dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS040

Inhibited defense system

CLAN ID

CLAN030

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
IMGVR_UViG_2778261704_000001\|2778261704\|2781089226	gene_page:	142	15541.78	6.6684	0.5

Phage property

Phage	Assembly id
	IMGVR_UViG_2778261704_000001

PMID/References

PDB structures

;

Pfam domains

PF14354.9

Phrog

phrog_6422,phrog_599

Host taxa

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

Gene Location

Start: 3768; End: 4196; 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 APIS033 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_2778261704_000001	1	618	-	IMGVR_UViG_2778261704_000001\|2778261704\|2781089220	206	22937.34	4.5	9.7270	phage antirepressor YoqD-like protein	phrog_5689 ; phrog_15709 ; phrog_9438 ; phrog_4936 ; phrog_15968 ; phrog_63 ; phrog_10324	PF03374.17
IMGVR_UViG_2778261704_000001	1	618	-	IMGVR_UViG_2778261704_000001\|2778261704\|2781089220	206	22937.34	4.5	9.7270	phage antirepressor YoqD-like protein	phrog_5689 ; phrog_15709 ; phrog_9438 ; phrog_4936 ; phrog_15968 ; phrog_63 ; phrog_10324	PF09669.13
IMGVR_UViG_2778261704_000001	693	1373	-	IMGVR_UViG_2778261704_000001\|2778261704\|2781089221	226	26347.07	6.0	8.5952	phage anti-repressor protein	phrog_7755 ; phrog_4936 ; phrog_2812 ; phrog_8244 ; phrog_4792 ; phrog_2379 ; phrog_15086 ; phrog_2127 ; phrog_1760 ; phrog_377 ; phrog_22471 ; phrog_5060 ; phrog_1726	PF10543.12
IMGVR_UViG_2778261704_000001	693	1373	-	IMGVR_UViG_2778261704_000001\|2778261704\|2781089221	226	26347.07	6.0	8.5952	phage anti-repressor protein	phrog_7755 ; phrog_4936 ; phrog_2812 ; phrog_8244 ; phrog_4792 ; phrog_2379 ; phrog_15086 ; phrog_2127 ; phrog_1760 ; phrog_377 ; phrog_22471 ; phrog_5060 ; phrog_1726	PF10548.12
IMGVR_UViG_2778261704_000001	1629	2387	-	IMGVR_UViG_2778261704_000001\|2778261704\|2781089222	252	29143.28	8.5	9.5155	ORF6N domain-containing protein	phrog_463 ; phrog_7755 ; phrog_4936 ; phrog_450 ; phrog_995 ; phrog_24476 ; phrog_8244 ; phrog_4792 ; phrog_2379 ; phrog_15086 ; phrog_2127 ; phrog_1760 ; phrog_377 ; phrog_22471 ; phrog_17980 ; phrog_1726	PF10543.12
IMGVR_UViG_2778261704_000001	2440	2523	-	IMGVR_UViG_2778261704_000001\|2778261704\|2781089223					(miscRNA )
IMGVR_UViG_2778261704_000001	2841	3368	-	IMGVR_UViG_2778261704_000001\|2778261704\|2781089224	175	19737.60	-1.5	5.6965	phage N-6-adenine-methyltransferase	phrog_6083 ; phrog_11720 ; phrog_111 ; phrog_33262 ; phrog_22740	PF05869.14
IMGVR_UViG_2778261704_000001	3365	3811	-	IMGVR_UViG_2778261704_000001\|2778261704\|2781089225	148	17363.98	8.5	10.6047	NinB protein	phrog_72	PF05772.15
IMGVR_UViG_2778261704_000001	3768	4196	-	IMGVR_UViG_2778261704_000001\|2778261704\|2781089226	142	15541.78	0.5	6.6684	endodeoxyribonuclease RalR	phrog_6422 ; phrog_1603 ; phrog_599	PF14354.9

Seed genomic context- JBrowse

Predicted 3D structure by alphafold2 with pTM = 0.42 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

No homologs found in AlphaFold database

No homologs found in esmfold database

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS040	IMGVR_UViG_2778261704_000001\|2778261704\|2781089226	8	HMM model	Member alignment

Host Taxa distribution

Length distribution

Homology to other families download full data without filtering help

Clan ID: CLAN030

Hit APIS family	E-Value	Query Start	Query End	Hit Start	Hit End	Immune system	Seed protein
APIS033	7.99E-52	63	142	1	80	restriction-modification (RM)	YP_009168126.1

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_2513237251_000011\|2513237251\|2514251218	97.872	9.16e-98	285	99%	Escherichia coli	IMGVR	PF14354	phrog_6422 phrog_599
IMGVR_UViG_2519899560_000002\|2519899560\|2520119982	99.291	1.32e-99	290	99%	Escherichia coli	IMGVR	PF14354	phrog_6422 phrog_599
IMGVR_UViG_2529292905_000008\|2529292905\|2530448621	97.500	1.57e-80	241	85%	Escherichia coli	IMGVR	PF14354	phrog_6422 phrog_599
IMGVR_UViG_2534682324_000030\|2534682324\|2537377010	98.333	2.54e-81	243	85%	Escherichia coli	IMGVR	PF14354	phrog_6422 phrog_599
IMGVR_UViG_2537562191_000049\|2537562191\|2540114087	99.167	1.60e-82	246	85%	Escherichia coli	IMGVR	PF14354	phrog_6422 phrog_599
IMGVR_UViG_2562617085_000012\|2562617085\|2562934667	100.000	4.19e-83	248	85%	Escherichia coli	IMGVR	PF14354	phrog_6422 phrog_599
IMGVR_UViG_2778261704_000001\|2778261704\|2781089226	100.000	5.03e-101	293	100%	Escherichia coli	IMGVR	PF14354	phrog_6422 phrog_599
IMGVR_UViG_2974711179_000001\|2974711179\|2974711208	98.582	6.79e-99	288	99%	Salmonella	IMGVR	PF14354	phrog_6422 phrog_599