CAZyme Information: MGYG000001417_01046

Basic Information

• Species: Noviherbaspirillum massiliense
• Lineage: Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Noviherbaspirillum; Noviherbaspirillum massiliense
• CAZyme ID: MGYG000001417_01046
• CAZy Family: GH1
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
734		82769.7	6.8847

Genome Property

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

• Gene Location: Start: 1055258; End: 1057462 Strand: +

Full Sequence      

MNSINNNTSDVSTQQTLELWGGIECTVVRIQDQYRNQIKETGHADRMEDLDAIAALGIKT
LRYPVLWETISPDHPDQAEWGWHDKRLARLRELGIAPIAGLVHHGSGPRYTNLLDPNFPQ
MLARHAERVARRYPWIDMFTPVNEPLTTARFSALYGHWYPHARDTLTMLRALYIECRATA
LSMEAIRKVTPHARLVQTEDLGKTFSFPDLKHQADYENERRWLSFDLLCGRIDARHPWYD
TFIKAGIGKSELAFFTEQPCAPDIIGINHYVTSERFLDRRAREYPPEFWTDAVPYVDVHA
TRVPYVEGLTGPEARLREVWERYRLPIAVTEAHLGGSRDDQLRWLNQIWKAAVKLKGEGV
DIRAVTIWSIFGCVDWNSLLLQNSGFYESGVFDVRGGQPRPTALAHAAASLAKNGEFDHP
VLDGLGWWHRPDRYFQRPSQAVEAPQIIRSDRRLVITGARGTLGQALSRICSARSLEHDL
LSRAEMDIADQASVEAALMRHRPWAVINAAGYVRVADAHRESERCMRENAMGAEVLAKAC
AKLGIPYVTFSSDLVFDGKLGRAYVESDKLSPLCVYGNSKAEAERRVMAAFPDALVVRTS
AFFGPWDRYNFVHAILRELAAGRRVEASDDAHVSPTYVPDLAHAVLDLLIDRANGIWHLA
NQGALSWYEFAERAAREARLDASALVKTHGGGRSITALSSERGLLLPTFGNAFDRYFREN
TIAWDADPAERAVA

Enzyme Prediction     

No EC number prediction in MGYG000001417_01046.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
GH1	23	388	5e-38	0.8531468531468531

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd05254	dTDP_HR_like_SDR_e	6.37e-66	453	685	1	239	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	2.64e-64	453	681	2	229	dTDP-4-dehydrorhamnose reductase [Cell wall/membrane/envelope biogenesis].
pfam04321	RmlD_sub_bind	4.58e-58	454	683	1	234	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	7.45e-56	453	678	1	228	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	5.32e-19	453	687	2	265	Nucleoside-diphosphate-sugar epimerase [Cell wall/membrane/envelope biogenesis].

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QFU17850.1	0.0	14	734	2	723
QRM34426.1	0.0	17	726	7	715
QGM97233.1	0.0	17	719	9	710
QAY76666.1	3.99e-292	8	718	2	712
BBD68245.1	1.81e-285	4	721	12	756

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
3SC6_A	5.01e-27	453	719	7	283	2.65Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames],3SC6_B 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames],3SC6_C 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames],3SC6_D 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames],3SC6_E 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames],3SC6_F 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames]
1VL0_A	4.67e-26	453	681	14	240	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]
2GGS_A	7.41e-19	453	671	2	218	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]
1KBZ_A	3.07e-17	487	679	39	235	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]
3ZJK_A	2.21e-09	48	387	61	404	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     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P39631	8.73e-34	453	688	3	236	Spore coat polysaccharide biosynthesis protein SpsK OS=Bacillus subtilis (strain 168) OX=224308 GN=spsK PE=3 SV=3
P9WH09	6.69e-33	453	681	7	238	dTDP-4-dehydrorhamnose reductase OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) OX=83332 GN=rmlD PE=1 SV=1
P9WH08	6.69e-33	453	681	7	238	dTDP-4-dehydrorhamnose reductase OS=Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) OX=83331 GN=rmlD PE=3 SV=1
Q9L9E9	8.62e-31	453	676	4	227	dTDP-4-keto-6-deoxy-D-glucose reductase OS=Streptomyces niveus OX=193462 GN=novS PE=3 SV=1
O66251	2.43e-28	453	671	3	227	dTDP-4-dehydrorhamnose reductase OS=Aggregatibacter actinomycetemcomitans OX=714 GN=rmlD PE=1 SV=1

SignalP and Lipop Annotations

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
1.000054	0.000002	0.000000	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000001417_01046.