CAZyme Information: MGYG000000044_00258

Basic Information

• Species: Parabacteroides merdae
• Lineage: Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Tannerellaceae; Parabacteroides; Parabacteroides merdae
• CAZyme ID: MGYG000000044_00258
• CAZy Family: GH43
• CAZyme Description: Non-reducing end alpha-L-arabinofuranosidase BoGH43A

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
313		35862.71	5.0354

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000000044	4300426	Isolate	United Kingdom	Europe

• Gene Location: Start: 294043; End: 294984 Strand: +

Full Sequence      

MKTDTLKKMLLMLLCVVSVNMTALGKELVSDVLPIADPYILFYNDTYYAYGTSRADGFEV
YSSKDMKSWERSPRLALSKEDSYGDKWFWAPEVYYVEEDKKFYMFYSVEEHVCVATSDSP
LGPFVQDEKKPIREEKGIDTSVFFDEDGKAYLYFVRFTNGNVIWCAELKDNLKEIKEETL
TQCVEATEPWELVFGKVVEGPSIVKQGGLYYMFYSANDFRSQDYAVGYATSDSPFGPWRK
SEKNPLLHKVEELVGTGHGAPFLDKAGRYRYIFHAHKSQTEVNQRNSYIIDMSLTGKDRV
SIGGGLIRPEVVK

Enzyme Prediction     

No EC number prediction in MGYG000000044_00258.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
GH43	34	292	3.1e-105	0.9850746268656716

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd08991	GH43_HoAraf43-like	2.21e-124	36	304	1	281	Glycosyl hydrolase family 43 protein such as Halothermothrix orenii H 168 alpha-L-arabinofuranosidase (HoAraf43;Hore_20580). This glycosyl hydrolase family 43 (GH43) subgroup includes Halothermothrix orenii H 168 alpha-L-arabinofuranosidase (EC 3.2.1.55) (HoAraf43;Hore_20580). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. This GH43_ HoAraf43-like subgroup includes enzymes that have been annotated as having xylan-digesting beta-xylosidase (EC 3.2.1.37) and xylanase (endo-alpha-L-arabinanase, EC 3.2.1.8) activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.
cd08978	GH_F	9.00e-66	36	276	1	251	Glycosyl hydrolase families 43 and 62 form CAZY clan GH-F. This glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) includes family 43 (GH43) and 62 (GH62). GH43 includes enzymes with beta-xylosidase (EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanases (beta-xylanases) and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. GH62 includes enzymes characterized as arabinofuranosidases (alpha-L-arabinofuranosidases; EC 3.2.1.55) that specifically cleave either alpha-1,2 or alpha-1,3-L-arabinofuranose side chains from xylans. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many of the enzymes in this family display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. GH62 are also predicted to be inverting enzymes. A common structural feature of both, GH43 and GH62 enzymes, is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.
cd08999	GH43_ABN-like	1.91e-65	36	296	9	280	Glycosyl hydrolase family 43 protein such as endo-alpha-L-arabinanase. This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes with alpha-L-arabinofuranosidase (ABF; EC 3.2.1.55) and endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the ABF enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.
cd09004	GH43_bXyl-like	5.41e-59	36	262	1	223	Glycosyl hydrolase family 43 protein such as Bacteroides thetaiotaomicron VPI-5482 alpha-L-arabinofuranosidases (BT3675;BT_3675) and (BT3662;BT_3662); includes mostly xylanases. This glycosyl hydrolase family 43 (GH43) subgroup includes enzymes that have been annotated as xylan-digesting beta-xylosidase (EC 3.2.1.37) and xylanase (endo-alpha-L-arabinanase, EC 3.2.1.8) activities, as well the Bacteroides thetaiotaomicron VPI-5482 alpha-L-arabinofuranosidases (EC 3.2.1.55) (BT3675;BT_3675) and (BT3662;BT_3662). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.
pfam04616	Glyco_hydro_43	5.09e-48	36	275	11	254	Glycosyl hydrolases family 43. The glycosyl hydrolase family 43 contains members that are arabinanases. Arabinanases hydrolyze the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The structure of arabinanase Arb43A from Cellvibrio japonicus reveals a five-bladed beta-propeller fold. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QUT48797.1	2.92e-229	1	313	1	313
QUT51345.1	5.87e-148	30	312	43	324
QDO68170.1	9.15e-129	27	313	34	324
QQD13991.1	9.37e-124	27	313	34	324
AIM37610.1	1.39e-123	29	313	18	305

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
3KST_A	5.85e-117	30	313	19	306	Crystalstructure of Endo-1,4-beta-xylanase (NP_811807.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.70 A resolution [Bacteroides thetaiotaomicron VPI-5482],3KST_B Crystal structure of Endo-1,4-beta-xylanase (NP_811807.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.70 A resolution [Bacteroides thetaiotaomicron VPI-5482]
4QQS_A	1.55e-41	29	276	9	275	Crystalstructure of a thermostable family-43 glycoside hydrolase [Halothermothrix orenii H 168],4QQS_B Crystal structure of a thermostable family-43 glycoside hydrolase [Halothermothrix orenii H 168]
3QZ4_A	1.48e-22	36	260	16	259	Crystalstructure of an Endo-1,4-beta-xylanase D (BT_3675) from Bacteroides thetaiotaomicron VPI-5482 at 1.74 A resolution [Bacteroides thetaiotaomicron],3QZ4_B Crystal structure of an Endo-1,4-beta-xylanase D (BT_3675) from Bacteroides thetaiotaomicron VPI-5482 at 1.74 A resolution [Bacteroides thetaiotaomicron]
4NOV_A	7.09e-20	36	274	55	304	Xsa43E,a GH43 family enzyme from Butyrivibrio proteoclasticus [Butyrivibrio proteoclasticus B316]
5C0P_A	6.88e-19	33	281	24	284	Thecrystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482 [Bacteroides thetaiotaomicron VPI-5482]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P48791	3.41e-13	96	274	89	287	Beta-xylosidase OS=Prevotella ruminicola OX=839 GN=xynB PE=3 SV=1
P49943	8.04e-11	58	238	52	259	Xylosidase/arabinosidase OS=Bacteroides ovatus OX=28116 GN=xsa PE=2 SV=1
P45982	1.87e-08	37	258	15	248	Xylosidase/arabinosidase OS=Butyrivibrio fibrisolvens OX=831 GN=xylB PE=3 SV=1
B0XTS5	1.95e-08	33	254	55	317	Probable arabinan endo-1,5-alpha-L-arabinosidase B OS=Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) OX=451804 GN=abnB PE=3 SV=2
Q4X0A5	2.62e-08	33	254	55	317	Probable arabinan endo-1,5-alpha-L-arabinosidase B OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) OX=330879 GN=abnB PE=3 SV=2

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.000270	0.999109	0.000168	0.000147	0.000137	0.000126

TMHMM  Annotations     

There is no transmembrane helices in MGYG000000044_00258.