dbCAN-seq: a database of CAZyme sequence and annotation

Basic Information help

Species

Vibrio parahaemolyticus

Lineage

Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Vibrionaceae; Vibrio; Vibrio parahaemolyticus

CAZyme ID

MGYG000002331_00505

CAZy Family

GH13

CAZyme Description

Alpha-amylase

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
449	MGYG000002331_3\|CGC10	51392.39	5.3552

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000002331	5262465	Isolate	Bangladesh	Asia

Gene Location

Start: 519259; End: 520608 Strand: +

Enzyme Prediction help

EC	3.2.1.1

CAZyme Signature Domains help

Family	Start	End	Evalue	family coverage
GH13	25	341	2e-162	0.9968553459119497

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd11315	AmyAc_bac1_AmyA	8.05e-147	12	384	1	352	Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.
cd11317	AmyAc_bac_euk_AmyA	2.81e-42	12	377	1	329	Alpha amylase catalytic domain found in bacterial and eukaryotic Alpha amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes AmyA proteins from bacteria, fungi, mammals, insects, mollusks, and nematodes. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.
smart00642	Aamy	1.55e-20	14	102	2	97	Alpha-amylase domain.
COG0366	AmyA	3.62e-17	20	367	27	379	Glycosidase [Carbohydrate transport and metabolism].
cd00551	AmyAc_family	4.60e-15	17	341	20	252	Alpha amylase catalytic domain family. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.

CAZyme Hits help

Hit ID	Query Start	Query End	Hit Start	Hit End
QEL42185.1	1	449	1	449
QQD01198.1	1	449	1	449
ALM68337.1	1	449	1	449
AWJ81145.1	1	449	1	449
AWG81165.1	1	449	1	449

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
3DC0_A	2.53e-27	9	418	2	385	Crystalstructure of native alpha-amylase from Bacillus sp. KR-8104 [Bacillus sp. KR-8104]
1G94_A	8.54e-27	16	418	6	395	CRYSTALSTRUCTURE ANALYSIS OF THE TERNARY COMPLEX BETWEEN PSYCHROPHILIC ALPHA AMYLASE FROM PSEUDOALTEROMONAS HALOPLANCTIS IN COMPLEX WITH A HEPTA-SACCHARIDE AND A TRIS MOLECULE [Pseudoalteromonas haloplanktis],1G9H_A TERNARY COMPLEX BETWEEN PSYCHROPHILIC ALPHA-AMYLASE, COMII (PSEUDO TRI-SACCHARIDE FROM BAYER) AND TRIS (2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL) [Pseudoalteromonas haloplanktis],1L0P_A Crystal Structure Analysis Of The Complex Between Psychrophilic Alpha Amylase From Pseudoalteromonas Haloplanctis And Nitrate [Pseudoalteromonas haloplanktis]
1JD9_A	8.98e-27	16	418	6	395	ChainA, ALPHA-AMYLASE [Pseudoalteromonas haloplanktis]
1JD7_A	8.98e-27	16	418	6	395	ChainA, ALPHA-AMYLASE [Pseudoalteromonas haloplanktis]
1AQH_A	8.98e-27	16	418	6	395	ALPHA-AMYLASEFROM ALTEROMONAS HALOPLANCTIS [Pseudoalteromonas haloplanktis],1AQM_A ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS COMPLEXED WITH TRIS [Pseudoalteromonas haloplanktis],1B0I_A ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS [Pseudoalteromonas haloplanktis]

Swiss-Prot Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P22630	1.77e-128	1	422	10	430	Alpha-amylase OS=Aeromonas hydrophila OX=644 PE=3 SV=1
P29750	1.24e-31	9	417	36	436	Alpha-amylase OS=Thermomonospora curvata OX=2020 GN=tam PE=1 SV=1
P76616	9.38e-31	7	406	211	676	Putative uncharacterized protein YgaQ OS=Escherichia coli (strain K12) OX=83333 GN=ygaQ PE=5 SV=2
Q8X958	3.09e-30	7	406	211	676	Putative uncharacterized protein YgaQ OS=Escherichia coli O157:H7 OX=83334 GN=ygaQ PE=5 SV=2
O18420	5.16e-30	13	417	31	440	Alpha-amylase-related protein OS=Drosophila subobscura OX=7241 GN=Amyrel PE=3 SV=1

SignalP and Lipop Annotations help

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
1.000056	0.000000	0.000000	0.000000	0.000000	0.000000

TMHMM Annotations help

There is no transmembrane helices in MGYG000002331_00505.

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