dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS069

Inhibited defense system

CLAN ID

CLAN003

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_343_774	gene_page:	143	15871.7	6.1247	-1.5

Phage property

Phage	Assembly id
	IMGVR_UViG_3300036792_000137

PMID/References

PDB structures

;

Pfam domains

PF03230.16

Phrog

phrog_10132

Host taxa

Gene Location

Start: 343; End: 774; 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.

Seed genomic context Download table help

Genome accession	Start	End	Strand	Protein ID	Length	Molecular weight	Charge	Isoelectric point	Function	Phrog	PFAM
IMGVR_UViG_3300036792_000137	1288	1587	-	IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_1288_1587	99	10715.93	-5.0	4.5468	hypothetical protein
IMGVR_UViG_3300036792_000137	1598	1840	-	IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_1598_1840	80	8401.68	4.5	10.7162	hypothetical protein
IMGVR_UViG_3300036792_000137	1837	2442	-	IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_1837_2442	201	22012.79	10.5	10.2799	hypothetical protein	phrog_17923
IMGVR_UViG_3300036792_000137	2439	2636	-	IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_2439_2636	65	7101.94	-1.0	5.5707	hypothetical protein
IMGVR_UViG_3300036792_000137	343	774	+	IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_343_774	143	15871.73	-1.5	6.1247	hypothetical protein	phrog_10132	PF03230.16
IMGVR_UViG_3300036792_000137	42	218	+	IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_42_218	58	6319.69	4.0	10.1264	hypothetical protein	phrog_1039 ; phrog_1584	PF14373.9
IMGVR_UViG_3300036792_000137	796	1029	+	IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_796_1029	77	8472.94	-0.5	5.7905	antitoxin HicB

Seed genomic context- JBrowse

Predicted 3D structure by alphafold2 with pTM = 0.77 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-Q93GQ0-F1-model_v4	1	143	5	144	0.9302	0.9149
AF-A0A077ZNG7-F1-model_v4	1	143	5	141	0.9165	0.8953
AF-A0A0H3GW18-F1-model_v4	4	143	8	141	0.8769	0.8531
AF-A0A0H3GVF3-F1-model_v4	4	143	3	132	0.8722	0.8195
AF-P52139-F1-model_v4	4	143	18	152	0.8586	0.818
AF-P75676-F1-model_v4	4	143	18	152	0.8567	0.8156
AF-Q327Q6-F1-model_v4	4	143	21	157	0.8514	0.7979
AF-A0A0H3GZ47-F1-model_v4	1	143	84	221	0.9197	0.7523
AF-Q32HM6-F1-model_v4	4	143	45	181	0.8529	0.7521

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP000816921373.pdb	1	143	1	139	0.9505	0.9242
MGYP000611349549.pdb	4	143	8	145	0.9519	0.9177
MGYP000112106482.pdb	4	143	4	140	0.9387	0.917
MGYP001142107270.pdb	4	143	5	141	0.9397	0.9161
MGYP003561631401.pdb	3	143	5	142	0.9326	0.9098
MGYP002759879196.pdb	4	143	5	141	0.9348	0.9097
MGYP001611400893.pdb	6	143	1	138	0.9368	0.9088
MGYP000926023203.pdb	5	143	1	136	0.9411	0.9047
MGYP000465578469.pdb	3	143	6	143	0.9307	0.9043
MGYP001044518354.pdb	5	143	7	143	0.9261	0.9035

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS069	IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_343_774	5	HMM model	Member alignment

Host Taxa distribution

Length distribution

Homology to other families download full data without filtering help

Clan ID: CLAN003

Hit APIS family	E-Value	Query Start	Query End	Hit Start	Hit End	Immune system	Seed protein
APIS007	1.77E-47	2	143	18	151	restriction-modification (RM)	BAF33451.1
APIS038	2.29E-40	3	143	11	150		IMGVR_UViG_2576861805_000002\|2576861805\|2579667884
APIS039	1.79E-25	3	143	44	179		IMGVR_UViG_2751185776_000007\|2751185776\|2753238834
APIS037	3.95E-25	7	143	8	141		IMGVR_UViG_2541047688_000003\|2541047688\|2543982737
APIS055	2.07E-23	3	143	7	142		OL763419_00042

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_2852743531_000002\|2852743531\|2852746060	40.299	1.06e-22	95.5	91%	Paraburkholderia tuberum	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2921707344_000004\|2921707344\|2921709599	40.146	1.51e-21	92.8	93%	Paraburkholderia tuberum	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2921707344_000005\|2921707344\|2921712269	41.606	3.63e-24	99.4	93%	Paraburkholderia tuberum	IMGVR	PF03230	phrog_10132
IMGVR_UViG_3300033475_000967\|3300033475\|Ga0310811_1000048848	64.789	2.53e-59	188	99%		IMGVR	PF03230	phrog_10132
IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_343_774	100.000	6.76e-101	293	100%		IMGVR	PF03230	phrog_10132