dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS073

Inhibited defense system

CLAN ID

CLAN001

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_37885_38742	gene_page:	285	32666.12	6.0793	-3.0

Phage property

Phage	Assembly id
	IMGVR_UViG_3300042197_004918

PMID/References

PDB structures

;

Pfam domains

PF00753.30

Phrog

Host taxa

Gene Location

Start: 37885; End: 38742; 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_3300042197_004918	33450	35534	+	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_33450_35534	694	77488.02	2.5	6.9721	hypothetical protein
IMGVR_UViG_3300042197_004918	35606	36028	+	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_35606_36028	140	14944.05	7.5	10.4737	hypothetical protein
IMGVR_UViG_3300042197_004918	36062	36295	-	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_36062_36295	77	8947.46	5.0	9.7718	hypothetical protein
IMGVR_UViG_3300042197_004918	36313	37494	+	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_36313_37494	393	45743.05	6.5	8.2669	hypothetical protein	phrog_19197	PF14236.9
IMGVR_UViG_3300042197_004918	37478	37882	+	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_37478_37882	134	15650.73	2.5	8.0003	hypothetical protein
IMGVR_UViG_3300042197_004918	37885	38742	+	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_37885_38742	285	32666.12	-3.0	6.0793	ribonuclease BN (tRNA processing enzyme)	phrog_392	PF00753.30
IMGVR_UViG_3300042197_004918	38778	38948	-	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_38778_38948	56	6828.99	8.0	9.3387	hypothetical protein
IMGVR_UViG_3300042197_004918	38864	39079	+	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_38864_39079	71	7972.13	8.0	11.7940	hypothetical protein
IMGVR_UViG_3300042197_004918	39335	39823	+	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_39335_39823	162	18541.20	5.0	8.5563	hypothetical protein
IMGVR_UViG_3300042197_004918	39810	40427	+	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_39810_40427	205	23747.18	4.0	8.3087	hypothetical protein
IMGVR_UViG_3300042197_004918	40793	41191	+	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_40793_41191	132	15289.49	8.0	9.6701	hypothetical protein

Seed genomic context- JBrowse

Predicted 3D structure by alphafold2 with pTM = 0.89 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-P9WGC1-F1-model_v4	10	285	6	270	0.7718	0.7363
AF-P50474-F1-model_v4	10	285	15	279	0.749	0.7273
AF-Q329H1-F1-model_v4	24	285	1	252	0.7844	0.7255
AF-A0A0H3GM29-F1-model_v4	24	285	1	252	0.7841	0.7251
AF-A0A133CTF0-F1-model_v4	26	284	1	246	0.7954	0.7247
AF-A0A0H3GHL8-F1-model_v4	30	285	1	242	0.7813	0.7178
AF-Q58769-F1-model_v4	24	285	1	257	0.7607	0.7165
AF-O74545-F1-model_v4	23	285	3	300	0.7514	0.7149
AF-P9WGZ5-F1-model_v4	25	285	1	271	0.7243	0.686
AF-Q2G2U5-F1-model_v4	22	284	1	266	0.723	0.6818

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP001420084740.pdb	1	283	2	283	0.9519	0.9413
MGYP001772298923.pdb	1	284	2	282	0.9271	0.9123
MGYP001165362474.pdb	1	283	1	282	0.9166	0.9001
MGYP003590904441.pdb	1	284	2	280	0.909	0.8905
MGYP001261411007.pdb	1	285	4	300	0.9102	0.8761
MGYP001202930834.pdb	1	284	1	278	0.8902	0.8627
MGYP003319870133.pdb	1	284	1	279	0.8863	0.8596
MGYP001595459157.pdb	14	284	1	271	0.8915	0.8569
MGYP000874665675.pdb	1	284	6	285	0.8711	0.8548
MGYP003452926687.pdb	25	285	1	266	0.8927	0.8512

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS073	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_37885_38742	14	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
APIS058	9.36E-53	22	285	12	269		IMGVR_UViG_3300022562_000702\|3300022562\|Ga0247387_1000200120
APIS001	1.09E-52	25	284	19	270	pyrimidine cyclase system for antiphage resistance (Pycsar)	YP_009840594.1
APIS076	1.16E-47	26	284	6	259		IMGVR_UViG_3300044693_000096\|3300044693\|Ga0466961_0000159_42271_43065
APIS054	1.66E-43	26	284	3	262		IMGVR_UViG_3300014204_000482\|3300014204\|Ga0172381_1000105623
APIS060	5.08E-37	26	284	1	259		IMGVR_UViG_3300024258_000005\|3300024258\|Ga0233440_1000037199
APIS062	9.17E-37	26	284	1	263		IMGVR_UViG_3300028374_000006\|3300028374\|Ga0306906_100003345
APIS066	3.42E-35	26	284	1	293		IMGVR_UViG_3300035396_000446\|3300035396\|Ga0393109_006065_59543_60412
APIS064	1.82E-30	26	284	1	258		IMGVR_UViG_3300033145_003233\|3300033145\|Ga0366840_1000004654
APIS041	7.54E-25	25	284	1	249		IMGVR_UViG_2832702071_000001\|2832702071\|2832704097
APIS044	1.99E-17	28	273	2	233		HM144387_00160

Family members, sources, and their hosts help

Results of representative protein blast against members.
Member	pident	evalue	bitscore	qcovs	SourceDB	Pfam	Phrog
IMGVR_UViG_3300005077_000004\|3300005077\|Ga0071116_1000032245	38.519	1.23e-55	189	91%	IMGVR	PF00753	phrog_392
IMGVR_UViG_3300007735_000950\|3300007735\|Ga0104988_1091613	84.912	4.78e-177	498	100%	IMGVR	PF00753	phrog_392
IMGVR_UViG_3300017766_004476\|3300017766\|Ga0181343_1000008189	48.438	4.82e-90	277	89%	IMGVR	PF00753	phrog_392
IMGVR_UViG_3300017960_000507\|3300017960\|Ga0180429_10000248101	42.754	1.28e-58	197	91%	IMGVR	PF00753	phrog_392
IMGVR_UViG_3300017963_000203\|3300017963\|Ga0180437_100001849	39.194	9.87e-51	177	91%	IMGVR	PF00753	phrog_392
IMGVR_UViG_3300017987_000005\|3300017987\|Ga0180431_1000002932	40.559	3.49e-66	216	96%	IMGVR	PF12706	phrog_392
IMGVR_UViG_3300025012_000030\|3300025012\|Ga0209727_100004580	40.845	4.48e-53	183	94%	IMGVR	PF00753	phrog_392
IMGVR_UViG_3300030616_000016\|3300030616\|Ga0272442_1000002153	40.824	4.78e-56	190	90%	IMGVR	PF12706	phrog_392
IMGVR_UViG_3300035698_020072\|3300035698\|Ga0374944_615467_46640_47488	37.132	1.85e-50	176	92%	IMGVR	PF00753	phrog_392
IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_37885_38742	100.000	0.0	592	100%	IMGVR	PF00753	phrog_
IMGVR_UViG_3300044954_000152\|3300044954\|Ga0438285_002856_21869_22723	81.053	8.43e-170	479	100%	IMGVR	PF00753	phrog_
IMGVR_UViG_3300045538_000426\|3300045538\|Ga0466424_000001_29103_29957	76.761	1.61e-160	456	100%	IMGVR	PF00753	phrog_
IMGVR_UViG_3300046092_000171\|3300046092\|Ga0456271_000015_27156_28010	80.282	1.94e-166	471	100%	IMGVR	PF00753	phrog_
IMGVR_UViG_3300047476_000993\|3300047476\|Ga0485304_004108_3925_4782	95.439	0.0	547	100%	IMGVR	PF00753	phrog_