Seed protein information help

APIS family ID APIS062
Inhibited defense system
CLAN ID CLAN001
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300028374_000006|3300028374|Ga0306906_100003345
gene_page: 266 29693.55 5.1357 -9.0
Phage property
Phage Assembly id
PMID/References
PDB structures ;
Pfam domains PF00753.30
Phrog phrog_392,phrog_14556
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 = 0.89 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 1 266 1 246 0.825 0.7772
AF-A0A0H3GHL8-F1-model_v4 5 266 1 240 0.8064 0.7661
AF-P9WGC1-F1-model_v4 1 266 18 269 0.79 0.7627
AF-K0EUK8-F1-model_v4 24 266 1 232 0.8196 0.7525
AF-P50474-F1-model_v4 1 266 27 278 0.7906 0.75
AF-P16692-F1-model_v4 1 266 3 251 0.7839 0.7474
AF-A0A0H3GM29-F1-model_v4 1 266 3 251 0.7826 0.7462
AF-Q329H1-F1-model_v4 1 266 3 251 0.7824 0.746
AF-Q58769-F1-model_v4 1 266 3 255 0.7654 0.7421
AF-Q9HYM9-F1-model_v4 1 266 1 256 0.7716 0.7409

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 1 266 3 255 0.9139 0.8866
MGYP001465423269.pdb 1 266 1 253 0.873 0.8388
MGYP003952926961.pdb 1 266 2 253 0.8723 0.8385
MGYP000228473758.pdb 1 266 1 253 0.8658 0.8348
MGYP000856702051.pdb 1 266 3 267 0.851 0.8335
MGYP000246945288.pdb 1 266 2 255 0.8659 0.8329
MGYP003624123598.pdb 1 266 1 258 0.8548 0.8299
MGYP001333914959.pdb 1 266 3 243 0.8809 0.8294
MGYP000134058721.pdb 1 266 1 259 0.8433 0.8288
MGYP001159265950.pdb 1 266 2 251 0.8651 0.8263

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS062 IMGVR_UViG_3300028374_000006|3300028374|Ga0306906_100003345 6 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_3300011187_000002|3300011187|Ga0136596_100000964 100.000 0.0 551 100% IMGVR PF00753 phrog_392 phrog_14556
IMGVR_UViG_3300011189_000017|3300011189|Ga0136558_100014736 50.549 4.60e-86 266 100% IMGVR PF00753 phrog_392
IMGVR_UViG_3300028374_000006|3300028374|Ga0306906_100003345 100.000 0.0 551 100% IMGVR PF00753 phrog_392 phrog_14556
IMGVR_UViG_3300028374_000796|3300028374|Ga0306906_100001918 50.549 4.45e-86 266 100% IMGVR PF00753 phrog_392
IMGVR_UViG_3300028410_000013|3300028410|Ga0306866_100003517 59.023 5.39e-107 318 100% IMGVR PF12706 phrog_392
IMGVR_UViG_3300031216_000010|3300031216|Ga0307980_100003053 58.647 1.93e-105 315 100% IMGVR PF12706 phrog_392