dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS067

Inhibited defense system

CLAN ID

CLAN004

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_6069_6716	gene_page:	215	25113.6	3.9397	-29

Phage property

Phage	Assembly id
	IMGVR_UViG_3300035506_000204

PMID/References

PDB structures

;

Pfam domains

PF07275.14

Phrog

phrog_2059

Host taxa

Gene Location

Start: 6069; End: 6716; 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_3300035506_000204	10713	11669	+	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_10713_11669	318	35543.45	-8.0	4.7897	hypothetical protein
IMGVR_UViG_3300035506_000204	11770	12363	+	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_11770_12363	197	21122.49	-6.5	4.4764	hypothetical protein
IMGVR_UViG_3300035506_000204	3654	3965	+	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_3654_3965	103	11771.41	-1.0	5.2600	DNA-binding XRE family transcriptional regulator	phrog_38027 ; phrog_1373 ; phrog_2439 ; phrog_3 ; phrog_29047 ; phrog_6831 ; phrog_11553 ; phrog_24325 ; phrog_5823 ; phrog_2339 ; phrog_1381	PF01381.25
IMGVR_UViG_3300035506_000204	4146	4622	+	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_4146_4622	158	19114.97	6.0	8.9352	hypothetical protein
IMGVR_UViG_3300035506_000204	4632	4757	+	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_4632_4757	41	4601.38	-5.5	3.8121	hypothetical protein
IMGVR_UViG_3300035506_000204	4760	5188	+	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_4760_5188	142	15933.44	1.5	7.1875	hypothetical protein
IMGVR_UViG_3300035506_000204	5461	5832	-	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_5461_5832	123	14044.42	-2.0	5.1657	hypothetical protein
IMGVR_UViG_3300035506_000204	6069	6716	+	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_6069_6716	215	25113.60	-29.0	3.9397	antirestriction protein	phrog_2059	PF07275.14
IMGVR_UViG_3300035506_000204	6790	7458	-	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_6790_7458	222	26369.84	0.5	6.6193	hypothetical protein
IMGVR_UViG_3300035506_000204	7698	9344	-	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_7698_9344	548	62551.21	-6.0	5.1316	hypothetical protein	phrog_8741	PF08238.15
IMGVR_UViG_3300035506_000204	7698	9344	-	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_7698_9344	548	62551.21	-6.0	5.1316	hypothetical protein	phrog_8741	PF08238.15
IMGVR_UViG_3300035506_000204	7698	9344	-	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_7698_9344	548	62551.21	-6.0	5.1316	hypothetical protein	phrog_8741	PF08238.15
IMGVR_UViG_3300035506_000204	7698	9344	-	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_7698_9344	548	62551.21	-6.0	5.1316	hypothetical protein	phrog_8741	PF08238.15
IMGVR_UViG_3300035506_000204	7698	9344	-	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_7698_9344	548	62551.21	-6.0	5.1316	hypothetical protein	phrog_8741	PF08238.15
IMGVR_UViG_3300035506_000204	7698	9344	-	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_7698_9344	548	62551.21	-6.0	5.1316	hypothetical protein	phrog_8741	PF08238.15
IMGVR_UViG_3300035506_000204	9450	10571	+	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_9450_10571	373	40537.68	-11.5	4.7223	ATP-dependent protease ClpP protease subunit	phrog_94 ; phrog_1684 ; phrog_3348 ; phrog_133 ; phrog_2976 ; phrog_53	PF00574.26

Seed genomic context- JBrowse

Predicted 3D structure by alphafold2 with pTM = 0.82 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	49	214	5	168	0.8453	0.7359

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP002619016300.pdb	6	215	1	211	0.9465	0.9277
MGYP003538369595.pdb	28	215	1	186	0.8888	0.8145
MGYP000693494289.pdb	4	215	2	205	0.8558	0.8121
MGYP002521666680.pdb	8	215	1	200	0.8541	0.8009
MGYP002519753648.pdb	21	215	1	188	0.8717	0.7998
MGYP002523803474.pdb	21	215	16	207	0.8568	0.7947
MGYP003228289826.pdb	28	215	2	190	0.8598	0.7937
MGYP003324507119.pdb	18	215	14	205	0.8442	0.7931
MGYP003510632526.pdb	24	215	1	190	0.8578	0.79
MGYP003439714399.pdb	12	215	1	208	0.8281	0.7883

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS067	IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_6069_6716	15	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	4.57E-69	48	215	36	203	restriction-modification (RM)	AAB36891.1
APIS063	5.95E-54	46	215	8	174		IMGVR_UViG_3300031923_000006\|3300031923\|Ga0326331_1000015821
APIS051	9.64E-54	48	214	54	222		IMGVR_UViG_3300012016_000701\|3300012016\|Ga0120387_100082722
APIS072	2.75E-41	47	214	48	223		IMGVR_UViG_3300039331_000150\|3300039331\|Ga0169804_01911_10006_10671

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_3300007669_000275\|3300007669\|Ga0105546_10007546	59.296	1.92e-76	237	92%	Muribaculaceae	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300008268_000462\|3300008268\|Ga0111491_100004980	53.488	6.76e-75	233	99%	Muribaculaceae	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300013414_001143\|3300013414\|Ga0177923_108916522	53.589	2.52e-68	217	92%	CAG-485	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300035428_000204\|3300035428\|Ga0247197_01065_5309_5935	53.488	3.79e-75	234	99%	Muribaculaceae	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300035501_000804\|3300035501\|Ga0376455_0008063_329_934	52.821	2.37e-61	198	89%		IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_6069_6716	100.000	3.87e-158	444	100%		IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300045988_155923\|3300045988\|Ga0495776_113777_35447_36073	56.500	1.68e-72	227	96%	Muribaculaceae	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300045988_165293\|3300045988\|Ga0495776_184413_31235_31861	53.023	7.05e-75	233	99%	Muribaculaceae	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300045988_185973\|3300045988\|Ga0495776_114647_14749_15378	55.941	1.15e-68	217	96%	CAG-485	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300045988_187022\|3300045988\|Ga0495776_071467_36894_37544	65.278	3.52e-95	285	99%		IMGVR	PF07275	phrog_2059
MGV-GENOME-0268661_41	65.278	3.63e-95	285	99%	Muribaculaceae	MGV	PF07275	phrog_2059
MGV-GENOME-0272767_35	56.500	1.79e-72	227	92%	Muribaculaceae	MGV	PF07275	phrog_2059
MGV-GENOME-0290063_36	53.023	7.54e-75	233	99%	Muribaculaceae	MGV	PF07275	phrog_2059
MGV-GENOME-0316874_15	55.941	1.22e-68	217	93%	CAG-873	MGV	PF07275	phrog_2059
uvig_403301_1	49.254	5.20e-59	192	93%		GPD	PF07275	phrog_2059