dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS044

Inhibited defense system

CLAN ID

CLAN030

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
HM144387_00160	gene_page:	247	28728.7	6.1665	-2

Phage property

Phage	Assembly id
Bacillus phage W.Ph.	HM144387

PMID/References

PDB structures

;

Pfam domains

PF12706.10

Phrog

phrog_392,phrog_14429

Host taxa

d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus;

Gene Location

Start: 109111; End: 109854; Strand: +

Description

Note

This family does not have seed protein, but we infer its function is defending pyrimidine cyclase system for antiphage resistance (Pycsar) because it belongs to the same clan as family APIS001 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
HM144387	108161	108340	+	HM144387_00155	59	6929.03	6929.03	4.5702	hypothetical protein	phrog_2637
HM144387	108337	108507	+	HM144387_00156	56	6777.53	6777.53	4.2258	hypothetical protein	phrog_13947 ; phrog_5688
HM144387	108510	108770	+	HM144387_00157	86	10318.77	10318.77	7.3125	hypothetical protein	phrog_4388
HM144387	108770	108892	+	HM144387_00158	40	4589.62	4589.62	5.8806	hypothetical protein	phrog_4169
HM144387	108896	109108	+	HM144387_00159	70	7553.95	7553.95	8.5062	hypothetical protein	phrog_5623
HM144387	109111	109854	+	HM144387_00160	247	28728.72	28728.72	6.1665	metal-dependent hydrolase	phrog_35014 ; phrog_14429 ; phrog_392	PF12706.10
HM144387	109874	110092	+	HM144387_00161	72	8684.76	8684.76	4.2293	hypothetical protein	phrog_8000
HM144387	110104	111309	+	HM144387_00162	401	47165.28	47165.28	7.8003	hypothetical protein	phrog_30990 ; phrog_2475 ; phrog_13564 ; phrog_6266 ; phrog_14061
HM144387	111336	111761	+	HM144387_00163	141	16203.97	16203.97	7.2776	hypothetical protein	phrog_2574 ; phrog_6841
HM144387	111886	112485	+	HM144387_00164	199	23582.42	23582.42	4.3065	hypothetical protein	phrog_4518
HM144387	112463	112981	+	HM144387_00165	172	19217.69	19217.69	5.0827	hypothetical protein	phrog_10728 ; phrog_5566

Seed genomic context- JBrowse

Predicted 3D structure by alphafold2 with pTM = 0.92 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-A0A133CTF0-F1-model_v4	1	245	2	243	0.8144	0.7901
AF-A0A0H3GHL8-F1-model_v4	4	245	1	237	0.8045	0.7759
AF-Q58769-F1-model_v4	1	247	4	266	0.8058	0.7557
AF-P16692-F1-model_v4	1	245	4	248	0.7805	0.752
AF-Q329H1-F1-model_v4	1	245	4	248	0.7798	0.7514
AF-A0A0H3GM29-F1-model_v4	1	245	4	248	0.7792	0.7508
AF-P50474-F1-model_v4	1	245	28	275	0.814	0.7454
AF-Q9HYM9-F1-model_v4	1	245	2	253	0.7772	0.7437
AF-K0EUK8-F1-model_v4	21	245	1	229	0.7871	0.7435
AF-A0A0P0W0M3-F1-model_v4	1	245	6	307	0.8354	0.7354

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP000539623615.pdb	1	247	5	236	0.9235	0.8922
MGYP001339465194.pdb	1	247	2	242	0.914	0.888
MGYP001434148013.pdb	1	247	1	237	0.9124	0.8778
MGYP001084414565.pdb	1	247	1	240	0.908	0.8773
MGYP000970277262.pdb	1	247	1	235	0.9102	0.8736
MGYP000109510454.pdb	1	245	1	240	0.8924	0.8691
MGYP000890762165.pdb	1	247	8	244	0.8886	0.868
MGYP000867902925.pdb	1	247	1	247	0.8822	0.8653
MGYP001053807098.pdb	1	247	3	232	0.9053	0.8628
MGYP003548652537.pdb	1	243	1	240	0.8909	0.8611

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS044	HM144387_00160	9	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
APIS001	4.00E-31	2	229	22	253	pyrimidine cyclase system for antiphage resistance (Pycsar)	YP_009840594.1
APIS076	3.02E-28	2	240	8	253		IMGVR_UViG_3300044693_000096\|3300044693\|Ga0466961_0000159_42271_43065
APIS058	4.62E-27	2	236	18	257		IMGVR_UViG_3300022562_000702\|3300022562\|Ga0247387_1000200120
APIS062	2.16E-22	2	226	3	244		IMGVR_UViG_3300028374_000006\|3300028374\|Ga0306906_100003345
APIS060	1.47E-21	2	238	3	250		IMGVR_UViG_3300024258_000005\|3300024258\|Ga0233440_1000037199
APIS073	9.07E-19	2	229	25	269		IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_37885_38742
APIS041	1.34E-18	2	229	4	231		IMGVR_UViG_2832702071_000001\|2832702071\|2832704097
APIS054	1.41E-17	2	236	5	251		IMGVR_UViG_3300014204_000482\|3300014204\|Ga0172381_1000105623
APIS064	4.65E-17	2	223	3	227		IMGVR_UViG_3300033145_003233\|3300033145\|Ga0366840_1000004654
APIS066	2.22E-14	2	228	3	262		IMGVR_UViG_3300035396_000446\|3300035396\|Ga0393109_006065_59543_60412

Family members, sources, and their hosts help

Results of representative protein blast against members.
Member	pident	evalue	bitscore	qcovs	phage	host	SourceDB	Pfam	Phrog
HM144387_00160	100.000	0.0	516	100%	Bacillus phage W.Ph.	Bacillus	INPHARED	PF12706	phrog_392 phrog_14429
IMGVR_UViG_2936514734_000001\|2936514734\|2936514924	42.915	3.82e-55	185	100%		Priestia megaterium	IMGVR	PF12706	phrog_392
IMGVR_UViG_3300007790_000074\|3300007790\|Ga0105679_1013100840	99.595	0.0	514	99%			IMGVR	PF12706	phrog_392 phrog_14429
IMGVR_UViG_3300011497_000002\|3300011497\|Ga0120869_1002699	40.476	5.37e-49	169	98%			IMGVR	PF12706	phrog_392
IMGVR_UViG_3300024999_000038\|3300024999\|Ga0209728_1000028178	39.592	6.53e-43	154	98%			IMGVR	PF12706	phrog_392
IMGVR_UViG_3300026493_000016\|3300026493\|Ga0256786_1000025144	68.016	3.63e-121	353	100%			IMGVR	PF12706	phrog_392 phrog_14429
IMGVR_UViG_3300027858_000004\|3300027858\|Ga0209013_10000004126	40.164	5.43e-50	172	96%			IMGVR	PF12706	phrog_392
IMGVR_UViG_3300047323_000304\|3300047323\|Ga0495683_0000015_159496_160188	39.834	3.62e-49	169	98%			IMGVR	PF12706	phrog_392
ON366411_00087	50.826	3.93e-73	231	97%	Bacillus phage vB_BceH_LY2	Bacillus	INPHARED	PF12706	phrog_392 phrog_14429