CAZyme Information: MGYG000003237_03324

Basic Information

• Species: Victivallis sp002998355
• Lineage: Bacteria; Verrucomicrobiota; Lentisphaeria; Victivallales; Victivallaceae; Victivallis; Victivallis sp002998355
• CAZyme ID: MGYG000003237_03324
• CAZy Family: PL11
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
1288		141917.36	6.0941

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000003237	4618450	MAG	United States	North America

• Gene Location: Start: 64637; End: 68503 Strand: +

Full Sequence      

MWKAICLCCAVASTLAAAEMRQFEVENVVVEREKLNRDRLSSSAWDIWTTDPEGRRWSEG
TVLRIGGPKSDRNPQDPASAMLTLRLPLEDGVYRISATGGRTFGISADGGRNFARIDARG
VVAGRVEVRGGVLELKLANCYAEANPANYGLVYVDRITAERLADLPKAVAPAVLKPGVPR
RFEAEDFVVEREKLARNRISSAAWDVWDEDRKGVWSGDRVLRIAGPRRDREPGDPASAAL
TIRIPVENGSYRVSASGGRSFGISLDGKTFRRISGHGVAAGRFEVKDGRLELTLSNCFAE
KDPAKYGAVYLDCITLERLDGAAAATKIVPVLPPPVKYPDPGVNWLKNDGNSRKFEAEEC
VVNRELLTWDVAQRGKWELWSKDENASRWSGRKVLRALACDTDRPAADSDSALLKFRVPV
EKGAKYTVFCAGGRSYGVSRDGKEFRKFSDGATIFEDVSSDTGFFEFYVANCFRHDPGPG
AVYLDYFQVMKQRELRDLPRVRGWAKERVRERLGRGVVALPADGGGAYISWRLLREDPAK
IGFDVFRIRDGRETRLNREAVVRTCDFTDPGAKEGDRYAVRPAAGFTGKAGESALLKEKY
ISFKLPDPKTNIMRVGVGDLDGDGTYDYIFKTPDANIDPWEAYWYPTPEPYRLEAFRSDG
THLWTKSYGWAIERGVWYSPFIVYDFDGDGRAEVALKMGEGDPRAKDGRVFTGPEYLVIL
DGMTGEEIARAPWPSREGFESYNLVNRNQLAMAYLDGKTPCVVALRGTYGLMKAEAWQLK
DGKLENVWKFSNEGLGDKCRGQGAHATIVADLDDDGRDEILLGSMALDDNGEVLWTTGMG
HNDYMYLSDIMPENPGLEVAYIYETPQRKNGVCVADAKTGRILWGLGEQTWHVNDGYAID
LDPALPGMEVMGLDFDGRGPSKERRWLFSGSGRLLNRGASVGPMRRGVYWDADLEKEECT
GLIRDFDGGPVGGMFAGNWVTTADLFGDWREELVVSLPGEVRIYATSIPAMDRRPSLMQE
HSYRTGVLNNAQGYPSDACLPCLPTQESDNFSLIHRSGGDPHIQVTVSASRHGALAGRVR
LAAPAGVTLEPAEWDVDLKAGGVSVTRVAASGDVKTGLLVRGEFAGRDGERLLRGQVPLY
RKKTRTVAPGAVTVPAAKFSSEKGGNVKIEAGRSLAKDGCMLGWDEKGHALSWSFRVPAA
GKYRLTMLRASARLAERKLTVAGKEYGIFAFPPTGGFGHSPEEWVLEGFEREGAELVFDL
PAGEVTVSMENTNSGSMNLAYLYLEPVR

Enzyme Prediction     

No EC number prediction in MGYG000003237_03324.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL11	508	1035	8.2e-126	0.9191419141914191

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10318	RGL11	2.33e-120	511	1034	2	556	Rhamnogalacturonan lyase of the polysaccharide lyase family 11. The rhamnogalacturonan lyase of the polysaccharide lyase family 11 (RGL11) cleaves glycoside bonds in polygalacturonan as well as RG (rhamnogalacturonan) type-I through a beta-elimination reaction. Functionally characterized members of this family, YesW and YesX from Bacillus subtilis, cleave glycoside bonds between rhamnose and galacturonic acid residues in the RG-I region of plant cell wall pectin. YesW and YesX work synergistically, with YesW cleaving the glycoside bond of the RG chain endolytically, and YesX converting the resultant oligosaccharides through an exotype reaction. This domain is sometimes found in architectures with non-catalytic carbohydrate-binding modules (CBMs). There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain through a beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.
pfam18370	RGI_lyase	1.54e-15	508	582	1	70	Rhamnogalacturonan I lyases beta-sheet domain. This is the beta-sheet domain found in rhamnogalacturonan (RG) lyases, which are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Polysaccharide lyase family 11 carrying this domain, such as YesW (EC:4.2.2.23) and YesX (EC:4.2.2.24), cleave glycoside bonds between rhamnose and galacturonic acid residues in RG-I through a beta-elimination reaction. Other family members carrying this domain are hemagglutinin A, lysine gingipain (Kgp) and Chitinase C (EC:3.2.1.14).
cd04082	CBM35_pectate_lyase-like	2.12e-04	1188	1284	35	124	Carbohydrate Binding Module family 35 (CBM35), pectate lyase-like; appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans. This family includes carbohydrate binding module family 35 (CBM35) domains that are non-catalytic carbohydrate binding domains that are appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans. Included in this family are CBM35s of pectate lyases, including pectate lyase 10A from Cellvibrio japonicas, these enzymes release delta-4,5-anhydrogalaturonic acid (delta4,5-GalA) from pectin, thus identifying a signature molecule for plant cell wall degradation. CBM35s are unique in that they display conserved specificity through extensive sequence similarity but divergent function through their appended catalytic modules. They are known to bind alpha-D-galactose (Gal), mannan (Man), xylan, glucuronic acid (GlcA), a beta-polymer of mannose, and possibly glucans, forming four subfamilies based on general ligand specificities (galacto, urono, manno, and gluco configurations). In contrast to most CBMs that are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. Some CBM35s bind their ligands in a calcium-dependent manner, especially those binding uronic acids.
cd04080	CBM6_cellulase-like	0.003	1183	1282	51	141	Carbohydrate Binding Module 6 (CBM6); appended to glycoside hydrolase (GH) domains, including GH5 (cellulase). This family includes carbohydrate binding module 6 (CBM6) domains that are appended to several glycoside hydrolase (GH) domains, including GH5 (cellulase) and GH16, as well as to coagulation factor 5/8 carbohydrate-binding domains. CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. The CBM6s are appended to GHs that display a diversity of substrate specificities. For some members of this family information is available about the specific substrates of the appended GH domains. It includes the CBM domains of various enzymes involved in cell wall degradation including, an extracellular beta-1,3-glucanase from Lysobacter enzymogenes encoded by the gluC gene (its catalytic domain belongs to the GH16 family), the tandem CBM domains of Pseudomonas sp. PE2 beta-1,3(4)-glucanase A (its catalytic domain also belongs to GH16), and a family 6 CBM from Cellvibrio mixtus Endoglucanase 5A (CmCBM6) which binds to the beta1,4-beta1,3-mixed linked glucans lichenan, and barley beta-glucan, cello-oligosaccharides, insoluble forms of cellulose, the beta1,3-glucan laminarin, and xylooligosaccharides, and the CBM6 of Fibrobacter succinogenes S85 XynD xylanase, appended to a GH10 domain, and Cellvibrio japonicas Cel5G appended to a GH5 (cellulase) domain. GH5 (cellulase) family includes enzymes with several known activities such as endoglucanase, beta-mannanase, and xylanase, which are involved in the degradation of cellulose and xylans. GH16 family includes enzymes with lichenase, xyloglucan endotransglycosylase (XET), and beta-agarase activities. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. For CmCBM6 it has been shown that these two binding sites have different ligand specificities.
pfam13517	VCBS	0.004	619	696	1	61	Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella. This domain of about 100 residues is found in multiple (up to 35) copies in long proteins from several species of Vibrio, Colwellia, Bradyrhizobium, and Shewanella (hence the name VCBS) and in smaller copy numbers in proteins from several other bacteria. The large protein size and repeat copy numbers, species distribution, and suggested activities of several member proteins suggests a role for this domain in adhesion (TIGR).

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
AVM44648.1	0.0	1	1288	1	1288
ASV76202.1	3.06e-170	507	1034	37	574
SCD19742.1	1.15e-148	486	1035	28	599
QNN21898.1	2.33e-148	505	1040	27	579
ADY37514.1	1.74e-147	486	1035	31	598

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2Z8R_A	9.39e-84	511	1027	6	551	Crystalstructure of rhamnogalacturonan lyase YesW at 1.40 A resolution [Bacillus subtilis],2Z8R_B Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution [Bacillus subtilis],2Z8S_A Crystal structure of rhamnogalacturonan lyase YesW complexed with digalacturonic acid [Bacillus subtilis],2Z8S_B Crystal structure of rhamnogalacturonan lyase YesW complexed with digalacturonic acid [Bacillus subtilis],2ZUX_A Crystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose [Bacillus subtilis],2ZUX_B Crystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose [Bacillus subtilis]
4CAG_A	2.10e-78	505	1034	6	565	Bacilluslicheniformis Rhamnogalacturonan Lyase PL11 [Bacillus licheniformis]
2ZUY_A	1.85e-73	506	1035	4	582	Crystalstructure of exotype rhamnogalacturonan lyase YesX [Bacillus subtilis]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
O31526	1.06e-82	511	1027	43	588	Rhamnogalacturonan endolyase YesW OS=Bacillus subtilis (strain 168) OX=224308 GN=yesW PE=1 SV=1
O31527	8.45e-73	506	1035	4	582	Rhamnogalacturonan exolyase YesX OS=Bacillus subtilis (strain 168) OX=224308 GN=yesX PE=1 SV=1

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
0.000291	0.999112	0.000155	0.000145	0.000138	0.000131

TMHMM  Annotations     

There is no transmembrane helices in MGYG000003237_03324.