dbCAN-seq: a database of CAZyme sequence and annotation

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CAZyme Information: MGYG000003172_00048

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Basic Information help

Species

CAG-485 sp900555915

Lineage

Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Muribaculaceae; CAG-485; CAG-485 sp900555915

CAZyme ID

MGYG000003172_00048

CAZy Family

PL4

CAZyme Description

Rhamnogalacturonate lyase

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
638		69707.88	5.0126

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000003172	1933519	MAG	United States	North America

Gene Location

Start: 17397; End: 19313 Strand: -

Full Sequence Download help

Enzyme Prediction help

No EC number prediction in MGYG000003172_00048.

CAZyme Signature Domains help

Family	Start	End	Evalue	family coverage
PL4	30	574	1.4e-117	0.9836660617059891

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10320	RGL4_N	5.88e-38	30	289	6	259	N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold; the middle and C-terminal domains are both putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.
cd10317	RGL4_C	7.58e-33	426	579	1	161	C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.
pfam14683	CBM-like	9.33e-30	425	578	2	157	Polysaccharide lyase family 4, domain III. CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion.
cd10316	RGL4_M	1.42e-12	323	389	1	68	Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle domain represented by this model and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.
pfam14686	fn3_3	6.23e-06	344	389	9	54	Polysaccharide lyase family 4, domain II. FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits.

CAZyme Hits help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
BBH93641.1	4.82e-112	35	586	58	587
APC39134.1	2.57e-97	36	580	16	563
BAV08848.1	5.61e-88	81	580	103	595
CAD27359.1	6.18e-77	35	578	39	573
ADM97186.1	6.18e-77	35	578	39	573

PDB Hits help

has no PDB hit.

Swiss-Prot Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q8RJP2	1.24e-77	35	578	39	573	Rhamnogalacturonate lyase OS=Dickeya dadantii (strain 3937) OX=198628 GN=rhiE PE=1 SV=1

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
0.000240	0.999117	0.000178	0.000160	0.000150	0.000141

TMHMM Annotations help

There is no transmembrane helices in MGYG000003172_00048.