dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS037

Inhibited defense system

CLAN ID

CLAN003

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
IMGVR_UViG_2541047688_000003\|2541047688\|2543982737	gene_page:	141	16245.5	4.7142	-6

Phage property

Phage	Assembly id
	IMGVR_UViG_2541047688_000003

PMID/References

PDB structures

;

Pfam domains

PF03230.16

Phrog

phrog_10132

Host taxa

d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli

Gene Location

Start: 142165; End: 142590; 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_2541047688_000003	138994	139197	+	IMGVR_UViG_2541047688_000003\|2541047688\|2543982732	67	7305.88	-12.5	3.3580	hypothetical protein	phrog_37043
IMGVR_UViG_2541047688_000003	139581	140264	+	IMGVR_UViG_2541047688_000003\|2541047688\|2543982733	227	25436.93	8.0	9.2535	site-specific DNA-methyltransferase (adenine-specific)	phrog_23085 ; phrog_3008 ; phrog_18293 ; phrog_6025 ; phrog_498 ; phrog_6952 ; phrog_8769 ; phrog_23148 ; phrog_67 ; phrog_12862	PF01555.21
IMGVR_UViG_2541047688_000003	140265	140486	+	IMGVR_UViG_2541047688_000003\|2541047688\|2543982734	73	8674.86	-2.0	5.1002	hypothetical protein	phrog_4830
IMGVR_UViG_2541047688_000003	140500	140934	+	IMGVR_UViG_2541047688_000003\|2541047688\|2543982735	144	16127.30	-7.5	4.4673	Protein of unknown function (DUF1380)	phrog_9024	PF07128.15
IMGVR_UViG_2541047688_000003	140979	141749	+	IMGVR_UViG_2541047688_000003\|2541047688\|2543982736	256	28725.97	-1.0	6.1331	hypothetical protein	phrog_8919
IMGVR_UViG_2541047688_000003	142165	142590	+	IMGVR_UViG_2541047688_000003\|2541047688\|2543982737	141	16245.46	-6.0	4.7142	Antirestriction protein	phrog_10132	PF03230
IMGVR_UViG_2541047688_000003	142637	143059	+	IMGVR_UViG_2541047688_000003\|2541047688\|2543982738	140	15641.69	-14.5	4.1242	Protein of unknown function (DUF1380)
IMGVR_UViG_2541047688_000003	143056	143247	+	IMGVR_UViG_2541047688_000003\|2541047688\|2543982739	63	7264.29	3.5	9.9914	hypothetical protein

Seed genomic context- JBrowse

Predicted 3D structure by alphafold2 with pTM = 0.7 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	3	141	6	144	0.9678	0.9404
AF-A0A077ZNG7-F1-model_v4	5	141	5	141	0.9703	0.9367
AF-A0A0H3GW18-F1-model_v4	7	141	10	141	0.8924	0.8519
AF-A0A0H3GVF3-F1-model_v4	7	141	5	132	0.8497	0.8024
AF-P52139-F1-model_v4	7	141	20	152	0.8506	0.7993
AF-P75676-F1-model_v4	7	141	20	152	0.8455	0.793
AF-Q327Q6-F1-model_v4	7	141	23	157	0.8383	0.78
AF-A0A0H3GZ47-F1-model_v4	3	141	83	221	0.9301	0.7593
AF-Q32HM6-F1-model_v4	7	141	47	181	0.8393	0.7351

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP001142107270.pdb	6	141	6	141	0.9716	0.9314
MGYP003561631401.pdb	6	141	7	142	0.9718	0.9286
MGYP000112106482.pdb	7	141	6	140	0.9681	0.9223
MGYP002759879196.pdb	7	141	7	141	0.9676	0.9186
MGYP000816921373.pdb	6	141	5	139	0.9509	0.9134
MGYP000926023203.pdb	6	141	1	136	0.9402	0.912
MGYP000465578469.pdb	6	141	8	143	0.9545	0.9041
MGYP001044518354.pdb	7	141	8	143	0.9428	0.9006
MGYP000611349549.pdb	7	141	10	145	0.9557	0.9005
MGYP000014743116.pdb	7	141	9	143	0.9549	0.8977

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS037	IMGVR_UViG_2541047688_000003\|2541047688\|2543982737	3	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	1.98E-30	5	141	20	151	restriction-modification (RM)	BAF33451.1
APIS069	5.96E-27	4	141	7	144		IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_343_774
APIS038	9.50E-21	4	141	11	150		IMGVR_UViG_2576861805_000002\|2576861805\|2579667884
APIS039	2.94E-17	6	141	46	179		IMGVR_UViG_2751185776_000007\|2751185776\|2753238834
APIS055	2.42E-15	12	141	16	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_2541047688_000003\|2541047688\|2543982737	100.000	3.62e-102	296	100%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2609460178_000003\|2609460178\|2611808575	65.248	2.38e-63	198	100%	Klebsiella pneumoniae	IMGVR	PF03230	phrog_10132
uvig_397292_14	98.582	4.82e-101	293	100%	Escherichia coli	GPD	PF03230	phrog_10132