CAZyme3D

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Entry ID

Information for CAZyme ID: AFV00107.2

Basic Information

GenBank IDAFV00107.2
FamilyCBM2, GH5_1
Sequence Length565
UniProt IDK4KM49(100,100)Download
Average pLDDT?89.66
CAZy50 ID57214
CAZy50 RepYes, AFV00107.2
Structure ClusterSC_CBM2_clus17, SC_GH5_clus299
EC Number(s)-
Substrates(s)-

Taxonomy

Tax ID1117647
KingdomBacteria
PhylumPseudomonadota
ClassGammaproteobacteria
OrderCellvibrionales
FamilyCellvibrionaceae
GenusSimiduia
SpeciesSimiduia agarivorans
PDB file does not exist: ../CAZyme3D/mapped_uniprot_cazy/K4KM49.pdb

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

MKRKILGMAM  AGLFATFAEA  AQVSMSASGD  WGSAFQGDTK  ITNDEAGAVN  GWTITFGASF60
TIDQIWNARI  ISKTGNTYVI  GNLDYNGAIN  PGESVNFGFI  GSPGNAMMPV  DIVFNGGAAP120
TPTPTPTPTP  TPTPTPTPTP  TPTPTPTPTP  GNGLPGDDWL  SVSGNTIVNK  SGQPVWLTGA180
NWFGFNTTER  VFHGLWSVNL  DATVKAMADR  GINLVRVPFS  TELVKEWMAG  QFKAININTH240
ANPELTGMNS  LQVFDAFLAA  CKKYGVKVLL  DAHSAEADNS  GHVQPLWTKG  NITEADFINT300
WVWLAERYKN  DDTIVAFDLE  NEPHGKAHSD  TVFAKWDGST  DANNWKHVSE  KTAKAVLAAN360
PEILIMIEGI  EVYPIDGLSW  DSKNEKSYHF  NWWGGNLRGV  ADHPVLVPGH  QNKIMYSPHD420
YGPLVFAQDW  FYPGFSKETL  INDVWQDNWL  YIHTQGISPL  LMGEWGGFLD  GGDNEKWMLA480
LRELMNDYKI  HHTFWCLNPN  SGDTGGLLTG  DWTNWDEAKY  KVLEPVLWQN  AAGAYIGLDH540
EVPLGANGIT  VKQHYLNGGA  RPIGL565

Predicted 3D structure by AlphaFold2 with pLDDT = 89.66 ; 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

MKRKILGMAM  AGLFATFAEA  AQVSMSASGD  WGSAFQGDTK  ITNDEAGAVN  GWTITFGASF60
TIDQIWNARI  ISKTGNTYVI  GNLDYNGAIN  PGESVNFGFI  GSPGNAMMPV  DIVFNGGAAP120
TPTPTPTPTP  TPTPTPTPTP  TPTPTPTPTP  GNGLPGDDWL  SVSGNTIVNK  SGQPVWLTGA180
NWFGFNTTER  VFHGLWSVNL  DATVKAMADR  GINLVRVPFS  TELVKEWMAG  QFKAININTH240
ANPELTGMNS  LQVFDAFLAA  CKKYGVKVLL  DAHSAEADNS  GHVQPLWTKG  NITEADFINT300
WVWLAERYKN  DDTIVAFDLE  NEPHGKAHSD  TVFAKWDGST  DANNWKHVSE  KTAKAVLAAN360
PEILIMIEGI  EVYPIDGLSW  DSKNEKSYHF  NWWGGNLRGV  ADHPVLVPGH  QNKIMYSPHD420
YGPLVFAQDW  FYPGFSKETL  INDVWQDNWL  YIHTQGISPL  LMGEWGGFLD  GGDNEKWMLA480
LRELMNDYKI  HHTFWCLNPN  SGDTGGLLTG  DWTNWDEAKY  KVLEPVLWQN  AAGAYIGLDH540
EVPLGANGIT  VKQHYLNGGA  RPIGL565

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) : CBM2(22-117)+GH5_1(170-506)

0

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