dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS094

Inhibited defense system

Retron

CLAN ID

CLAN037

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
YP_009829723.1	gene_page: Rad	189	21059.21	6.4794	0.0

Phage property

Phage	Assembly id
Escherichia phage SP15	GCF_004768945.1

PMID/References

Azam et al., 2023

PDB structures

;

Pfam domains

PF13155.11,PF13155.11

Phrog

phrog_849,phrog_849,phrog_14043,phrog_14043,phrog_17952,phrog_17952

Host taxa

d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;

Gene Location

Start: 35930; End: 36499; Strand: -

Description

Rad inhibited retron function by degrading noncoding RNA, the precursor of msDNA.

Seed genomic context Download table help

Genome accession	Start	End	Strand	Protein ID	Length	Molecular weight	Charge	Isoelectric point	Function	Phrog	PFAM
NC_048627.1	33935	34207	-	YP_009829718.1	90	10872.68	11.0	10.1441	hypothetical protein	phrog_5876
NC_048627.1	34696	34971	-	YP_009829719.1	91	10200.65	-10.0	3.9759	hypothetical protein	phrog_4991 ; phrog_4551
NC_048627.1	35062	35268	-	YP_009829720.1	68	7442.57	-3.5	4.5125	hypothetical protein	phrog_5153
NC_048627.1	35261	35377	-	YP_009829721.1	38	4463.16	-1.0	5.5929	hypothetical protein	phrog_7716
NC_048627.1	35528	35716	-	YP_009829722.1	62	7404.41	-4.5	4.3138	hypothetical protein	phrog_10617
NC_048627.1	35930	36499	-	YP_009829723.1	189	21059.21	0.0	6.4794	DNA primase	phrog_14043 ; phrog_14043 ; phrog_17952 ; phrog_17952 ; phrog_849 ; phrog_849	PF13155.11 ;PF13155.11
NC_048627.1	36714	37697	+	YP_009829724.1	327	34694.35	-10.5	4.6672	hypothetical protein	phrog_8119 ; phrog_16490
NC_048627.1	37719	38135	+	YP_009829725.1	138	15370.19	-1.0	4.8282	hypothetical protein	phrog_7894
NC_048627.1	38460	39407	-	YP_009829726.1	315	35302.41	3.5	9.3132	lipoprotein		PF01145.30
NC_048627.1	40366	40809	-	YP_009829727.1	147	16863.21	-0.5	5.9391	tRNA amidotransferase	phrog_1460	PF09424.15
NC_048627.1	40809	40979	-	YP_009829728.1	56	6130.23	6.0	11.1710	hypothetical protein	phrog_5077

Seed genomic context- JBrowse

Predicted 3D structure by alphafold2 with pTM = 0.85 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-Q8DPW1-F1-model_v4	18	188	135	365	0.7578	0.495
AF-P0ABS5-F1-model_v4	18	189	134	365	0.7501	0.4916
AF-Q32BQ1-F1-model_v4	18	189	134	365	0.75	0.4915
AF-A0A0H3GVT7-F1-model_v4	18	189	134	365	0.7499	0.4914
AF-P07362-F1-model_v4	18	189	134	365	0.7498	0.4913
AF-P56064-F1-model_v4	19	189	124	349	0.7416	0.4906
AF-Q08346-F1-model_v4	19	189	136	366	0.7494	0.4887
AF-Q9PM37-F1-model_v4	19	189	124	351	0.748	0.4854
AF-A0A132Z8R3-F1-model_v4	18	188	137	374	0.7477	0.4838
AF-Q9I5W0-F1-model_v4	18	189	136	369	0.749	0.4755

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP001916582558.pdb	12	189	12	189	0.9562	0.893
MGYP000909425859.pdb	16	189	3	172	0.9346	0.888
MGYP000119266823.pdb	17	189	1	172	0.9225	0.8735
MGYP003650345132.pdb	17	189	1	173	0.9003	0.8554
MGYP000220139417.pdb	18	189	1	172	0.9108	0.8525
MGYP000550666186.pdb	20	189	1	176	0.8931	0.8479
MGYP001152145515.pdb	18	189	1	173	0.8922	0.8419
MGYP001944544822.pdb	13	185	1	180	0.8777	0.8411
MGYP000682962050.pdb	22	189	1	175	0.8863	0.839
MGYP000155127275.pdb	23	189	1	165	0.9081	0.8375

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS094	YP_009829723.1	95	HMM model	Member alignment

Host Taxa distribution

Length distribution

Homology to other families help

Clan ID: CLAN037

APIS094 has no similar APIS family.

Family members, sources, and their hosts help

Results of representative protein blast against members.
Member	pident	evalue	bitscore	qcovs	phage	host	SourceDB	Pfam	Phrog
IMGVR_UViG_3300041405_000299\|3300041405\|Ga0439438_000009_5754_6251	45.300	1.451E-36	134	0.852%			IMGVR		phrog_14043 phrog_17952
IMGVR_UViG_3300045988_167117\|3300045988\|Ga0495776_031990_33662_34171	39.900	1.278E-29	114	0.852%			IMGVR		phrog_14043 phrog_17952
MGV-GENOME-0378604_77	39.900	1.278E-29	114	0.852%			MGV		phrog_14043 phrog_17952
MGV-GENOME-0288342_34	42.800	2.447E-35	130	0.894%		Escherichia	MGV		phrog_14043 phrog_17952 phrog_849
IMGVR_UViG_3300045988_006100\|3300045988\|Ga0495776_014478_17347_17862	43.700	3.348E-35	130	0.868%		Escherichia	IMGVR		phrog_14043 phrog_17952 phrog_849
uvig_146039_24	43.500	6.272E-35	129	0.868%			GPD		phrog_14043 phrog_17952 phrog_849
MN927225_00074	44.600	1.986E-36	134	0.868%	Escherichia phage vB_EcoS_XY1	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
OQ442786_00042	44.600	1.986E-36	134	0.868%	Escherichia phage JSSK01	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MGV-GENOME-0290406_43	44.600	1.986E-36	134	0.868%		Escherichia	MGV	PF13155	phrog_14043 phrog_17952 phrog_849
ON001686_00032	45.900	3.352E-38	139	0.868%	Escherichia phage vB_EcoS_SCS44	Escherichia	INPHARED		phrog_14043 phrog_17952 phrog_849
OM632668_00028	45.100	4.134E-37	136	0.868%	Escherichia phage BEU35	Escherichia	INPHARED		phrog_14043 phrog_17952 phrog_849
uvig_584053_71	44.400	3.722E-36	133	0.868%			GPD	PF13155	phrog_14043 phrog_17952 phrog_849
uvig_420133_53	43.400	8.583E-35	129	0.868%			GPD	PF13155	phrog_14043 phrog_17952 phrog_849
MZ576217_00033	44.200	6.972E-36	132	0.868%	Escherichia phage vB_EcoS-phiEc3	Escherichia	INPHARED		phrog_14043 phrog_17952 phrog_849
IMGVR_UViG_2974654489_000001\|2974654489\|2974654519	44.100	9.543E-36	132	0.868%		Escherichia	IMGVR	PF13155	phrog_14043 phrog_17952 phrog_849
MK972700_00012	43.000	1.306E-35	131	0.894%	Salmonella phage SS1	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MW331437_00036	43.500	6.272E-35	129	0.868%	Escherichia phage phiWAO78-1	Escherichia	INPHARED		phrog_14043 phrog_17952 phrog_849
MT653144_00036	44.000	1.306E-35	131	0.868%	Salmonella phage 5sent1	Salmonella	INPHARED		phrog_14043 phrog_17952 phrog_849
MK737937_00034	44.100	9.543E-36	132	0.868%	Raoultella phage RP180	Raoultella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
uvig_385574_49	43.700	3.348E-35	130	0.868%			GPD		phrog_14043 phrog_17952 phrog_849
uvig_552390_68	44.600	1.986E-36	134	0.868%			GPD	PF13155	phrog_14043 phrog_17952 phrog_849
MGV-GENOME-4420767_53	43.400	8.583E-35	129	0.868%		Enterobacteriaceae	MGV	PF13155	phrog_14043 phrog_17952 phrog_849
MK759883_00032	42.400	8.583E-35	129	0.894%	Salmonella phage vB_SenS_SB15	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MGV-GENOME-4421334_66	44.000	1.306E-35	131	0.868%		Enterobacteriaceae	MGV		phrog_14043 phrog_17952 phrog_849
uvig_70836_34	44.000	1.306E-35	131	0.868%			GPD		phrog_14043 phrog_17952 phrog_849
IMGVR_UViG_3300045988_012343\|3300045988\|Ga0495776_020668_22221_22736	42.800	2.447E-35	130	0.894%		Escherichia	IMGVR		phrog_14043 phrog_17952 phrog_849
MZ576218_00032	44.500	2.719E-36	133	0.868%	Escherichia phage vB_EcoS-phiEc4	Escherichia	INPHARED		phrog_14043 phrog_17952 phrog_849
MGV-GENOME-0292928_66	43.500	6.272E-35	129	0.868%		Escherichia	MGV		phrog_14043 phrog_17952 phrog_849
MG099933_00032	44.800	1.060E-36	134	0.868%	Escherichia phage VB_EcoS-Golestan	Escherichia	INPHARED		phrog_14043 phrog_17952 phrog_849
MZ234010_00046	44.600	1.986E-36	134	0.868%	Escherichia phage vB_EcoS-22664BS2	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MGV-GENOME-0293638_35	43.700	3.348E-35	130	0.868%		Escherichia	MGV		phrog_14043 phrog_17952 phrog_849
MT632020_00005	44.900	7.746E-37	135	0.868%	Salmonella phage UPWr_S5	Salmonella	INPHARED		phrog_14043 phrog_17952 phrog_849
IMGVR_UViG_3300045988_058438\|3300045988\|Ga0495776_007465_18400_18897	44.700	2.705E-33	124	0.804%		Klebsiella	IMGVR		phrog_14043 phrog_17952
MGV-GENOME-0270442_31	44.700	2.705E-33	124	0.804%		Enterobacteriaceae	MGV		phrog_14043 phrog_17952
MH830339_00069	39.900	8.357E-29	111	0.820%	Proteus phage Stubb	Proteus	INPHARED	PF13155	phrog_14043 phrog_849
YP_009829723.1	100.000	2.838E-128	398	1.000%	Escherichia phage SP15	Escherichia	NCBI	PF13155 PF13155	phrog_14043 phrog_14043 phrog_17952 phrog_17952 phrog_849 phrog_849
MK373796_00094	98.700	4.038E-115	361	0.910%	Escherichia phage vB_EcoS_HdH2	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
KR233164_00013	99.300	6.083E-116	363	0.910%	Salmonella phage NR01	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MZ398246_00084	96.700	3.043E-112	352	0.910%	Escherichia phage IME178	Escherichia	INPHARED	PF13155	phrog_14043 phrog_849
MK373792_00083	97.800	6.906E-114	357	0.910%	Escherichia phage vB_EcoS_VAH1	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MF774688_00026	99.500	3.236E-116	364	0.910%	Salmonella phage SP1a	Salmonella	INPHARED	PF13155	phrog_14043 phrog_849
MF431735_00104	97.700	9.467E-114	357	0.910%	Bacteriophage T5-like poul124	Unspecified	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
OK272477_00089	98.500	7.588E-115	360	0.910%	Escherichia phage JLBYU43	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MN316588_00100	99.700	1.722E-116	364	0.910%	Escherichia phage VEc33	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MGV-GENOME-0370602_50	99.700	1.722E-116	364	0.910%			MGV	PF13155	phrog_14043 phrog_17952 phrog_849
MT577844_00080	97.300	4.584E-113	355	0.910%	Salmonella phage vB_StyS-LmqsSP1	Salmonella	INPHARED	PF13155	phrog_14043 phrog_849
MN026741_00095	99.800	1.256E-116	365	0.910%	Salmonella phage Th1	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MT080103_00124	99.500	3.236E-116	364	0.910%	Escherichia phage ECOP18	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
OK254197_00076	99.800	1.256E-116	365	0.910%	Escherichia phage PNJ1902	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
OM386660_00071	97.900	5.037E-114	357	0.910%	Escherichia phage vB_EcoS_ESCO40	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
HQ665011_00100	98.500	7.588E-115	360	0.910%	Escherichia phage vB_EcoS_AKFV33	Escherichia	INPHARED		phrog_14043 phrog_849
MK867835_00090	98.800	2.945E-115	361	0.910%	Salmonella phage vB_SenS_SB9	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
AC171169_00055	97.500	1.779E-113	356	0.910%	Escherichia phage H8	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
KM979355_00067	96.700	3.043E-112	352	0.910%	Escherichia phage DT571/2	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MW149273_00132	98.600	5.535E-115	360	0.910%	Salmonella phage vB_SalS_ABTNLsp4	Salmonella	INPHARED		phrog_14043 phrog_849
OM386657_00106	99.300	6.083E-116	363	0.910%	Escherichia phage vB_EcoS_ESCO30	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MN994504_00103	99.500	3.236E-116	364	0.910%	Phage NBSal005	Unspecified	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
IMGVR_UViG_2974599810_000001\|2974599810\|2974599885	97.300	2.933E-125	390	1.000%			IMGVR		phrog_14043 phrog_849
MN994502_00100	99.300	6.083E-116	363	0.910%	Phage NBSal003	Unspecified	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MT074468_00109	88.300	1.842E-100	318	0.910%	Salmonella phage rutana	Salmonella	INPHARED	PF13155 PF01751	phrog_14043
IMGVR_UViG_2974645054_000001\|2974645054\|2974645117	98.700	1.884E-127	396	1.000%			IMGVR	PF13155	phrog_14043 phrog_17952 phrog_849
MT311645_00017	99.500	3.236E-116	364	0.910%	Salmonella phage vB_Sen-E22	Salmonella	INPHARED	PF13155	phrog_14043 phrog_849
IMGVR_UViG_2974662754_000001\|2974662754\|2974662805	94.600	5.185E-121	377	1.000%			IMGVR	PF13155	phrog_14043 phrog_17952 phrog_849
OQ680481_00057	99.200	8.339E-116	362	0.910%	Salmonella phage phC17	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
KP143763_00079	97.800	6.906E-114	357	0.910%	Salmonella phage Shivani	Salmonella	INPHARED		phrog_14043 phrog_17952 phrog_849
MF402939_00043	97.900	5.037E-114	357	0.910%	Escherichia phage OSYSP	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
OQ680480_00063	96.500	5.718E-112	351	0.910%	Salmonella phage phC11	Salmonella	INPHARED	PF13155	phrog_14043 phrog_849
LR027384_00038	97.400	3.344E-113	355	0.910%	Escherichia phage vB_Eco_mar004NP2	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
OQ680478_00102	96.700	3.043E-112	352	0.910%	Salmonella phage phA11	Salmonella	INPHARED	PF13155	phrog_14043 phrog_849
ON526840_00092	88.500	9.799E-101	319	0.910%	Salmonella phage GRNsp8	Salmonella	INPHARED	PF13155 PF01751	phrog_14043 phrog_17952 phrog_849
MH203051_00068	96.800	2.220E-112	353	0.910%	Escherichia phage Gostya9	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MZ501075_00084	97.300	4.584E-113	355	0.910%	Escherichia phage IrisVonRoten	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MH370378_00078	97.500	1.779E-113	356	0.910%	Salmonella phage S131	Salmonella	INPHARED		phrog_14043 phrog_849
OQ031075_00136	99.700	1.722E-116	364	0.910%	Klebsiella phage KPP2018	Klebsiella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
OK143207_00079	99.200	8.339E-116	362	0.910%	Escherichia phage Lindwurm	Escherichia	INPHARED	PF13155	phrog_14043 phrog_849
MN445182_00086	97.600	1.298E-113	356	0.910%	Salmonella phage vB_SalS_SA001	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MT074448_00101	97.700	9.467E-114	357	0.910%	Salmonella phage oldekolle	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MG387042_00080	97.500	2.439E-113	355	0.910%	Salmonella phage SP3	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
OQ359888_00101	100.000	4.875E-117	366	0.910%	Salmonella phage vB_SenS_UTK0008	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MZ501058_00083	98.900	2.148E-115	361	0.910%	Escherichia phage DaisyDussoix	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
KR422353_00001	97.400	3.344E-113	355	0.910%	Escherichia phage phiAPCEc03	Escherichia	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
OQ383622_00079	88.300	2.525E-100	318	0.910%	Salmonella phage MET_P1_179_112	Salmonella	INPHARED	PF13155 PF01751	phrog_14043 phrog_17952
MT843274_00017	99.500	3.236E-116	364	0.910%	Escherichia phage BB1	Escherichia	INPHARED		phrog_14043 phrog_849
MK972716_00001	99.600	2.361E-116	364	0.910%	Salmonella phage SE8	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
OQ383621_00086	89.400	5.731E-102	323	0.910%	Salmonella phage MET_P1_137_112	Salmonella	INPHARED	PF13155 PF01751 PF13662	phrog_14043 phrog_849
OL800604_00081	99.000	1.567E-115	362	0.910%	Salmonella phage vB_STy-RN29	Salmonella	INPHARED		phrog_14043 phrog_17952 phrog_849
MK972709_00123	88.900	2.775E-101	321	0.910%	Salmonella phage SE20	Salmonella	INPHARED	PF13155 PF01751 PF13662	phrog_14043
OQ383620_00078	98.400	1.040E-114	359	0.910%	Salmonella phage MET_P1_100_107	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MT233524_00161	98.500	7.588E-115	360	0.910%	Salmonella phage vB_Sen_I1	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
KY114934_00106	97.800	6.906E-114	357	0.910%	Salmonella phage SP01	Salmonella	INPHARED	PF13155	phrog_14043 phrog_17952 phrog_849
MGV-GENOME-4430145_42	40.200	3.701E-33	124	0.910%		Escherichia	MGV		phrog_14043 phrog_17952 phrog_849
IMGVR_UViG_3300045988_149821\|3300045988\|Ga0495776_095910_91875_92417	40.100	5.064E-33	124	0.910%		Escherichia	IMGVR		phrog_14043 phrog_17952 phrog_849
IMGVR_UViG_3300045988_126325\|3300045988\|Ga0495776_066294_40338_40880	40.200	3.701E-33	124	0.910%		Escherichia	IMGVR		phrog_14043 phrog_17952 phrog_849
IMGVR_UViG_3300045988_158509\|3300045988\|Ga0495776_102224_35888_36430	40.000	6.929E-33	123	0.910%		Escherichia	IMGVR		phrog_14043 phrog_17952 phrog_849
uvig_585840_21	40.000	6.929E-33	123	0.910%			GPD		phrog_14043 phrog_17952 phrog_849