dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS055

Inhibited defense system

CLAN ID

CLAN003

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
OL763419_00042	gene_page:	137	15688.8	4.381	-7.5

Phage property

Phage	Assembly id
Pseudomonas phage Churro	OL763419

PMID/References

PDB structures

;

Pfam domains

PF03230.16

Phrog

phrog_10132

Host taxa

d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;

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 APIS007,ArdB which has seed protein.

Predicted 3D structure by alphafold2 with pTM = 0.88 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-A0A0H3GW18-F1-model_v4	1	137	6	141	0.9313	0.9039
AF-P52139-F1-model_v4	1	137	16	152	0.9259	0.8679
AF-P75676-F1-model_v4	1	137	16	152	0.9255	0.867
AF-Q93GQ0-F1-model_v4	3	137	7	144	0.8948	0.8558
AF-Q327Q6-F1-model_v4	1	137	19	157	0.9249	0.8539
AF-A0A0H3GVF3-F1-model_v4	1	137	1	132	0.8913	0.8522
AF-A0A077ZNG7-F1-model_v4	6	137	7	141	0.878	0.8488
AF-Q32HM6-F1-model_v4	1	137	43	181	0.9244	0.8028
AF-A0A0H3GZ47-F1-model_v4	3	137	87	221	0.8742	0.7011

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP001248649841.pdb	1	137	1	137	0.9885	0.9841
MGYP001201501853.pdb	1	137	2	134	0.9757	0.9591
MGYP003390684032.pdb	1	137	2	135	0.9609	0.9433
MGYP000117479218.pdb	1	137	1	133	0.9646	0.939
MGYP000412510903.pdb	3	137	1	131	0.9696	0.9384
MGYP001120502683.pdb	1	137	1	133	0.9622	0.9363
MGYP001487061361.pdb	3	137	1	132	0.9652	0.9361
MGYP001335377403.pdb	2	137	1	131	0.9674	0.936
MGYP001992189960.pdb	1	137	2	134	0.9554	0.9322
MGYP003460860055.pdb	1	137	2	135	0.9462	0.9317

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS055	OL763419_00042	20	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	2.99E-39	2	142	14	151	restriction-modification (RM)	BAF33451.1
APIS038	9.43E-29	4	142	8	150		IMGVR_UViG_2576861805_000002\|2576861805\|2579667884
APIS069	1.64E-22	7	142	7	144		IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_343_774
APIS039	8.76E-20	2	142	39	179		IMGVR_UViG_2751185776_000007\|2751185776\|2753238834
APIS037	1.90E-15	12	142	9	141		IMGVR_UViG_2541047688_000003\|2541047688\|2543982737

Family members, sources, and their hosts help

Results of representative protein blast against members.
Member	pident	evalue	bitscore	qcovs	phage	host	SourceDB	Pfam	Phrog
DQ163916_00002	99.270	3.15e-98	286	100%	Pseudomonas phage M6	Pseudomonas	INPHARED	PF03230	phrog_10132
IMGVR_UViG_2595698855_000001\|2595698855\|2596517448	97.810	4.06e-97	283	96%		Burkholderiaceae	IMGVR	PF03230	phrog_10132
IMGVR_UViG_3300015607_001032\|3300015607\|Ga0182412_11370211	97.080	4.84e-95	278	96%			IMGVR	PF03230	phrog_10132
IMGVR_UViG_3300028603_000095\|3300028603\|Ga0265293_1000173436	94.161	2.45e-93	274	100%		Gammaproteobacteria	IMGVR	PF03230	phrog_10132
IMGVR_UViG_3300033074_000335\|3300033074\|Ga0364573_111686	87.591	6.85e-86	255	100%		Proteobacteria	IMGVR	PF03230	phrog_10132
IMGVR_UViG_641509461_000001\|641509461\|641514143	89.781	2.40e-87	259	96%		Gammaproteobacteria	IMGVR	PF03230	phrog_10132
JX131330_00045	97.810	3.23e-97	283	100%	Pseudomonas phage MP1412	Pseudomonas	INPHARED	PF03230	phrog_10132
KX198613_00078	98.540	9.44e-98	285	100%	Pseudomonas phage AN14	Pseudomonas	INPHARED	PF03230	phrog_10132
KX961385_00071	97.810	2.46e-96	281	100%	Bordetella phage LK3	Bordetella	INPHARED	PF03230	phrog_10132
KY000221_00043	96.350	1.54e-95	279	100%	Bordetella phage CN1	Bordetella	INPHARED	PF03230	phrog_10132
MH791406_00059	88.321	3.55e-86	256	100%	Pseudomonas phage PaSz-4	Pseudomonas	INPHARED	PF03230	phrog_10132
MN871456_00032	89.781	1.03e-86	257	100%	Pseudomonas phage Pa-C	Pseudomonas	INPHARED	PF03230	phrog_10132
MN871469_00034	89.781	1.97e-87	259	100%	Pseudomonas phage Pa-S	Pseudomonas	INPHARED	PF03230	phrog_10132
MN871478_00030	97.810	2.71e-97	284	100%	Pseudomonas phage PaSt-2_45_61k	Pseudomonas	INPHARED	PF03230	phrog_10132
MN871482_00028	90.511	4.02e-88	260	100%	Pseudomonas virus PaSz-6	Pseudomonas	INPHARED	PF03230	phrog_10132
MN871486_00009	89.051	4.30e-87	258	100%	Pseudomonas phage PaSz-9_45_61k	Pseudomonas	INPHARED	PF03230	phrog_10132
MZ089741_00002	99.270	1.67e-97	284	100%	Pseudomonas phage PSA39	Pseudomonas	INPHARED	PF03230	phrog_10132
OL763419_00042	100.000	1.11e-98	287	100%	Pseudomonas phage Churro	Pseudomonas	INPHARED	PF03230	phrog_10132
OM809160_00032	92.701	6.68e-91	268	100%	Pseudomonas phage 185	Pseudomonas	INPHARED	PF03230	phrog_10132
ON165687_00074	97.080	2.72e-96	281	100%	Sphaerotilus phage SN1	Sphaerotilus	INPHARED	PF03230	phrog_10132

APIS	Contig	Range
APIS055		-