND SPECIFICITY IN ENZYMATIC GLYCOSIDE HYDROLASES: A 2,5B CONFORMATION FOR THE GLYCOSYL-ENZYME INTERMIDIATE REVEALED BY THE STRUCTURE OF THE BACILLUS AGARADHAERENS FAMILY 11 XYLANASE [Salipaludibacillus agaradhaerens]
4IXL_A	4.64e-80	34	240	36	236	Crystalstructure of endo-beta-1,4-xylanase from the alkaliphilic Bacillus sp. SN5 [Bacillus sp. (in: Bacteria)],4IXL_B Crystal structure of endo-beta-1,4-xylanase from the alkaliphilic Bacillus sp. SN5 [Bacillus sp. (in: Bacteria)]

Swiss-Prot Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q53317	1.68e-105	1	406	1	407	Xylanase/beta-glucanase OS=Ruminococcus flavefaciens OX=1265 GN=xynD PE=3 SV=2
P83513	1.02e-85	24	240	8	217	Bifunctional xylanase/deacetylase OS=Pseudobutyrivibrio xylanivorans OX=185007 GN=xyn11A PE=1 SV=2
Q8GJ44	2.38e-83	30	245	30	237	Endo-1,4-beta-xylanase A OS=Thermoclostridium stercorarium OX=1510 GN=xynA PE=1 SV=2
P17137	5.78e-82	21	239	49	260	Endo-1,4-beta-xylanase OS=Clostridium saccharobutylicum OX=169679 GN=xynB PE=3 SV=1
P33558	2.75e-81	30	245	30	238	Endo-1,4-beta-xylanase A OS=Thermoclostridium stercorarium OX=1510 GN=xynA PE=1 SV=2

SignalP and Lipop Annotations help

This protein is predicted as SP

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.000277	0.999006	0.000165	0.000212	0.000167	0.000149

TMHMM Annotations download full data without filtering help

start	end
13	35

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