CAZyme Information: PHYCI_394861T0-p1

Basic Information

• Species: Phytophthora cinnamomi
• Lineage: Oomycota; NA; ; Peronosporaceae; Phytophthora; Phytophthora cinnamomi
• CAZyme ID: PHYCI_394861T0-p1
• CAZy Family: GH6
• CAZyme Description: unspecified product

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
602		65894.41	9.5504

Genome Property

Genome Version/Assembly ID	Genes	Strain NCBI Taxon ID	Non Protein Coding Genes	Protein Coding Genes
FungiDB-61_PcinnamomiCBS144-22	26201	1048749	70	26131

• Gene Location: location=PcinCBS144-22_SC0180:62216-66437(-)

Full Sequence      

MLSGRLFRAALLLTSGLLAVAQANTKQLTSNLNFQSEEERGATSSFGYKANGKSWVIDSG
AGLTVKVSQGSCDITSMVWNKAELQIKQKMTHINSGLGKVTSSIQELKDKTIQISCKTKG
LEHTYLFRPNENAIYMGTHHTTEMQLGELRFLARLARKPMNNPMVTASNIDGMKPIEAHD
VYADSKGVTASKFYSGIPFIDDRVHGVTGDAGGVYFVMSDYAYEKSVGGPFFRDINNQCT
EANELTFYMFSDHTRTEDYRFGFHGPYALVFTDGKTPPTVSDVDFDFFQDLTLAGFVPEA
ERGSWTGSITDKNGVLSNSSVVVGFSNAEAQYWVKLNSTTGSFTSPMMIAGSYNATIYKN
QLPVSSEAVTISGASGSTPASTKAAPETQTSHTPTPTHASYQGQSRRTQSVQNAQTLTVT
YEPAAKPIWRIGKWDGTPDGFLNADKIHTAHPSDSRMEAWKPLNFTIGTDKDSIFPMAMF
RAVNDPITINFELTKQQVGDRTLKIGVPLAQNSGRCRVTVNKYSAKVPLSAAVKTRGVTR
GVTVVATRTRWASGCRPRSCSRSLVATRTRWASGCRPRSCLTLSSLCSAVNLYNFSLERK
QF

Enzyme Prediction     

EC	4.2.2.23:4

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL4	43	389	6.3e-107	0.6793587174348698

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
401282	RhgB_N	3.44e-132	46	295	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).
199907	RGL4_N	5.05e-47	46	279	1	264	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.
199905	RGL4_C	2.47e-34	429	551	1	120	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	1.93e-31	427	543	1	112	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.
405387	fn3_3	6.50e-12	312	378	5	72	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     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
CCA68112.1|PL4_1	2.79e-111	45	541	22	472
CDJ79831.1|PL4_1	4.67e-107	41	541	18	476
QRV98672.1|PL4_1	7.52e-106	41	541	23	463
QRW13230.1|PL4_1	1.30e-105	67	541	23	451
QRW22552.1|PL4_1	9.64e-105	42	541	15	471

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1NKG_A	2.50e-89	45	541	1	456	Rhamnogalacturonan lyase from Aspergillus aculeatus [Aspergillus aculeatus]
2XHN_A	1.92e-88	45	541	1	456	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	7.46e-88	45	541	1	456	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|Q0CVU1|RGLA_ASPTN	1.80e-96	42	541	18	476	Probable rhamnogalacturonate lyase A OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) OX=341663 GN=rglA PE=3 SV=2
sp|Q5AX45|RGLA_EMENI	1.35e-94	40	541	16	475	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|A1C995|RGLA_ASPCL	1.95e-94	42	541	18	476	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|Q2U0Q1|RGLA_ASPOR	1.07e-93	40	541	16	476	Probable rhamnogalacturonate lyase A OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) OX=510516 GN=rglA PE=3 SV=1
sp|B8NCU7|RGLA_ASPFN	1.51e-93	40	541	16	476	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

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	CS Position
0.000236	0.999770	CS pos: 23-24. Pr: 0.9544

TMHMM  Annotations     

There is no transmembrane helices in PHYCI_394861T0-p1.