CAZyme Information: PHYSODRAFT_553407-t26_1-p1

Basic Information

• Species: Phytophthora sojae
• Lineage: Oomycota; NA; ; Peronosporaceae; Phytophthora; Phytophthora sojae
• CAZyme ID: PHYSODRAFT_553407-t26_1-p1
• CAZy Family: PL1
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
591		64229.23	6.7770

Genome Property

Genome Version/Assembly ID	Genes	Strain NCBI Taxon ID	Non Protein Coding Genes	Protein Coding Genes
FungiDB-61_PsojaeP6497	28142	1094619	1653	26489

• Gene Location: location=JH159151:12269206-12270981(-)

Full Sequence      

MLSGRLFRAAFLLTSGLLAVTLADTNPQTSNLNFQSEEERGATSSFGYKQNGGAWVIDSG
AGLTVTVSQRSCDITSMVWNKAELQIKKKMTHINSGLGKVTSSIQELKDKTVQISCKTKG
LEHTYLFRPNENAIYMGTHHTTEMQLGELRFLARLNRTPMKNPMVPASNIDGMNAIEAHD
VYADSKGVTASKFYSGIPFIDDQVHGVTGDAGGVFFVMSDYAYEKSVGGPFFRDINNQCT
EANELTFYMFSDHTRAEDYRYGFHGPYALVFTDGKTPAVSDVDFDFFQDLTLTGFVPEAE
RGSWTGTITDKNGVLSNSSVVVGFSNAEAQYWVKLNSITGSFTSPMMIAGSYNATIYKNQ
LPVSSEAITIGSGSTPASSEAASAAPSTNAPTPAPASHQSHSRRTQSTQNAPTLTVTYEP
AAKPIWRIGEWDGTPDGFLNADKIHTAHPSDSRMEAWTPLNFTIGTDKDSVFPMALFRAV
NDPITINFELTKEQVGDRTLKIGIPLSQNNGRCSVTVNKFSAKSPLSAAVKTRGVTRGVT
VGKYMFYDYAIPKSALVEGKNQIKLSIVSGNKDTLGKWLSASVVFDALELV

Enzyme Prediction     

No EC number prediction in PHYSODRAFT_553407-t26_1-p1.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL4	43	379	1.2e-107	0.6633266533066132

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
401282	RhgB_N	5.50e-135	46	294	1	251	Rhamnogalacturonan lyase B, N-terminal. Members of this family are found in both fungi, bacteria and wood-eating arthropods. The domain is found at the N-terminus of rhamnogalacturonase B, a member of the polysaccharide lyase family 4. The domain adopts a structure consisting of a beta super-sandwich, with eighteen strands in two beta-sheets. The three domains of the whole protein rhamnogalacturonan lyase (RGL4), are involved in the degradation of rhamnogalacturonan-I, RG-I, an important pectic plant cell-wall polysaccharide. The active-site residues are a lysine at position 169 in UniProtKB:Q00019 and a histidine at 229, Lys169 is likely to be a proton abstractor, His229 a proton donor in the mechanism. The substrate is a disaccharide, and RGL4, in contrast to other rhamnogalacturonan hydrolases, cleaves the alpha-1,4 linkages of RG-I between Rha and GalUA through a beta-elimination resulting in a double bond in the nonreducing GalUA residue, and is thus classified as a polysaccharide lyase (PL).
199905	RGL4_C	1.37e-49	426	591	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.
405384	CBM-like	3.65e-45	424	590	1	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.
199907	RGL4_N	2.61e-44	46	278	1	263	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.
199904	RGL4_M	1.22e-11	300	373	1	84	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.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
CCA68112.1|PL4_1	5.52e-124	44	590	21	522
QRW20454.1|PL4_1	3.27e-120	41	590	17	513
CDJ79831.1|PL4_1	4.29e-118	41	590	18	526
BAO51935.1|PL4_1|4.2.2.23	6.75e-114	42	590	18	526
QRW23656.1|PL4_1	1.58e-113	42	590	20	521

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1NKG_A	3.53e-105	45	590	1	506	Rhamnogalacturonan lyase from Aspergillus aculeatus [Aspergillus aculeatus]
2XHN_A	2.76e-104	45	590	1	506	Rhamnogalacturonan lyase from Aspergillus aculeatus K150A active site mutant [Aspergillus aculeatus],2XHN_B Rhamnogalacturonan lyase from Aspergillus aculeatus K150A active site mutant [Aspergillus aculeatus],3NJV_A Rhamnogalacturonan lyase from Aspergillus aculeatus K150A substrate complex [Aspergillus aculeatus]
3NJX_A	1.09e-103	45	590	1	506	Rhamnogalacturonan Lyase from Aspergillus aculeatus mutant H210A [Aspergillus aculeatus]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
sp|A1C995|RGLA_ASPCL	7.14e-110	42	590	18	526	Probable rhamnogalacturonate lyase A OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1 / QM 1276 / 107) OX=344612 GN=rglA PE=3 SV=1
sp|Q5AX45|RGLA_EMENI	5.44e-109	40	590	16	525	Rhamnogalacturonate lyase A OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) OX=227321 GN=rglA PE=2 SV=1
sp|P78710|ASD1_NEUCR	1.58e-108	41	590	20	538	Putative rhamnogalacturonase OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) OX=367110 GN=asd-1 PE=2 SV=1
sp|B8NCU7|RGLA_ASPFN	8.71e-108	40	590	16	526	Probable rhamnogalacturonate lyase A OS=Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167) OX=332952 GN=rglA PE=3 SV=1
sp|Q2U0Q1|RGLA_ASPOR	1.23e-107	40	590	16	526	Probable rhamnogalacturonate lyase A OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) OX=510516 GN=rglA PE=3 SV=1

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	CS Position
0.000273	0.999694	CS pos: 23-24. Pr: 0.9807

TMHMM  Annotations     

There is no transmembrane helices in PHYSODRAFT_553407-t26_1-p1.