CAZyme Information: MGYG000002358_00356

Basic Information

• Species: Pelistega indica
• Lineage: Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Pelistega; Pelistega indica
• CAZyme ID: MGYG000002358_00356
• CAZy Family: CBM50
• CAZyme Description: Murein hydrolase activator NlpD

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
243		25307.53	10.6964

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000002358	2504912	Isolate	India	Asia

• Gene Location: Start: 3110; End: 3841 Strand: +

Full Sequence      

MFKKSKILGLTLITVVLAGCAGSGNKAPISTIGGGYSGGSSAVSGNGIHVVQRGDTMYSI
ARRYNVPVSRLLSMNNLSNPSQIEVGQRIRVGAGSSVSGSSSAVTQPKDSSYANVTPPKA
ADASAISWTWPHKGNIISSYSESTRGIDIAGNLGDPVKAAASGTVSYVGNGLRGLGNLVL
ITHSNGFISAYAHNQRLLVKQNQRVSAGDKIAELGQSDTTSPRLHFEIRRNGTPVNPVSY
LPR

Enzyme Prediction     

No EC number prediction in MGYG000002358_00356.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CBM50	49	91	6.4e-16	0.95

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
PRK10871	nlpD	6.09e-43	1	243	7	318	murein hydrolase activator NlpD.
pfam01551	Peptidase_M23	1.53e-39	145	237	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.
COG0739	NlpD	1.71e-39	48	243	3	266	Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contain LysM domain [Cell wall/membrane/envelope biogenesis].
COG4942	EnvC	2.32e-31	130	243	301	420	Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning].
cd12797	M23_peptidase	7.29e-30	145	228	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
QPT40033.1	4.84e-90	1	243	1	237
AVL71145.1	3.85e-85	1	243	1	240
AHG64220.1	3.39e-84	7	243	13	252
QIM49640.1	1.08e-80	16	242	35	263
AWB35670.1	5.23e-76	15	242	2	217

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
4BH5_A	7.87e-15	130	243	23	142	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	1.45e-13	130	243	267	386	EnvCbound to the FtsX periplasmic domain [Escherichia coli K-12]
3SLU_A	6.31e-13	146	239	248	340	Crystalstructure of NMB0315 [Neisseria meningitidis ATCC 13091],3SLU_B Crystal structure of NMB0315 [Neisseria meningitidis ATCC 13091]
6MUK_A	6.90e-13	146	239	268	360	1.93Angstrom Resolution Crystal Structure of Peptidase M23 from Neisseria gonorrhoeae. [Neisseria gonorrhoeae FA 1090]
5J1L_A	1.14e-12	146	240	67	163	Crystalstructure of Csd1-Csd2 dimer I [Helicobacter pylori 26695],5J1L_C Crystal structure of Csd1-Csd2 dimer I [Helicobacter pylori 26695],5J1M_A Crystal structure of Csd1-Csd2 dimer II [Helicobacter pylori 26695],5J1M_C Crystal structure of Csd1-Csd2 dimer II [Helicobacter pylori 26695]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q46798	2.24e-48	3	242	9	243	Uncharacterized lipoprotein YgeR OS=Escherichia coli (strain K12) OX=83333 GN=ygeR PE=3 SV=2
P45682	2.69e-45	46	243	66	296	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	8.25e-39	51	243	149	404	Outer membrane antigenic lipoprotein B OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=lppB PE=3 SV=1
Q56131	2.82e-35	104	243	226	372	Murein hydrolase activator NlpD OS=Salmonella typhi OX=90370 GN=nlpD PE=3 SV=2
P40827	3.03e-35	104	243	230	376	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	0.000000	1.000063	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000002358_00356.