Seed protein information help

APIS family ID APIS060
Inhibited defense system
CLAN ID CLAN001
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300024258_000005|3300024258|Ga0233440_1000037199
gene_page: 263 29902.25 4.5051 -17.5
Phage property
Phage Assembly id
PMID/References
PDB structures ;
Pfam domains PF00753.30
Phrog phrog_392
Host taxa
Gene Location Start: ;  End: ;  Strand: 
Description
Note This family does not have seed protein, but we infer its function is defending pyrimidine cyclase system for antiphage resistance (Pycsar) because it belongs to the same clan as family APIS001 which has seed protein.

Predicted 3D structure by alphafold2 with pTM = 0.9 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-A0A133CTF0-F1-model_v4 1 259 1 246 0.8428 0.7954
AF-A0A0H3GHL8-F1-model_v4 5 263 1 244 0.8257 0.7871
AF-O74545-F1-model_v4 1 261 6 301 0.8416 0.7757
AF-P9WGC1-F1-model_v4 1 262 18 272 0.8097 0.7739
AF-Q58769-F1-model_v4 1 263 3 260 0.7998 0.7715
AF-I1KRW8-F1-model_v4 1 261 3 311 0.8437 0.7661
AF-I1K3H5-F1-model_v4 1 261 3 308 0.8375 0.7639
AF-A0A1P8B5J8-F1-model_v4 1 261 11 318 0.8486 0.7637
AF-P50474-F1-model_v4 1 263 27 282 0.8106 0.7615
AF-A0A0P0W0M3-F1-model_v4 1 261 5 312 0.8387 0.7603

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP002654867125.pdb 1 259 3 255 0.9415 0.9194
MGYP000856702051.pdb 1 260 3 268 0.8858 0.8648
MGYP000228473758.pdb 1 261 1 255 0.8908 0.8634
MGYP001465423269.pdb 1 259 1 253 0.8918 0.8615
MGYP003624123598.pdb 1 260 1 259 0.8802 0.8609
MGYP003194564429.pdb 1 259 1 252 0.8939 0.8594
MGYP001278173685.pdb 1 259 1 252 0.8927 0.8585
MGYP003452926687.pdb 1 260 2 266 0.8755 0.8581
MGYP003606950373.pdb 1 261 4 256 0.8816 0.8564
MGYP003952926961.pdb 1 260 2 254 0.8857 0.8558

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS060 IMGVR_UViG_3300024258_000005|3300024258|Ga0233440_1000037199 3 HMM model Member alignment

Host Taxa distribution

Length distribution

Length Distribution Bar chart

Family members, sources, and their hosts        help

Results of representative protein blast against members.

Member pident evalue bitscore qcovs phage host SourceDB Pfam Phrog
IMGVR_UViG_3300013795_000141|3300013795|Ga0180408_1001003 42.593 8.76e-55 185 99% IMGVR PF00753 phrog_392
IMGVR_UViG_3300024258_000005|3300024258|Ga0233440_1000037199 100.000 0.0 542 100% IMGVR PF00753 phrog_392
IMGVR_UViG_3300035188_001312|3300035188|Ga0335059_0000026_130956_131816 41.219 2.02e-60 201 97% IMGVR PF12706 phrog_392