dbCAN-seq: a database of CAZyme sequence and annotation

Basic Information help

Species

Noviherbaspirillum massiliense

Lineage

Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Noviherbaspirillum; Noviherbaspirillum massiliense

CAZyme ID

MGYG000001417_01158

CAZy Family

GH1

CAZyme Description

hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
753	MGYG000001417_1\|CGC11	84070.1	5.9611

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001417	4171493	Isolate	not provided	not provided

Gene Location

Start: 1181737; End: 1183998 Strand: -

Enzyme Prediction help

No EC number prediction in MGYG000001417_01158.

CAZyme Signature Domains help

Family	Start	End	Evalue	family coverage
GH1	15	382	3e-39	0.8554778554778555

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd05254	dTDP_HR_like_SDR_e	3.35e-78	460	715	2	263	dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs. dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended SDR, synthesizes dTDP-L-rhamnose from alpha-D-glucose-1-phosphate, providing the precursor of L-rhamnose, an essential cell wall component of many pathogenic bacteria. This subgroup has the characteristic active site tetrad and NADP-binding motif. This subgroup also contains human MAT2B, the regulatory subunit of methionine adenosyltransferase (MAT); MAT catalyzes S-adenosylmethionine synthesis. The human gene encoding MAT2B encodes two major splicing variants which are induced in human cell liver cancer and regulate HuR, an mRNA-binding protein which stabilizes the mRNA of several cyclins, to affect cell proliferation. Both MAT2B variants include this extended SDR domain. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
COG1091	RfbD	3.61e-72	459	730	2	277	dTDP-4-dehydrorhamnose reductase [Cell wall/membrane/envelope biogenesis].
pfam04321	RmlD_sub_bind	3.46e-64	460	730	1	280	RmlD substrate binding domain. L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesized by four different enzymes the final one of which is RmlD. The RmlD substrate binding domain is responsible for binding a sugar nucleotide.
TIGR01214	rmlD	2.26e-62	460	730	2	284	dTDP-4-dehydrorhamnose reductase. This enzyme catalyzes the last of 4 steps in making dTDP-rhamnose, a precursor of LPS core antigen, O-antigen, etc. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]
COG0451	WcaG	2.76e-24	460	710	3	282	Nucleoside-diphosphate-sugar epimerase [Cell wall/membrane/envelope biogenesis].

CAZyme Hits help

Hit ID	Query Start	Query End	Hit Start	Hit End
ALK96169.1	11	735	12	736
ATQ74756.1	13	748	13	748
QYF94144.1	13	748	13	748
QJD98907.1	10	753	11	755
QYG01613.1	9	738	8	738

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1VL0_A	5.79e-27	460	713	15	265	CrystalStructure Of A Dtdp-4-dehydrorhamnose Reductase, Rfbd Ortholog (ca_c2315) From Clostridium Acetobutylicum Atcc 824 At 2.05 A Resolution [Clostridium acetobutylicum ATCC 824],1VL0_B Crystal Structure Of A Dtdp-4-dehydrorhamnose Reductase, Rfbd Ortholog (ca_c2315) From Clostridium Acetobutylicum Atcc 824 At 2.05 A Resolution [Clostridium acetobutylicum ATCC 824],1VL0_C Crystal Structure Of A Dtdp-4-dehydrorhamnose Reductase, Rfbd Ortholog (ca_c2315) From Clostridium Acetobutylicum Atcc 824 At 2.05 A Resolution [Clostridium acetobutylicum ATCC 824]
4WPG_A	1.82e-21	456	729	3	282	GroupA Streptococcus GacA is an essential dTDP-4-dehydrorhamnose reductase (RmlD) [Streptococcus pyogenes]
1KBZ_A	2.94e-21	460	730	3	290	ChainA, dTDP-glucose oxidoreductase [Salmonella enterica subsp. enterica serovar Typhimurium],1KC1_A Chain A, dTDP-glucose oxidoreductase [Salmonella enterica subsp. enterica serovar Typhimurium],1KC3_A Chain A, dTDP-glucose oxidoreductase [Salmonella enterica subsp. enterica serovar Typhimurium],1N2S_A Chain A, dTDP-glucose oxidoreductase [Salmonella enterica subsp. enterica serovar Typhimurium]
2GGS_A	6.86e-20	461	723	4	262	crystalstructure of hypothetical dTDP-4-dehydrorhamnose reductase from sulfolobus tokodaii [Sulfurisphaera tokodaii],2GGS_B crystal structure of hypothetical dTDP-4-dehydrorhamnose reductase from sulfolobus tokodaii [Sulfurisphaera tokodaii]
3ZJK_A	2.99e-16	15	394	32	415	crystalstructure of Ttb-gly F401S mutant [Thermus thermophilus],3ZJK_B crystal structure of Ttb-gly F401S mutant [Thermus thermophilus],3ZJK_C crystal structure of Ttb-gly F401S mutant [Thermus thermophilus]

Swiss-Prot Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q9RR27	2.24e-35	461	724	4	270	Probable dTDP-4,6-dihydroxy-2-methyloxan-3-one 4-ketoreductase OS=Streptomyces antibioticus OX=1890 GN=oleU PE=3 SV=1
Q9L9E9	1.21e-34	461	712	6	257	dTDP-4-keto-6-deoxy-D-glucose reductase OS=Streptomyces niveus OX=193462 GN=novS PE=3 SV=1
A0QTF8	2.18e-32	414	727	3	308	dTDP-4-dehydrorhamnose reductase OS=Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) OX=246196 GN=rmlD PE=1 SV=1
P29781	1.12e-31	461	715	10	269	dTDP-4-dehydrorhamnose reductase OS=Streptomyces griseus OX=1911 GN=strL PE=1 SV=1
O66251	1.92e-30	460	678	4	228	dTDP-4-dehydrorhamnose reductase OS=Aggregatibacter actinomycetemcomitans OX=714 GN=rmlD PE=1 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
1.000060	0.000000	0.000000	0.000000	0.000000	0.000000

TMHMM Annotations help

There is no transmembrane helices in MGYG000001417_01158.

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