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Seed proteins  | Seed protein 3D structures  |  Structural homologs  |  Family infomation  | Homology to other families  | Family members, sources, and their hosts  

Seed protein information help

APIS family ID APIS064
Inhibited defense system
CLAN ID CLAN030
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300033145_003233|3300033145|Ga0366840_1000004654
gene_page: 276 32163.5 5.7244 -5
Phage property
Phage Assembly id
PMID/References
PDB structures ;
Pfam domains PF12706.10
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 = 0.85 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 2 276 1 246 0.8237 0.7647
AF-A0A0H3GHL8-F1-model_v4 6 276 1 240 0.7991 0.7465
AF-O74545-F1-model_v4 1 276 5 299 0.788 0.7407
AF-Q58769-F1-model_v4 1 276 2 255 0.7646 0.7321
AF-A0A0P0W0M3-F1-model_v4 1 276 4 310 0.7796 0.7214
AF-A0A1P8B5J8-F1-model_v4 1 276 10 316 0.7856 0.7209
AF-A0A0H3GR46-F1-model_v4 2 276 1 305 0.7742 0.7188
AF-P60195-F1-model_v4 2 276 1 305 0.7714 0.7159
AF-K7M157-F1-model_v4 1 276 14 319 0.7828 0.7153
AF-P0A8V0-F1-model_v4 2 276 1 305 0.7707 0.7151

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 1 276 2 255 0.9237 0.8813
MGYP003624123598.pdb 2 276 1 258 0.8885 0.8484
MGYP001465423269.pdb 2 276 1 253 0.8885 0.8392
MGYP000856702051.pdb 1 276 2 267 0.8639 0.8383
MGYP003670084134.pdb 1 276 1 242 0.8972 0.8302
MGYP001478949968.pdb 2 275 1 259 0.8705 0.8285
MGYP003952926961.pdb 1 276 1 253 0.8712 0.8234
MGYP001278173685.pdb 2 276 1 252 0.8743 0.8228
MGYP003194564429.pdb 2 276 1 252 0.8728 0.821
MGYP000246945288.pdb 1 276 1 255 0.868 0.821

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS064 IMGVR_UViG_3300033145_003233|3300033145|Ga0366840_1000004654 4 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN030

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS058 4.59E-67 2 276 16 268 IMGVR_UViG_3300022562_000702|3300022562|Ga0247387_1000200120
APIS054 2.00E-49 2 275 3 261 IMGVR_UViG_3300014204_000482|3300014204|Ga0172381_1000105623
APIS066 1.24E-43 2 276 1 293 IMGVR_UViG_3300035396_000446|3300035396|Ga0393109_006065_59543_60412
APIS060 5.63E-40 2 276 1 259 IMGVR_UViG_3300024258_000005|3300024258|Ga0233440_1000037199
APIS001 1.88E-33 1 245 19 251 pyrimidine cyclase system for antiphage resistance (Pycsar) YP_009840594.1
APIS062 1.51E-30 2 243 1 243 IMGVR_UViG_3300028374_000006|3300028374|Ga0306906_100003345
APIS073 4.84E-30 2 276 23 285 IMGVR_UViG_3300042197_004918|3300042197|Ga0451494_0000046_37885_38742
APIS076 2.78E-28 3 247 7 240 IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_42271_43065
APIS041 6.89E-24 1 244 1 228 IMGVR_UViG_2832702071_000001|2832702071|2832704097
APIS044 2.89E-18 4 265 2 233 HM144387_00160

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_3300024259_002152|3300024259|Ga0233437_1000033161 60.806 6.65e-109 323 99% IMGVR PF00753 phrog_392
IMGVR_UViG_3300033145_003233|3300033145|Ga0366840_1000004654 100.000 0.0 573 100% IMGVR PF12706 phrog_392
IMGVR_UViG_3300035698_029839|3300035698|Ga0374944_284892_60618_61400 53.986 2.51e-80 251 99% IMGVR PF00753 phrog_392
IMGVR_UViG_3300037247_001786|3300037247|Ga0392330_0000001_218554_219357 49.291 2.94e-77 244 99% IMGVR PF00753 phrog_392