dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS020

Inhibited defense system

RecBCD

CLAN ID

CLAN019

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
NP_059594.1	gene_page: Abc2	97	11620.18	8.9809	3.5

Phage property

Phage	Assembly id
Salmonella phage P22	GCF_000845765.1

PMID/References

PMID:10669596 36533901

PDB structures

8B1T;

Pfam domains

PF11043.11

Phrog

phrog_656

Host taxa

d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;

Gene Location

Start: 26630; End: 26923; Strand: -

Description

Bacteriophage P22 Abc2 protein binds to the RecBCD enzyme from E. coli to promote phage growth and recombination; the RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products.

Seed genomic context Download table help

Genome accession	Start	End	Strand	Protein ID	Length	Molecular weight	Charge	Isoelectric point	Function	Phrog	PFAM
NC_002371.2	25964	26461	-	NP_059592.1	165	18147.16	-17.0	4.0025	EaE	phrog_368 ; phrog_31590 ; phrog_492 ; phrog_614 ; phrog_14548 ; phrog_26126 ; phrog_10746
NC_002371.2	26449	26619	-	NP_059593.1	56	6633.80	5.5	10.4591	hypothetical protein	phrog_4684 ; phrog_1117	PF10930.11
NC_002371.2	26630	26923	-	NP_059594.1	97	11620.18	3.5	8.9809	abc2 anti-RecBCD	phrog_656	PF11043.11
NC_002371.2	26970	27254	-	NP_059595.1	94	10894.72	11.5	10.9204	Abc1	phrog_323 ; phrog_31591
NC_002371.2	27254	27871	-	NP_059596.1	205	23000.72	-1.5	6.0295	Erf-like ssDNA annealing protein	phrog_1097 ; phrog_10003 ; phrog_34817 ; phrog_2324 ; phrog_155	PF04404.15
NC_002371.2	27868	28011	-	NP_059597.1	47	5516.99	-10.5	3.4959	Erf recombination cofactor Arf	phrog_2445	PF17585.5
NC_002371.2	28001	28189	-	NP_059598.1	62	6949.59	-4.5	4.1520	Kil protein for bacterial septation inhibition	phrog_2394	PF17519.5
NC_002371.2	28170	28328	-	NP_059599.1	52	5733.73	4.0	9.3916	CIII anti-termination	phrog_550 ; phrog_2461	PF02061.19
NC_002371.2	24906	25499	-	YP_063721.1	197	22345.14	-6.0	4.9106	EaD	phrog_34708 ; phrog_250 ; phrog_11761 ; phrog_38306 ; phrog_1138 ; phrog_19867 ; phrog_32305 ; phrog_20344	PF13935.9
NC_002371.2	25496	25855	-	YP_063722.1	119	13909.77	-7.5	4.4910	EaF	phrog_6018	PF17526.5
NC_002371.2	25830	25967	-	YP_063723.1	45	5081.57	-2.0	4.8084	hypothetical protein	phrog_25957

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-Q32CA2-F1-model_v4	1	601	1	606	0.9876	0.9796
AF-Q8ZMB7-F1-model_v4	1	601	2	606	0.9812	0.9699
AF-P04993-F1-model_v4	1	601	2	606	0.9731	0.9627
AF-A0A0H3H2A9-F1-model_v4	1	601	2	610	0.9762	0.9619
AF-A0A0H3GX23-F1-model_v4	1	1080	1	1121	0.9808	0.9589
AF-Q8ZMB4-F1-model_v4	1	1080	1	1121	0.9793	0.9581
AF-Q32C99-F1-model_v4	1	1080	1	1121	0.9783	0.9573
AF-P07648-F1-model_v4	1	1080	1	1121	0.9682	0.9462
AF-Q32CA1-F1-model_v4	1	1141	5	1174	0.9558	0.9349
AF-A0A0H3GSM0-F1-model_v4	1	1135	5	1162	0.9432	0.9291

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP000868799281.pdb	1	601	2	606	0.9735	0.9641
MGYP002472884262.pdb	1	601	2	605	0.97	0.961
MGYP001104396436.pdb	1	601	2	611	0.9691	0.9549
MGYP001152395759.pdb	1	601	2	610	0.967	0.9528
MGYP001073940060.pdb	1	601	2	609	0.9627	0.9504
MGYP000627624437.pdb	1	601	2	610	0.9664	0.9499
MGYP001095023059.pdb	1	601	1	616	0.9663	0.9476
MGYP000933771875.pdb	1	601	3	611	0.9652	0.9461
MGYP003365269547.pdb	2	601	1	614	0.9626	0.9451
MGYP000368278305.pdb	2	601	1	638	0.9674	0.9347

Fam ID	Seed protein	Member count	Model	Alignment
APIS020	NP_059594.1	65	HMM model	Member alignment

Homology to other families help

Clan ID: CLAN019

APIS020 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
AY052766_00015	94.845	6.75e-64	196	100%	Salmonella phage ST64T	Salmonella	INPHARED	PF11043	phrog_656
FJ000341_00023	95.876	1.39e-64	198	100%	Salmonella phage g341c	Salmonella	INPHARED	PF11043	phrog_656
IMGVR_UViG_2526164688_000036\|2526164688\|2526973919	93.814	1.99e-61	190	100%		Escherichia coli	IMGVR	PF11043	phrog_656
IMGVR_UViG_2529292729_000007\|2529292729\|2529749295	93.814	4.57e-62	191	100%		Escherichia coli	IMGVR	PF11043	phrog_656
IMGVR_UViG_2529292934_000004\|2529292934\|2530582789	94.845	4.35e-64	197	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2529292964_000003\|2529292964\|2530674819	93.814	8.81e-63	193	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2531839281_000006\|2531839281\|2532920724	93.814	1.03e-62	193	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2534681712_000004\|2534681712\|2535163245	93.814	2.91e-63	194	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2534681952_000002\|2534681952\|2536102514	93.814	1.09e-62	193	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2537561642_000010\|2537561642\|2538080042	93.814	1.17e-63	196	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2541047592_000015\|2541047592\|2543543060	93.814	1.04e-62	193	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2551306401_000003\|2551306401\|2552940337	92.784	7.47e-63	193	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2554235233_000004\|2554235233\|2555255608	98.969	7.16e-66	201	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2554235428_000004\|2554235428\|2555951937	91.753	1.16e-62	193	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2558860365_000002\|2558860365\|2559643376	93.814	8.18e-62	191	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2558860438_000004\|2558860438\|2559848087	95.876	1.97e-64	197	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2558860440_000007\|2558860440\|2559859069	93.814	5.55e-63	194	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2558860441_000018\|2558860441\|2559865402	95.876	2.46e-63	195	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2558860448_000006\|2558860448\|2559894977	93.814	3.43e-63	194	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2558860453_000005\|2558860453\|2559918391	94.845	3.87e-63	194	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2558860463_000002\|2558860463\|2559964348	95.876	1.77e-64	197	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2562617076_000006\|2562617076\|2562916525	95.876	7.53e-64	196	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2563367061_000009\|2563367061\|2565312821	94.845	4.25e-64	197	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2568526051_000005\|2568526051\|2568734086	97.938	1.27e-65	201	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2571042321_000004\|2571042321\|2572119373	92.784	1.09e-62	193	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2571042474_000005\|2571042474\|2572653972	94.845	4.71e-63	194	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2579778613_000007\|2579778613\|2580252917	93.814	1.80e-61	190	100%		Escherichia coli	IMGVR	PF11043	phrog_656
IMGVR_UViG_2600255161_000002\|2600255161\|2601131084	96.907	3.27e-64	197	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2600255197_000002\|2600255197\|2601297917	94.845	6.72e-62	191	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2630968702_000010\|2630968702\|2632897043	92.784	6.84e-63	194	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2636415526_000004\|2636415526\|2636931379	94.845	2.72e-63	194	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2636415722_000006\|2636415722\|2637731720	94.845	1.23e-63	196	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2639762794_000001\|2639762794\|2640741481	94.845	2.85e-62	192	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2654587610_000002\|2654587610\|2655066076	95.876	6.11e-64	196	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2657244928_000007\|2657244928\|2657412357	96.907	3.53e-64	197	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2657245436_000003\|2657245436\|2658969070	92.784	1.92e-62	192	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2663763153_000010\|2663763153\|2665861020	93.814	4.51e-63	194	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2684622651_000004\|2684622651\|2685238307	94.845	1.65e-62	192	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2711768112_000006\|2711768112\|2712316136	95.876	2.43e-64	197	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2731957936_000005\|2731957936\|2733836628	92.784	9.94e-63	193	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2737471863_000004\|2737471863\|2738099920	93.814	1.26e-61	190	100%		Escherichia coli	IMGVR	PF11043	phrog_656
IMGVR_UViG_2740892417_000006\|2740892417\|2743350916	93.814	1.72e-63	195	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2744054625_000009\|2744054625\|2745029640	94.845	1.23e-63	196	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2744054867_000002\|2744054867\|2745935876	92.784	1.72e-62	192	100%		Salmonella enterica	IMGVR	PF11043	phrog_656
IMGVR_UViG_2778261630_000006\|2778261630\|2780794918	93.814	4.78e-62	191	100%		Escherichia coli	IMGVR	PF11043	phrog_656
IMGVR_UViG_641228505_000002\|641228505\|641305831	97.938	6.16e-65	199	100%		Salmonella arizonae	IMGVR	PF11043	phrog_656
ivig_4422_8	93.814	1.19e-61	191	100%		Escherichia coli	GPD	PF11043	phrog_656
JQ086372_00028	93.814	1.82e-61	190	100%	Escherichia phage HK446	Escherichia	INPHARED	PF11043	phrog_656
JQ806763_00037	94.845	7.87e-64	196	100%	Salmonella phage vB_SemP_Emek	Salmonella	INPHARED	PF11043	phrog_656
JQ806764_00041	92.784	1.14e-61	191	100%	Salmonella phage vB_SosS_Oslo	Salmonella	INPHARED	PF11043	phrog_656
KU927498_00032	96.907	8.10e-65	198	100%	Salmonella phage 64795_sal4	Salmonella	INPHARED	PF11043	phrog_656
KX776161_00063	91.753	2.85e-62	192	100%	Salmonella phage UPF_BP1	Salmonella	INPHARED	PF11043	phrog_656
KY709687_00033	95.876	6.04e-64	196	100%	Salmonella phage 29485	Salmonella	INPHARED	PF11043	phrog_656
LC645441_00006	93.814	1.19e-61	191	100%	Stx2a-converting phage Stx2_EH2085		INPHARED	PF11043	phrog_656
MGV-GENOME-0189209_43	93.814	1.61e-61	190	100%		Escherichia	MGV	PF11043	phrog_656
MGV-GENOME-0264182_6	94.845	1.76e-62	192	100%		Escherichia	MGV	PF11043	phrog_656
MGV-GENOME-0279163_46	93.814	1.23e-61	191	100%		Escherichia	MGV	PF11043	phrog_656
MH370364_00049	94.845	2.55e-63	195	100%	Salmonella phage S107	Salmonella	INPHARED	PF11043	phrog_656
MK972694_00062	95.876	3.24e-63	194	100%	Salmonella phage SE22	Salmonella	INPHARED	PF11043	phrog_656
NP_059594.1	100.000	6.02e-73	202	100%	Salmonella phage P22	Salmonella	NCBI	PF11043	phrog_656
OP265889_00040	95.876	4.21e-64	197	100%	Salmonella phage P6	Salmonella	INPHARED	PF11043	phrog_656
uvig_127144_9	93.814	3.22e-62	192	100%			GPD	PF11043	phrog_656
uvig_203138_29	93.814	1.56e-61	190	100%			GPD	PF11043	phrog_656
uvig_316968_55	93.814	1.02e-61	191	100%			GPD	PF11043	phrog_656
uvig_320512_27	94.845	1.70e-62	192	100%			GPD	PF11043	phrog_656

APIS	Contig	Range
APIS020	NC_002371.2	25964 - 25967

Seed protein information help

Seed genomic context Download table help

Seed genomic context- JBrowse

PDB structure: 8B1T ; 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 help

Clan ID: CLAN019

Family members, sources, and their hosts help

Results of representative protein blast against members.

Gene cluster comparison plot by clinker Download html