Seed protein information help

APIS family ID APIS056
Inhibited defense system
CLAN ID CLAN007
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300020049_002891|3300020049|Ga0206652_100507913
gene_page: 364 41704.94 4.6222 -15.5
Phage property
Phage Assembly id
PMID/References
PDB structures ;
Pfam domains
Phrog phrog_18122,phrog_27100,phrog_4400,phrog_25514,phrog_37109,phrog_16176
Host taxa
Gene Location Start: ;  End: ;  Strand: 
Description
Note This family does not have seed protein, but we infer its function is defending Gabija because it belongs to the same clan as family APIS008 which has seed protein.

Predicted 3D structure by alphafold2 with pTM = 0.75 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-Q55D09-F1-model_v4 1 329 601 1152 0.4784 0.3103

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP003537377462.pdb 2 352 1 267 0.8469 0.7266
MGYP000373333736.pdb 1 223 1 204 0.9324 0.7243
MGYP003394315973.pdb 1 229 4 202 0.91 0.7026
MGYP001439174798.pdb 2 228 1 229 0.858 0.7
MGYP000999235125.pdb 3 221 1 205 0.8998 0.6991
MGYP000376116683.pdb 1 248 1 248 0.8366 0.6961
MGYP001760742232.pdb 12 225 1 235 0.8353 0.6816
MGYP001197111591.pdb 1 364 5 272 0.7415 0.6772
MGYP001238726922.pdb 1 221 1 226 0.8643 0.6721
MGYP001240424264.pdb 1 227 1 229 0.8262 0.6717

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS056 IMGVR_UViG_3300020049_002891|3300020049|Ga0206652_100507913 6 HMM model Member alignment

Host Taxa distribution

Length distribution

Length Distribution Bar chart

Homology to other families       download full data without filtering help

Clan ID: CLAN007

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS008 3.90E-81 1 357 23 418 Gabija Gad2
APIS059 1.49E-66 2 346 20 399 - KF302034_00153
APIS089 6.71E-28 3 348 2 390 - uvig_330502_68