dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS138

Inhibited defense system

CLAN ID

CLAN057

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
JN882284_00173	gene_page:	270	29465.77	5.9792	-3.0

Phage property

Phage	Assembly id
	JN882284

PMID/References

PDB structures

;

Pfam domains

PF00156.32,PF14572.11,PF13793.11,PF00156.32,PF14572.11,PF13793.11

Phrog

phrog_619,phrog_619

Host taxa

d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter;s__unclassified Cronobacter species

Gene Location

Start: 79935; End: 80747; Strand: +

Description

Note

This family does not have seed protein, but we infer its function is defending NAD+ reconstitution pathway (NARP) because it belongs to the same clan as family APIS160 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
JN882284	78089	78328	-	JN882284_00168	79	9369.92	7.0	10.5587	hypothetical protein	phrog_17653
JN882284	78325	78609	-	JN882284_00169	94	11109.92	4.5	9.7809	hypothetical protein	phrog_6208
JN882284	78606	78881	-	JN882284_00170	91	10675.35	1.5	7.2391	hypothetical protein	phrog_7684
JN882284	78993	79337	-	JN882284_00171	114	13130.03	2.0	7.7498	hypothetical protein	phrog_4868
JN882284	79616	79933	+	JN882284_00172	105	12236.95	8.0	9.5243	replication initiation protein	phrog_8102	PF22182.1 ;PF09339.15
JN882284	79935	80747	+	JN882284_00173	270	29465.77	-3.0	5.9792	Ribose-phosphate pyrophosphokinase	phrog_619 ; phrog_619	PF00156.32 ;PF14572.11 ;PF13793.11 ;PF00156.32 ;PF14572.11 ;PF13793.11
JN882284	80747	81280	+	JN882284_00174	177	20219.65	-10.0	4.4858	hypothetical protein	phrog_23621
JN882284	81334	83037	+	JN882284_00175	567	64331.11	-11.5	5.2130	nicotinamide phosphoribosyl transferase	phrog_15800 ; phrog_12872 ; phrog_448 ; phrog_16547	PF04095.21
JN882284	83182	83397	+	JN882284_00176	71	7860.95	-4.5	4.5777	hypothetical protein	phrog_23579 ; phrog_12146
JN882284	83390	83599	+	JN882284_00177	69	7895.75	-6.0	4.3875	hypothetical protein	phrog_5724 ; phrog_1359 ; phrog_15229 ; phrog_4586
JN882284	83679	83924	+	JN882284_00178	81	9258.25	-6.0	4.4763	hypothetical protein	phrog_38874 ; phrog_5676

Seed genomic context- JBrowse

Predicted 3D structure by alphafold2 with pTM = 0.88 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-Q58761-F1-model_v4	1	268	7	270	0.8387	0.8018
AF-Q9HVC5-F1-model_v4	1	270	10	280	0.842	0.77
AF-I1KY16-F1-model_v4	1	270	17	298	0.8449	0.7666
AF-Q9PP15-F1-model_v4	1	269	10	277	0.8339	0.766
AF-Q2G0S2-F1-model_v4	1	270	17	289	0.8467	0.766
AF-K0FCQ4-F1-model_v4	1	270	18	291	0.8513	0.7654
AF-I1N0W9-F1-model_v4	1	270	17	298	0.8433	0.765
AF-P65240-F1-model_v4	1	270	12	285	0.8455	0.7633
AF-Q6ZFT5-F1-model_v4	1	270	21	303	0.8451	0.7614
AF-P56184-F1-model_v4	1	269	19	286	0.8382	0.7612

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP002795671682.pdb	1	269	1	268	0.9537	0.9426
MGYP000566046755.pdb	2	270	1	266	0.9266	0.9084
MGYP000548379464.pdb	3	268	1	257	0.9413	0.9075
MGYP001593485562.pdb	1	269	2	270	0.921	0.8927
MGYP000845279644.pdb	3	270	1	269	0.9166	0.892
MGYP000364272986.pdb	1	269	2	270	0.9087	0.8852
MGYP001553664353.pdb	1	270	1	269	0.9169	0.885
MGYP002537967899.pdb	1	269	3	269	0.9169	0.8815
MGYP001255384670.pdb	1	270	2	267	0.9229	0.8811
MGYP000334889950.pdb	3	269	1	271	0.912	0.8797

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS138	JN882284_00173	21	HMM model	Member alignment

Host Taxa distribution

Length distribution

Homology to other families help

Clan ID: CLAN057

APIS138 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_3300029922_000003\|3300029922\|Ga0311363_1000006153	43.200	5.402E-60	206	0.974%			IMGVR	PF00156 PF14572	phrog_619
IMGVR_UViG_3300005573_000052\|3300005573\|Ga0078972_100038892	45.300	1.011E-59	205	0.919%			IMGVR	PF14572 PF13793 PF00156	phrog_619
IMGVR_UViG_3300045919_000631\|3300045919\|Ga0485834_0000010_7162_8040	44.800	1.383E-59	205	0.933%			IMGVR	PF00156 PF14572 PF13793	phrog_619
IMGVR_UViG_3300038548_000082\|3300038548\|Ga0392322_0000001_89024_89830	44.700	1.128E-60	208	0.952%			IMGVR	PF13793 PF00156 PF14572	phrog_619
IMGVR_UViG_3300034171_000021\|3300034171\|Ga0314773_001424_8417_9271	39.700	5.468E-49	174	0.933%			IMGVR	PF14572 PF00156 PF13793	phrog_619
IMGVR_UViG_3300005330_000014\|3300005330\|Ga0070690_100000001206	39.100	3.026E-52	183	0.993%			IMGVR	PF14572 PF13793 PF00156	phrog_619
KX452695_00096	83.100	1.254E-149	465	1.000%	Klebsiella phage KNP2	Klebsiella	INPHARED	PF00156 PF14572 PF13793	phrog_619
JN882284_00173	100.000	2.716E-180	553	1.000%	Cronobacter phage vB_CsaM_GAP31	Cronobacter	INPHARED	PF00156 PF14572 PF13793 PF00156 PF14572 PF13793	phrog_619 phrog_619
OP819284_00109	83.100	1.254E-149	465	1.000%	Cronobacter phage EspYZU12	Cronobacter	INPHARED	PF00156 PF14572 PF13793	phrog_619
MZ311864_00097	96.600	1.800E-179	551	1.000%	Escherichia phage vB_EcoM_LNA4	Escherichia	INPHARED	PF00156 PF14572 PF13793	phrog_619
KF550303_00114	85.500	5.756E-155	480	1.000%	Escherichia phage 4MG	Escherichia	INPHARED	PF00156 PF14572 PF13793	phrog_619
IMGVR_UViG_3300026472_000003\|3300026472\|Ga0256410_1000091232	76.300	1.011E-137	430	0.996%			IMGVR	PF00156 PF14572 PF13793	phrog_619
IMGVR_UViG_3300011114_000773\|3300011114\|Ga0151515_1000337	42.500	2.480E-53	186	0.911%			IMGVR	PF00156 PF14572	phrog_619
IMGVR_UViG_3300024999_000001\|3300024999\|Ga0209728_100004224	44.300	1.239E-58	202	0.933%			IMGVR	PF13793 PF00156 PF14572	phrog_619
IMGVR_UViG_3300001041_000001\|3300001041\|C687J13239_1000017119	44.300	1.239E-58	202	0.933%			IMGVR	PF13793 PF00156 PF14572	phrog_619
IMGVR_UViG_3300020047_010159\|3300020047\|Ga0206650_100083444	39.500	3.561E-48	171	0.926%			IMGVR	PF13793 PF00156	phrog_619
IMGVR_UViG_3300036944_001289\|3300036944\|Ga0377190_000032_14167_15033	43.400	1.857E-56	196	0.926%			IMGVR	PF14572 PF00156 PF13793	phrog_619
IMGVR_UViG_3300029826_000005\|3300029826\|Ga0134619_100004957	48.300	4.991E-68	229	0.948%			IMGVR	PF13793 PF00156 PF14572	phrog_619
IMGVR_UViG_3300016771_000001\|3300016771\|Ga0182082_101116249	45.400	4.455E-64	218	0.978%			IMGVR	PF13793 PF00156 PF14572	phrog_619
IMGVR_UViG_3300037575_000021\|3300037575\|Ga0394428_000074_41321_42130	44.600	1.917E-62	213	0.978%			IMGVR	PF13793 PF00156 PF14572	phrog_619
IMGVR_UViG_3300018421_000001\|3300018421\|Ga0181592_1000001540	46.300	3.589E-62	212	0.926%			IMGVR	PF13793 PF00156 PF14572	phrog_619