sublogo
Home Family list Seed list Statistics Download Help About Annotate
Links
dbAPIS github
PADLOC
DefenseFinder
Tracking Anti-CRISPR Names
anti-CRISPRdb
AcrDB
Cite us: nar/gkad932

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 APIS100
Inhibited defense system
CLAN ID CLAN006
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_2838756947_000002|2838756947|2838760980
gene_page: 143 16857.90 4.6547 -5.5
Phage property
Phage Assembly id
IMGVR_UViG_2838756947_000002
PMID/References
PDB structures ;
Pfam domains PF03230.18
Phrog
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus;s__Xenorhabdus innexi
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 APIS007,ArdB which has seed protein.

Predicted 3D structure by alphafold2 with pTM = 0.87 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-A0A0H3GW18-F1-model_v4 1 143 1 141 0.891 0.8621
AF-Q93GQ0-F1-model_v4 6 143 7 144 0.8778 0.8424
AF-A0A077ZNG7-F1-model_v4 10 143 7 141 0.8655 0.8211
AF-P75676-F1-model_v4 1 143 12 152 0.8599 0.8144
AF-A0A0H3GVF3-F1-model_v4 4 143 1 132 0.8669 0.8115
AF-P52139-F1-model_v4 1 143 9 152 0.8523 0.806
AF-Q327Q6-F1-model_v4 3 143 17 157 0.8366 0.7793
AF-Q32HM6-F1-model_v4 2 143 40 181 0.8404 0.7372
AF-A0A0H3GZ47-F1-model_v4 7 143 88 221 0.8636 0.6889

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP001044518354.pdb 2 143 1 143 0.9205 0.9009
MGYP002643039375.pdb 1 143 14 159 0.9557 0.8977
MGYP000666839751.pdb 1 143 8 150 0.9296 0.8915
MGYP001560098228.pdb 5 143 1 139 0.9133 0.8829
MGYP001992189960.pdb 4 143 1 134 0.9245 0.8801
MGYP000611349549.pdb 1 143 2 145 0.9069 0.8792
MGYP001307263660.pdb 6 143 1 138 0.9098 0.8734
MGYP001809940848.pdb 3 143 1 140 0.9033 0.8733
MGYP000949801973.pdb 3 143 1 139 0.9071 0.8732
MGYP002759879196.pdb 3 143 1 141 0.9022 0.8731

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS100 IMGVR_UViG_2838756947_000002|2838756947|2838760980 3 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN006

APIS100 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_2838756947_000002|2838756947|2838760980 100.000 5.037E-97 306 1.000% Xenorhabdus innexi IMGVR PF03230 phrog_
IMGVR_UViG_2848576382_000012|2848576382|2848578646 81.800 2.420E-72 235 0.965% Xenorhabdus stockiae IMGVR PF03230 phrog_
IMGVR_UViG_2896227970_000003|2896227970|2896227985 39.600 3.066E-24 96 0.951% Providencia alcalifaciens IMGVR PF03230 phrog_