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Seed proteins  | Seed protein 3D structures  |  Structural homologs

Seed protein information help

APIS family ID ArdB
Inhibited defense system restriction-modification (RM)
CLAN ID CLAN006
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
AAB36887.1 gene_page: ArdB 141 16479.50 4.4957 -6.0
Phage property
Phage Genbank id
plasmid pKM101 of E. coli U72482.2
PMID/References PMID:8393008
PDB structures ;
Pfam domains PF03230
Phrog
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli
Gene Location Start: ;  End: ;  Strand: 
Description Like ArdA, ArdB efficiently inhibits restriction by members of the three known families of type I systems of E. coli and only slightly affects the type II enzyme, EcoRI.

Predicted 3D structure by alphafold2 with pTM = 0.86 Download help

pTM is for the estimate of the TM-score, which is obtained from a pairwise error prediction. The higher pTM score indicates better model quality.

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
90 < plddt <=100 ;
70 < plddt <= 90 ;
50 < plddt <= 70 ;
0 <= plddt <= 50 ;      Download help

Structural homologs

Structure homologs against by afdb (html) ; download full result table

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
AF-A0A0H3GW18-F1-model_v4 5 142 6 141 0.8672 0.8327
AF-A0A0H3GVF3-F1-model_v4 5 142 1 132 0.8766 0.8198
AF-Q93GQ0-F1-model_v4 2 142 3 144 0.8489 0.8146
AF-P52139-F1-model_v4 3 142 14 152 0.8471 0.7976
AF-P75676-F1-model_v4 4 142 15 152 0.8456 0.7957
AF-Q327Q6-F1-model_v4 5 142 19 157 0.8478 0.7874
AF-A0A077ZNG7-F1-model_v4 11 142 9 141 0.8503 0.784
AF-Q32HM6-F1-model_v4 5 142 43 181 0.8523 0.7464
AF-A0A0H3GZ47-F1-model_v4 5 142 87 221 0.83 0.6657

Structure homologs against by esmdb (html) ; download full result table

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP001487061361.pdb 7 142 1 132 0.948 0.8993
MGYP003639530229.pdb 2 142 1 137 0.9285 0.8929
MGYP001183799919.pdb 2 142 3 140 0.9174 0.8919
MGYP001809940848.pdb 1 142 1 140 0.9181 0.889
MGYP001201501853.pdb 1 142 1 134 0.9341 0.8886
MGYP003692230177.pdb 1 142 3 142 0.9092 0.8876
MGYP000848125219.pdb 1 142 1 135 0.9276 0.8864
MGYP001225601631.pdb 1 142 1 137 0.9216 0.8863
MGYP000947783961.pdb 1 142 1 138 0.9182 0.8848
MGYP000175629856.pdb 1 142 3 144 0.9122 0.8847