dbAPIS: a database of anti-prokaryotic immune systems

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

Homology to other families download full data without filtering help

Clan ID: CLAN001

Hit APIS family	E-Value	Query Start	Query End	Hit Start	Hit End	Immune system	Seed protein
APIS001	1.76E-65	2	260	18	273	pyrimidine cyclase system for antiphage resistance (Pycsar)	YP_009840594.1
APIS058	6.21E-48	4	262	16	273		IMGVR_UViG_3300022562_000702\|3300022562\|Ga0247387_1000200120
APIS073	1.33E-47	3	259	22	287		IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_37885_38742
APIS062	1.49E-43	4	257	1	263		IMGVR_UViG_3300028374_000006\|3300028374\|Ga0306906_100003345
APIS054	2.00E-35	3	261	2	266		IMGVR_UViG_3300014204_000482\|3300014204\|Ga0172381_1000105623
APIS060	2.59E-34	4	261	1	263		IMGVR_UViG_3300024258_000005\|3300024258\|Ga0233440_1000037199
APIS066	6.52E-31	4	259	1	295		IMGVR_UViG_3300035396_000446\|3300035396\|Ga0393109_006065_59543_60412
APIS044	6.97E-30	6	243	2	232		HM144387_00160
APIS041	1.45E-28	3	257	1	249		IMGVR_UViG_2832702071_000001\|2832702071\|2832704097
APIS064	8.17E-28	4	257	1	258		IMGVR_UViG_3300033145_003233\|3300033145\|Ga0366840_1000004654

Family members, sources, and their hosts help

Results of representative protein blast against members.
Member	pident	evalue	bitscore	qcovs	host	SourceDB	Pfam	Phrog
IMGVR_UViG_2879469214_000007\|2879469214\|2879476043	71.648	9.83e-139	399	99%	Paenibacillus amylolyticus_B	IMGVR	PF00753	phrog_392
IMGVR_UViG_3300019124_000038\|3300019124\|Ga0193592_100007933	55.556	7.89e-95	288	98%	Streptococcus	IMGVR	PF12706	phrog_392
IMGVR_UViG_3300037312_000317\|3300037312\|Ga0395899_0000358_21814_22602	57.600	4.95e-96	291	95%		IMGVR	PF00753	phrog_392
IMGVR_UViG_3300037312_001887\|3300037312\|Ga0395899_0000079_29822_30592	59.200	8.96e-101	302	95%		IMGVR	PF00753	phrog_392
IMGVR_UViG_3300037467_003075\|3300037467\|Ga0395902_0000054_74092_74880	73.563	8.95e-138	396	99%		IMGVR	PF00753	phrog_392
IMGVR_UViG_3300038393_001170\|3300038393\|Ga0395904_0005874_145_930	59.922	7.24e-104	310	97%		IMGVR	PF00753	phrog_392
IMGVR_UViG_3300042923_000408\|3300042923\|Ga0456365_0001500_26198_26986	82.443	7.13e-162	457	99%		IMGVR	PF00753	phrog_392
IMGVR_UViG_3300043749_000020\|3300043749\|Ga0456118_0000004_28205_28981	59.459	4.81e-104	311	98%		IMGVR	PF00753	phrog_392
IMGVR_UViG_3300044693_000096\|3300044693\|Ga0466961_0000159_42271_43065	100.000	0.0	547	100%		IMGVR	PF00753	phrog_392
IMGVR_UViG_3300046492_000319\|3300046492\|Ga0495585_0002691_1738_2526	75.191	7.38e-144	412	100%		IMGVR	PF00753	phrog_392