CAZyme3D

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Entry ID

Information for CAZyme ID: SLM46173.1

Basic Information

GenBank IDSLM46173.1
FamilyGT4
Sequence Length381
UniProt IDA0A1W1I001(100,100)Download
Average pLDDT?92.73
CAZy50 ID111126
CAZy50 RepYes, SLM46173.1
Structure ClusterSC_GT4_clus864
EC Number(s)-
Substrates(s)-

Taxonomy

Tax ID1325564
KingdomBacteria
PhylumNitrospirota
ClassNitrospiria
OrderNitrospirales
FamilyNitrospiraceae
GenusNitrospira
SpeciesNitrospira japonica

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

MKRWSNSGAG  MRIGIDASPI  VGDRGGVGWH  TYYLLEAMLA  GADDVEFIGY  LRPGSVLPDD60
ARSWRTGGRI  TWVEAAKWAM  RWRGRTDRLD  LYHGTNFKLH  TVGRYGGIVT  IHDLWLERFP120
QYSTKVLGQG  LASMKARRTA  GRARTVVTVS  EFSARELSEL  YAVPRERLSV  IPNGVADDFS180
VRRDDRAMAE  LRARIRLPDG  PYLLFIGGAD  PRKNHRRFLE  AAHLMRGPLQ  GRRLLLVGSP240
DHAFGSYQES  AKTYGLTAQV  CCPGRLGRAD  LQLLYTYADQ  FVFPSLYEGF  GMPVLEAMAC300
GTPVITSRTT  GVAEAAGDAA  LLVDPEDARS  VGEAMVSLLE  DASLRASLTA  KGFERVKRFS360
WRSAAAKTLD  VYRRLCQERG  S381

Predicted 3D structure by AlphaFold2 with pLDDT = 92.73 ; 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

MKRWSNSGAG  MRIGIDASPI  VGDRGGVGWH  TYYLLEAMLA  GADDVEFIGY  LRPGSVLPDD60
ARSWRTGGRI  TWVEAAKWAM  RWRGRTDRLD  LYHGTNFKLH  TVGRYGGIVT  IHDLWLERFP120
QYSTKVLGQG  LASMKARRTA  GRARTVVTVS  EFSARELSEL  YAVPRERLSV  IPNGVADDFS180
VRRDDRAMAE  LRARIRLPDG  PYLLFIGGAD  PRKNHRRFLE  AAHLMRGPLQ  GRRLLLVGSP240
DHAFGSYQES  AKTYGLTAQV  CCPGRLGRAD  LQLLYTYADQ  FVFPSLYEGF  GMPVLEAMAC300
GTPVITSRTT  GVAEAAGDAA  LLVDPEDARS  VGEAMVSLLE  DASLRASLTA  KGFERVKRFS360
WRSAAAKTLD  VYRRLCQERG  S381

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) : GT4(199-347)

MKRWSNSGAG  MRIGIDASPI  VGDRGGVGWH  TYYLLEAMLA  GADDVEFIGY  LRPGSVLPDD60
ARSWRTGGRI  TWVEAAKWAM  RWRGRTDRLD  LYHGTNFKLH  TVGRYGGIVT  IHDLWLERFP120
QYSTKVLGQG  LASMKARRTA  GRARTVVTVS  EFSARELSEL  YAVPRERLSV  IPNGVADDFS180
VRRDDRAMAE  LRARIRLPDG  PYLLFIGGAD  PRKNHRRFLE  AAHLMRGPLQ  GRRLLLVGSP240
DHAFGSYQES  AKTYGLTAQV  CCPGRLGRAD  LQLLYTYADQ  FVFPSLYEGF  GMPVLEAMAC300
GTPVITSRTT  GVAEAAGDAA  LLVDPEDARS  VGEAMVSLLE  DASLRASLTA  KGFERVKRFS360
WRSAAAKTLD  VYRRLCQERG  S381

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