dbCAN-seq: a database of CAZyme sequence and annotation

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CAZyme Information: MGYG000001328_01000

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Basic Information help

Species

Clostridium tertium

Lineage

Bacteria; Firmicutes_A; Clostridia; Clostridiales; Clostridiaceae; Clostridium; Clostridium tertium

CAZyme ID

MGYG000001328_01000

CAZy Family

CBM50

CAZyme Description

Trifunctional nucleotide phosphoesterase protein YfkN

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
504	MGYG000001328_3\|CGC12	58012.62	4.7099

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001328	3807822	Isolate	not provided	not provided

Gene Location

Start: 713175; End: 714689 Strand: +

Full Sequence Download help

Enzyme Prediction help

No EC number prediction in MGYG000001328_01000.

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
COG0737	UshA	9.75e-73	1	468	25	509	2',3'-cyclic-nucleotide 2'-phosphodiesterase/5'- or 3'-nucleotidase, 5'-nucleotidase family [Nucleotide transport and metabolism, Defense mechanisms].
PRK09419	PRK09419	1.83e-71	2	492	41	592	multifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase/5'-nucleotidase.
cd07410	MPP_CpdB_N	9.54e-65	3	268	1	273	Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain. CpdB is a bacterial periplasmic protein with an N-terminal metallophosphatase domain and a C-terminal 3'-nucleotidase domain. This alignment model represents the N-terminal metallophosphatase domain, which has 2',3'-cyclic phosphodiesterase activity, hydrolyzing the 2',3'-cyclic phosphates of adenosine, guanosine, cytosine and uridine to yield nucleoside and phosphate. CpdB also hydrolyzes the chromogenic substrates p-nitrophenyl phosphate (PNPP), bis(PNPP) and p-nitrophenyl phosphorylcholine (NPPC). CpdB is thought to play a scavenging role during RNA hydrolysis by converting the non-transportable nucleotides produced by RNaseI to nucleosides which can easily enter a cell for use as a carbon source. This family also includes YfkN, a Bacillus subtilis nucleotide phosphoesterase with two copies of each of the metallophosphatase and 3'-nucleotidase domains. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.
PRK09418	PRK09418	4.27e-48	1	503	38	608	bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase.
PRK11907	PRK11907	5.87e-46	5	485	118	662	bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase.

CAZyme Hits help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
APT74155.1	3.00e-129	1	504	19	535
ANQ54130.1	6.72e-125	1	500	19	529
APT72575.1	6.72e-125	1	500	19	529
QTA38048.1	3.25e-121	1	500	22	536
AGB41602.1	1.95e-67	3	455	37	495

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
4Q7F_A	3.92e-119	2	495	19	518	ChainA, 5' nucleotidase family protein [Staphylococcus aureus subsp. aureus COL]
3QFK_A	3.92e-119	2	495	19	518	ChainA, Uncharacterized protein [Staphylococcus aureus subsp. aureus NCTC 8325]
3GVE_A	1.93e-27	1	267	10	305	Crystalstructure of calcineurin-like phosphoesterase YfkN from Bacillus subtilis [Bacillus subtilis subsp. subtilis str. 168],3GVE_B Crystal structure of calcineurin-like phosphoesterase YfkN from Bacillus subtilis [Bacillus subtilis subsp. subtilis str. 168]
5EQV_A	7.84e-19	1	246	8	268	1.45Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site [Yersinia pestis CO92]
3IVD_A	1.11e-17	3	492	7	487	Putative5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine [Escherichia coli O6],3IVD_B Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine [Escherichia coli O6],3IVE_A Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Cytidine [Escherichia coli O6]

Swiss-Prot Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
O34313	1.98e-49	1	502	43	609	Trifunctional nucleotide phosphoesterase protein YfkN OS=Bacillus subtilis (strain 168) OX=224308 GN=yfkN PE=1 SV=1
P44764	5.84e-35	1	491	32	590	2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=cpdB PE=3 SV=1
P08331	1.73e-32	1	456	22	546	2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase OS=Escherichia coli (strain K12) OX=83333 GN=cpdB PE=1 SV=2
P26265	8.51e-31	1	456	22	546	2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) OX=99287 GN=cpdB PE=3 SV=2
P53052	5.92e-28	1	472	27	586	2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase OS=Yersinia enterocolitica OX=630 GN=cpdB 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
1.000067	0.000001	0.000000	0.000000	0.000000	0.000000

TMHMM Annotations help

There is no transmembrane helices in MGYG000001328_01000.