dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS039

Inhibited defense system

CLAN ID

CLAN003

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
IMGVR_UViG_2751185776_000007\|2751185776\|2753238834	gene_page:	141	16050.8	3.9947	-12.5

Phage property

Phage	Assembly id
	IMGVR_UViG_2751185776_000007

PMID/References

PDB structures

;

Pfam domains

PF03230.16

Phrog

phrog_10132

Host taxa

d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella;s__Morganella psychrotolerans_B

Gene Location

Start: 10487; End: 10912; Strand: -

Description

Note

This family does not have seed protein, but we infer its function is defending restriction-modification (RM) because it belongs to the same clan as family APIS007,ArdB 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
IMGVR_UViG_2751185776_000007	6914	7336	-	IMGVR_UViG_2751185776_000007\|2751185776\|2753238829	140	15209.04	-9.5	4.2611	hypothetical protein
IMGVR_UViG_2751185776_000007	7431	7916	-	IMGVR_UViG_2751185776_000007\|2751185776\|2753238830	161	17967.29	13.5	10.1417	hypothetical protein
IMGVR_UViG_2751185776_000007	8073	8540	-	IMGVR_UViG_2751185776_000007\|2751185776\|2753238831	155	17383.10	6.0	9.6596	hypothetical protein
IMGVR_UViG_2751185776_000007	8718	9425	-	IMGVR_UViG_2751185776_000007\|2751185776\|2753238832	235	27363.89	15.5	10.0618	predicted DNA-binding transcriptional regulator YafY	phrog_13105	PF13280.9
IMGVR_UViG_2751185776_000007	9637	10473	-	IMGVR_UViG_2751185776_000007\|2751185776\|2753238833	278	31760.34	12.0	9.9993	uncharacterized protein DUF932	phrog_12094	PF06067.14
IMGVR_UViG_2751185776_000007	10487	10912	-	IMGVR_UViG_2751185776_000007\|2751185776\|2753238834	141	16050.82	-12.5	3.9947	antirestriction protein	phrog_10132	PF03230.16
IMGVR_UViG_2751185776_000007	11004	11876	-	IMGVR_UViG_2751185776_000007\|2751185776\|2753238835	290	32663.10	-2.5	5.8864	hypothetical protein	phrog_11431 ; phrog_16468	PF01926.26
IMGVR_UViG_2751185776_000007	11938	12870	-	IMGVR_UViG_2751185776_000007\|2751185776\|2753238836	310	36472.83	8.5	9.2282	hypothetical protein
IMGVR_UViG_2751185776_000007	13307	13885	+	IMGVR_UViG_2751185776_000007\|2751185776\|2753238837	192	22808.02	15.5	9.9478	uncharacterized protein DUF3296	phrog_25019	PF11726.11
IMGVR_UViG_2751185776_000007	13991	14200	+	IMGVR_UViG_2751185776_000007\|2751185776\|2753238838	69	8143.46	2.0	9.8652	AlpA family transcriptional regulator	phrog_9834 ; phrog_66 ; phrog_2790	PF05930.15
IMGVR_UViG_2751185776_000007	14562	15002	-	IMGVR_UViG_2751185776_000007\|2751185776\|2753238839	146	16592.06	-6.5	4.3904	arsenate reductase	phrog_16693	PF03960.18

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

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
AF-P75676-F1-model_v4	1	141	10	152	0.9559	0.9109
AF-P52139-F1-model_v4	1	141	9	152	0.9532	0.909
AF-A0A0H3GW18-F1-model_v4	1	141	1	141	0.9167	0.8995
AF-Q327Q6-F1-model_v4	2	141	15	157	0.9473	0.8897
AF-Q32HM6-F1-model_v4	1	141	38	181	0.951	0.8384
AF-Q93GQ0-F1-model_v4	7	141	7	144	0.8636	0.838
AF-A0A0H3GVF3-F1-model_v4	6	141	1	132	0.882	0.8309
AF-A0A077ZNG7-F1-model_v4	12	141	9	141	0.8676	0.829
AF-A0A0H3GZ47-F1-model_v4	2	141	35	221	0.8463	0.686

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP000479619222.pdb	3	141	1	141	0.9517	0.9427
MGYP000901984350.pdb	2	141	1	138	0.9621	0.9411
MGYP000931080388.pdb	1	141	6	146	0.9653	0.9383
MGYP003365227403.pdb	1	141	3	143	0.951	0.9311
MGYP001992189960.pdb	5	141	1	134	0.9624	0.9271
MGYP001201501853.pdb	5	141	1	134	0.9598	0.9243
MGYP001037997637.pdb	3	141	1	135	0.9571	0.9242
MGYP000589756821.pdb	1	141	6	149	0.9606	0.9238
MGYP001120502683.pdb	6	141	1	133	0.9599	0.9212
MGYP001805956192.pdb	1	141	6	147	0.9529	0.9208

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS039	IMGVR_UViG_2751185776_000007\|2751185776\|2753238834	49	HMM model	Member alignment

Host Taxa distribution

Length distribution

Homology to other families download full data without filtering help

Clan ID: CLAN003

Hit APIS family	E-Value	Query Start	Query End	Hit Start	Hit End	Immune system	Seed protein
APIS007	9.89E-74	2	141	14	151	restriction-modification (RM)	BAF33451.1
APIS069	1.27E-25	6	141	6	144		IMGVR_UViG_3300036792_000137\|3300036792\|Ga0376663_0000427_343_774
APIS038	1.91E-25	4	141	8	150		IMGVR_UViG_2576861805_000002\|2576861805\|2579667884
APIS055	4.85E-21	2	141	2	142		OL763419_00042
APIS037	1.52E-16	10	141	7	141		IMGVR_UViG_2541047688_000003\|2541047688\|2543982737

Family members, sources, and their hosts help

Results of representative protein blast against members.
Member	pident	evalue	bitscore	qcovs	host	SourceDB	Pfam	Phrog
IMGVR_UViG_2511231170_000001\|2511231170\|2511870096	47.020	2.78e-35	129	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2529292882_000013\|2529292882\|2530356395	47.552	6.08e-37	132	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2529293076_000023\|2529293076\|2531131775	50.382	4.14e-36	130	91%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2534682236_000019\|2534682236\|2537093308	48.201	2.85e-37	133	96%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2534682325_000015\|2534682325\|2537385693	49.265	5.79e-37	132	94%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2537562092_000001\|2537562092\|2539773385	46.853	2.70e-36	130	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2541047498_000018\|2541047498\|2543234824	48.889	6.65e-36	129	94%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2541047684_000005\|2541047684\|2543962383	47.682	6.57e-37	132	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2541047721_000001\|2541047721\|2544145901	47.020	1.95e-35	128	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2541047742_000006\|2541047742\|2544253806	48.344	1.15e-39	139	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2541047802_000015\|2541047802\|2544556426	50.382	4.21e-36	130	91%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2541047851_000005\|2541047851\|2544797335	46.358	4.49e-34	125	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2541047893_000009\|2541047893\|2545003977	46.154	2.64e-35	128	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2547132277_000010\|2547132277\|2548114485	49.265	5.99e-37	132	94%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2547132398_000002\|2547132398\|2548602399	51.064	2.28e-43	148	99%	Cronobacter sakazakii	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2548876858_000014\|2548876858\|2550148890	48.529	2.34e-36	130	94%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2562617085_000012\|2562617085\|2562934603	48.529	1.63e-36	131	94%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2563366805_000004\|2563366805\|2564130911	55.319	9.16e-46	154	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2565956581_000001\|2565956581\|2566253699	51.799	4.63e-43	147	99%	Yersinia similis	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2571042794_000002\|2571042794\|2573734993	48.936	4.67e-39	137	99%	Enterobacter hormaechei	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2579778730_000001\|2579778730\|2580747249	50.355	1.82e-41	143	99%	Siccibacter colletis	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2579778842_000011\|2579778842\|2581214126	45.833	9.68e-36	129	100%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2627854164_000002\|2627854164\|2630474902	49.645	9.88e-42	144	99%	Citrobacter_A amalonaticus_C	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2636416160_000022\|2636416160\|2639573815	46.617	3.79e-36	130	94%	Yersinia pestis	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2639763134_000006\|2639763134\|2642124910	47.552	4.50e-39	137	99%	Salmonella enterica	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2671180458_000011\|2671180458\|2672855773	48.252	1.07e-39	139	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2690316149_000015\|2690316149\|2692446076	46.479	4.49e-37	132	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2718218402_000003\|2718218402\|2721315463	48.951	2.42e-40	140	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2721755658_000005\|2721755658\|2723459047	51.064	6.15e-44	149	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2721755711_000001\|2721755711\|2723685156	52.672	1.50e-39	139	91%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2721755725_000016\|2721755725\|2723748035	48.252	1.14e-39	139	99%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2744054944_000002\|2744054944\|2746270176	93.617	6.84e-97	283	100%	Providencia rettgeri_A	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2751185776_000007\|2751185776\|2753238834	100.000	2.02e-102	297	100%	Morganella psychrotolerans_B	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2751185922_000002\|2751185922\|2753877244	50.355	3.11e-41	143	93%	Enterobacter chengduensis	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2802429241_000010\|2802429241\|2804655210	51.773	6.31e-42	144	93%	Escherichia marmotae	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2802429245_000006\|2802429245\|2804670716	49.007	2.00e-40	141	96%	Escherichia marmotae	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2872185964_000007\|2872185964\|2872187687	50.000	5.16e-40	139	100%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2874927903_000002\|2874927903\|2874928327	50.000	4.94e-40	140	86%	Escherichia coli	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2878868365_000004\|2878868365\|2878870336	50.355	9.87e-42	144	93%	Citrobacter braakii	IMGVR	PF03230	phrog_10132
IMGVR_UViG_2922317101_000007\|2922317101\|2922321092	50.355	1.33e-41	144	93%	Citrobacter braakii	IMGVR	PF03230	phrog_10132
IMGVR_UViG_3300011617_000014\|3300011617\|Ga0120835_1000499	51.064	2.35e-43	148	99%	Enterobacteriaceae	IMGVR	PF03230	phrog_10132
IMGVR_UViG_3300011754_000012\|3300011754\|Ga0122284_10010317	47.143	1.76e-37	133	99%	Serratia	IMGVR	PF03230	phrog_10132
IMGVR_UViG_3300011875_000025\|3300011875\|Ga0121110_10002051	50.355	1.06e-41	144	99%	Enterobacter	IMGVR	PF03230	phrog_10132
IMGVR_UViG_3300017814_000038\|3300017814\|Ga0183095_107935	53.901	1.18e-44	151	99%	Enterobacteriaceae	IMGVR	PF03230	phrog_10132
IMGVR_UViG_651053023_000006\|651053023\|651239028	48.951	2.12e-40	141	89%	Escherichia	IMGVR	PF03230	phrog_10132
MGV-GENOME-0167262_5	50.355	5.65e-42	144	99%	Escherichia	MGV	PF03230	phrog_10132
MGV-GENOME-0272743_7	50.355	1.05e-41	144	99%	Escherichia	MGV	PF03230	phrog_10132
uvig_327479_5	50.355	1.02e-41	144	99%		GPD	PF03230	phrog_10132
uvig_577415_2	50.355	1.03e-41	144	99%		GPD	PF03230	phrog_10132