CAZyme Information: MGYG000002331_01462

Basic Information

• Species: Vibrio parahaemolyticus
• Lineage: Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Vibrionaceae; Vibrio; Vibrio parahaemolyticus
• CAZyme ID: MGYG000002331_01462
• CAZy Family: CBM50
• CAZyme Description: putative L,D-transpeptidase YcfS

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
308	MGYG000002331_3|CGC16	33891.17	7.5145

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000002331	5262465	Isolate	Bangladesh	Asia

• Gene Location: Start: 1627261; End: 1628187 Strand: -

Full Sequence      

MLSKKRSMSFAKRTLLSVSLSLVSGLSFAKMYELPEDGSRLIGRLENHVVQEGETMANIA
KHYDVGMLALMAANKGVDPFLPQEGRVLTIPSQLILPEVPHQGIVINLAELRLYYFPEGE
DVVHVFPVGIGRIGRDTPVMTTSISQKRPNPTWTPPASIRAEYRAKGVDLPAVVPAGPDN
PLGLFALRLAYGNGEYLIHGTNKDFGIGMRVSAGCIRMDPSDIEWLFDKVRRGEKVNIIN
QPVKVSLEPDRSVFVEAHEPLTRSNGEKDHLQVPKELGWWLNEFGLTNVKAKAVIAAQNG
VPVEITAP

Enzyme Prediction     

No EC number prediction in MGYG000002331_01462.

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
PRK10260	PRK10260	4.80e-101	29	267	24	262	L,D-transpeptidase; Provisional
PRK10190	PRK10190	4.37e-89	29	308	21	305	L,D-transpeptidase; Provisional
COG1376	ErfK	5.15e-52	28	242	22	232	Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis].
cd16913	YkuD_like	3.88e-40	104	239	2	121	L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD. Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.
pfam17969	Ldt_C	5.78e-24	242	305	1	67	L,D-transpeptidase C-terminal domain. This is the C-terminal domain found in d-transpeptidases (Ldt) homologues from E.coli. Three of these enzymes (YbiS, ErfK, YcfS) have been shown to cross-link Braun's lipoprotein to the peptidoglycan (PG), while the other two (YnhG, YcbB) form direct meso-diaminopimelate (DAP-DAP, or 3-3) cross-links within the PG. Family members include erfK (ldtA), ybiS (ldtB), ycfS (ldtC), and ynhG (ldtE).

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QUY00823.1	3.47e-149	29	308	20	299
QPC55488.1	3.47e-149	29	308	20	299
QTV10206.1	3.47e-149	29	308	20	299
QLK92159.1	3.47e-149	29	308	20	299
QTV04013.1	3.47e-149	29	308	20	299

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
4LZH_A	1.59e-77	27	267	1	241	ChainA, L,D-transpeptidase [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P75954	1.97e-94	29	305	28	310	Probable L,D-transpeptidase YcfS OS=Escherichia coli (strain K12) OX=83333 GN=ycfS PE=1 SV=1
P76193	7.79e-87	18	262	7	256	Probable L,D-transpeptidase YnhG OS=Escherichia coli (strain K12) OX=83333 GN=ynhG PE=1 SV=1
P0AAX8	6.77e-84	8	267	1	262	Probable L,D-transpeptidase YbiS OS=Escherichia coli (strain K12) OX=83333 GN=ybiS PE=1 SV=1
P0AAX9	6.77e-84	8	267	1	262	Probable L,D-transpeptidase YbiS OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) OX=199310 GN=ybiS PE=3 SV=1
P0AAY0	6.77e-84	8	267	1	262	Probable L,D-transpeptidase YbiS OS=Escherichia coli O157:H7 OX=83334 GN=ybiS PE=3 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
0.003199	0.994399	0.001593	0.000303	0.000257	0.000209

TMHMM  Annotations     

There is no transmembrane helices in MGYG000002331_01462.