CAZyme Information: MGYG000002382_03253

Basic Information

• Species: Stenotrophomonas maltophilia_AK
• Lineage: Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Stenotrophomonas; Stenotrophomonas maltophilia_AK
• CAZyme ID: MGYG000002382_03253
• CAZy Family: CBM50
• CAZyme Description: Murein hydrolase activator NlpD

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
260		27020.73	10.4739

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000002382	4489830	Isolate	not provided	not provided

• Gene Location: Start: 38863; End: 39645 Strand: -

Full Sequence      

MNPDRLSKGVRIGALALLVSTLAACGTATVVRPGGGNAGGVTTPKTSVPKPGQTVVVRKG
DTIYALARIHDITPADLIAWNRLDNPSTIYPGQVIRLYPQGATSGRAPTTVVTPPRSAGS
SGGSTAPAPAPVGPVKSNIAWRWPADGAIVGRYVAGDATKQGVDIAGTSGQPVKATANGV
VVYSGAGLVGYGELIIIKHSDQWLSAYGHNRKRLVNEGQSVKAGEQIAEMGRTGANRDMV
HFEIRYNGKPVDPQQYLPAR

Enzyme Prediction     

No EC number prediction in MGYG000002382_03253.

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
PRK10871	nlpD	3.26e-51	11	260	12	319	murein hydrolase activator NlpD.
COG0739	NlpD	1.45e-38	54	260	3	267	Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contain LysM domain [Cell wall/membrane/envelope biogenesis].
pfam01551	Peptidase_M23	1.62e-36	161	253	4	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.
COG4942	EnvC	4.57e-34	96	257	263	418	Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning].
cd12797	M23_peptidase	4.14e-25	161	244	2	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.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
AYA90288.1	6.38e-186	1	260	1	260
QCZ96865.1	6.38e-186	1	260	1	260
QGL79961.1	2.60e-185	1	260	1	260
QNG77479.1	2.60e-185	1	260	1	260
QNA95495.1	3.69e-185	1	260	1	260

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
4BH5_A	1.02e-16	143	257	23	140	LytMdomain of EnvC, an activator of cell wall amidases in Escherichia coli [Escherichia coli K-12],4BH5_B LytM domain of EnvC, an activator of cell wall amidases in Escherichia coli [Escherichia coli K-12],4BH5_C LytM domain of EnvC, an activator of cell wall amidases in Escherichia coli [Escherichia coli K-12],4BH5_D LytM domain of EnvC, an activator of cell wall amidases in Escherichia coli [Escherichia coli K-12]
6TPI_A	2.75e-15	143	257	267	384	EnvCbound to the FtsX periplasmic domain [Escherichia coli K-12]
2B44_A	1.06e-10	151	260	19	133	TruncatedS. aureus LytM, P 32 2 1 crystal form [Staphylococcus aureus],2B44_B Truncated S. aureus LytM, P 32 2 1 crystal form [Staphylococcus aureus]
2B0P_A	1.08e-10	151	260	20	134	truncatedS. aureus LytM, P212121 crystal form [Staphylococcus aureus],2B0P_B truncated S. aureus LytM, P212121 crystal form [Staphylococcus aureus],2B13_A Truncated S. aureus LytM, P41 crystal form [Staphylococcus aureus],2B13_B Truncated S. aureus LytM, P41 crystal form [Staphylococcus aureus],4ZYB_A Chain A, Glycyl-glycine endopeptidase LytM [Staphylococcus aureus subsp. aureus NCTC 8325],4ZYB_B Chain B, Glycyl-glycine endopeptidase LytM [Staphylococcus aureus subsp. aureus NCTC 8325],4ZYB_C Chain C, Glycyl-glycine endopeptidase LytM [Staphylococcus aureus subsp. aureus NCTC 8325],4ZYB_D Chain D, Glycyl-glycine endopeptidase LytM [Staphylococcus aureus subsp. aureus NCTC 8325]
3SLU_A	6.15e-10	162	253	248	338	Crystalstructure of NMB0315 [Neisseria meningitidis ATCC 13091],3SLU_B Crystal structure of NMB0315 [Neisseria meningitidis ATCC 13091]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P45682	1.26e-51	5	260	18	297	Lipoprotein NlpD/LppB homolog OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA3623 PE=3 SV=1
P44833	4.61e-41	52	258	144	403	Outer membrane antigenic lipoprotein B OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=lppB PE=3 SV=1
P36685	3.32e-40	44	252	100	337	Outer membrane antigenic lipoprotein B (Fragment) OS=Histophilus somni OX=731 GN=lppB PE=3 SV=2
Q56131	1.40e-39	52	260	114	373	Murein hydrolase activator NlpD OS=Salmonella typhi OX=90370 GN=nlpD PE=3 SV=2
P40827	1.52e-39	52	260	118	377	Murein hydrolase activator NlpD OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) OX=99287 GN=nlpD PE=3 SV=2

SignalP and Lipop Annotations

This protein is predicted as LIPO

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.000000	0.000008	1.000033	0.000000	0.000000	0.000000

TMHMM  Annotations     

start	end
12	31