dbAPIS: a database of anti-prokaryotic immune systems

Seed protein information help

APIS family ID

APIS105

Inhibited defense system

CLAN ID

CLAN039

Seed protein property

Accession ID	Gene name	Protein length	Molecular weight	Isoelectric point	Charge
MN988543_00081	gene_page:	411	45524.92	6.5704	0.5

Phage property

Phage	Assembly id
	MN988543

PMID/References

PDB structures

;

Pfam domains

PF07728.19,PF08406.15,PF07728.19,PF08406.15

Phrog

phrog_249,phrog_249

Host taxa

d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Hyphomicrobiales;f__Rhizobiaceae;g__Rhizobium;s__unclassified Rhizobium species

Gene Location

Start: 65262; End: 66497; 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 APIS166 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
MN988543	59934	61037	-	MN988543_00076	367	41118.65	6.5	8.8613	replication protein	phrog_391 ; phrog_22671	PF03428.18 ;PF11800.13 ;PF13730.11
MN988543	61211	61417	-	MN988543_00077	68	7436.26	0.5	7.0114	hypothetical protein
MN988543	61810	62214	+	MN988543_00078	134	15000.24	2.0	8.0296	hypothetical protein
MN988543	62333	62563	+	MN988543_00079	76	8494.67	-3.0	4.8979	hypothetical protein
MN988543	62606	65149	+	MN988543_00080	847	92940.90	-111.0	3.9879	hypothetical protein	phrog_26570 ; phrog_1576	PF11775.13 ;PF05762.19
MN988543	65262	66497	+	MN988543_00081	411	45524.92	0.5	6.5704	porphyrin biosynthesis	phrog_249 ; phrog_249	PF07728.19 ;PF08406.15 ;PF07728.19 ;PF08406.15
MN988543	66494	67129	+	MN988543_00082	211	24081.74	2.0	7.3613	RNA polymerase sigma factor		PF04542.19
MN988543	67126	67656	+	MN988543_00083	176	19042.17	11.0	10.0827	hypothetical protein	phrog_3616
MN988543	67656	67850	+	MN988543_00084	64	7153.20	2.0	7.3208	hypothetical protein
MN988543	67850	68086	+	MN988543_00085	78	8780.00	0.5	6.6407	hypothetical protein
MN988543	68086	71493	+	MN988543_00086	1135	126390.66	-2.5	6.3644	DNA polymerase III subunit alpha	phrog_405 ; phrog_21652	PF07733.17 ;PF17657.6 ;PF02811.24 ;PF14579.11 ;PF03167.24

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-A0A0H3H502-F1-model_v4	80	411	1	281	0.9715	0.8156
AF-Q2G2J8-F1-model_v4	123	410	1	263	0.9301	0.7588
AF-Q51481-F1-model_v4	119	411	1	260	0.9216	0.7477
AF-X8F327-F1-model_v4	76	411	2	289	0.7994	0.6731
AF-P71922-F1-model_v4	76	411	4	291	0.7963	0.6723
AF-K0EW51-F1-model_v4	75	411	5	294	0.7899	0.6701
AF-O53705-F1-model_v4	81	411	1	294	0.7842	0.67
AF-K0FAA2-F1-model_v4	78	411	1	288	0.7851	0.6656
AF-Q9I0D5-F1-model_v4	83	404	1	274	0.7781	0.6479
AF-P33348-F1-model_v4	77	411	33	355	0.6884	0.6382

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

Hit	Query start	Query end	Hit start	Hit end	TMscore(ali)	TMscore(avg)
MGYP000353374853.pdb	60	411	7	328	0.9389	0.8409
MGYP000610236305.pdb	81	411	1	318	0.9458	0.8354
MGYP000487978036.pdb	69	411	1	318	0.9183	0.8126
MGYP001467461195.pdb	73	411	1	322	0.9118	0.8115
MGYP000487869468.pdb	78	411	1	318	0.9143	0.8112
MGYP002646372076.pdb	80	411	2	322	0.907	0.8103
MGYP001389673498.pdb	63	411	1	325	0.9037	0.8102
MGYP000704697880.pdb	72	411	1	319	0.9123	0.8102
MGYP000467473224.pdb	78	411	1	318	0.9125	0.8095
MGYP001281949795.pdb	73	411	1	318	0.912	0.8088

Family information Download help

Fam ID	Seed protein	Member count	Model	Alignment
APIS105	MN988543_00081	37	HMM model	Member alignment

Host Taxa distribution

Length distribution

Homology to other families help

Clan ID: CLAN039

APIS105 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_3300037258_000313\|3300037258\|Ga0376646_0012491_11718_12860	51.100	2.456E-120	388	0.988%			IMGVR	PF07728 PF08406	phrog_249
IMGVR_UViG_3300002542_000198\|3300002542\|JGI25328J35697_10010683	52.700	2.491E-126	405	0.993%		Rhizobiales	IMGVR	PF07728 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300025529_000146\|3300025529\|Ga0207865_1029202	52.700	2.491E-126	405	0.993%		Rhizobiales	IMGVR	PF07728 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300017649_000001\|3300017649\|Ga0182741_100014817	46.400	1.526E-107	351	0.995%			IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_3300005281_000202\|3300005281\|Ga0065720_100358013	52.600	3.409E-126	405	0.993%		Rhizobiales	IMGVR	PF07728 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300002042_000001\|3300002042\|LBB12012_10000057143	41.700	7.475E-88	293	0.973%			IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_3300046507_000489\|3300046507\|Ga0495606_0000871_14605_15804	73.600	1.861E-197	611	0.998%			IMGVR	PF07728	phrog_30335 phrog_249
IMGVR_UViG_2671180612_000001\|2671180612\|2673478899	53.100	8.778E-129	412	1.000%		Aureimonas sp001442755	IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_2751185817_000001\|2751185817\|2753435482	88.000	2.828E-246	752	0.998%		Ensifer sp001695855	IMGVR	PF07728 PF08406	phrog_249
IMGVR_UViG_3300048856_000029\|3300048856\|Ga0496066_000420_38155_39426	77.000	1.399E-210	649	0.995%			IMGVR	PF07728 PF08406	phrog_249
MN988543_00081	100.000	4.659E-277	841	1.000%	Rhizobium phage RHph_N2_6	Rhizobium	INPHARED	PF07728 PF08406 PF07728 PF08406	phrog_249 phrog_249
IMGVR_UViG_3300012794_000008\|3300012794\|Ga0160493_10028520	52.600	1.471E-124	400	0.981%			IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_3300037423_002313\|3300037423\|Ga0395907_0003220_7148_8359	45.000	1.597E-99	327	0.983%			IMGVR	PF07728 PF07726 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300037312_001329\|3300037312\|Ga0395899_0000135_94769_95968	41.300	1.395E-87	293	0.985%			IMGVR	PF07728 PF05443 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300028588_000076\|3300028588\|Ga0265780_100020515	44.200	8.307E-97	319	0.983%			IMGVR	PF07728 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300048914_000231\|3300048914\|Ga0496111_0000005_21366_22568	40.600	2.055E-85	286	0.985%			IMGVR	PF07728 PF05443 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300017553_000003\|3300017553\|Ga0182744_10001079	44.500	8.307E-97	319	0.973%			IMGVR	PF07728 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300033142_001075\|3300033142\|Ga0366826_100001043	44.500	4.981E-98	323	0.983%			IMGVR	PF07728 PF08406	phrog_30335 phrog_249
uvig_342642_10	42.200	9.453E-90	299	0.978%			GPD	PF07728 PF08406	phrog_30335 phrog_249
MGV-GENOME-0340637_29	42.200	9.453E-90	299	0.978%			MGV	PF07728 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300019124_000003\|3300019124\|Ga0193592_1000107103	51.900	2.013E-124	400	0.998%			IMGVR	PF07728 PF08406	phrog_30335 phrog_249
IMGVR_UViG_2565956984_000003\|2565956984\|2567878516	41.800	3.705E-90	300	0.993%		Acinetobacter baumannii	IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_3300012075_000001\|3300012075\|Ga0153917_100007620	41.100	1.395E-87	293	0.993%			IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_3300012079_000001\|3300012079\|Ga0153918_100005030	41.100	2.807E-85	286	0.968%			IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_2531839636_000005\|2531839636\|2534277668	43.500	1.537E-80	272	0.852%		Acinetobacter baumannii	IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_2645727582_000005\|2645727582\|2646091864	41.800	3.705E-90	300	0.993%		Acinetobacter baumannii	IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_2505119019_000001\|2505119019\|2505193897	41.700	9.453E-90	299	0.993%		Acinetobacter baumannii	IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_2565957004_000004\|2565957004\|2567958375	43.500	1.537E-80	272	0.852%		Acinetobacter baumannii	IMGVR	PF07728 PF08406 PF07726	phrog_30335 phrog_249
IMGVR_UViG_3300016664_000173\|3300016664\|Ga0186811_10273321	41.500	1.395E-87	293	0.978%			IMGVR	PF07728 PF07726	phrog_30335 phrog_249
IMGVR_UViG_3300037313_000659\|3300037313\|Ga0395908_0000226_33039_34253	42.900	1.832E-92	307	0.981%			IMGVR	PF07728 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300028603_001620\|3300028603\|Ga0265293_1000223121	41.100	3.161E-86	289	0.978%			IMGVR	PF07728 PF08406 PF07726 PF00437	phrog_30335 phrog_249
IMGVR_UViG_3300046557_000512\|3300046557\|Ga0495622_0000093_14699_15973	39.600	1.271E-81	275	0.973%			IMGVR	PF07728	phrog_30335
IMGVR_UViG_3300034069_000130\|3300034069\|Ga0370205_000460_9083_10024	43.300	7.906E-66	229	0.720%			IMGVR	PF07728 PF13191 PF00004 PF07726	phrog_249
IMGVR_UViG_3300029818_000001\|3300029818\|Ga0246095_10020363	46.100	7.824E-102	334	0.971%			IMGVR	PF07728 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300002242_002192\|3300002242\|KVWGV2_1032770115	42.100	1.149E-88	296	0.968%			IMGVR	PF07728 PF08406	phrog_30335 phrog_249
IMGVR_UViG_3300049846_002076\|3300049846\|Ga0499941_000028_5854_7050	47.300	1.367E-106	348	0.978%			IMGVR	PF07728 PF08406	phrog_249
IMGVR_UViG_3300034072_000578\|3300034072\|Ga0310127_000210_6963_7904	41.200	7.558E-68	235	0.791%			IMGVR	PF07728	phrog_249