CAZyme3D

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Entry ID

Information for CAZyme ID: AYD00179.1

Basic Information

GenBank IDAYD00179.1
FamilyGT51
Sequence Length762
UniProt IDAYD00179.1(MOD)Download
Average pLDDT?82.33
CAZy50 ID31439
CAZy50 RepYes, AYD00179.1
Structure ClusterSC_GT51_clus109
EC Number(s)-
Substrates(s)-

Taxonomy

Tax ID1825976
KingdomBacteria
PhylumPseudomonadota
ClassAlphaproteobacteria
OrderHyphomicrobiales
FamilyRhizobiaceae
GenusNeorhizobium
SpeciesNeorhizobium sp. NCHU2750

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

MQDEPKDRST  SPEERPRKKR  HLLLRIDSWI  DSTVWNLGFK  LAELWEEITI  FFRRFRVRGW60
KKLVFELAGE  AMTLGTAGAL  VLLALAMPAF  EETKEDWRNR  GDFAVTFLDR  YGNVIGHRGI120
IHEDSVPIDQ  LPDTLIKAVL  ATEDRRFFDH  YGIDFIGLAR  ALTENAKAGG  VVQGGSTLTQ180
QLAKNLFLTN  ERSIERKVKE  AFLSVWLEAN  LSKKEILSLY  LDRAYMGGGT  FGVAAAAQFY240
FGKNVTDINL  AESAMLAGLF  KAPAKYAPHV  NLPAARARAN  DVLSNLVQSG  FMSEGQVIGA300
RRNPATAIDR  AEVKAPDYFL  DWAFDEVQRL  AAEGKIKEHS  LVVRTTIDTG  LQQAADAAME360
SSLREYGENY  KVKQGALVMI  ENGGAVRAMV  GGRDYGESQF  NRATKALRQP  GSSFKLYTYS420
TAMEHGFTPE  TTISDAPITW  NGWSPQNYER  SYKGKVTLLA  AMAASLNTVP  VRLAKEYLGI480
DAIVKTAKAF  GVETPLRKDK  TVPLGTSEVT  VLDQATGYAV  MPAGGMQSRR  HGIEQVQGYG540
GEVLYDFNRD  EPAAKRVLSE  QAVSSMNRIL  TQIPVIGTAR  RAALDGGIVT  GGKTGTSQNY600
RDAWFIGFTG  NYTTAVWFGN  DDYSPMNNMT  GGTLPAMAFK  KLMDYAHQGV  ELRAIPGIDN660
PLPTGTHRKG  DTVAERKDTD  PAILALTRPR  SLSSETTRVL  KQIAQMLKTA  PPITADPEKF720
ADAAKPAAVP  ASLLGPGTDS  LRTGDVRKGK  AVVSPIRTNT  IP762

Predicted 3D structure by AlphaFold2 with pLDDT = 82.33 ; 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

MQDEPKDRST  SPEERPRKKR  HLLLRIDSWI  DSTVWNLGFK  LAELWEEITI  FFRRFRVRGW60
KKLVFELAGE  AMTLGTAGAL  VLLALAMPAF  EETKEDWRNR  GDFAVTFLDR  YGNVIGHRGI120
IHEDSVPIDQ  LPDTLIKAVL  ATEDRRFFDH  YGIDFIGLAR  ALTENAKAGG  VVQGGSTLTQ180
QLAKNLFLTN  ERSIERKVKE  AFLSVWLEAN  LSKKEILSLY  LDRAYMGGGT  FGVAAAAQFY240
FGKNVTDINL  AESAMLAGLF  KAPAKYAPHV  NLPAARARAN  DVLSNLVQSG  FMSEGQVIGA300
RRNPATAIDR  AEVKAPDYFL  DWAFDEVQRL  AAEGKIKEHS  LVVRTTIDTG  LQQAADAAME360
SSLREYGENY  KVKQGALVMI  ENGGAVRAMV  GGRDYGESQF  NRATKALRQP  GSSFKLYTYS420
TAMEHGFTPE  TTISDAPITW  NGWSPQNYER  SYKGKVTLLA  AMAASLNTVP  VRLAKEYLGI480
DAIVKTAKAF  GVETPLRKDK  TVPLGTSEVT  VLDQATGYAV  MPAGGMQSRR  HGIEQVQGYG540
GEVLYDFNRD  EPAAKRVLSE  QAVSSMNRIL  TQIPVIGTAR  RAALDGGIVT  GGKTGTSQNY600
RDAWFIGFTG  NYTTAVWFGN  DDYSPMNNMT  GGTLPAMAFK  KLMDYAHQGV  ELRAIPGIDN660
PLPTGTHRKG  DTVAERKDTD  PAILALTRPR  SLSSETTRVL  KQIAQMLKTA  PPITADPEKF720
ADAAKPAAVP  ASLLGPGTDS  LRTGDVRKGK  AVVSPIRTNT  IP762

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) : GT51(122-286)

MQDEPKDRST  SPEERPRKKR  HLLLRIDSWI  DSTVWNLGFK  LAELWEEITI  FFRRFRVRGW60
KKLVFELAGE  AMTLGTAGAL  VLLALAMPAF  EETKEDWRNR  GDFAVTFLDR  YGNVIGHRGI120
IHEDSVPIDQ  LPDTLIKAVL  ATEDRRFFDH  YGIDFIGLAR  ALTENAKAGG  VVQGGSTLTQ180
QLAKNLFLTN  ERSIERKVKE  AFLSVWLEAN  LSKKEILSLY  LDRAYMGGGT  FGVAAAAQFY240
FGKNVTDINL  AESAMLAGLF  KAPAKYAPHV  NLPAARARAN  DVLSNLVQSG  FMSEGQVIGA300
RRNPATAIDR  AEVKAPDYFL  DWAFDEVQRL  AAEGKIKEHS  LVVRTTIDTG  LQQAADAAME360
SSLREYGENY  KVKQGALVMI  ENGGAVRAMV  GGRDYGESQF  NRATKALRQP  GSSFKLYTYS420
TAMEHGFTPE  TTISDAPITW  NGWSPQNYER  SYKGKVTLLA  AMAASLNTVP  VRLAKEYLGI480
DAIVKTAKAF  GVETPLRKDK  TVPLGTSEVT  VLDQATGYAV  MPAGGMQSRR  HGIEQVQGYG540
GEVLYDFNRD  EPAAKRVLSE  QAVSSMNRIL  TQIPVIGTAR  RAALDGGIVT  GGKTGTSQNY600
RDAWFIGFTG  NYTTAVWFGN  DDYSPMNNMT  GGTLPAMAFK  KLMDYAHQGV  ELRAIPGIDN660
PLPTGTHRKG  DTVAERKDTD  PAILALTRPR  SLSSETTRVL  KQIAQMLKTA  PPITADPEKF720
ADAAKPAAVP  ASLLGPGTDS  LRTGDVRKGK  AVVSPIRTNT  IP762

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