CAZyme Information: PHPALM_14940-t46_1-p1

Basic Information

• Species: Phytophthora palmivora
• Lineage: Oomycota; NA; ; Peronosporaceae; Phytophthora; Phytophthora palmivora
• CAZyme ID: PHPALM_14940-t46_1-p1
• CAZy Family: AA7
• CAZyme Description: Polysaccharide lyase

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
582		63582.08	7.5001

Genome Property

Genome Version/Assembly ID	Genes	Strain NCBI Taxon ID	Non Protein Coding Genes	Protein Coding Genes
FungiDB-61_Ppalmivorasbr112.9	28185	N/A	3511	24674

• Gene Location: location=NCKW01008021:1190-2938(+)

Full Sequence      

MLSGRLFRTALLLTSGLLAVAQANTKQLTSNLNFQTEERAANTTSFGYKENGGSWVIDSG
AGLTVKVNQGTCDITSMVWNKAELQISKKMTHINSGLGKVKTSIESLKDKTIQISCKATG
LEHTYLFRPNENAIYMGTHHTKEMQLGELRFLARLDRKPLNKPMVPASNIDGMSAIEAHD
VYADKKGVTASKFYSGIPFIDDQVHGVTGDAGGVFFIMSDYAYERSVGGPFFRDINNQCT
EANELTFYMFSDHTRAEDYRYGFHGPYALVFTDGKQPAVSEVDFDFFQDLTLTGFIPEAE
RGSWTGTITDKNGVLSNSSIVVGFSNAEAQYWVKVKSTTEPFTSPKMVAGTYNATIYKNQ
LPVSSEAITIGGGSTTPAASPSTPPSTEAPASRRMESAQSAQTLTVTYEPVAKPIWRIGV
WDGTPDGFLNADKIHTAHPSDSRMEPWKPLNFTIGTDKDSIFPMAMFRAVNDPITINFEL
TKEQIGMDRTLKLGIPLAQNNGRCSVTVNKFSAKTPLSAAVKTRGVTRGVTVGKYMFYDY
AIPKTALVEGTNKVVLSIVSGNKDTLGKWLSASVVFDALELV

Enzyme Prediction     

No EC number prediction in PHPALM_14940-t46_1-p1.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL4	44	571	2.8e-159	0.9919839679358717

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
401282	RhgB_N	2.37e-136	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	9.59e-52	416	582	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	1.04e-45	414	581	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	1.30e-45	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	4.81e-12	300	376	1	87	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	5.25e-125	45	581	22	522
QRW20454.1|PL4_1	3.50e-120	45	581	21	513
CDJ79831.1|PL4_1	1.26e-114	45	581	22	526
QRW22552.1|PL4_1	1.79e-109	30	539	4	481
UJO24073.1|PL4_1	2.45e-109	45	581	20	530

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1NKG_A	2.66e-98	45	581	1	506	Rhamnogalacturonan lyase from Aspergillus aculeatus [Aspergillus aculeatus]
2XHN_A	2.07e-97	45	581	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	8.11e-97	45	581	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|P78710|ASD1_NEUCR	8.16e-106	45	581	24	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|A1C995|RGLA_ASPCL	1.96e-103	45	581	21	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	7.48e-103	39	581	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|Q0CVU1|RGLA_ASPTN	3.62e-101	43	562	19	509	Probable rhamnogalacturonate lyase A OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) OX=341663 GN=rglA PE=3 SV=2
sp|Q4W9T6|RGLA_ASPFU	6.59e-101	45	581	21	526	Probable rhamnogalacturonate lyase A OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) OX=330879 GN=rglA PE=3 SV=1

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	CS Position
0.000299	0.999683	CS pos: 23-24. Pr: 0.9532

TMHMM  Annotations     

There is no transmembrane helices in PHPALM_14940-t46_1-p1.