CAZyme3D

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Entry ID

Information for CAZyme ID: QFT54545.1

Basic Information

GenBank IDQFT54545.1
FamilyCBM2, GH5_2
Sequence Length593
UniProt IDA0A5P9EVE1(100,100)Download
Average pLDDT?77.79
CAZy50 ID53312
CAZy50 RepYes, QFT54545.1
Structure ClusterSC_CBM2_clus17, SC_CBM2_clus2, SC_GH5_clus134
EC Number(s)-
Substrates(s)-

Taxonomy

Tax ID2587856
KingdomBacteria
PhylumPseudomonadota
ClassGammaproteobacteria
OrderCellvibrionales
FamilyMicrobulbiferaceae
GenusMicrobulbifer
SpeciesMicrobulbifer sp. THAF38

Protein Sequence:
90 < plddt <=100;
70 < plddt <= 90;
50 < plddt <= 70;
0 <= plddt <= 50;     Download help

MLKVKRKNKS  LQVILALSIG  FSAGISNIHS  VFAASDSNPV  GYFGEMQVEG  NKINGSKTGE60
PMQVKGMSFF  WSNWTTYYNS  ETVDRMVDEF  QVEILRASYG  VDDNGSPYDS  DEDKIRTVVE120
AAIDRGVYII  IDWHTHGAHN  NVDAAKEFFA  RMAMDYGSYD  NVIFEIYNEP  TYVSWSVVKD180
YAEEVISEIR  KHSDNLVVVG  SPTWSQDVGA  AANDRINDEN  VAYSLHFYAG  THFSSLRDKA240
DYALSQGVAL  FVTEWGSVNA  DGNGSINYDS  TGDWLAWMDE  NEISWANWAI  NDKAESSSIF300
NSDGSVTETG  SFLKSIFESA  VPGRIWDDAG  IDGGTIGDDD  VDSGNEGAGN  TGSANGEEGG360
EADNGSGGAI  DGENDNVDLV  SGSSVGFSKA  SDWGAGFNGS  FTINNTGSSD  IEGWVLEFDF420
DGQINSFWTA  QIVSHSGNHY  VVKPHDWNST  VNAGKSLDLG  FTATGGQTVT  NITLGGNSDV480
GQSTGNTNEG  DTVVGATSLA  PIVEFSVSKD  WGAGFNGEFT  IKNTGSTDLS  GWTLEFDYDG540
QIDSFWTAKI  ISHSEGHYVV  KPLDWNSTIK  PGDSLKLGFT  ATGSKNVSNS  TLK593

Predicted 3D structure by AlphaFold2 with pLDDT = 77.79 ; Download help

pLDDT is for per-residue accuracy of the structure, which representes the quality of the residue. A higher value indicates better prediction accuracy. More detail please see AlphaFold .

Residues were colored according to plddt ( blue-> high quality; red-> low quality ).

Full Sequence:
CAPSIF:V and CAPSIF:G =99.9;
CAPSIF:V =59.9;
CAPSIF:G =40;
Non-Binding=0;     Download help

MLKVKRKNKS  LQVILALSIG  FSAGISNIHS  VFAASDSNPV  GYFGEMQVEG  NKINGSKTGE60
PMQVKGMSFF  WSNWTTYYNS  ETVDRMVDEF  QVEILRASYG  VDDNGSPYDS  DEDKIRTVVE120
AAIDRGVYII  IDWHTHGAHN  NVDAAKEFFA  RMAMDYGSYD  NVIFEIYNEP  TYVSWSVVKD180
YAEEVISEIR  KHSDNLVVVG  SPTWSQDVGA  AANDRINDEN  VAYSLHFYAG  THFSSLRDKA240
DYALSQGVAL  FVTEWGSVNA  DGNGSINYDS  TGDWLAWMDE  NEISWANWAI  NDKAESSSIF300
NSDGSVTETG  SFLKSIFESA  VPGRIWDDAG  IDGGTIGDDD  VDSGNEGAGN  TGSANGEEGG360
EADNGSGGAI  DGENDNVDLV  SGSSVGFSKA  SDWGAGFNGS  FTINNTGSSD  IEGWVLEFDF420
DGQINSFWTA  QIVSHSGNHY  VVKPHDWNST  VNAGKSLDLG  FTATGGQTVT  NITLGGNSDV480
GQSTGNTNEG  DTVVGATSLA  PIVEFSVSKD  WGAGFNGEFT  IKNTGSTDLS  GWTLEFDYDG540
QIDSFWTAKI  ISHSEGHYVV  KPLDWNSTIK  PGDSLKLGFT  ATGSKNVSNS  TLK593

Carbohydrate binding residues Predicted by CAPSIF from 3D structure; Download help

Residues were colored according to prediction score:

Nonbinder, CAPSIF:G Predicted Binder, CAPSIF:V Predicted Binder, CAPSIF:V and CAPSIF:G Predicted Binder

CArbohydrate–Protein interaction Site IdentiFier (CAPSIF) that predicts non-covalent carbohydrate-binding sites on proteins: (1) a 3D-UNet voxel-based neural network model (CAPSIF:V) and (2) an equivariant graph neural network model (CAPSIF:G).

Details:
⋆B-Factor = 0.0 : Nonbinder.
⋆B-Factor = 40.0 : CAPSIF:G Predicted Binder.
⋆B-Factor = 59.9 : CAPSIF:V Predicted Binder.
⋆B-Factor = 99.9 : CAPSIF:V and CAPSIF:G Predicted Binder.

For more detail please see CAPSIF.

Full Sequence:
AA;
CE;
PL;
GH;
GT;
CBM;     Download structure help

dbCAN3 predicted domain(s) : GH5_2(58-287)+CBM2(384-476)+CBM2(503-586)

MLKVKRKNKS  LQVILALSIG  FSAGISNIHS  VFAASDSNPV  GYFGEMQVEG  NKINGSKTGE60
PMQVKGMSFF  WSNWTTYYNS  ETVDRMVDEF  QVEILRASYG  VDDNGSPYDS  DEDKIRTVVE120
AAIDRGVYII  IDWHTHGAHN  NVDAAKEFFA  RMAMDYGSYD  NVIFEIYNEP  TYVSWSVVKD180
YAEEVISEIR  KHSDNLVVVG  SPTWSQDVGA  AANDRINDEN  VAYSLHFYAG  THFSSLRDKA240
DYALSQGVAL  FVTEWGSVNA  DGNGSINYDS  TGDWLAWMDE  NEISWANWAI  NDKAESSSIF300
NSDGSVTETG  SFLKSIFESA  VPGRIWDDAG  IDGGTIGDDD  VDSGNEGAGN  TGSANGEEGG360
EADNGSGGAI  DGENDNVDLV  SGSSVGFSKA  SDWGAGFNGS  FTINNTGSSD  IEGWVLEFDF420
DGQINSFWTA  QIVSHSGNHY  VVKPHDWNST  VNAGKSLDLG  FTATGGQTVT  NITLGGNSDV480
GQSTGNTNEG  DTVVGATSLA  PIVEFSVSKD  WGAGFNGEFT  IKNTGSTDLS  GWTLEFDYDG540
QIDSFWTAKI  ISHSEGHYVV  KPLDWNSTIK  PGDSLKLGFT  ATGSKNVSNS  TLK593

Predicted CAZyme domains from dbCAN; Download help

Domains were colored according to CAZyme classification: (AA), (CE), (PL), (GH), (GT), (CBM), & (Null)

dbCAN3 server is a web server for automated Carbohydrate-active enzyme ANnotation.

Details:
dbCAN3 server integrates three state-of-the-art tools/databases for automated CAZyme annotation:
⋆HMMER search for CAZyme family annotation vs. dbCAN CAZyme domain HMM database
⋆DIAMOND search for BLAST hits in the CAZy database
⋆HMMER search for CAZyme subfamily annotation vs. dbCAN-sub HMM database of CAZyme subfamilies (derived from eCAMI classification of CAZyDB families)

For more details, please see dbCAN3.

Similarites between the same cluster seqeunces from DIAMOND; Download help