dbAPIS: a database of anti-prokaryotic immune systems

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Seed protein information help

APIS family ID

APIS051

Inhibited defense system

CLAN ID

CLAN004

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
IMGVR_UViG_3300012016_000701\|3300012016\|Ga0120387_100082722	gene_page:	223	26277.5	3.5608	-44

Phage property

Phage	Assembly id

PMID/References

PDB structures

;

Pfam domains

PF07275.14

Phrog

phrog_14321,phrog_2059

Host taxa

Gene Location

Start: ; End: ; 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.

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-A0A0H3GZQ3-F1-model_v4	55	223	5	168	0.7952	0.6754

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP003228289826.pdb	37	223	1	190	0.9258	0.8467
MGYP002627441165.pdb	36	221	1	189	0.9162	0.8361
MGYP003538369595.pdb	39	223	1	186	0.9113	0.8242
MGYP002522264593.pdb	29	222	2	195	0.8904	0.8233
MGYP002523803474.pdb	41	223	23	207	0.9271	0.8031
MGYP002855897325.pdb	34	223	34	223	0.944	0.7996
MGYP003306129017.pdb	27	222	10	202	0.8456	0.7918
MGYP002624915303.pdb	20	223	9	205	0.8283	0.7829
MGYP000232002069.pdb	55	222	2	166	0.9078	0.7805
MGYP003298723900.pdb	54	222	1	170	0.9003	0.78

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS051	IMGVR_UViG_3300012016_000701\|3300012016\|Ga0120387_100082722	6	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	1.95E-67	54	222	36	202	restriction-modification (RM)	AAB36891.1
APIS067	5.57E-55	45	222	32	206		IMGVR_UViG_3300035506_000204\|3300035506\|Ga0376461_0000200_6069_6716
APIS063	4.49E-54	50	222	6	173		IMGVR_UViG_3300031923_000006\|3300031923\|Ga0326331_1000015821
APIS072	2.37E-41	55	222	50	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_2799112676_000001\|2799112676\|2800327525	93.722	5.71e-149	421	99%	Bacteroidales	IMGVR	PF07275	phrog_14321 phrog_2059
IMGVR_UViG_2799112753_000001\|2799112753\|2800520724	93.274	2.81e-149	422	100%	Bacteroidales	IMGVR	PF07275	phrog_14321 phrog_2059
IMGVR_UViG_3300012016_000701\|3300012016\|Ga0120387_100082722	100.000	7.86e-162	454	100%		IMGVR	PF07275	phrog_14321 phrog_2059
IMGVR_UViG_3300014043_000317\|3300014043\|Ga0120385_100021611	48.498	4.36e-60	197	100%	Muribaculaceae	IMGVR	PF07275	phrog_2059
IMGVR_UViG_3300014057_000711\|3300014057\|Ga0120384_100018520	94.608	9.89e-138	392	99%		IMGVR	PF07275	phrog_14321 phrog_2059
IMGVR_UViG_3300028591_008370\|3300028591\|Ga0247611_1000073715	65.333	9.92e-101	300	99%	Muribaculaceae	IMGVR	PF07275	phrog_2059