dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS077

Inhibited defense system

CLAN ID

CLAN009

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
KU946962_00005	gene_page:	109	12584.91	3.3526	-22.5

Phage property

Phage	Assembly id
Proteus phage PM 116	KU946962

PMID/References

PDB structures

;

Pfam domains

PF08684.13

Phrog

phrog_2568

Host taxa

d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus;

Gene Location

Start: 2028; End: 2357; Strand: +

Description

Note

This family does not have seed protein, but we infer its function is defending restriction-modification (RM);bacteriophage exclusion (BREX) because it belongs to the same clan as family APIS010 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
KU946962	619	882	+	KU946962_00001	87	10056.97	10056.97	10.5254	hypothetical protein	phrog_23827
KU946962	884	1096	+	KU946962_00002	70	8106.36	8106.36	5.5127	hypothetical protein	phrog_6403
KU946962	1096	1305	+	KU946962_00003	69	8340.47	8340.47	4.0090	hypothetical protein	phrog_6403
KU946962	1463	1963	+	KU946962_00004	166	19922.16	19922.16	4.0843	hypothetical protein	phrog_23478
KU946962	2028	2357	+	KU946962_00005	109	12584.91	12584.91	3.3526	ocr-like anti-restriction	phrog_2568	PF08684.13
KU946962	2542	2754	+	KU946962_00006	70	8067.37	8067.37	4.8430	hypothetical protein	phrog_19783
KU946962	2825	3670	+	KU946962_00007	281	32073.50	32073.50	4.8246	hypothetical protein	phrog_22983 ; phrog_4571
KU946962	3744	6371	+	KU946962_00008	875	99624.91	99624.91	6.8163	RNA polymerase	phrog_2166 ; phrog_414 ; phrog_2051	PF00940.22
KU946962	3744	6371	+	KU946962_00008	875	99624.91	99624.91	6.8163	RNA polymerase	phrog_2166 ; phrog_414 ; phrog_2051	PF14700.9
KU946962	6674	7087	+	KU946962_00009	137	15817.92	15817.92	10.2744	HNH endonuclease	phrog_37683 ; phrog_4578 ; phrog_99 ; phrog_1492 ; phrog_959 ; phrog_59 ; phrog_14913	PF13392.9
KU946962	7089	7217	+	KU946962_00010	42	5196.09	5196.09	11.1658	hypothetical protein	phrog_4383 ; phrog_2490	PF08200.14

Seed genomic context- JBrowse

Predicted 3D structure by alphafold2 with pTM = 0.79 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

No homologs found in AlphaFold database

No homologs found in esmfold database

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS077	KU946962_00005	81	HMM model	Member alignment

Host Taxa distribution

Length distribution

Homology to other families download full data without filtering help

Clan ID: CLAN009

Hit APIS family	E-Value	Query Start	Query End	Hit Start	Hit End	Immune system	Seed protein
APIS010	6.23E-55	2	109	6	112	restriction-modification (RM);bacteriophage exclusion (BREX)	NP_041954.1
APIS087	3.93E-50	2	109	6	112		ON528733_00011
APIS085	2.01E-49	2	108	6	111		OL964750_00001

Family members, sources, and their hosts help

Results of representative protein blast against members.
Member	pident	evalue	bitscore	qcovs	phage	host	SourceDB	Pfam	Phrog
EU734174_00002	50.467	1.05e-24	98.6	91%	Escherichia phage 13a	Escherichia	INPHARED	PF08684	phrog_2568
GU595417_00004	48.980	5.88e-21	89.0	90%	Escherichia phage UAB_Phi78	Escherichia	INPHARED	PF08684	phrog_2568
HG818823_00001	40.449	7.40e-12	65.9	82%	Citrobacter phage CR44b	Citrobacter	INPHARED	PF08684	phrog_2568
IMGVR_UViG_2627853805_000003\|2627853805\|2629048919	43.810	6.91e-17	79.0	87%		Yersinia pestis	IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300013307_000052\|3300013307\|Ga0157372_1000212327	43.750	1.84e-15	74.7	87%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300013837_000006\|3300013837\|Ga0120084_100057	43.396	8.87e-18	81.3	88%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300029310_000088\|3300029310\|Ga0134545_100214110	40.000	6.85e-12	65.9	81%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300031087_000014\|3300031087\|Ga0308161_1000186228	43.158	1.03e-14	73.2	83%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300031087_000234\|3300031087\|Ga0308161_100037196	42.708	8.43e-14	70.9	86%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300031151_000001\|3300031151\|Ga0308162_100006695	43.158	8.45e-15	73.2	85%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300045988_000522\|3300045988\|Ga0495776_019744_25048_25395	43.925	1.47e-17	80.5	92%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300045988_000532\|3300045988\|Ga0495776_056017_25063_25398	42.991	5.92e-19	84.0	95%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300045988_001011\|3300045988\|Ga0495776_127866_4638_4970	48.598	3.60e-22	92.0	96%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300045988_002335\|3300045988\|Ga0495776_012863_5059_5415	42.056	7.66e-19	84.0	90%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300045988_004017\|3300045988\|Ga0495776_020355_15974_16330	41.441	7.29e-17	79.0	89%			IMGVR	PF08684	phrog_2568
IMGVR_UViG_3300045988_011354\|3300045988\|Ga0495776_092730_36573_36920	46.729	2.93e-18	82.4	92%			IMGVR	PF08684	phrog_2568
JN986844_00006	41.509	1.51e-15	75.5	89%	Escherichia phage vB_EcoP_ACG-C91	Escherichia	INPHARED	PF08684	phrog_2568
KM819695_00006	50.000	1.16e-22	93.6	93%	Proteus phage PM 85	Proteus	INPHARED	PF08684	phrog_2568
KT852574_00001	47.664	5.28e-21	89.4	88%	Yersinia phage vB_YenP_AP10	Yersinia	INPHARED	PF08684	phrog_2568
KU946962_00005	100.000	2.57e-71	216	100%	Proteus phage PM 116	Proteus	INPHARED	PF08684	phrog_2568
KX279892_00004	41.509	2.78e-16	77.0	93%	Escherichia phage AAPEc6	Escherichia	INPHARED	PF08684	phrog_2568
KY084243_00001	35.556	9.48e-11	63.2	83%	Pectobacterium phage PP74	Pectobacterium	INPHARED	PF08684	phrog_2568
KY295894_00010	39.560	4.35e-12	66.2	83%	Escherichia phage vB_EcoP_F	Escherichia	INPHARED	PF08684	phrog_2568
KY295899_00034	38.889	1.38e-12	67.4	82%	Escherichia phage vB_EcoP_R	Escherichia	INPHARED	PF08684	phrog_2568
KY435490_00051	42.453	4.98e-17	79.3	89%	Escherichia phage K1E	Escherichia	INPHARED	PF08684	phrog_2568
LC730323_00005	44.898	2.46e-17	80.1	90%	Salmonella phage SP6	Salmonella	INPHARED	PF08684	phrog_2568
MGV-GENOME-0199759_10	37.778	6.78e-11	63.5	83%			MGV	PF08684	phrog_2568
MGV-GENOME-0218412_33	47.664	5.96e-18	81.6	91%			MGV	PF08684	phrog_2568
MGV-GENOME-0263483_7	48.598	4.06e-22	92.0	91%			MGV	PF08684	phrog_2568
MGV-GENOME-0265351_44	47.664	8.06e-22	91.7	86%			MGV	PF08684	phrog_2568
MGV-GENOME-0279303_7	43.519	5.84e-17	79.0	92%			MGV	PF08684	phrog_2568
MGV-GENOME-0286050_29	42.991	6.68e-19	84.0	92%			MGV	PF08684	phrog_2568
MGV-GENOME-0286366_31	43.925	1.52e-17	80.5	91%			MGV	PF08684	phrog_2568
MGV-GENOME-0286693_16	42.453	5.16e-17	79.3	88%			MGV	PF08684	phrog_2568
MGV-GENOME-0286695_22	41.441	7.54e-17	79.0	88%			MGV	PF08684	phrog_2568
MGV-GENOME-0290208_38	42.453	4.23e-17	79.3	89%		Treponema_D	MGV	PF08684	phrog_2568
MGV-GENOME-0291317_9	42.056	7.93e-19	84.0	89%			MGV	PF08684	phrog_2568
MGV-GENOME-0291506_39	46.729	3.04e-18	82.4	91%			MGV	PF08684	phrog_2568
MGV-GENOME-0292351_18	43.925	2.73e-17	79.7	91%			MGV	PF08684	phrog_2568
MH382198_00008	48.980	4.04e-21	89.7	90%	Salmonella phage 3A_8767	Salmonella	INPHARED	PF08684	phrog_2568
MH400309_00003	37.778	2.83e-11	64.3	83%	Escherichia phage Vec13	Escherichia	INPHARED	PF08684	phrog_2568
MH729818_00006	43.564	9.91e-16	75.9	93%	Escherichia phage LL11	Escherichia	INPHARED	PF08684	phrog_2568
MK033136_00018	40.449	1.60e-13	70.1	80%	Enterobacter phage EcpYZU01	Enterobacter	INPHARED	PF08684	phrog_2568
MK373771_00004	43.564	5.04e-16	76.6	84%	Escherichia phage vB_EcoP_R4596	Escherichia	INPHARED	PF08684	phrog_2568
MK380014_00006	45.794	1.47e-17	80.5	92%	Klebsiella phage K1-ULIP33	Klebsiella	INPHARED	PF08684	phrog_2568
MK521905_00043	40.000	1.26e-11	65.1	83%	Klebsiella phage vB_KpnP_FZ12	Klebsiella	INPHARED	PF08684	phrog_2568
MK903279_00003	38.889	2.59e-12	67.0	83%	Escherichia phage Peacock	Escherichia	INPHARED	PF08684	phrog_2568
MN067430_00002	38.889	7.49e-12	65.9	83%	Escherichia phage vB_EcoP-Ro103C3lw	Escherichia	INPHARED	PF08684	phrog_2568
MW358931_00007	56.364	2.25e-28	107	100%	Providencia phage PSTRCR_128	Providencia	INPHARED	PF08684	phrog_2568
MW883060_00049	48.515	5.56e-22	91.7	93%	Escherichia phage vB_EcoP_SYGE1	Escherichia	INPHARED	PF08684	phrog_2568
MZ031013_00007	42.453	3.32e-17	79.7	97%	Escherichia phage vB_EcoA_fTuEco01	Escherichia	INPHARED	PF08684	phrog_2568
MZ234012_00051	44.000	6.56e-16	76.3	92%	Escherichia phage vB_EcoP-101101UKE1	Escherichia	INPHARED	PF08684	phrog_2568
MZ234032_00048	44.144	5.22e-17	79.0	98%	Escherichia phage vB_EcoP-G3A1	Escherichia	INPHARED	PF08684	phrog_2568
MZ234050_00054	42.574	4.79e-17	79.3	93%	Escherichia phage vB_EcoP-UTI89UKE3	Escherichia	INPHARED	PF08684	phrog_2568
MZ398244_00050	43.925	6.87e-17	78.6	98%	Klebsiella phage IME184	Klebsiella	INPHARED	PF08684	phrog_2568
MZ573924_00040	45.918	5.43e-17	79.0	90%	Salmonella phage vB_SenAt-pSL2	Salmonella	INPHARED	PF08684	phrog_2568
OK499982_00001	55.046	6.92e-29	109	100%	Morganella phage vB_MmoP_Lilpapawes	Morganella	INPHARED	PF08684	phrog_2568
OL362272_00015	44.762	7.00e-17	78.6	96%	Escherichia phage 6948	Escherichia	INPHARED	PF08684	phrog_2568
OL362273_00015	44.660	1.72e-16	77.8	94%	Escherichia phage 6949	Escherichia	INPHARED	PF08684	phrog_2568
OL416096_00008	42.453	9.59e-16	75.9	97%	Proteus phage 309	Proteus	INPHARED	PF08684	phrog_2568
OL539729_00049	39.623	1.34e-13	70.5	97%	Salmonella phage PRF-SP3	Salmonella	INPHARED	PF08684	phrog_2568
OM194188_00009	38.889	8.72e-12	65.5	83%	Klebsiella phage Shaphc-168R	Klebsiella	INPHARED	PF08684	phrog_2568
ON148529_00001	37.778	8.15e-11	63.2	83%	Klebsiella phage Kp9	Klebsiella	INPHARED	PF08684	phrog_2568
ON210145_00004	44.000	2.84e-16	77.0	92%	Escherichia phage EEc4	Escherichia	INPHARED	PF08684	phrog_2568
ON526839_00042	45.918	1.79e-17	80.1	90%	Salmonella phage GRNsp51	Salmonella	INPHARED	PF08684	phrog_2568
ON548433_00010	40.659	1.56e-12	67.4	83%	Escherichia phage vB_EcoP_FFK3	Escherichia	INPHARED	PF08684	phrog_2568
ON602753_00002	38.889	8.59e-13	68.2	83%	Klebsiella phage VLCpiA3d	Klebsiella	INPHARED	PF08684	phrog_2568
OP013026_00009	36.667	1.56e-15	58.2	82%	Klebsiella phage NK20	Klebsiella	INPHARED	PF08684	phrog_2568
OP018999_00008	40.566	5.24e-17	79.0	97%	Escherichia phage NTNC80A	Escherichia	INPHARED	PF08684	phrog_2568
OP038547_00030	45.918	6.12e-17	79.0	90%	Salmonella phage GRNsp03	Salmonella	INPHARED	PF08684	phrog_2568
OP413828_00048	41.584	5.56e-17	79.0	93%	Klebsiella phage pKP-M186-2.1	Klebsiella	INPHARED	PF08684	phrog_2568
OX335382_00005	44.860	1.67e-17	80.1	98%	Klebsiella phage cp4	Klebsiella	INPHARED	PF08684	phrog_2568
uvig_220123_45	42.453	4.09e-17	79.3	90%			GPD	PF08684	phrog_2568
uvig_230064_18	43.925	2.64e-17	79.7	92%			GPD	PF08684	phrog_2568
uvig_255282_14	42.056	3.02e-18	82.0	93%			GPD	PF08684	phrog_2568
uvig_286192_10	37.778	6.63e-11	63.5	83%			GPD	PF08684	phrog_2568
uvig_290651_23	39.326	3.29e-12	66.6	82%			GPD	PF08684	phrog_2568
uvig_374109_8	47.664	5.76e-18	81.6	92%			GPD	PF08684	phrog_2568
uvig_475627_7	43.519	5.64e-17	79.0	93%			GPD	PF08684	phrog_2568
uvig_481475_40	37.778	4.24e-16	59.7	79%			GPD	PF08684	phrog_2568
uvig_575770_11	43.925	3.57e-20	87.0	92%			GPD	PF08684	phrog_2568

APIS	Contig	Range
APIS077	KU946962	619 - 7217