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_00540

CAZy Family

CBM35

CAZyme Description

hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
537	MGYG000001375_1\|CGC5	58899.45	4.2632

Genome Property

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

Gene Location

Start: 602774; End: 604387 Strand: -

Enzyme Prediction help

No EC number prediction in MGYG000001375_00540.

CAZyme Signature Domains help

Family	Start	End	Evalue	family coverage
CBM35	118	239	5.8e-23	0.9915966386554622

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd04082	CBM35_pectate_lyase-like	2.12e-51	116	239	1	124	Carbohydrate Binding Module family 35 (CBM35), pectate lyase-like; appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans. This family includes carbohydrate binding module family 35 (CBM35) domains that are non-catalytic carbohydrate binding domains that are appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans. Included in this family are CBM35s of pectate lyases, including pectate lyase 10A from Cellvibrio japonicas, these enzymes release delta-4,5-anhydrogalaturonic acid (delta4,5-GalA) from pectin, thus identifying a signature molecule for plant cell wall degradation. CBM35s are unique in that they display conserved specificity through extensive sequence similarity but divergent function through their appended catalytic modules. They are known to bind alpha-D-galactose (Gal), mannan (Man), xylan, glucuronic acid (GlcA), a beta-polymer of mannose, and possibly glucans, forming four subfamilies based on general ligand specificities (galacto, urono, manno, and gluco configurations). In contrast to most CBMs that are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. Some CBM35s bind their ligands in a calcium-dependent manner, especially those binding uronic acids.
cd04083	CBM35_Lmo2446-like	1.02e-19	116	237	1	123	Carbohydrate Binding Module 35 (CBM35) domains similar to Lmo2446. This family includes carbohydrate binding module 35 (CBM35) domains that are appended to several carbohydrate binding enzymes. Some CBM35 domains belonging to this family are appended to glycoside hydrolase (GH) family domains, including glycoside hydrolase family 31 (GH31), for example the CBM35 domain of Lmo2446, an uncharacterized protein from Listeria monocytogenes EGD-e. These CBM35s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. GH31 has a wide range of hydrolytic activities such as alpha-glucosidase, alpha-xylosidase, 6-alpha-glucosyltransferase, or alpha-1,4-glucan lyase, cleaving a terminal carbohydrate moiety from a substrate that may be a starch or a glycoprotein. Most characterized GH31 enzymes are alpha-glucosidases.
cd02795	CBM6-CBM35-CBM36_like	2.08e-18	120	239	4	124	Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily. Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules. This alignment model also contains the C-terminal domains of bacterial insecticidal toxins, where they may be involved in determining insect specificity through carbohydrate binding functionality.
cd14256	Dockerin_I	1.65e-13	44	100	1	56	Type I dockerin repeat domain. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. This subfamily represents type I dockerins, which are responsible for anchoring a variety of enzymatic domains to the complex.
cd04080	CBM6_cellulase-like	2.61e-12	141	240	38	144	Carbohydrate Binding Module 6 (CBM6); appended to glycoside hydrolase (GH) domains, including GH5 (cellulase). This family includes carbohydrate binding module 6 (CBM6) domains that are appended to several glycoside hydrolase (GH) domains, including GH5 (cellulase) and GH16, as well as to coagulation factor 5/8 carbohydrate-binding domains. CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. The CBM6s are appended to GHs that display a diversity of substrate specificities. For some members of this family information is available about the specific substrates of the appended GH domains. It includes the CBM domains of various enzymes involved in cell wall degradation including, an extracellular beta-1,3-glucanase from Lysobacter enzymogenes encoded by the gluC gene (its catalytic domain belongs to the GH16 family), the tandem CBM domains of Pseudomonas sp. PE2 beta-1,3(4)-glucanase A (its catalytic domain also belongs to GH16), and a family 6 CBM from Cellvibrio mixtus Endoglucanase 5A (CmCBM6) which binds to the beta1,4-beta1,3-mixed linked glucans lichenan, and barley beta-glucan, cello-oligosaccharides, insoluble forms of cellulose, the beta1,3-glucan laminarin, and xylooligosaccharides, and the CBM6 of Fibrobacter succinogenes S85 XynD xylanase, appended to a GH10 domain, and Cellvibrio japonicas Cel5G appended to a GH5 (cellulase) domain. GH5 (cellulase) family includes enzymes with several known activities such as endoglucanase, beta-mannanase, and xylanase, which are involved in the degradation of cellulose and xylans. GH16 family includes enzymes with lichenase, xyloglucan endotransglycosylase (XET), and beta-agarase activities. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. For CmCBM6 it has been shown that these two binding sites have different ligand specificities.

CAZyme Hits help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
CBL16774.1	0.0	1	537	1	537
ADU22444.1	2.35e-115	264	536	46	318
ADU21954.1	7.31e-93	261	536	38	314
CDM67270.1	1.51e-91	259	536	43	305
QGI94971.1	8.15e-46	266	534	61	300

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2W47_A	7.20e-23	117	239	6	128	ChainA, Lipolytic Enzyme, G-d-s-l [Acetivibrio thermocellus]
2W1W_A	7.60e-23	117	239	6	128	ChainA, LIPOLYTIC ENZYME, G-D-S-L [Acetivibrio thermocellus],2W1W_B Chain B, LIPOLYTIC ENZYME, G-D-S-L [Acetivibrio thermocellus]
2VZP_A	5.31e-19	118	239	6	127	AtomicResolution Structure of the C-terminal CBM35 from Amycolatopsis orientalis exo-chitosanase CsxA [Amycolatopsis orientalis],2VZP_B Atomic Resolution Structure of the C-terminal CBM35 from Amycolatopsis orientalis exo-chitosanase CsxA [Amycolatopsis orientalis],2VZQ_A C-terminal CBM35 from Amycolatopsis orientalis exo-chitosanase CsxA in complex with digalacturonic acid [Amycolatopsis orientalis],2VZQ_B C-terminal CBM35 from Amycolatopsis orientalis exo-chitosanase CsxA in complex with digalacturonic acid [Amycolatopsis orientalis],2VZR_A C-terminal CBM35 from Amycolatopsis orientalis exo-chitosanase CsxA in complex with glucuronic acid [Amycolatopsis orientalis],2VZR_B C-terminal CBM35 from Amycolatopsis orientalis exo-chitosanase CsxA in complex with glucuronic acid [Amycolatopsis orientalis]
2VZU_A	1.80e-16	118	239	911	1032	Complexof Amycolatopsis orientalis exo-chitosanase CsxA D469A with PNP-beta-D-glucosamine [Amycolatopsis orientalis],2VZU_B Complex of Amycolatopsis orientalis exo-chitosanase CsxA D469A with PNP-beta-D-glucosamine [Amycolatopsis orientalis]
2VZO_A	1.80e-16	118	239	911	1032	Crystalstructure of Amycolatopsis orientalis exo-chitosanase CsxA [Amycolatopsis orientalis],2VZO_B Crystal structure of Amycolatopsis orientalis exo-chitosanase CsxA [Amycolatopsis orientalis]