dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS072

Inhibited defense system

CLAN ID

CLAN004

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_10006_10671	gene_page:	221	26491.3	4.3157	-19.5

Phage property

Phage	Assembly id
	IMGVR_UViG_3300039331_000150

PMID/References

PDB structures

;

Pfam domains

PF07275.14

Phrog

phrog_2059

Host taxa

d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;;

Gene Location

Start: 10006; End: 10671; 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 APIS003 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_3300039331_000150	10006	10671	+	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_10006_10671	221	26491.29	-19.5	4.3157	antirestriction protein	phrog_14321 ; phrog_2059	PF07275.14
IMGVR_UViG_3300039331_000150	10750	10947	+	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_10750_10947	65	7891.15	7.0	9.0610	hypothetical protein
IMGVR_UViG_3300039331_000150	10952	11164	+	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_10952_11164	70	8281.41	3.5	8.6909	hypothetical protein
IMGVR_UViG_3300039331_000150	11184	11663	+	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_11184_11663	159	18218.69	-5.5	4.6052	hypothetical protein
IMGVR_UViG_3300039331_000150	11805	11954	+	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_11805_11954	50	5838.62	-1.0	4.9828	hypothetical protein
IMGVR_UViG_3300039331_000150	7365	7949	+	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_7365_7949	194	22166.94	9.0	9.7115	integrase	phrog_216	PF00589.25
IMGVR_UViG_3300039331_000150	7961	8467	+	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_7961_8467	168	19794.94	-0.5	6.2522	hypothetical protein	phrog_4792	PF10543.12
IMGVR_UViG_3300039331_000150	8726	8842	+	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_8726_8842	38	4427.15	1.0	8.6630	hypothetical protein
IMGVR_UViG_3300039331_000150	8863	9183	+	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_8863_9183	106	11725.49	-0.5	6.3709	DNA repair protein RadC	phrog_10276	PF04002.18
IMGVR_UViG_3300039331_000150	9217	9660	-	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_9217_9660	147	16450.58	7.5	10.1014	uncharacterized membrane protein YdbT with pleckstrin-like domain	phrog_3707	PF03703.17

Seed genomic context- JBrowse

Predicted 3D structure by alphafold2 with pTM = 0.58 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-A0A0H3GZQ3-F1-model_v4	46	220	3	168	0.8542	0.7345

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP001001204165.pdb	41	221	1	178	0.9595	0.8588
MGYP000507340143.pdb	43	221	1	176	0.9559	0.8512
MGYP000968187613.pdb	43	221	1	178	0.9507	0.8491
MGYP001035038468.pdb	47	221	1	175	0.9522	0.8447
MGYP001358281342.pdb	41	221	1	182	0.926	0.8355
MGYP000424701238.pdb	45	220	1	175	0.9415	0.8333
MGYP001260782423.pdb	44	221	1	177	0.9245	0.8198
MGYP000918656566.pdb	42	221	1	177	0.9229	0.8191
MGYP001260855221.pdb	44	221	1	178	0.9201	0.8168
MGYP002611320555.pdb	43	220	1	176	0.9175	0.8118

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS072	IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_10006_10671	14	HMM model	Member alignment

Host Taxa distribution

Length distribution

Homology to other families download full data without filtering help

Clan ID: CLAN004

Hit APIS family	E-Value	Query Start	Query End	Hit Start	Hit End	Immune system	Seed protein
APIS003	1.03E-65	40	220	26	202	restriction-modification (RM)	AAB36891.1
APIS063	3.64E-62	42	220	3	173		IMGVR_UViG_3300031923_000006\|3300031923\|Ga0326331_1000015821
APIS051	1.74E-42	49	220	54	222		IMGVR_UViG_3300012016_000701\|3300012016\|Ga0120387_100082722
APIS067	2.86E-42	50	220	41	206		IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_6069_6716

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_2873698837_000006\|2873698837\|2873702461	69.540	2.05e-82	251	98%	Parabacteroides distasonis	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300029333_000176\|3300029333\|Ga0243760_1048344	91.351	1.69e-122	353	84%	Bacteroidaceae	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300029464_000078\|3300029464\|Ga0244165_10048050	43.956	8.61e-42	148	80%	Phocaeicola	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300029487_000150\|3300029487\|Ga0244179_1009185	43.956	4.79e-42	149	80%	Phocaeicola	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300029543_000089\|3300029543\|Ga0244989_10084611	43.407	1.28e-40	145	80%	Phocaeicola	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_10006_10671	100.000	5.90e-163	456	100%	Bacteroidaceae	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300045988_149569\|3300045988\|Ga0495776_155429_59017_59559	44.505	6.57e-42	148	100%	Phocaeicola	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300045988_156592\|3300045988\|Ga0495776_141324_99854_100396	43.956	1.19e-41	147	100%	Phocaeicola	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300045988_160714\|3300045988\|Ga0495776_183503_25718_26284	44.262	1.55e-42	150	96%	Phocaeicola	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300045988_164858\|3300045988\|Ga0495776_168682_71409_71951	42.308	2.18e-40	144	100%	Phocaeicola	IMGVR	PF07275	phrog_2059
MGV-GENOME-0351977_76	44.505	8.31e-42	148	80%	Bacteroides	MGV	PF07275	phrog_2059
MGV-GENOME-0368690_47	43.956	8.87e-42	148	80%	Bacteroides	MGV	PF07275	phrog_2059
MGV-GENOME-0370255_146	43.956	1.51e-41	147	80%	Bacteroides	MGV	PF07275	phrog_2059
MGV-GENOME-0374647_97	42.308	2.75e-40	144	80%	Bacteroides	MGV	PF07275	phrog_2059