dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS001

Inhibited defense system

pyrimidine cyclase system for antiphage resistance (Pycsar)

CLAN ID

CLAN001

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
YP_009840594.1	gene_page: Apyc1	256	29051.70	4.8545	-9.5

Phage property

Phage	Assembly id
Bsp38 of Bacillus subtilis	GCF_003367035.1

PMID/References

PMID:35395152

PDB structures

7T28,Bsp38;7U2R,Paenibacillus J14;7U2S,Paenibacillus xerothermodurans;

Pfam domains

PF00753.30

Phrog

phrog_392

Host taxa

d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus;s__Bacillus subtilis

Gene Location

Start: 92525; End: 93295; Strand: +

Description

SBSphiJ Apyc1 efficiently hydrolyses a wide range of cyclic mononucleotides; 273 Acb1 and 107 Apyc1 phage proteins were identified.

Seed genomic context Download table help

Search:

Genome accession	Start	End	Strand	Protein ID	Length	Molecular weight	Charge	Isoelectric point	Function	Phrog	PFAM
NC_048726.1	90711	90842	+	YP_009840589.1	43	5432.17	1.5	7.3202	hypothetical protein
NC_048726.1	90832	91815	+	YP_009840590.1	327	37645.45	-14.5	4.4760	ribonucleotide reductase class Ia beta subunit	phrog_10582 ; phrog_24856 ; phrog_7909 ; phrog_86 ; phrog_9465 ; phrog_9530	PF00268.24
NC_048726.1	91815	92051	+	YP_009840591.1	78	8693.89	-7.5	4.0742	putative thioredoxin
NC_048726.1	92152	92349	+	YP_009840592.1	65	7822.74	-4.5	4.5778	hypothetical protein	phrog_24464
NC_048726.1	92346	92525	+	YP_009840593.1	59	7041.92	-14.5	3.3286	hypothetical protein
NC_048726.1	92525	93295	+	YP_009840594.1	256	29051.70	-9.5	4.8545	metal-dependent hydrolase	phrog_392	PF00753.30
NC_048726.1	93311	93502	+	YP_009840595.1	63	6927.92	-3.5	4.4895	hypothetical protein	phrog_11210
NC_048726.1	93502	93657	+	YP_009840596.1	51	5795.81	-4.5	4.2507	hypothetical protein	phrog_28167 ; phrog_19268 ; phrog_21011
NC_048726.1	93654	93848	+	YP_009840597.1	64	7430.41	-1.5	5.6149	hypothetical protein
NC_048726.1	93845	94063	+	YP_009840598.1	72	8315.41	-8.0	4.0078	acetyltransferase	phrog_5504
NC_048726.1	94066	94446	+	YP_009840599.1	126	14832.61	-12.0	4.1674	hypothetical protein	phrog_17088

Showing 1 to 11 of 11 entries

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Seed genomic context- JBrowse

PDB structure: 7T28 ; Download help

Full Sequence Download help

MLHTTQIRMV GTGSAFSKKF YNNSALVTFT NGYNLLIDCG HSVPKGLHDA DIPLESIDGI	60
LITHTHADHI GGLEEVALYN KFVLGGRKID LLVPNTLVES LWENSLKGGL RYSDTYDDLS	120
LSDYFTVRSL KTFTSGAART QLEENIAIKL YPTFHVSHMA SYAVGLEDRG EDKVFYSSDT	180
IFDEYLIDYA LTYSWVFHDC QFFTGGVHAS LDELLNYIPE EDQDRVFLMH YGDNMEDFFT	240
KTGRMRFALQ GRTYIL	256

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-A0A0H3GHL8-F1-model_v4	5	238	1	238	0.8284	0.7878
AF-A0A133CTF0-F1-model_v4	1	238	1	244	0.8176	0.7862
AF-P9WGC1-F1-model_v4	1	238	18	267	0.8368	0.7674
AF-Q58769-F1-model_v4	1	238	3	253	0.816	0.7554
AF-P50474-F1-model_v4	1	238	27	276	0.8371	0.7551
AF-P16692-F1-model_v4	1	238	3	249	0.7862	0.7487
AF-A0A0H3GM29-F1-model_v4	1	238	3	249	0.7863	0.7487
AF-Q329H1-F1-model_v4	1	238	3	249	0.7848	0.747
AF-O74545-F1-model_v4	1	238	6	297	0.8418	0.7433
AF-K0EUK8-F1-model_v4	22	238	1	230	0.7727	0.742

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP001101967902.pdb	1	238	5	254	0.9231	0.8778
MGYP002654867125.pdb	1	238	3	253	0.9006	0.8575
MGYP003952926961.pdb	1	238	2	251	0.8769	0.8337
MGYP001424664394.pdb	1	238	1	240	0.857	0.8335
MGYP000754846076.pdb	1	238	3	243	0.8585	0.8314
MGYP000856702051.pdb	1	238	3	265	0.8913	0.8294
MGYP001478949968.pdb	1	238	1	258	0.8806	0.8291
MGYP001450167839.pdb	1	238	1	245	0.8676	0.8291
MGYP000956383480.pdb	1	238	1	240	0.853	0.8289
MGYP001465423269.pdb	1	238	1	251	0.8711	0.8287

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS001	YP_009840594.1	26	HMM model	Member alignment

Host Taxa distribution

Length distribution

Homology to other families download full data without filtering help

Clan ID: CLAN001

Search:

Hit APIS family	E-Value	Query Start	Query End	Hit Start	Hit End	Seed protein
APIS041	9.01E-43	19	271	1	249	IMGVR_UViG_2832702071_000001\|2832702071\|2832704097
APIS044	7.63E-31	22	260	2	233	HM144387_00160
APIS054	1.35E-43	19	270	2	261	IMGVR_UViG_3300014204_000482\|3300014204\|Ga0172381_1000105623
APIS058	3.13E-56	18	271	14	268	IMGVR_UViG_3300022562_000702\|3300022562\|Ga0247387_1000200120
APIS060	2.90E-36	20	271	1	259	IMGVR_UViG_3300024258_000005\|3300024258\|Ga0233440_1000037199
APIS062	2.02E-54	20	271	1	263	IMGVR_UViG_3300028374_000006\|3300028374\|Ga0306906_100003345
APIS064	1.21E-35	20	271	1	258	IMGVR_UViG_3300033145_003233\|3300033145\|Ga0366840_1000004654
APIS066	2.83E-40	20	271	1	293	IMGVR_UViG_3300035396_000446\|3300035396\|Ga0393109_006065_59543_60412
APIS073	6.60E-53	19	271	22	285	IMGVR_UViG_3300042197_004918\|3300042197\|Ga0451494_0000046_37885_38742
APIS076	1.49E-66	17	271	3	259	IMGVR_UViG_3300044693_000096\|3300044693\|Ga0466961_0000159_42271_43065

Showing 1 to 10 of 10 entries

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Family members, sources, and their hosts help

Search:

Member	pident	evalue	bitscore	qcovs	phage	host	SourceDB	Pfam	Phrog
IMGVR_UViG_2974673286_000001\|2974673286\|2974673417	100.000	0.0	528	99%			IMGVR	PF00753	phrog_392
IMGVR_UViG_3300027628_000019\|3300027628\|Ga0209463_100018292	50.973	3.06e-78	245	98%			IMGVR	PF12706	phrog_392
IMGVR_UViG_3300049046_000017\|3300049046\|Ga0498743_000341_2770_3534	51.362	6.47e-77	241	98%			IMGVR	PF12706	phrog_392
JN638751_00385	41.494	7.02e-41	149	90%	Bacillus phage G	Bacillus	INPHARED	PF12706	phrog_392
KF669652_00121	87.938	1.32e-164	464	99%	Bacillus phage Grass	Bacillus	INPHARED	PF00753	phrog_392
KM236245_00126	50.000	2.13e-78	245	97%	Bacillus phage Mater	Bacillus	INPHARED	PF12706	phrog_392
KY368640_00118	78.846	2.48e-144	412	99%	Bacillus phage vB_BsuM-Goe3	Bacillus	INPHARED	PF00753	phrog_392
LT960608_00153	87.549	4.12e-163	460	99%	Bacillus phage SBSphiJ	Bacillus	INPHARED	PF00753	phrog_392
MH606185_00128	100.000	0.0	528	99%	Bacillus phage BSP38	Bacillus	INPHARED	PF00753	phrog_392
MT151604_00140	54.365	1.09e-79	248	98%	Bacillus phage P59	Bacillus	INPHARED	PF00753	phrog_392

Showing 1 to 10 of 26 entries

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APIS	Contig	Range
APIS001	NC_048726.1	90711 - 94446

Seed protein information help

Seed genomic context Download table help

Seed genomic context- JBrowse

PDB structure: 7T28 ; Download help

Full Sequence Download help

Structural homologs

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

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

Family information Download help

Host Taxa distribution

Length distribution

Homology to other families download full data without filtering help

Clan ID: CLAN001

Family members, sources, and their hosts help

Results of representative protein blast against members.

Gene cluster comparison plot by clinker Download html