Seed protein information help

APIS family ID APIS076
Inhibited defense system
CLAN ID CLAN001
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_42271_43065
gene_page: 264 30317.55 4.9035 -9.0
Phage property
Phage Assembly id
IMGVR_UViG_3300044693_000096
PMID/References
PDB structures ;
Pfam domains PF00753.30
Phrog phrog_392
Host taxa
Gene Location Start: 42271;  End: 43065;  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.

Seed genomic context      Download table help

Genome accession Start End Strand Protein ID Length Molecular weight Charge Isoelectric point Function Phrog PFAM
IMGVR_UViG_3300044693_000096 40061 40273 + IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_40061_40273 70 7935.09 0.5 6.9781 hypothetical protein
IMGVR_UViG_3300044693_000096 40330 40839 + IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_40330_40839 169 19380.90 -4.5 5.3200 guanylate kinase phrog_1815 PF00625.24
IMGVR_UViG_3300044693_000096 40841 41605 + IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_40841_41605 254 29020.23 -4.0 5.7653 predicted phosphodiesterase phrog_246 ; phrog_1649 PF12850.10
IMGVR_UViG_3300044693_000096 41595 42092 + IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_41595_42092 165 18961.54 0.5 6.6855 hypothetical protein
IMGVR_UViG_3300044693_000096 42092 42265 + IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_42092_42265 57 7031.15 2.0 8.0308 hypothetical protein
IMGVR_UViG_3300044693_000096 42271 43065 + IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_42271_43065 264 30317.55 -9.0 4.9035 ribonuclease BN (tRNA processing enzyme) phrog_392 PF00753.30
IMGVR_UViG_3300044693_000096 43606 45096 + IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_43606_45096 496 55752.31 11.5 9.4071 hypothetical protein phrog_850 PF11443.11
IMGVR_UViG_3300044693_000096 43606 45096 + IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_43606_45096 496 55752.31 11.5 9.4071 hypothetical protein phrog_850 PF11443.11
IMGVR_UViG_3300044693_000096 45158 45442 + IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_45158_45442 94 11059.63 -3.5 4.9149 hypothetical protein
IMGVR_UViG_3300044693_000096 45494 45579 + IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_45494_45579 tRNA_His_GTG

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.9 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-A0A0H3GHL8-F1-model_v4 8 260 1 244 0.8247 0.7857
AF-A0A133CTF0-F1-model_v4 4 257 1 246 0.821 0.7764
AF-P9WGC1-F1-model_v4 2 259 16 271 0.8004 0.7673
AF-O74545-F1-model_v4 1 259 3 301 0.8286 0.7641
AF-A0A0H3GM29-F1-model_v4 2 258 1 252 0.7949 0.7591
AF-Q329H1-F1-model_v4 2 258 1 252 0.7938 0.7584
AF-P16692-F1-model_v4 2 258 1 252 0.7938 0.7579
AF-P50474-F1-model_v4 2 259 25 280 0.8007 0.7546
AF-A0A0P0W0M3-F1-model_v4 2 259 3 312 0.8315 0.7541
AF-I1KRW8-F1-model_v4 2 259 1 311 0.8263 0.7494

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 2 257 1 255 0.906 0.8798
MGYP003590904441.pdb 1 257 15 280 0.8934 0.8591
MGYP003670084134.pdb 3 257 1 242 0.9096 0.8579
MGYP001090083249.pdb 4 260 1 249 0.895 0.8537
MGYP003194564429.pdb 4 257 1 252 0.884 0.85
MGYP001214891407.pdb 2 258 1 244 0.8963 0.8472
MGYP000754846076.pdb 2 257 1 245 0.8932 0.8469
MGYP001333914959.pdb 2 257 1 243 0.8966 0.8463
MGYP002619530386.pdb 4 257 1 245 0.8927 0.8462
MGYP001772298923.pdb 1 257 18 282 0.8827 0.8456

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS076 IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_42271_43065 10 HMM model Member alignment

Host Taxa distribution

Length distribution

Length Distribution Bar chart