CAZyme3D

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Entry ID

Information for CAZyme ID: VDD12656.1

Basic Information

GenBank IDVDD12656.1
FamilyPL4
Sequence Length606
UniProt IDA0A3P6CBA9(100,100)Download
Average pLDDT?86.56
CAZy50 ID51555
CAZy50 RepYes, VDD12656.1
Structure ClusterSC_PL4_clus6
EC Number(s)-
Substrates(s)-

Taxonomy

Tax ID3712
KingdomEukaryota
PhylumStreptophyta
ClassMagnoliopsida
OrderBrassicales
FamilyBrassicaceae
GenusBrassica
SpeciesBrassica oleracea

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

MKVGAPRKIR  SWVVFQVLLL  HLLPQAVHSQ  RSQNKLNITK  PGENISSLTI  QLRGVVVDNG60
IVQVTFSSPQ  GSITGIKYDG  IDNVLDDEVD  ERRRGYWDVA  WYEPEKKFKT  DKLEGTRFEI120
ITQNEEQVEI  SFTRTWTISK  RGSLVPLNVD  KRYIIRSGVS  GIYIYCIMER  LEGWPDVDMD180
QIRIVFKLNH  TIFNFMAISD  DRQRSMPSMA  DRNHAMQLAY  KEAVLLTNPR  NPMFKGEVDD240
KYMYSMEDKD  NNVHGWISSE  PPVGFWMITP  SDEFRLGGPI  KQDLTSHAGP  ITLSMFTSTH300
YAGKEMRMGY  RNGEPWKKVF  GPVLAYLNSV  SPNASTLRLW  RDAKRQGYQF  WTKADRKGRF360
IIENVRAGNY  SLYAWGIGFI  GDYKYEQNIT  ITPGTEMNVG  PIVYEPPRNG  PTLWEIGVPD420
RTAGEFYIPD  PYPTLMNNLY  VNPLQDRFRQ  YGLWDRYSDL  YPENDLVYTI  GLSNYRRDWF480
FAHVTRNVGN  NTYQPTTWQI  VFNLQNLNRV  GLYTLRVALA  SAADSELQVR  INDPESDHIF540
TTGLIGKDNA  IARHGIHGLY  RLYSIDVAGN  LLGAGDNTIY  LTQSRSTTPF  QGVMYDYIRL600
ESPFKT606

Predicted 3D structure by AlphaFold2 with pLDDT = 86.56 ; 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

MKVGAPRKIR  SWVVFQVLLL  HLLPQAVHSQ  RSQNKLNITK  PGENISSLTI  QLRGVVVDNG60
IVQVTFSSPQ  GSITGIKYDG  IDNVLDDEVD  ERRRGYWDVA  WYEPEKKFKT  DKLEGTRFEI120
ITQNEEQVEI  SFTRTWTISK  RGSLVPLNVD  KRYIIRSGVS  GIYIYCIMER  LEGWPDVDMD180
QIRIVFKLNH  TIFNFMAISD  DRQRSMPSMA  DRNHAMQLAY  KEAVLLTNPR  NPMFKGEVDD240
KYMYSMEDKD  NNVHGWISSE  PPVGFWMITP  SDEFRLGGPI  KQDLTSHAGP  ITLSMFTSTH300
YAGKEMRMGY  RNGEPWKKVF  GPVLAYLNSV  SPNASTLRLW  RDAKRQGYQF  WTKADRKGRF360
IIENVRAGNY  SLYAWGIGFI  GDYKYEQNIT  ITPGTEMNVG  PIVYEPPRNG  PTLWEIGVPD420
RTAGEFYIPD  PYPTLMNNLY  VNPLQDRFRQ  YGLWDRYSDL  YPENDLVYTI  GLSNYRRDWF480
FAHVTRNVGN  NTYQPTTWQI  VFNLQNLNRV  GLYTLRVALA  SAADSELQVR  INDPESDHIF540
TTGLIGKDNA  IARHGIHGLY  RLYSIDVAGN  LLGAGDNTIY  LTQSRSTTPF  QGVMYDYIRL600
ESPFKT606

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) : PL4_2(53-346)+PL4_2(346-586)

MKVGAPRKIR  SWVVFQVLLL  HLLPQAVHSQ  RSQNKLNITK  PGENISSLTI  QLRGVVVDNG60
IVQVTFSSPQ  GSITGIKYDG  IDNVLDDEVD  ERRRGYWDVA  WYEPEKKFKT  DKLEGTRFEI120
ITQNEEQVEI  SFTRTWTISK  RGSLVPLNVD  KRYIIRSGVS  GIYIYCIMER  LEGWPDVDMD180
QIRIVFKLNH  TIFNFMAISD  DRQRSMPSMA  DRNHAMQLAY  KEAVLLTNPR  NPMFKGEVDD240
KYMYSMEDKD  NNVHGWISSE  PPVGFWMITP  SDEFRLGGPI  KQDLTSHAGP  ITLSMFTSTH300
YAGKEMRMGY  RNGEPWKKVF  GPVLAYLNSV  SPNASTLRLW  RDAKRQGYQF  WTKADRKGRF360
IIENVRAGNY  SLYAWGIGFI  GDYKYEQNIT  ITPGTEMNVG  PIVYEPPRNG  PTLWEIGVPD420
RTAGEFYIPD  PYPTLMNNLY  VNPLQDRFRQ  YGLWDRYSDL  YPENDLVYTI  GLSNYRRDWF480
FAHVTRNVGN  NTYQPTTWQI  VFNLQNLNRV  GLYTLRVALA  SAADSELQVR  INDPESDHIF540
TTGLIGKDNA  IARHGIHGLY  RLYSIDVAGN  LLGAGDNTIY  LTQSRSTTPF  QGVMYDYIRL600
ESPFKT606

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