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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 APIS134
Inhibited defense system
CLAN ID CLAN039
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300005662_003648|3300005662|Ga0078894_100068595
gene_page: 346 37387.71 5.4730 -3.0
Phage property
Phage Assembly id
IMGVR_UViG_3300005662_003648
PMID/References
PDB structures ;
Pfam domains PF07728.19,PF08406.15,PF00004.34,PF13555.11
Phrog phrog_249
Host taxa ;;;;;;
Gene Location Start: ;  End: ;  Strand: 
Description
Note This family does not have seed protein, but we infer its function is defending restriction-modification (RM) because it belongs to the same clan as family APIS166 which has seed protein.

Predicted 3D structure by alphafold2 with pTM = 0.81 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-A0A0H3H502-F1-model_v4 39 344 1 281 0.9397 0.845
AF-Q51481-F1-model_v4 72 344 1 260 0.9311 0.8101
AF-Q2G2J8-F1-model_v4 76 343 1 263 0.9053 0.791
AF-X8F327-F1-model_v4 38 344 6 289 0.7903 0.7162
AF-P71922-F1-model_v4 38 344 8 291 0.7864 0.715
AF-K0EW51-F1-model_v4 38 344 9 294 0.7793 0.7118
AF-O53705-F1-model_v4 40 345 1 297 0.7749 0.711
AF-K0FAA2-F1-model_v4 38 345 3 288 0.7785 0.7095
AF-Q9I0D5-F1-model_v4 41 340 1 277 0.7667 0.6841
AF-P33348-F1-model_v4 36 345 29 352 0.7055 0.6759

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP003332725384.pdb 1 345 1 348 0.8973 0.8817
MGYP003345063198.pdb 68 345 1 279 0.968 0.8663
MGYP000129684018.pdb 37 345 2 332 0.8917 0.8611
MGYP000487978036.pdb 39 345 5 319 0.8983 0.8564
MGYP000665104057.pdb 21 345 41 374 0.9259 0.8563
MGYP002627237152.pdb 39 345 1 306 0.9042 0.853
MGYP003324878685.pdb 20 345 24 361 0.888 0.8492
MGYP000089807778.pdb 39 344 3 309 0.9019 0.8469
MGYP003663999631.pdb 38 345 8 308 0.899 0.8466
MGYP003125958051.pdb 38 345 7 310 0.8931 0.8428

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS134 IMGVR_UViG_3300005662_003648|3300005662|Ga0078894_100068595 3 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN039

APIS134 has no similar APIS family.

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_3300005662_003648|3300005662|Ga0078894_100068595 100.000 1.975E-228 696 1.000% IMGVR PF07728 PF08406 PF00004 PF13555 phrog_249
IMGVR_UViG_3300017766_000946|3300017766|Ga0181343_100021727 95.800 1.441E-228 697 0.997% IMGVR PF07728 PF08406 PF00004 PF13555 phrog_249
IMGVR_UViG_3300020042_006902|3300020042|Ga0206640_10060063 94.100 8.886E-224 683 0.997% IMGVR PF07728 PF08406 PF00004 PF13555 phrog_249