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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 APIS133
Inhibited defense system CRISPR-Cas evasion by DNA repair
CLAN ID CLAN056
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
YP_008997728.1 gene_page: vcrx092 343 39173.88 4.8053 -11.5
Phage property
Phage Assembly id
Vibrio cholerae
PMID/References PMID:32556263
PDB structures ;
Pfam domains PF03837.19
Phrog phrog_12233,phrog_252,phrog_8375,phrog_10056
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Vibrionales;f__Vibrionaceae;g__Vibrio;
Gene Location Start: ;  End: ;  Strand: 
Description CRISPR–Cas evasion by repairing double-strand DNA breaks via recombination between short sequence repeats

Predicted 3D structure by alphafold2 with pTM = 0.57 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-Q32GM7-F1-model_v4 15 223 2 193 0.8259 0.5916

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP001022669891.pdb 20 211 1 187 0.9335 0.7162
MGYP001049722605.pdb 16 212 7 202 0.9236 0.7111
MGYP000396468630.pdb 30 219 1 173 0.9255 0.6945
MGYP001042576686.pdb 15 223 8 198 0.8818 0.6904
MGYP001571145685.pdb 6 203 1 170 0.9254 0.6878
MGYP001563290713.pdb 15 220 9 191 0.8884 0.6871
MGYP003491535395.pdb 16 218 10 194 0.8722 0.6823
MGYP000196605117.pdb 15 219 6 186 0.8824 0.6819
MGYP000461655890.pdb 15 191 1 176 0.9071 0.6808
MGYP001010422329.pdb 22 274 1 200 0.8652 0.6788

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS133 YP_008997728.1 6 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN056

APIS133 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_3300002898_001291|3300002898|draft_100396202 57.000 1.100E-103 336 0.892% IMGVR PF03837 phrog_8375 phrog_252 phrog_10056 phrog_12233
IMGVR_UViG_3300006728_000014|3300006728|Ga0031676_13501792 77.100 8.139E-160 498 0.915% Pseudomonadales IMGVR PF03837 phrog_8375 phrog_252 phrog_10056 phrog_12233
IMGVR_UViG_3300006689_000003|3300006689|Ga0031669_11037932 77.300 3.165E-160 499 0.915% Pseudomonadales IMGVR PF03837 phrog_8375 phrog_252 phrog_10056 phrog_12233
YP_008997728.1 100.000 2.293E-231 705 1.000% Vibrio cholerae Vibrio NCBI PF03837 phrog_8375 phrog_252 phrog_10056 phrog_12233
IMGVR_UViG_3300025061_000136|3300025061|Ga0208300_1029442 50.100 1.456E-88 292 0.913% IMGVR PF03837 phrog_8375 phrog_252 phrog_10056 phrog_12233
IMGVR_UViG_3300043431_000434|3300043431|Ga0451754_0000020_7834_8796 58.600 3.479E-68 233 0.595% IMGVR PF03837 phrog_8375 phrog_252 phrog_10056 phrog_12233