dbCAN-seq: a database of CAZyme sequence and annotation

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CAZyme Information: MGYG000001323_02963

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Basic Information help

Species

Providencia rettgeri_D

Lineage

Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Providencia; Providencia rettgeri_D

CAZyme ID

MGYG000001323_02963

CAZy Family

CBM50

CAZyme Description

Murein DD-endopeptidase MepM

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
446	MGYG000001323_32\|CGC3	49182.63	9.904

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001323	4749568	Isolate	not provided	not provided

Gene Location

Start: 559947; End: 561287 Strand: -

Full Sequence Download help

Enzyme Prediction help

No EC number prediction in MGYG000001323_02963.

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
PRK11649	PRK11649	0.0	1	445	1	438	putative peptidase; Provisional
COG0739	NlpD	1.64e-50	232	429	69	274	Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contain LysM domain [Cell wall/membrane/envelope biogenesis].
pfam01551	Peptidase_M23	7.14e-49	319	413	2	96	Peptidase family M23. Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.
cd12797	M23_peptidase	3.75e-42	320	404	1	85	M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins. This model describes the metallopeptidase M23 family, which includes beta-lytic metallopeptidase and lysostaphin. Members of this family are zinc endopeptidases that lyse bacterial cell wall peptidoglycans; they cleave either the N-acylmuramoyl-Ala bond between the cell wall peptidoglycan and the cross-linking peptide (e.g. beta-lytic endopeptidase) or a bond within the cross-linking peptide (e.g. stapholysin, and lysostaphin). Beta-lytic metallopeptidase, formerly known as beta-lytic protease, has a preference for cleavage of Gly-X bonds and favors hydrophobic or apolar residues on either side. It inhibits growth of sensitive organisms and may potentially serve as an antimicrobial agent. Lysostaphin, produced by Staphylococcus genus, cleaves pentaglycine cross-bridges of cell wall peptidoglycan, acting as autolysins to maintain cell wall metabolism or as toxins and weapons against competing strains. Staphylolysin (also known as LasA) is implicated in a range of processes related to Pseudomonas virulence, including stimulating shedding of the ectodomain of cell surface heparan sulphate proteoglycan syndecan-1, and elastin degradation in connective tissue. Its active site is less constricted and contains a five-coordinate zinc ion with trigonal bipyramidal geometry and two metal-bound water molecules, possibly contributing to its activity against a wider range of substrates than those used by related lytic enzymes, consistent with its multiple roles in Pseudomonas virulence. The family includes members that do not appear to have the conserved zinc-binding site and might be lipoproteins lacking proteolytic activity.
PRK10871	nlpD	2.59e-14	321	414	220	313	murein hydrolase activator NlpD.

CAZyme Hits help

Hit ID	Query Start	Query End	Hit Start	Hit End
QNN31505.1	1	446	1	446
QKG45269.1	1	446	1	446
BBV04666.1	1	446	1	446
BBV12786.1	1	446	1	446
BBU95776.1	1	446	1	446

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
6UE4_A	2.07e-83	101	438	43	384	ShyAEndopeptidase from Vibrio cholerae (Closed form) [Vibrio cholerae O1 biovar El Tor str. N16961],6UE4_B ShyA Endopeptidase from Vibrio cholerae (Closed form) [Vibrio cholerae O1 biovar El Tor str. N16961]
6U2A_A	2.26e-83	101	438	40	381	ShyAendopeptidase from Vibrio cholera (open form) [Vibrio cholerae]
2GU1_A	4.48e-78	103	438	10	350	Crystalstructure of a zinc containing peptidase from vibrio cholerae [Vibrio cholerae]
4RNY_A	2.81e-26	218	443	117	343	Structureof Helicobacter pylori Csd3 from the orthorhombic crystal [Helicobacter pylori 26695],4RNY_B Structure of Helicobacter pylori Csd3 from the orthorhombic crystal [Helicobacter pylori 26695],4RNZ_A Structure of Helicobacter pylori Csd3 from the hexagonal crystal [Helicobacter pylori 26695]
3SLU_A	1.60e-24	105	420	19	345	Crystalstructure of NMB0315 [Neisseria meningitidis ATCC 13091],3SLU_B Crystal structure of NMB0315 [Neisseria meningitidis ATCC 13091]

Swiss-Prot Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P0AFT1	2.62e-189	1	444	1	438	Murein DD-endopeptidase MepM OS=Shigella flexneri OX=623 GN=mepM PE=3 SV=1
P0AFT0	2.62e-189	1	444	1	438	Murein DD-endopeptidase MepM OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) OX=199310 GN=mepM PE=3 SV=1
P0AFS9	2.62e-189	1	444	1	438	Murein DD-endopeptidase MepM OS=Escherichia coli (strain K12) OX=83333 GN=mepM PE=1 SV=1
P44693	4.73e-99	62	444	97	474	Uncharacterized metalloprotease HI_0409 OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=HI_0409 PE=3 SV=1
Q8K9M4	1.81e-82	101	444	77	415	Uncharacterized metalloprotease BUsg_310 OS=Buchnera aphidicola subsp. Schizaphis graminum (strain Sg) OX=198804 GN=BUsg_310 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
0.998801	0.001129	0.000018	0.000008	0.000004	0.000071

TMHMM Annotations help

There is no transmembrane helices in MGYG000001323_02963.