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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 APIS169
Inhibited defense system
CLAN ID CLAN038
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300044551_000136|3300044551|Ga0455787_00181_52848_53810
gene_page: 320 36532.91 5.3287 -6.0
Phage property
Phage Assembly id
IMGVR_UViG_3300044551_000136
PMID/References
PDB structures ;
Pfam domains PF09588.15
Phrog
Host taxa ;;;;;;
Gene Location Start: ;  End: ;  Strand: 
Description
Note This family does not have seed protein, but we infer its function is defending CRISPR-Cas evasion by DNA repair because it belongs to the same clan as family APIS185 which has seed protein.

Predicted 3D structure by alphafold2 with pTM = 0.78 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-K7K9X8-F1-model_v4 22 221 18 233 0.7347 0.5792
AF-I1KRY7-F1-model_v4 7 222 62 283 0.7401 0.552
AF-Q4DEY6-F1-model_v4 21 299 2 446 0.5349 0.451

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP001560186693.pdb 9 317 1 292 0.8788 0.824
MGYP003757534971.pdb 9 303 1 297 0.8531 0.8085
MGYP001614786375.pdb 22 312 1 276 0.8789 0.803
MGYP000292165069.pdb 9 317 4 318 0.8189 0.7983
MGYP000646640369.pdb 1 320 17 345 0.8436 0.7976
MGYP000367821159.pdb 8 316 1 296 0.8424 0.7969
MGYP003654241378.pdb 9 314 1 320 0.8136 0.7959
MGYP000331096436.pdb 2 320 5 335 0.8298 0.7936
MGYP000170097161.pdb 9 312 1 317 0.8141 0.7913
MGYP001136335699.pdb 23 318 1 317 0.8131 0.7907

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS169 IMGVR_UViG_3300044551_000136|3300044551|Ga0455787_00181_52848_53810 20 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN038

APIS169 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_3300044551_000136|3300044551|Ga0455787_00181_52848_53810 100.000 2.509E-217 663 1.000% IMGVR PF09588 phrog_
IMGVR_UViG_2600255079_000001|2600255079|2600868391 63.200 1.411E-121 387 0.966% Bifidobacterium bombi IMGVR PF09588 phrog_
MGV-GENOME-0262487_5 51.900 4.745E-96 313 0.978% Bifidobacterium MGV PF09588 phrog_
uvig_396285_95 53.300 4.738E-99 321 0.978% Bifidobacterium longum GPD PF09588 phrog_8474
IMGVR_UViG_3300045988_076561|3300045988|Ga0495776_049500_5379_6347 53.700 5.256E-100 324 0.978% Bifidobacterium IMGVR PF09588 phrog_8474
uvig_233391_8 56.300 2.804E-100 325 0.938% Bifidobacterium longum GPD PF09588 phrog_8474
uvig_576839_56 53.400 3.461E-99 322 0.978% Bifidobacterium longum GPD PF09588 phrog_8474
uvig_297080_54 52.500 1.096E-97 317 0.978% Bifidobacterium longum GPD PF09588 phrog_
MGV-GENOME-0261211_51 54.000 5.830E-101 327 0.978% Bifidobacterium MGV PF09588 phrog_8474
IMGVR_UViG_3300029325_000116|3300029325|Ga0242844_1027724 53.500 1.846E-99 323 0.978% Bifidobacterium IMGVR PF09588 phrog_8474
IMGVR_UViG_3300045988_071707|3300045988|Ga0495776_009075_31027_31995 54.000 5.830E-101 327 0.978% Bifidobacterium IMGVR PF09588 phrog_8474
uvig_450334_17 52.600 8.003E-98 318 0.978% Bifidobacterium longum GPD PF09588 phrog_
uvig_452566_30 52.100 1.351E-96 314 0.978% Bifidobacterium longum GPD PF09588 phrog_
uvig_165585_49 51.900 4.745E-96 313 0.978% Bifidobacterium longum GPD PF09588 phrog_
uvig_314501_58 52.300 3.848E-97 316 0.978% Bifidobacterium longum GPD PF09588 phrog_
uvig_424581_10 52.300 5.267E-97 316 0.978% Bifidobacterium longum GPD PF09588 phrog_
MGV-GENOME-0182231_9 53.700 5.256E-100 324 0.978% Bifidobacterium MGV PF09588 phrog_8474
MGV-GENOME-0214287_10 53.700 5.256E-100 324 0.978% Bifidobacterium MGV PF09588 phrog_8474
uvig_482582_51 54.000 5.830E-101 327 0.978% Bifidobacterium longum GPD PF09588 phrog_8474
IMGVR_UViG_3300045988_071735|3300045988|Ga0495776_115182_4289_5257 53.700 5.256E-100 324 0.978% Bifidobacterium IMGVR PF09588 phrog_8474