The following contents displays predicted prophage regions
first line of each prophage describes the prophage information and the following lines describe the proteins and homology proteins in uniprot database
bacteria_id bac_def genome_size prophage_start  prophage_end    key_proteins    best_hit_species    CDS_number  attl_region attr_region
>prophage 1
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	266834	331120	4586233	tRNA,transposase,protease	Paramecium_bursaria_Chlorella_virus(20.0%)	46	NA	NA
AZG49243.1|266834_268355_+|protease	ATP-dependent protease	protease	NA	NA	NA	NA
AZG49244.1|268379_268718_-	DUF413 domain-containing protein	NA	NA	NA	NA	NA
AZG49245.1|268836_269676_+	transcriptional regulator	NA	NA	NA	NA	NA
AZG49246.1|275476_276169_+	FadR family transcriptional regulator	NA	NA	NA	NA	NA
AZG49247.1|276191_277619_+	DHA2 family efflux MFS transporter permease subunit	NA	NA	NA	NA	NA
AZG49248.1|277584_278577_-	ribose operon repressor	NA	NA	NA	NA	NA
AZG52773.1|278580_279510_-	ribokinase	NA	NA	NA	NA	NA
AZG49249.1|280550_281516_-	ribose ABC transporter permease	NA	NA	NA	NA	NA
AZG49250.1|283445_283802_-	ATP-binding cassette domain-containing protein	NA	G3M9Y6	Bacillus_virus	29.2	5.0e-05
AZG52774.1|283809_284229_-	D-ribose pyranase	NA	NA	NA	NA	NA
AZG49251.1|284395_286264_-	low affinity potassium transporter Kup	NA	M1I6H8	Paramecium_bursaria_Chlorella_virus	30.3	8.7e-64
AZG49252.1|286421_287750_-|transposase	IS4 family transposase	transposase	NA	NA	NA	NA
AZG49253.1|287870_289700_-	glutamine--fructose-6-phosphate aminotransferase	NA	A7IW18	Paramecium_bursaria_Chlorella_virus	43.2	5.6e-132
AZG49254.1|289861_291232_-	bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase	NA	A0A0N7G7I9	Chrysochromulina_ericina_virus	36.7	3.1e-34
AZG49255.1|291582_292002_-	ATP synthase epsilon chain	NA	NA	NA	NA	NA
AZG49256.1|292022_293405_-	F0F1 ATP synthase subunit beta	NA	NA	NA	NA	NA
AZG49257.1|293431_294295_-	ATP synthase subunit gamma	NA	NA	NA	NA	NA
AZG49258.1|294345_295887_-	F0F1 ATP synthase subunit alpha	NA	NA	NA	NA	NA
AZG49259.1|295899_296433_-	ATP synthase subunit delta	NA	NA	NA	NA	NA
AZG49260.1|296447_296918_-	ATP synthase subunit B	NA	NA	NA	NA	NA
AZG49261.1|296979_297219_-	ATP synthase subunit C	NA	NA	NA	NA	NA
AZG49262.1|297265_298081_-	F0F1 ATP synthase subunit A	NA	NA	NA	NA	NA
AZG49263.1|298089_298470_-	ATP synthase I	NA	NA	NA	NA	NA
AZG49264.1|299086_299710_-	ribosomal RNA small subunit methyltransferase G	NA	NA	NA	NA	NA
AZG49265.1|299773_301663_-|tRNA	tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG	tRNA	NA	NA	NA	NA
AZG49266.1|302041_302485_-	FMN-binding protein MioC	NA	NA	NA	NA	NA
AZG49267.1|302574_303033_-	AsnC family transcriptional regulator	NA	NA	NA	NA	NA
AZG49268.1|303184_304177_+	aspartate--ammonia ligase	NA	A0A1C9C5F0	Heterosigma_akashiwo_virus	38.0	3.4e-51
AZG49269.1|304181_305633_-	protein viaA	NA	NA	NA	NA	NA
AZG49270.1|305626_307123_-	ATPase RavA	NA	NA	NA	NA	NA
AZG49271.1|307296_308625_+|transposase	IS4 family transposase	transposase	NA	NA	NA	NA
AZG49272.1|308916_309489_+	fimbrial protein	NA	NA	NA	NA	NA
AZG49273.1|310254_311528_-|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	98.7	1.5e-176
AZG49274.1|315780_316821_+	phosphate-binding protein	NA	A0A1D7SRJ6	Cyanophage	38.3	2.7e-51
AZG49275.1|316907_317867_+	phosphate ABC transporter permease	NA	NA	NA	NA	NA
AZG49276.1|317866_318757_+	phosphate ABC transporter permease PstA	NA	NA	NA	NA	NA
AZG49277.1|318848_319622_+	phosphate ABC transporter ATP-binding protein PstB	NA	G9BWD6	Planktothrix_phage	31.1	1.1e-17
AZG49278.1|319636_320362_+	phosphate-specific transport system accessory protein PhoU	NA	NA	NA	NA	NA
AZG49279.1|320648_321470_+	transcriptional antiterminator BglG	NA	NA	NA	NA	NA
AZG49280.1|321603_323481_+	PTS beta-glucoside transporter subunit IIABC	NA	NA	NA	NA	NA
AZG49281.1|323499_324894_+	glycoside hydrolase family 1 protein	NA	NA	NA	NA	NA
AZG49282.1|324979_326596_+	carbohydrate porin	NA	NA	NA	NA	NA
AZG49283.1|327795_328518_+	glucosamine-6-phosphate deaminase	NA	NA	NA	NA	NA
AZG49284.1|328571_329117_-	hypothetical protein	NA	NA	NA	NA	NA
AZG49285.1|329171_330773_-|transposase	IS66-like element ISSfl3 family transposase	transposase	A0A0P0ZEB3	Stx2-converting_phage	61.5	4.9e-148
AZG49286.1|330769_331120_-|transposase	transposase	transposase	A0A0P0ZDM8	Stx2-converting_phage	68.7	3.5e-27
>prophage 2
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	801300	864312	4586233	protease,tRNA,transposase	Stx2-converting_phage(25.0%)	53	NA	NA
AZG49678.1|801300_802902_-|transposase	IS66-like element ISSfl3 family transposase	transposase	A0A0P0ZBS5	Stx2-converting_phage	61.6	1.1e-147
AZG49679.1|802898_803249_-|transposase	transposase	transposase	A0A0P0ZDM8	Stx2-converting_phage	67.5	1.3e-26
AZG49680.1|803245_803920_-	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZCV4	Stx2-converting_phage	30.1	5.8e-10
AZG49681.1|804100_805477_-	trk system potassium uptake protein trkA	NA	NA	NA	NA	NA
AZG49682.1|805498_806788_-	16S rRNA m5C967 methyltransferase	NA	NA	NA	NA	NA
AZG49683.1|806833_807781_-|tRNA	methionyl-tRNA formyltransferase	tRNA	E3SNR5	Prochlorococcus_phage	34.7	1.9e-06
AZG49684.1|807795_808305_-	peptide deformylase	NA	E3SLL2	Synechococcus_phage	41.1	1.1e-18
AZG49685.1|808452_809577_+	DNA-protecting protein DprA	NA	NA	NA	NA	NA
AZG49686.1|809548_810022_+	DUF494 domain-containing protein	NA	NA	NA	NA	NA
AZG49687.1|810050_810593_+	DNA topoisomerase	NA	NA	NA	NA	NA
AZG49688.1|810597_811170_+	L-threonylcarbamoyladenylate synthase type 1 TsaC	NA	NA	NA	NA	NA
AZG49689.1|811174_811993_+	shikimate dehydrogenase	NA	NA	NA	NA	NA
AZG49690.1|811989_812247_+	DUF1488 domain-containing protein	NA	NA	NA	NA	NA
AZG49691.1|812222_812777_-	gamma carbonic anhydrase family protein	NA	NA	NA	NA	NA
AZG49692.1|818655_819414_-	amino acid ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	37.7	9.7e-30
AZG49693.1|819421_820525_-	amino acid ABC transporter permease	NA	NA	NA	NA	NA
AZG49694.1|822548_823574_-	amino acid ABC transporter substrate-binding protein	NA	A0A1B1IT51	uncultured_Mediterranean_phage	39.5	1.2e-70
AZG49695.1|824500_824701_-	DUF2556 domain-containing protein	NA	NA	NA	NA	NA
AZG49696.1|824784_825669_-	adenine-specific DNA-methyltransferase	NA	M4QNN5	Ostreococcus_lucimarinus_virus	30.2	2.4e-24
AZG49697.1|825754_826051_-	DNA-binding transcriptional regulator Fis	NA	NA	NA	NA	NA
AZG49698.1|826076_827042_-|tRNA	tRNA dihydrouridine synthase DusB	tRNA	NA	NA	NA	NA
AZG49699.1|827370_828252_-	50S ribosomal protein L11 methyltransferase	NA	NA	NA	NA	NA
AZG49700.1|828263_829715_-	sodium/pantothenate symporter	NA	NA	NA	NA	NA
AZG49701.1|829704_829947_-	DUF997 family protein	NA	NA	NA	NA	NA
AZG49702.1|830055_831405_-	acetyl-CoA carboxylase biotin carboxylase subunit	NA	NA	NA	NA	NA
AZG49703.1|831415_831886_-	acetyl-CoA carboxylase biotin carboxyl carrier protein	NA	NA	NA	NA	NA
AZG49704.1|832863_833838_-	oxidoreductase	NA	NA	NA	NA	NA
AZG49705.1|833989_835930_+	RNase E specificity factor CsrD	NA	NA	NA	NA	NA
AZG49706.1|835938_836127_-	hypothetical protein	NA	NA	NA	NA	NA
AZG49707.1|836234_837278_+	rod shape-determining protein	NA	F2Y0P3	Organic_Lake_phycodnavirus	22.3	6.7e-05
AZG49708.1|837343_838447_+	rod shape-determining protein MreC	NA	NA	NA	NA	NA
AZG49709.1|838446_838935_+	rod shape-determining protein MreD	NA	NA	NA	NA	NA
AZG49710.1|838943_839537_+	septum formation inhibitor Maf	NA	NA	NA	NA	NA
AZG49711.1|839526_840996_+	ribonuclease G	NA	NA	NA	NA	NA
AZG49712.1|841063_844864_+	AsmA2 domain-containing protein	NA	NA	NA	NA	NA
AZG49713.1|845019_846465_+|protease	metalloprotease TldD	protease	NA	NA	NA	NA
AZG49714.1|846592_847522_-	HTH-type transcriptional activator AaeR	NA	NA	NA	NA	NA
AZG49715.1|847704_847908_+	protein AaeX	NA	NA	NA	NA	NA
AZG49716.1|847915_848848_+	p-hydroxybenzoic acid efflux pump subunit AaeA	NA	NA	NA	NA	NA
AZG49717.1|848853_850821_+	p-hydroxybenzoic acid efflux pump subunit AaeB	NA	NA	NA	NA	NA
AZG49718.1|850912_851185_+	hypothetical protein	NA	NA	NA	NA	NA
AZG52794.1|851240_851504_-	DUF1471 domain-containing protein	NA	NA	NA	NA	NA
AZG49719.1|851868_852339_-	transcriptional regulator ArgR	NA	NA	NA	NA	NA
AZG49720.1|852773_853712_+	malate dehydrogenase	NA	NA	NA	NA	NA
AZG49721.1|853773_854841_-|protease	serine endoprotease DegS	protease	A0A1S5Y2X3	uncultured_archaeal_virus	24.2	6.8e-05
AZG49722.1|856431_856830_-	DUF1043 family protein	NA	NA	NA	NA	NA
AZG49723.1|857023_858151_+	cell division protein ZapE	NA	NA	NA	NA	NA
AZG49724.1|858370_858799_+	50S ribosomal protein L13	NA	NA	NA	NA	NA
AZG49725.1|858814_859207_+	30S ribosomal protein S9	NA	NA	NA	NA	NA
AZG49726.1|859601_860240_+	stringent starvation protein A	NA	NA	NA	NA	NA
AZG49727.1|860245_860743_+|protease	ClpXP protease specificity-enhancing factor	protease	A0A1S5R3H3	Pseudomonas_phage	42.9	3.3e-26
AZG49728.1|860785_862153_-	C4-dicarboxylate transporter DcuC	NA	NA	NA	NA	NA
AZG49729.1|863039_864312_+|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	99.0	3.0e-177
>prophage 3
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	1335603	1345500	4586233	transposase	Pseudomonas_phage(50.0%)	6	NA	NA
AZG50116.1|1335603_1336167_-	hypothetical protein	NA	A0A2D1GNR8	Pseudomonas_phage	55.8	1.1e-35
AZG50117.1|1336331_1336583_+	DNA-binding protein	NA	A0A2D1GNH1	Pseudomonas_phage	53.0	1.1e-17
AZG50118.1|1336584_1338681_+|transposase	transposase	transposase	A0A2D1GNK9	Pseudomonas_phage	48.7	1.2e-173
AZG50119.1|1338820_1339977_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	1.4e-67
AZG50120.1|1340258_1341167_-	NAD(P)-dependent oxidoreductase	NA	A0A077SLF7	Escherichia_phage	76.2	5.6e-117
AZG50121.1|1342938_1345500_-	DNA mismatch repair protein MutS	NA	E3T5Q7	Cafeteria_roenbergensis_virus	20.6	1.7e-30
>prophage 4
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	1475805	1536367	4586233	tail,tRNA,transposase	Aeromonas_phage(10.53%)	50	NA	NA
AZG50230.1|1475805_1476066_-	4Fe-4S dicluster ferredoxin YfhL	NA	A0A1B1IWY9	uncultured_Mediterranean_phage	53.5	4.9e-18
AZG50231.1|1477420_1478577_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	2.6e-66
AZG50232.1|1478656_1479343_+	hypothetical protein	NA	A0A077KGW9	Edwardsiella_phage	43.1	7.6e-42
AZG50233.1|1479344_1479950_+	DUF2612 domain-containing protein	NA	H9C0Y0	Aeromonas_phage	43.2	1.0e-29
AZG50234.1|1480847_1482121_-|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	99.0	3.0e-177
AZG50235.1|1482184_1482658_+|tail	phage tail protein	tail	Q7Y4D4	Escherichia_virus	50.9	1.6e-35
AZG50236.1|1482660_1483206_+|tail	tail fiber assembly protein	tail	Q8W612	Enterobacteria_phage	72.5	7.3e-72
AZG50237.1|1483229_1484498_+|tail	phage tail protein	tail	Q8W611	Enterobacteria_phage	43.2	6.7e-76
AZG50238.1|1485253_1487080_-	invasion protein	NA	NA	NA	NA	NA
AZG50239.1|1488470_1489319_-	MurR/RpiR family transcriptional regulator	NA	NA	NA	NA	NA
AZG50240.1|1489527_1490163_+	phosphatidylglycerophosphatase C	NA	NA	NA	NA	NA
AZG50241.1|1490187_1490724_+|tRNA	tRNA adenosine(34) deaminase TadA	tRNA	NA	NA	NA	NA
AZG50242.1|1490720_1492277_-	membrane-bound lytic murein transglycosylase MltF	NA	NA	NA	NA	NA
AZG50243.1|1492535_1496423_+	phosphoribosylformylglycinamidine synthase	NA	A9YX36	Burkholderia_phage	58.4	6.5e-130
AZG50244.1|1496998_1498426_+	two component system sensor histidine kinase QseE/GlrK	NA	W8CYF6	Bacillus_phage	24.5	3.9e-16
AZG50245.1|1498590_1499304_+	two-component system QseEF-associated lipoprotein QseG	NA	NA	NA	NA	NA
AZG50246.1|1499293_1500628_+	two-component system response regulator GlrR	NA	W8CYM9	Bacillus_phage	37.3	3.9e-10
AZG50247.1|1500688_1501027_+	nitrogen regulatory protein P-II 1	NA	NA	NA	NA	NA
AZG50248.1|1501071_1502262_-	NO-inducible flavohemoprotein	NA	NA	NA	NA	NA
AZG50249.1|1502588_1503842_+	serine hydroxymethyltransferase	NA	A0A240F3L3	Aeromonas_phage	52.7	7.8e-101
AZG50250.1|1504039_1505233_-	ROK family protein	NA	NA	NA	NA	NA
AZG50251.1|1505530_1508632_+	DUF5107 domain-containing protein	NA	NA	NA	NA	NA
AZG50252.1|1508728_1509712_+	sugar ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AZG50253.1|1509734_1511246_+	sugar ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	27.3	8.7e-14
AZG50254.1|1511270_1512269_+	ABC transporter permease	NA	NA	NA	NA	NA
AZG52816.1|1512334_1513396_+	alcohol dehydrogenase	NA	NA	NA	NA	NA
AZG50255.1|1513407_1514280_+	aldose 1-epimerase	NA	NA	NA	NA	NA
AZG50256.1|1514327_1514750_-	DoxX family protein	NA	NA	NA	NA	NA
AZG50257.1|1514846_1516049_-	phenylpropionate dioxygenase ferredoxin reductase subunit	NA	NA	NA	NA	NA
AZG50258.1|1516058_1516871_-	3-phenylpropionate-dihydrodiol/cinnamic acid-dihydrodiol dehydrogenase	NA	NA	NA	NA	NA
AZG50259.1|1516867_1517188_-	3-phenylpropionate/cinnamic acid dioxygenase ferredoxin subunit	NA	NA	NA	NA	NA
AZG50260.1|1517187_1517706_-	3-phenylpropionate/cinnamic acid dioxygenase subunit beta	NA	NA	NA	NA	NA
AZG50261.1|1517702_1519064_-	3-phenylpropionate/cinnamic acid dioxygenase subunit alpha	NA	NA	NA	NA	NA
AZG50262.1|1519199_1520090_+	DNA-binding transcriptional regulator HcaR	NA	NA	NA	NA	NA
AZG50263.1|1520249_1521389_+	3-phenylpropionate MFS transporter	NA	NA	NA	NA	NA
AZG50264.1|1521380_1522661_-	stationary phase inducible protein CsiE	NA	NA	NA	NA	NA
AZG50265.1|1522851_1523706_-	alpha/beta hydrolase	NA	A0A1V0SD13	Indivirus	28.6	2.0e-15
AZG50266.1|1523850_1524654_-	inositol-1-monophosphatase	NA	NA	NA	NA	NA
AZG50267.1|1524772_1525513_+|tRNA	tRNA (cytosine(32)/uridine(32)-2'-O)-methyltransferase TrmJ	tRNA	NA	NA	NA	NA
AZG50268.1|1525782_1526271_+	Fe-S cluster assembly transcriptional regulator IscR	NA	NA	NA	NA	NA
AZG50269.1|1526382_1527597_+	IscS subfamily cysteine desulfurase	NA	A0A1X7C038	Faustovirus	31.8	8.8e-33
AZG50270.1|1527624_1528011_+	iron-sulfur cluster scaffold-like protein	NA	A0A218MKD1	uncultured_virus	78.9	1.4e-53
AZG50271.1|1528027_1528351_+	iron-sulfur cluster assembly protein IscA	NA	A0A2H4N7N5	Lake_Baikal_phage	48.6	5.4e-22
AZG50272.1|1528446_1528962_+	co-chaperone HscB	NA	NA	NA	NA	NA
AZG50273.1|1528978_1530829_+	molecular chaperone HscA	NA	A0A0N9QXN8	Chrysochromulina_ericina_virus	41.6	7.2e-103
AZG50274.1|1530830_1531166_+	ISC system 2Fe-2S type ferredoxin	NA	NA	NA	NA	NA
AZG50275.1|1531177_1531378_+	Fe-S assembly protein IscX	NA	NA	NA	NA	NA
AZG50276.1|1531436_1532720_+	aminopeptidase PepB	NA	Q6GYZ8	Mycoplasma_phage	37.8	1.7e-34
AZG50277.1|1532861_1533638_+	protein SseB	NA	NA	NA	NA	NA
AZG50278.1|1535170_1536367_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
>prophage 5
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	1918399	1957202	4586233	integrase,tail,tRNA,lysis,transposase	Enterobacteria_phage(69.23%)	32	1937298:1937317	1949152:1949171
AZG50581.1|1918399_1919095_-|lysis	CidB/LrgB family autolysis modulator	lysis	NA	NA	NA	NA
AZG50582.1|1919091_1919490_-	hypothetical protein	NA	NA	NA	NA	NA
AZG52826.1|1919728_1920676_+|tRNA	tRNA dihydrouridine(16) synthase DusC	tRNA	NA	NA	NA	NA
AZG50583.1|1921046_1921130_-	protein YohP	NA	NA	NA	NA	NA
AZG50584.1|1922040_1923567_+	multidrug resistance outer membrane protein MdtQ	NA	NA	NA	NA	NA
AZG50585.1|1924497_1925076_-	DedA family protein	NA	NA	NA	NA	NA
AZG50586.1|1925245_1925833_+	YIP1 family protein	NA	NA	NA	NA	NA
AZG50587.1|1926006_1926939_+	D-alanyl-D-alanine endopeptidase	NA	NA	NA	NA	NA
AZG50588.1|1926976_1928692_-	D-lactate dehydrogenase	NA	NA	NA	NA	NA
AZG50589.1|1928887_1931185_+	beta-glucosidase BglX	NA	NA	NA	NA	NA
AZG50590.1|1931436_1932354_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AZG50591.1|1932360_1933518_+	ABC transporter permease	NA	NA	NA	NA	NA
AZG50592.1|1933510_1934437_+	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	34.6	9.7e-24
AZG50593.1|1934441_1935173_+	ABC transporter permease	NA	NA	NA	NA	NA
AZG50594.1|1935153_1935261_-	protein YohO	NA	NA	NA	NA	NA
AZG50595.1|1937053_1937335_-	MerR family transcriptional regulator	NA	Q9EYF2	Enterobacteria_phage	96.2	3.6e-38
1937298:1937317	attL	CACGCGCGTAACGTGACAGG	NA	NA	NA	NA
AZG50596.1|1937355_1938153_-|integrase	site-specific integrase	integrase	H6WZF6	Escherichia_phage	97.7	9.2e-148
AZG50597.1|1938191_1939347_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	6.1e-68
AZG50598.1|1942458_1942872_+	hypothetical protein	NA	Q7Y4D4	Escherichia_virus	47.8	3.5e-26
AZG50599.1|1942874_1943420_+|tail	tail fiber assembly protein	tail	Q8W612	Enterobacteria_phage	73.1	1.9e-72
AZG50600.1|1943443_1944730_+|tail	phage tail protein	tail	Q8W611	Enterobacteria_phage	73.5	2.0e-67
AZG50601.1|1945430_1945610_+	hypothetical protein	NA	NA	NA	NA	NA
AZG50602.1|1945610_1947254_-	E3 ubiquitin--protein ligase	NA	NA	NA	NA	NA
AZG50603.1|1947568_1948228_-	class I SAM-dependent methyltransferase	NA	NA	NA	NA	NA
AZG50604.1|1948292_1948562_+|tail	tail fiber assembly protein	tail	K7PMH7	Enterobacteria_phage	81.7	1.2e-19
AZG50605.1|1948677_1948926_-	damage-inducible protein DinI	NA	A5LH55	Enterobacteria_phage	97.6	4.1e-38
AZG50606.1|1949323_1950652_-|transposase	IS4 family transposase	transposase	NA	NA	NA	NA
1949152:1949171	attR	CACGCGCGTAACGTGACAGG	NA	NA	NA	NA
AZG52827.1|1950877_1952563_+	sensor histidine kinase	NA	Q9EYF3	Enterobacteria_phage	99.6	2.5e-304
AZG50607.1|1952559_1953279_+	DNA-binding response regulator	NA	NA	NA	NA	NA
AZG50608.1|1953325_1953796_+	DUF1456 family protein	NA	Q9EYF4	Enterobacteria_phage	98.7	2.6e-81
AZG50609.1|1953836_1954298_-	DUF1307 domain-containing protein	NA	Q9EYF5	Enterobacteria_phage	99.3	1.6e-75
AZG50610.1|1955198_1957202_-	hypothetical protein	NA	Q9EYF6	Enterobacteria_phage	96.3	0.0e+00
>prophage 6
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	2044257	2050564	4586233		Enterobacteria_phage(50.0%)	6	NA	NA
AZG50669.1|2044257_2045652_+	colanic acid biosynthesis protein WcaM	NA	A0A291LBB9	Klebsiella_phage	30.9	4.9e-19
AZG50670.1|2045826_2046720_+	GalU regulator GalF	NA	A0A127AW70	Bacillus_phage	42.0	1.3e-46
AZG50671.1|2047092_2048178_+	dTDP-glucose 4,6-dehydratase	NA	I7HTA3	Enterobacteria_phage	53.6	4.4e-100
AZG50672.1|2048177_2049077_+	dTDP-4-dehydrorhamnose reductase	NA	A0A291LA50	Escherichia_phage	35.6	4.4e-29
AZG50673.1|2049135_2050014_+	glucose-1-phosphate thymidylyltransferase RfbA	NA	I7I009	Enterobacteria_phage	64.1	1.1e-106
AZG50674.1|2050018_2050564_+	dTDP-4-dehydrorhamnose 3,5-epimerase	NA	I7HJC4	Enterobacteria_phage	57.3	3.5e-50
>prophage 7
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	2077587	2092441	4586233	transposase	Stx2-converting_phage(55.56%)	13	NA	NA
AZG50699.1|2077587_2078427_+	DUF4102 domain-containing protein	NA	A0A0P0ZDN8	Stx2-converting_phage	99.6	1.3e-160
AZG50700.1|2078505_2079180_+	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZCV4	Stx2-converting_phage	30.8	2.0e-10
AZG50701.1|2079176_2079527_+|transposase	transposase	transposase	A0A0P0ZDM8	Stx2-converting_phage	67.5	1.8e-26
AZG50702.1|2080473_2081746_+|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	98.7	6.8e-177
AZG50703.1|2082111_2083267_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	3.4e-66
AZG50704.1|2083324_2084524_-|transposase	IS66 family transposase	transposase	A0A0P0ZEB3	Stx2-converting_phage	62.6	1.4e-99
AZG50705.1|2086176_2086851_-	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZCV4	Stx2-converting_phage	30.8	2.0e-10
AZG50706.1|2086920_2087220_+	hypothetical protein	NA	NA	NA	NA	NA
AZG50707.1|2087391_2087721_+	DUF496 family protein	NA	NA	NA	NA	NA
AZG50708.1|2087821_2088004_-	ethanolamine utilization protein	NA	NA	NA	NA	NA
AZG50709.1|2089754_2090923_-|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG50710.1|2091048_2091270_-	hypothetical protein	NA	NA	NA	NA	NA
AZG50711.1|2091285_2092441_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	2.0e-66
>prophage 8
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	2103460	2142532	4586233	integrase,tail,holin,head,transposase	Enterobacteria_phage(29.63%)	39	2105171:2105230	2140239:2141488
AZG50720.1|2103460_2104617_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	8.9e-67
AZG50721.1|2104678_2105182_-	serine transporter	NA	NA	NA	NA	NA
2105171:2105230	attL	CTGAAGTGGCACACTGAATTTGGCCACCTGAACAGAGGTGATATGCTCACCTCAGAACAA	NA	NA	NA	NA
AZG50722.1|2105243_2106411_+|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG52833.1|2108118_2108916_-	DgsA anti-repressor MtfA	NA	NA	NA	NA	NA
AZG50723.1|2109126_2110167_-|integrase	integrase	integrase	A0A192Y7M7	Salmonella_phage	57.9	2.0e-102
AZG52834.1|2110333_2110750_+	hypothetical protein	NA	A0A076GCN9	Escherichia_phage	72.0	1.5e-24
AZG50724.1|2110962_2111142_+	hypothetical protein	NA	NA	NA	NA	NA
AZG50725.1|2111344_2111557_+	type I toxin-antitoxin system Hok family toxin	NA	A0A0U2QV81	Escherichia_phage	95.7	6.6e-29
AZG50726.1|2111598_2111784_-	hypothetical protein	NA	NA	NA	NA	NA
AZG50727.1|2111724_2112003_+	hypothetical protein	NA	I6PCV7	Cronobacter_phage	45.0	4.5e-09
AZG50728.1|2112004_2113063_+	DUF968 domain-containing protein	NA	A0A291AWV9	Escherichia_phage	48.0	2.6e-89
AZG50729.1|2113063_2113429_+	RusA family crossover junction endodeoxyribonuclease	NA	V5URS4	Shigella_phage	67.3	4.6e-38
AZG50730.1|2113425_2114109_+	antiterminator	NA	I6PDF8	Cronobacter_phage	49.8	2.0e-58
AZG50731.1|2114909_2115125_+|holin	holin	holin	M1FN85	Enterobacteria_phage	98.6	5.3e-34
AZG50732.1|2115223_2115898_+	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZCV4	Stx2-converting_phage	30.8	2.0e-10
AZG50733.1|2115894_2116245_+|transposase	transposase	transposase	A0A0P0ZDM8	Stx2-converting_phage	67.5	1.8e-26
AZG50734.1|2117207_2117531_+|head,tail	phage gp6-like head-tail connector protein	head,tail	Q8W626	Enterobacteria_phage	99.1	9.7e-56
AZG50735.1|2117527_2117944_+|head,tail	head-tail adaptor protein	head,tail	Q8HAC9	Salmonella_phage	69.1	9.0e-46
AZG50736.1|2117909_2118434_+	hypothetical protein	NA	Q8W625	Enterobacteria_phage	98.9	2.7e-95
AZG50737.1|2118720_2119876_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	8.9e-67
AZG50738.1|2120270_2120432_+	DUF2635 domain-containing protein	NA	Q8SBH3	Shigella_phage	76.6	9.2e-15
AZG50739.1|2120428_2121925_+|tail	phage tail protein	tail	Q8W623	Enterobacteria_phage	97.4	5.9e-273
AZG50740.1|2121924_2122281_+|tail	phage tail protein	tail	Q8W622	Enterobacteria_phage	98.3	5.3e-63
AZG52835.1|2122286_2122616_+|tail	phage tail assembly protein	tail	Q8W621	Enterobacteria_phage	97.2	7.3e-51
AZG50741.1|2122700_2124650_+|tail	phage tail tape measure protein	tail	Q8W620	Enterobacteria_phage	98.2	0.0e+00
AZG50742.1|2124717_2125200_+	hypothetical protein	NA	NA	NA	NA	NA
AZG52836.1|2126897_2127425_+	DUF4376 domain-containing protein	NA	A0A0U2QQK4	Escherichia_phage	81.0	1.3e-68
AZG50743.1|2127424_2127604_+	hypothetical protein	NA	NA	NA	NA	NA
AZG50744.1|2127604_2129248_-	E3 ubiquitin--protein ligase	NA	NA	NA	NA	NA
AZG50745.1|2129563_2130223_-	class I SAM-dependent methyltransferase	NA	NA	NA	NA	NA
AZG50746.1|2130287_2130557_+|tail	tail fiber assembly protein	tail	K7PMH7	Enterobacteria_phage	81.7	1.2e-19
AZG50747.1|2130529_2130709_+	hypothetical protein	NA	NA	NA	NA	NA
AZG50748.1|2131634_2132285_-	metal-binding protein ZinT	NA	NA	NA	NA	NA
AZG50749.1|2132542_2133178_-	protein-methionine-sulfoxide reductase heme-binding subunit MsrQ	NA	NA	NA	NA	NA
AZG50750.1|2134291_2134705_-	hydroxyisourate hydrolase	NA	NA	NA	NA	NA
AZG52837.1|2134837_2135509_+	DNA-binding response regulator HprR	NA	W8CYM9	Bacillus_phage	35.2	5.4e-32
AZG50751.1|2138065_2139293_+|transposase	IS3 family transposase	transposase	Q9ZXG3	Shigella_phage	96.7	9.8e-173
AZG50752.1|2140311_2141479_+|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG50753.1|2141403_2142532_+|transposase	IS3 family transposase	transposase	U5P429	Shigella_phage	92.2	1.4e-146
2140239:2141488	attR	CTGAAGTGGCACACTGAATTTGGCCACCTGAACAGAGGTGATATGCTCACCTCAGAACAACACAGGTGCTCCAATGAAAAAAAGAAATTTTAGCGCAGAGTTTAAACGCGAATCCGCTCAACTGGTTGTTGACCAGAAATACACGGTGGCAGATGCCGCCAAAGCTATGGATGTTGGCCTTTCCACAATGACAAGATGGGTCAAACAACTGCGTGATGAGCGTCAGGGCAAAACACCAAAAGCCTCCCCCATTACCCCGGAACAAATTGAAATCCGTGAGCTCAGGAAAAAGCTACAACGCATTGAAATGGAGAATGAAATATTAAAAAAGGCTACCGCGCTCTTGATGTCAGACTCCCTGAACAGTTCTCGATAATCGGGAAACTCAGAGCGCATTATCCTGTGGTCACACTCTGCCATGTGTTCGGGGTTCATCGCAGCAGCTACAGATACTGGAAAAACCGTCCTGAAAAACCAGACGGCAGACGGGCTGTATTACGCAGTCAGGTACTTGAGCTACATGGCATCAGCCACGGTTCGGCCGGAGCAAGAAGCATCGCCACAATGGCAACCCGGAGAGGCTACCAGATGGGACGCTGGCTTGCTGGCAGGCTCATGAAAGAGCTGGGGCTGGTCAGCTGTCAGCAGCCGACTCACCGGTATAAACGTGGTGGTCATGAACATGTTGCTATCCCTAACTACCTTGAAAGGCAGTTCGCCGTGACCGAGCCAAATCAGGTGTGGTGCGGTGATGTGACCTATATCTGGACGGGTAAGCGCTGGGCGTACCTCGCCGTTGTTCTCGACCTGTTCGCAAGAAAACCAGTGGGCTGGGCCATGTCGTTCTCGCCGGACAGCAGGCTCACCATGAAAGCGCTGGAAATGGCATGGGAAACCCGTGGTAAGCCCGGCGGGGTGATGTTCCACAGCGATCAGGGCAGTCATTATACGAGCAGGCAGTTCCGGCAGTTATTGTGGCGATACCAGATCAGACAGAGTATGAGCCGGCGCGGAAACTGCTGGGATAACAGCCCAATGGAACGCTTCTTCAGGAGTCTGAAGAACGAATGGATGCCGGTGGTGGGTTACGTAAGCTTCAGCGAGGCAGCTCACGCCATAACGGACTATATCGTTGGATATTACAGTGCACTAAGACCGCACGAATATAACGGTGGGTTACCCCCAAACGAATCGGAAAATCGATACTGGAAAAACTCTAACTCGGTGGCCAGTTTTTGTTGACCACTTCA	NA	NA	NA	NA
>prophage 9
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	2213992	2311791	4586233	tail,tRNA,transposase	Enterobacteria_phage(27.59%)	80	NA	NA
AZG50824.1|2213992_2215149_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	1.4e-67
AZG50825.1|2215200_2215596_-	hypothetical protein	NA	NA	NA	NA	NA
AZG50826.1|2215736_2216904_+|transposase	IS3 family transposase	transposase	Q716C2	Shigella_phage	99.3	2.6e-183
AZG50827.1|2216839_2217298_-	HD domain-containing protein	NA	NA	NA	NA	NA
AZG50828.1|2217533_2218727_+	flagellar type III secretion system protein FlhB	NA	NA	NA	NA	NA
AZG50829.1|2218772_2219372_+	hypothetical protein	NA	NA	NA	NA	NA
AZG50830.1|2219368_2220751_+	flagellar biosynthesis protein FlhA	NA	NA	NA	NA	NA
AZG50831.1|2220750_2221089_+	flagellar protein FlhE	NA	NA	NA	NA	NA
AZG50832.1|2222569_2223058_-	lysozyme inhibitor LprI family protein	NA	NA	NA	NA	NA
AZG50833.1|2223234_2224968_-|tRNA	arginine--tRNA ligase	tRNA	A0A2K9L6Z2	Tupanvirus	33.7	6.8e-87
AZG50834.1|2225183_2225750_+	VOC family protein	NA	NA	NA	NA	NA
AZG50835.1|2225763_2226510_+	copper homeostasis protein CutC	NA	NA	NA	NA	NA
AZG50836.1|2226897_2227998_+	cytochrome C	NA	NA	NA	NA	NA
AZG50837.1|2228022_2230452_+	molybdopterin guanine dinucleotide-containing S/N-oxide reductase	NA	NA	NA	NA	NA
AZG50838.1|2230616_2231588_-|tRNA	tRNA 5-methoxyuridine(34)/uridine 5-oxyacetic acid(34) synthase CmoB	tRNA	NA	NA	NA	NA
AZG50839.1|2231584_2232328_-	carboxy-S-adenosyl-L-methionine synthase CmoA	NA	F5B419	Synechococcus_phage	30.0	4.6e-24
AZG50840.1|2232368_2232764_-	hypothetical protein	NA	NA	NA	NA	NA
AZG50841.1|2232816_2233167_-	DUF72 domain-containing protein	NA	NA	NA	NA	NA
AZG50842.1|2233396_2234564_+|transposase	IS3 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG50843.1|2234602_2235292_+	antiterminator	NA	I6PDF8	Cronobacter_phage	49.4	1.0e-57
AZG50844.1|2236477_2237674_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AZG50845.1|2237937_2238339_+	DNA-packaging protein FI	NA	A0A2R9YJP4	Escherichia_phage	66.2	3.3e-37
AZG50846.1|2238350_2238722_+|tail	phage tail protein	tail	NA	NA	NA	NA
AZG50847.1|2238708_2239299_+|tail	phage tail protein	tail	A5LH33	Enterobacteria_phage	77.7	1.3e-77
AZG50848.1|2239295_2239697_+|tail	phage tail protein	tail	A0A291AWY2	Escherichia_phage	97.7	1.6e-71
AZG50849.1|2239707_2240448_+|tail	phage tail protein	tail	A5LH35	Enterobacteria_phage	96.7	1.5e-128
AZG50850.1|2240901_2241231_+|tail	phage tail assembly protein T	tail	A5LH37	Enterobacteria_phage	99.1	1.3e-55
AZG50851.1|2241202_2242150_+|tail	tail length tape measure protein	tail	A0A291AWX1	Escherichia_phage	66.6	5.1e-97
AZG50852.1|2243938_2244268_+|tail	phage tail protein	tail	A5LH39	Enterobacteria_phage	97.2	2.4e-57
AZG50853.1|2244267_2244966_+|tail	phage minor tail protein L	tail	A0A0K2FJ01	Enterobacteria_phage	89.7	8.4e-121
AZG50854.1|2244970_2245714_+|tail	phage tail protein	tail	K7PLW1	Enterobacteria_phage	94.7	6.8e-145
AZG50855.1|2245650_2246253_+|tail	tail assembly protein	tail	A5LH42	Enterobacteria_phage	85.6	8.1e-88
AZG52839.1|2251965_2252511_+	DUF4376 domain-containing protein	NA	A0A0U2QQK4	Escherichia_phage	77.2	3.2e-75
AZG50856.1|2252510_2252690_+	hypothetical protein	NA	NA	NA	NA	NA
AZG50857.1|2252690_2254442_-	invasion plasmid antigen	NA	NA	NA	NA	NA
AZG50858.1|2255041_2255290_-	DinI family protein	NA	K7PLW4	Enterobacteria_phage	98.8	4.1e-38
AZG50859.1|2256018_2257215_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AZG50860.1|2257406_2257661_-	isochorismatase family protein	NA	NA	NA	NA	NA
AZG50861.1|2257970_2259743_+|tRNA	aspartate--tRNA ligase	tRNA	NA	NA	NA	NA
AZG52840.1|2259860_2260313_+	NUDIX pyrophosphatase	NA	NA	NA	NA	NA
AZG50862.1|2260341_2261082_+	YebC/PmpR family DNA-binding transcriptional regulator	NA	NA	NA	NA	NA
AZG50863.1|2261116_2261638_+	crossover junction endodeoxyribonuclease RuvC	NA	G3MA90	Bacillus_virus	35.1	2.0e-10
AZG52841.1|2262302_2262368_+	hypothetical protein	NA	NA	NA	NA	NA
AZG50864.1|2262506_2263118_+	Holliday junction branch migration protein RuvA	NA	NA	NA	NA	NA
AZG50865.1|2263126_2264137_+	Holliday junction branch migration DNA helicase RuvB	NA	A0A127AWE7	Bacillus_phage	25.2	2.8e-08
AZG50866.1|2264283_2265069_-	zinc ABC transporter permease subunit ZnuB	NA	NA	NA	NA	NA
AZG50867.1|2265065_2265821_-	zinc ABC transporter ATP-binding protein ZnuC	NA	G3M9Y6	Bacillus_virus	28.3	3.8e-18
AZG52842.1|2265899_2266832_+	zinc ABC transporter substrate-binding protein ZnuA	NA	NA	NA	NA	NA
AZG50868.1|2266847_2268170_+	murein DD-endopeptidase MepM	NA	A8ATH6	Listeria_phage	40.9	1.2e-14
AZG50869.1|2268289_2269261_+	lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase	NA	NA	NA	NA	NA
AZG50870.1|2269391_2270834_-	pyruvate kinase II	NA	NA	NA	NA	NA
AZG50871.1|2270961_2271831_-	MurR/RpiR family transcriptional regulator	NA	NA	NA	NA	NA
AZG50872.1|2272167_2273643_+	glucose-6-phosphate dehydrogenase	NA	H6WFS4	Cyanophage	37.3	9.9e-79
AZG50873.1|2276502_2277144_+	KHG/KDPG aldolase	NA	NA	NA	NA	NA
AZG50874.1|2277199_2278378_-	phosphoribosylglycinamide formyltransferase 2	NA	NA	NA	NA	NA
AZG50875.1|2278868_2279225_+	protein YebF	NA	NA	NA	NA	NA
AZG50876.1|2279551_2280211_+	tellurite resistance TerB family protein	NA	NA	NA	NA	NA
AZG50877.1|2280420_2282481_+	oligopeptidase B	NA	NA	NA	NA	NA
AZG50878.1|2282477_2283140_-	exodeoxyribonuclease X	NA	Q6UAU3	Klebsiella_phage	41.6	3.5e-07
AZG50879.1|2283921_2284152_-	DNA polymerase III subunit theta	NA	H9C187	Pectobacterium_phage	61.8	1.3e-14
AZG50880.1|2284290_2284665_+	CopC domain-containing protein YobA	NA	NA	NA	NA	NA
AZG50881.1|2285553_2285895_+	DUF2511 domain-containing protein	NA	NA	NA	NA	NA
AZG50882.1|2287329_2287611_-	excisionase	NA	A0A2H4J5E1	uncultured_Caudovirales_phage	42.4	9.8e-12
AZG50883.1|2291060_2292674_+	peptide ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AZG50884.1|2292724_2293756_-	mechanosensitive ion channel family protein	NA	NA	NA	NA	NA
AZG50885.1|2294431_2295619_-|transposase	IS91 family transposase	transposase	NA	NA	NA	NA
AZG50886.1|2295618_2295984_-|transposase	transposase	transposase	NA	NA	NA	NA
AZG50887.1|2297387_2298338_-	universal stress protein E	NA	NA	NA	NA	NA
AZG50888.1|2298489_2299242_-	fumarate/nitrate reduction transcriptional regulator Fnr	NA	NA	NA	NA	NA
AZG50889.1|2299436_2299952_-	methylated-DNA--protein-cysteine methyltransferase	NA	M1PFU9	Streptococcus_phage	42.8	1.1e-24
AZG50890.1|2300495_2301311_-	AraC family transcriptional regulator	NA	NA	NA	NA	NA
AZG50891.1|2301407_2302055_+	HlyD family secretion protein	NA	NA	NA	NA	NA
AZG50892.1|2302218_2303417_-|transposase	IS91 family transposase	transposase	NA	NA	NA	NA
AZG50893.1|2303426_2303615_-	hypothetical protein	NA	NA	NA	NA	NA
AZG50894.1|2303670_2304123_+	HlyD family secretion protein	NA	NA	NA	NA	NA
AZG52843.1|2304122_2305574_+	DHA2 family efflux MFS transporter permease subunit	NA	NA	NA	NA	NA
AZG50895.1|2305827_2306391_+	DNA endonuclease SmrA	NA	NA	NA	NA	NA
AZG50896.1|2307898_2308882_+	zinc transporter ZntB	NA	NA	NA	NA	NA
AZG50897.1|2309359_2310727_+	ATP-dependent RNA helicase DbpA	NA	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	33.1	6.2e-51
AZG50898.1|2310855_2311791_-|tRNA	tRNA 2-thiocytidine(32) synthetase TtcA	tRNA	A0A0U2S5Z2	Escherichia_phage	97.3	3.2e-144
>prophage 10
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	2325306	2369807	4586233	transposase	Shigella_phage(33.33%)	36	NA	NA
AZG50905.1|2325306_2326463_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	1.4e-67
AZG50906.1|2327225_2327831_-	FMN-dependent NADH-azoreductase	NA	NA	NA	NA	NA
AZG50907.1|2328031_2331934_+	ATP-dependent RNA helicase HrpA	NA	A0A1V0SIV3	Klosneuvirus	29.5	2.2e-53
AZG50908.1|2332891_2334060_-|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG50909.1|2335323_2336763_+	aldehyde dehydrogenase	NA	NA	NA	NA	NA
AZG50910.1|2336804_2337806_-	type I glyceraldehyde-3-phosphate dehydrogenase	NA	NA	NA	NA	NA
AZG50911.1|2337994_2338525_+	cytochrome b561	NA	A0A0U2QLA7	Escherichia_phage	44.9	3.1e-19
AZG50912.1|2338769_2338943_+	hypothetical protein	NA	A0A0R6PKG1	Moraxella_phage	67.4	4.4e-07
AZG50913.1|2339014_2339164_-	type I toxin-antitoxin system Hok family toxin	NA	NA	NA	NA	NA
AZG50914.1|2339538_2340694_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	8.0e-68
AZG50915.1|2340892_2342061_-|transposase	IS3 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG50916.1|2344863_2346504_+	HAMP domain-containing protein	NA	NA	NA	NA	NA
AZG52844.1|2346541_2347465_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AZG50917.1|2347681_2349025_+	VOC family protein	NA	NA	NA	NA	NA
AZG50918.1|2349249_2350905_+	glucan biosynthesis protein D	NA	NA	NA	NA	NA
AZG50919.1|2351044_2351269_+	DUF465 domain-containing protein	NA	NA	NA	NA	NA
AZG50920.1|2351331_2351868_+	50S ribosomal protein L7/L12-serine acetyltransferase	NA	NA	NA	NA	NA
AZG50921.1|2351862_2352843_-	hypothetical protein	NA	NA	NA	NA	NA
AZG50922.1|2352966_2353959_+	TDT family transporter	NA	NA	NA	NA	NA
AZG50923.1|2353955_2354549_+	tellurite resistance methyltransferase TehB	NA	NA	NA	NA	NA
AZG50924.1|2354851_2355520_+	DUF3313 domain-containing protein	NA	NA	NA	NA	NA
AZG50925.1|2357132_2358320_-|transposase	IS91 family transposase	transposase	NA	NA	NA	NA
AZG50926.1|2358270_2358456_-	hypothetical protein	NA	NA	NA	NA	NA
AZG50927.1|2359158_2359953_+	ABC transporter permease	NA	NA	NA	NA	NA
AZG50928.1|2359974_2361399_+	aminobutyraldehyde dehydrogenase	NA	NA	NA	NA	NA
AZG50929.1|2361608_2362418_+	antibiotic acetyltransferase	NA	A0A2R8FE91	Brazilian_cedratvirus	41.0	5.9e-17
AZG50930.1|2362819_2362915_-	stress response membrane protein YncL	NA	NA	NA	NA	NA
AZG52845.1|2363109_2363283_+	GhoT/OrtT family toxin	NA	NA	NA	NA	NA
AZG50931.1|2363368_2363602_+	DUF2526 domain-containing protein	NA	NA	NA	NA	NA
AZG50932.1|2363602_2364052_-	DMT family transporter	NA	NA	NA	NA	NA
AZG50933.1|2364048_2364567_-	L-methionine sulfoximine/L-methionine sulfone acetyltransferase	NA	NA	NA	NA	NA
AZG50934.1|2364680_2365953_+|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	99.0	3.0e-177
AZG50935.1|2366083_2367121_+	NADP-dependent oxidoreductase	NA	NA	NA	NA	NA
AZG52846.1|2367318_2367984_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AZG50936.1|2368254_2369442_-|transposase	IS91 family transposase	transposase	NA	NA	NA	NA
AZG50937.1|2369441_2369807_-|transposase	transposase	transposase	NA	NA	NA	NA
>prophage 11
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	2520712	2589941	4586233	integrase,holin,transposase,protease	Escherichia_phage(25.0%)	64	2531921:2531935	2540091:2540105
AZG51052.1|2520712_2521534_-|protease	serine protease	protease	NA	NA	NA	NA
AZG51053.1|2521633_2521717_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51054.1|2521809_2522145_-	acid shock protein	NA	NA	NA	NA	NA
AZG51055.1|2523901_2524804_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AZG51056.1|2524938_2526159_+	ROK family transcriptional regulator	NA	NA	NA	NA	NA
AZG51057.1|2526283_2526979_+	ATP-dependent dethiobiotin synthetase BioD	NA	NA	NA	NA	NA
AZG52852.1|2526931_2528224_-	voltage-gated ClC-type chloride channel ClcB	NA	NA	NA	NA	NA
AZG51058.1|2528382_2528997_-	Tat proofreading chaperone DmsD	NA	A0A077SLS7	Escherichia_phage	36.3	8.7e-29
AZG51059.1|2529039_2529894_-	dimethyl sulfoxide reductase anchor subunit	NA	NA	NA	NA	NA
AZG51060.1|2529895_2530513_-	dimethylsulfoxide reductase	NA	A0A077SL61	Escherichia_phage	59.6	9.5e-76
2531921:2531935	attL	GCTGTTGCCATCATT	NA	NA	NA	NA
AZG51061.1|2532622_2533789_-	dimethyl sulfoxide reductase subunit A	NA	A0A077SK27	Escherichia_phage	46.6	2.3e-83
AZG51062.1|2533714_2534515_+|integrase	integrase	integrase	NA	NA	NA	NA
AZG51063.1|2535836_2536511_-	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZCV4	Stx2-converting_phage	30.8	2.0e-10
AZG51064.1|2538624_2538852_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51065.1|2540933_2541239_-	DUF1161 domain-containing protein	NA	NA	NA	NA	NA
2540091:2540105	attR	GCTGTTGCCATCATT	NA	NA	NA	NA
AZG51066.1|2541346_2542057_+	YnfC family lipoprotein	NA	NA	NA	NA	NA
AZG51067.1|2542654_2542996_-	DUF1283 family protein	NA	NA	NA	NA	NA
AZG51068.1|2543130_2543457_+	YnfA family protein	NA	A0A218MNG8	uncultured_virus	55.6	7.6e-24
AZG51069.1|2543662_2544877_+	D-galactonate dehydratase family protein	NA	Q6A202	Oenococcus_phage	29.0	2.4e-46
AZG51070.1|2544953_2546100_+|transposase	IS3 family transposase	transposase	U5P429	Shigella_phage	92.2	1.5e-146
AZG51071.1|2546150_2547424_-|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	98.7	3.0e-177
AZG51072.1|2548628_2549621_-	autoinducer 2 import system permease LsrD	NA	NA	NA	NA	NA
AZG51073.1|2549620_2550649_-	autoinducer 2 ABC transporter permease LsrC	NA	NA	NA	NA	NA
AZG51074.1|2550642_2552178_-	autoinducer 2 ABC transporter ATP-binding protein LsrA	NA	A0A2H4PQG7	Staphylococcus_phage	30.4	9.8e-21
AZG51075.1|2552426_2553380_+	transcriptional regulator LsrR	NA	NA	NA	NA	NA
AZG51076.1|2553458_2554361_+	carbohydrate kinase	NA	NA	NA	NA	NA
AZG51077.1|2555804_2556575_+	3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase	NA	NA	NA	NA	NA
AZG51078.1|2556598_2556889_+	autoinducer 2-degrading protein LsrG	NA	NA	NA	NA	NA
AZG51079.1|2556927_2557686_+	trans-aconitate 2-methyltransferase	NA	NA	NA	NA	NA
AZG51080.1|2557689_2558604_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51081.1|2558804_2558993_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51082.1|2560496_2561948_-	altronate oxidoreductase	NA	NA	NA	NA	NA
AZG51083.1|2562174_2563593_-	GGDEF domain-containing protein	NA	A0A127AWB9	Bacillus_phage	37.5	1.1e-18
AZG51084.1|2563746_2564091_-	DUF4186 domain-containing protein	NA	NA	NA	NA	NA
AZG51085.1|2564090_2565017_-	glutaminase 2	NA	NA	NA	NA	NA
AZG51086.1|2565080_2566016_-	aldehyde dehydrogenase family protein	NA	NA	NA	NA	NA
AZG51087.1|2566095_2567211_+	putative protein YneK	NA	NA	NA	NA	NA
AZG51088.1|2567360_2568551_+	sugar efflux transporter	NA	NA	NA	NA	NA
AZG51089.1|2568575_2569241_-	NAAT family transporter MarC	NA	NA	NA	NA	NA
AZG51090.1|2569452_2569887_+	multiple antibiotic resistance transcriptional regulator MarR	NA	NA	NA	NA	NA
AZG51091.1|2569906_2570290_+	MDR efflux pump AcrAB transcriptional activator MarA	NA	D0R0F8	Streptococcus_phage	32.3	4.7e-09
AZG51092.1|2570321_2570540_+	multiple antibiotic resistance protein MarB	NA	NA	NA	NA	NA
AZG51093.1|2570570_2571470_-	O-acetylserine/cysteine exporter	NA	NA	NA	NA	NA
AZG51094.1|2571733_2572852_+	efflux MFS transporter YdeE	NA	NA	NA	NA	NA
AZG51095.1|2572978_2573074_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51096.1|2573321_2574478_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	2.0e-66
AZG51097.1|2575043_2575562_+	2-oxo-tetronate isomerase	NA	NA	NA	NA	NA
AZG51098.1|2575606_2577652_-	peptidyl-dipeptidase Dcp	NA	NA	NA	NA	NA
AZG51099.1|2577788_2578535_+	NAD(P)-dependent oxidoreductase	NA	NA	NA	NA	NA
AZG51100.1|2578623_2579310_+	transcriptional regulator	NA	NA	NA	NA	NA
AZG51101.1|2579487_2579691_+	putative selenium delivery protein YdfZ	NA	J9Q802	Salmonella_phage	55.2	1.6e-11
AZG51102.1|2579726_2581187_-	mannitol dehydrogenase family protein	NA	H8ZJP8	Ostreococcus_tauri_virus	29.6	1.1e-42
AZG51103.1|2582356_2583512_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	7.5e-66
AZG51104.1|2583537_2583717_-|holin	holin	holin	A0A2R2Z340	Escherichia_phage	91.5	4.1e-24
AZG51105.1|2584024_2584213_-	DUF1737 domain-containing protein	NA	H6WZJ9	Escherichia_phage	95.2	7.2e-27
AZG51106.1|2584472_2584808_+	anti-adapter protein IraM	NA	Q8HAJ1	Enterobacteria_phage	74.8	5.2e-44
AZG51107.1|2585255_2585582_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51108.1|2586117_2586939_-	antitermination protein	NA	K7P7B9	Enterobacteria_phage	59.0	1.6e-78
AZG51109.1|2586953_2587310_-	RusA family crossover junction endodeoxyribonuclease	NA	V5URS4	Shigella_phage	62.7	6.1e-35
AZG51110.1|2587322_2588372_-	DUF968 domain-containing protein	NA	U5P0K4	Shigella_phage	54.3	3.2e-108
AZG51111.1|2588754_2588970_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51112.1|2589187_2589343_-	protein HokD	NA	A0A0U2QV81	Escherichia_phage	96.1	1.5e-17
AZG51113.1|2589414_2589702_-	type II toxin-antitoxin system mRNA interferase RelE	NA	A0A2H4JBF4	uncultured_Caudovirales_phage	66.0	1.4e-29
AZG51114.1|2589701_2589941_-	antitoxin RelB	NA	A0A2H4JBG1	uncultured_Caudovirales_phage	54.4	1.6e-18
>prophage 12
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	2688903	2767522	4586233	integrase,tail,tRNA,protease,transposase	Escherichia_phage(40.0%)	79	2737565:2737624	2763267:2764520
AZG51197.1|2688903_2690071_+|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51198.1|2690794_2690893_-	hypothetical protein	NA	NA	NA	NA	NA
AZG52855.1|2691104_2691671_+	XRE family transcriptional regulator	NA	A0A076FRF7	Pseudomonas_phage	51.8	1.8e-09
AZG52856.1|2692027_2692630_+	ring-hydroxylating oxygenase subunit alpha	NA	NA	NA	NA	NA
AZG51199.1|2692685_2693651_+	oxidoreductase	NA	NA	NA	NA	NA
AZG51200.1|2693704_2694820_-	ribonuclease D	NA	NA	NA	NA	NA
AZG52857.1|2694901_2696587_-	long-chain-fatty-acid--CoA ligase FadD	NA	A0A2H4PQM9	Staphylococcus_phage	25.7	1.2e-35
AZG51201.1|2696791_2697373_-	Slp family lipoprotein YeaY	NA	NA	NA	NA	NA
AZG51202.1|2697412_2698108_-|tRNA	tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 TsaB	tRNA	NA	NA	NA	NA
AZG51203.1|2698165_2700076_-	ATP-dependent DNA helicase	NA	A0A127AW80	Bacillus_phage	31.7	3.8e-91
AZG51204.1|2700207_2700552_+	RidA family protein	NA	NA	NA	NA	NA
AZG51205.1|2700913_2701273_+	DUF1889 family protein	NA	NA	NA	NA	NA
AZG51206.1|2701392_2701572_-	YoaH family protein	NA	NA	NA	NA	NA
AZG51207.1|2701645_2703007_+	aminodeoxychorismate synthase component 1	NA	S4VT78	Pandoravirus	41.7	6.4e-40
AZG51208.1|2703010_2703589_+	CoA pyrophosphatase	NA	NA	NA	NA	NA
AZG51209.1|2703772_2705137_+	L-serine ammonia-lyase	NA	NA	NA	NA	NA
AZG51210.1|2705267_2706866_+	cyclic diguanylate phosphodiesterase	NA	NA	NA	NA	NA
AZG51211.1|2706869_2708420_-	TerC family protein	NA	A0A0R6PEZ3	Moraxella_phage	45.4	1.7e-41
AZG51212.1|2708882_2709854_+	PTS mannose transporter subunit IIAB	NA	NA	NA	NA	NA
AZG51213.1|2709916_2710717_+	PTS mannose/fructose/sorbose transporter subunit IIC	NA	NA	NA	NA	NA
AZG51214.1|2710729_2711581_+	PTS mannose transporter subunit IID	NA	NA	NA	NA	NA
AZG51215.1|2711635_2712112_+	DUF986 domain-containing protein	NA	NA	NA	NA	NA
AZG51216.1|2713300_2713867_+	manganese efflux pump MntP	NA	NA	NA	NA	NA
AZG51217.1|2713863_2714673_-	23S rRNA (guanine(745)-N(1))-methyltransferase	NA	NA	NA	NA	NA
AZG51218.1|2714838_2715048_-	cold-shock protein CspC	NA	A0A1W6JNX5	Morganella_phage	78.1	1.6e-22
AZG51219.1|2715060_2715204_-	DUF2627 domain-containing protein	NA	NA	NA	NA	NA
AZG51220.1|2715782_2716070_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51221.1|2716144_2716288_-	PhoP/PhoQ regulator MgrB	NA	NA	NA	NA	NA
AZG51222.1|2716446_2716686_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51223.1|2716828_2717620_-	transcriptional regulator KdgR	NA	NA	NA	NA	NA
AZG51224.1|2717796_2719170_+	MFS transporter	NA	NA	NA	NA	NA
AZG51225.1|2719215_2720097_-|protease	protease HtpX	protease	NA	NA	NA	NA
AZG51226.1|2720288_2722337_-	carboxy terminal-processing peptidase	NA	A0A0R6PIZ1	Moraxella_phage	33.5	1.2e-85
AZG51227.1|2722356_2723055_-	RNA chaperone ProQ	NA	NA	NA	NA	NA
AZG51228.1|2723151_2723649_-	GAF domain-containing protein	NA	NA	NA	NA	NA
AZG51229.1|2723778_2725062_+	paraquat-inducible protein A	NA	NA	NA	NA	NA
AZG51230.1|2727730_2729170_+	16S rRNA (cytosine(1407)-C(5))-methyltransferase RsmF	NA	NA	NA	NA	NA
AZG51231.1|2729287_2729524_+	DUF1480 family protein	NA	NA	NA	NA	NA
AZG52858.1|2729628_2729820_+	DUF1482 family protein	NA	NA	NA	NA	NA
AZG51232.1|2730076_2731233_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	8.9e-67
AZG51233.1|2732494_2734201_+	E3 ubiquitin--protein ligase	NA	NA	NA	NA	NA
AZG51234.1|2734201_2734381_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51235.1|2734892_2735504_-	IS66 family insertion sequence hypothetical protein	NA	NA	NA	NA	NA
AZG51236.1|2736013_2736250_-	hypothetical protein	NA	NA	NA	NA	NA
2737565:2737624	attL	CTAGACTGGCCCCCTGAATCTCCAGACAACCAGTATCACTTATTTAAGTGATAGTCTTAA	NA	NA	NA	NA
AZG51237.1|2737611_2738884_+|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	99.0	3.0e-177
AZG51238.1|2738961_2739183_+	cell division protein FtsZ	NA	A0A0U2RTC4	Escherichia_phage	97.3	6.9e-37
AZG52859.1|2739182_2739353_+	hypothetical protein	NA	A0A0U2SHB5	Escherichia_phage	92.9	7.9e-25
AZG51239.1|2739427_2739703_+	hypothetical protein	NA	A0A0U2QW85	Escherichia_phage	93.4	4.4e-41
AZG51240.1|2741274_2742431_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	6.8e-67
AZG51241.1|2742818_2743986_+|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51242.1|2744096_2744336_+	hypothetical protein	NA	I6PCV5	Cronobacter_phage	68.4	1.3e-25
AZG51243.1|2745667_2745835_+	DNA-binding protein	NA	A0A0U2RY08	Escherichia_phage	100.0	1.3e-27
AZG51244.1|2746762_2747416_+|integrase	site-specific integrase	integrase	A0A0U2JGI6	Escherichia_phage	98.6	1.3e-120
AZG51245.1|2747888_2748803_+	metal ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AZG51246.1|2748802_2749630_+	manganese/iron ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	28.5	3.8e-11
AZG51247.1|2749626_2750484_+	metal ABC transporter permease	NA	NA	NA	NA	NA
AZG51248.1|2750480_2751338_+	metal ABC transporter permease	NA	NA	NA	NA	NA
AZG51249.1|2751538_2752162_-	DUF4376 domain-containing protein	NA	A0A0U2QQK4	Escherichia_phage	78.6	5.8e-81
AZG51250.1|2753325_2753697_-|tail	tail fiber assembly protein	tail	Q8W612	Enterobacteria_phage	82.9	6.8e-53
AZG51251.1|2753717_2753870_-|tail	phage tail protein	tail	A0A222YXY8	Escherichia_phage	68.0	1.1e-14
AZG51252.1|2753893_2754262_-	hypothetical protein	NA	A0A0C4UQV0	Shigella_phage	55.4	2.6e-20
AZG51253.1|2754289_2755446_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	8.9e-67
AZG51254.1|2755507_2755693_-	hypothetical protein	NA	A0A291AWU3	Escherichia_phage	63.4	1.5e-05
AZG51255.1|2755833_2756388_-	DUF1133 family protein	NA	A0A0U2S606	Escherichia_phage	70.5	3.7e-71
AZG51256.1|2756384_2756675_-	DUF1364 domain-containing protein	NA	A0A0U2KD41	Escherichia_phage	89.6	3.3e-47
AZG51257.1|2756674_2757274_-	DUF1367 family protein	NA	A0A0U2RT94	Escherichia_phage	94.5	1.4e-108
AZG51258.1|2758122_2758374_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51259.1|2758610_2758823_-	type I toxin-antitoxin system Hok family toxin	NA	A0A0U2QV81	Escherichia_phage	92.9	8.1e-27
AZG51260.1|2759220_2759586_-	DUF551 domain-containing protein	NA	Q08J61	Stx2-converting_phage	53.7	6.1e-30
AZG51261.1|2759585_2760251_-	hypothetical protein	NA	A0A076G611	Escherichia_phage	44.9	6.1e-36
AZG51262.1|2760247_2760613_-	HNH endonuclease	NA	A0A2R2Z2X9	Escherichia_phage	99.2	2.5e-68
AZG51263.1|2760614_2760833_-	DUF4014 domain-containing protein	NA	A0A1I9LJM2	Stx_converting_phage	90.3	1.2e-28
AZG51264.1|2760925_2761339_-	hypothetical protein	NA	A0A2R2Z307	Escherichia_phage	97.5	4.6e-58
AZG51265.1|2761339_2761762_-	DUF977 family protein	NA	A0A2I6TCA7	Escherichia_phage	76.6	5.9e-53
AZG51266.1|2761776_2762520_-	DNA replication protein DnaC	NA	V5UQI5	Shigella_phage	88.8	2.0e-120
AZG51267.1|2762526_2763165_-	hypothetical protein	NA	I6PDJ3	Cronobacter_phage	50.0	4.3e-15
AZG51268.1|2763313_2764535_+|transposase	IS3 family transposase	transposase	Q9ZXG3	Shigella_phage	98.9	1.1e-163
2763267:2764520	attR	CTAGACTGGCCCCCTGAATCTCCAGACAACCAGTATCACTTATTTAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCTCTGGCGTAAGCAATACCAGGAAGGAAGTCTTACTGCTGTGGCCGCCGGAGAACAGGTTGTTCCTGCCTCTGAACTTGCTGCCGCCATGAAGCAGATTAAAGAACTCCAGCGCCTGCTCGGCAAGAAAACGATGAAAAATGAACTCCTCAAAGAAGCCGTTGAATATGGACGGGCAAAAAAGTGGATAGCGCACGCGCCCTTATTGCCCGGGGATGGGGAGTAAGCTTAGTCAGCCGTTGTCTCCGGGTGTCGCGTGCGCAGTTGCACGTCATTCTCAGACGAACCGATGACTGGATGGATGGCCGCCGCAGTCGTCACACTGATGATACGGATGTGCTTCTCCGTATACACCATGTTATCGGAGAGCTGCCCACGTATGGTTATCGTCGGGTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGCTCATGCGCCAGAATGCGCTGTTGCTTGAGCGAAAACCTGCTGTACCGCCATCGAAACGGGCACATACAGGCAGAGTGGCCGTGAAAGAAAGCAATCAGCGATGGTGCTCTGACGGGTTCGAGTTCTGCTGTGATAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTGACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCAGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTC	NA	NA	NA	NA
AZG51269.1|2764592_2765760_+|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51270.1|2766366_2767522_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	8.9e-67
>prophage 13
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	2900435	2973947	4586233	tail,tRNA,protease,terminase,head,portal,transposase	uncultured_Caudovirales_phage(43.75%)	66	NA	NA
AZG51381.1|2900435_2901020_+|tRNA	aminoacyl-tRNA hydrolase	tRNA	NA	NA	NA	NA
AZG51382.1|2901136_2902228_+	redox-regulated ATPase YchF	NA	NA	NA	NA	NA
AZG51383.1|2903070_2905938_+	autotransporter outer membrane beta-barrel domain-containing protein	NA	NA	NA	NA	NA
AZG51384.1|2906037_2907957_-	PTS-dependent dihydroxyacetone kinase operon transcriptional regulator DhaR	NA	NA	NA	NA	NA
AZG51385.1|2908184_2909255_+	dihydroxyacetone kinase subunit DhaK	NA	NA	NA	NA	NA
AZG51386.1|2909265_2909898_+	dihydroxyacetone kinase subunit L	NA	NA	NA	NA	NA
AZG51387.1|2909908_2911327_+	dihydroxyacetone kinase subunit DhaM	NA	NA	NA	NA	NA
AZG51388.1|2911646_2913344_+	alpha,alpha-trehalase	NA	NA	NA	NA	NA
AZG51389.1|2915704_2916727_+	iron ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AZG51390.1|2916726_2917707_+	iron ABC transporter permease	NA	NA	NA	NA	NA
AZG51391.1|2917703_2918462_+	ABC transporter ATP-binding protein	NA	F2Y2R6	Organic_Lake_phycodnavirus	29.7	1.7e-13
AZG51392.1|2918471_2919281_+	methyltransferase domain-containing protein	NA	NA	NA	NA	NA
AZG51393.1|2919280_2920135_+	ModD protein	NA	NA	NA	NA	NA
AZG51394.1|2922164_2922419_-	GlsB/YeaQ/YmgE family stress response membrane protein	NA	NA	NA	NA	NA
AZG51395.1|2922619_2923354_+	flagellar brake protein	NA	NA	NA	NA	NA
AZG51396.1|2923355_2923967_-	murein transglycosylase	NA	NA	NA	NA	NA
AZG51397.1|2924066_2924981_+	muramoyltetrapeptide carboxypeptidase	NA	NA	NA	NA	NA
AZG51398.1|2925075_2926812_+	K+/H+ antiporter NhaP2	NA	NA	NA	NA	NA
AZG51399.1|2929004_2930075_-	alanine racemase	NA	NA	NA	NA	NA
AZG51400.1|2930084_2931383_-	D-amino acid dehydrogenase	NA	NA	NA	NA	NA
AZG51401.1|2931712_2933245_+	SpoVR family protein	NA	NA	NA	NA	NA
AZG51402.1|2933296_2934016_-	fatty acid metabolism transcriptional regulator FadR	NA	NA	NA	NA	NA
AZG51403.1|2934236_2935778_+	Na+/H+ antiporter NhaB	NA	NA	NA	NA	NA
AZG51404.1|2935923_2936454_+	disulfide bond formation protein DsbB	NA	NA	NA	NA	NA
AZG51405.1|2936499_2937768_-	translesion error-prone DNA polymerase V subunit UmuC	NA	I6RSM4	Salmonella_phage	83.2	2.3e-209
AZG51406.1|2937767_2938187_-	protein UmuD	NA	A0A1W6JNS2	Morganella_phage	62.1	6.9e-38
AZG51407.1|2939666_2940128_-	YcgN family cysteine cluster protein	NA	NA	NA	NA	NA
AZG51408.1|2940204_2940864_-	fumarylacetoacetate hydrolase family protein	NA	NA	NA	NA	NA
AZG51409.1|2940935_2941229_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51410.1|2941470_2941611_+	peptidase	NA	NA	NA	NA	NA
AZG51411.1|2941607_2942770_-|transposase	IS3-like element IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	40.6	4.0e-51
AZG51412.1|2943451_2944724_+|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	99.0	3.0e-177
AZG51413.1|2945447_2946143_+	septum site-determining protein MinC	NA	NA	NA	NA	NA
AZG51414.1|2946166_2946979_+	septum site-determining protein MinD	NA	NA	NA	NA	NA
AZG51415.1|2946982_2947249_+	cell division topological specificity factor	NA	NA	NA	NA	NA
AZG51416.1|2947620_2948064_-	autotransporter outer membrane beta-barrel domain-containing protein	NA	NA	NA	NA	NA
AZG51417.1|2948079_2948265_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51418.1|2948365_2948539_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51419.1|2948540_2948885_+	glycine zipper family protein	NA	NA	NA	NA	NA
AZG51420.1|2948894_2949224_+	YmgD family protein	NA	NA	NA	NA	NA
AZG51421.1|2949280_2951602_-	autotransporter outer membrane beta-barrel domain-containing protein	NA	A0A2L1IV18	Escherichia_phage	43.5	3.2e-92
AZG51422.1|2951718_2951928_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51423.1|2952678_2954202_-	cyclic diguanylate phosphodiesterase	NA	NA	NA	NA	NA
AZG51424.1|2955099_2956350_-	NADP-dependent isocitrate dehydrogenase	NA	Q77Z09	Phage_21	100.0	3.8e-23
AZG51425.1|2956521_2957175_+	23S rRNA pseudouridine synthase E	NA	NA	NA	NA	NA
AZG51426.1|2957184_2957646_+	NUDIX hydrolase	NA	NA	NA	NA	NA
AZG51427.1|2957699_2958806_+|tRNA	tRNA 2-thiouridine(34) synthase MnmA	tRNA	NA	NA	NA	NA
AZG52871.1|2958841_2959483_+	lysogenization regulator HflD	NA	NA	NA	NA	NA
AZG51428.1|2959486_2960857_+	adenylosuccinate lyase	NA	A0A2H4UUU6	Bodo_saltans_virus	44.9	7.2e-108
AZG51429.1|2961025_2961697_+	two-component system response regulator PhoP	NA	NA	NA	NA	NA
AZG51430.1|2961696_2963157_+	Virulence sensor protein PhoQ	NA	NA	NA	NA	NA
AZG51431.1|2963953_2964235_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51432.1|2964248_2965910_-|terminase	terminase large subunit	terminase	A0A2H4JB64	uncultured_Caudovirales_phage	81.4	4.4e-277
AZG51433.1|2965929_2966220_-|terminase	phage terminase small subunit P27 family	terminase	A0A2H4JHS3	uncultured_Caudovirales_phage	77.9	1.1e-39
AZG51434.1|2966275_2966458_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51435.1|2966441_2966882_-	HNH endonuclease	NA	A0A2H4JAS8	uncultured_Caudovirales_phage	72.6	2.5e-62
AZG51436.1|2966881_2967178_-|head,tail	phage gp6-like head-tail connector protein	head,tail	A0A2H4JD08	uncultured_Caudovirales_phage	62.2	2.2e-30
AZG51437.1|2967174_2967513_-|head,tail	head-tail adaptor protein	head,tail	A0A2H4JHK5	uncultured_Caudovirales_phage	52.7	1.7e-31
AZG52872.1|2967509_2968685_-|portal	phage portal protein	portal	A0A2H4JFJ9	uncultured_Caudovirales_phage	79.2	1.7e-182
AZG51438.1|2968722_2969295_-|head,protease	HK97 family phage prohead protease	head,protease	A0A2H4JB68	uncultured_Caudovirales_phage	63.5	1.6e-61
AZG52873.1|2970792_2971017_-	hypothetical protein	NA	NA	NA	NA	NA
AZG52874.1|2971057_2971171_-	trigger factor	NA	NA	NA	NA	NA
AZG51439.1|2971158_2971320_-	PerC family transcriptional regulator	NA	NA	NA	NA	NA
AZG51440.1|2971329_2971635_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51441.1|2971631_2971910_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51442.1|2972198_2973947_-	DNA primase	NA	Q7M2A8	Enterobacteria_phage	39.3	9.5e-89
>prophage 14
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	3052368	3097097	4586233	tail,transposase	Stx2-converting_phage(30.0%)	48	NA	NA
AZG51518.1|3052368_3053537_-|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51519.1|3053669_3055010_-|tail	phage tail tape measure protein	tail	K4HYW1	Escherichia_phage	33.1	1.0e-45
AZG51520.1|3055028_3055394_+|transposase	transposase	transposase	NA	NA	NA	NA
AZG51521.1|3056995_3059539_-	glucan biosynthesis protein H	NA	NA	NA	NA	NA
AZG52876.1|3059531_3061067_-	glucans biosynthesis protein MdoG	NA	NA	NA	NA	NA
AZG51522.1|3061460_3062618_+	glucan biosynthesis protein C	NA	NA	NA	NA	NA
AZG51523.1|3062625_3064107_-	phospholipase D family protein	NA	NA	NA	NA	NA
AZG51524.1|3064048_3064582_-	O-acetyl-ADP-ribose deacetylase	NA	Q71G61	Red_sea_bream_iridovirus	40.2	7.8e-26
AZG51525.1|3064646_3065815_-|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51526.1|3066079_3066445_-	major curlin subunit CsgA	NA	NA	NA	NA	NA
AZG51527.1|3067720_3068176_-	minor curlin subunit	NA	NA	NA	NA	NA
AZG51528.1|3068928_3069579_+	transcriptional regulator CsgD	NA	NA	NA	NA	NA
AZG51529.1|3069583_3069973_+	curli production assembly/transport protein CsgE	NA	NA	NA	NA	NA
AZG51530.1|3069997_3070414_+	curli production assembly/transport component CsgF	NA	NA	NA	NA	NA
AZG52877.1|3071279_3071771_-	DUF1097 domain-containing protein	NA	NA	NA	NA	NA
AZG51531.1|3071872_3072427_-	molecular chaperone	NA	NA	NA	NA	NA
AZG51532.1|3072450_3073188_-	phosphatase	NA	NA	NA	NA	NA
AZG51533.1|3075215_3076220_-|transposase	IS110-like element ISSfl8 family transposase	transposase	NA	NA	NA	NA
AZG52878.1|3076288_3076852_-	DUF4942 domain-containing protein	NA	NA	NA	NA	NA
AZG51534.1|3076936_3077134_-	DUF957 domain-containing protein	NA	NA	NA	NA	NA
AZG51535.1|3077145_3077637_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51536.1|3077633_3078008_-	toxin	NA	NA	NA	NA	NA
AZG51537.1|3078054_3078429_-	type IV toxin-antitoxin system YeeU family antitoxin	NA	NA	NA	NA	NA
AZG51538.1|3078591_3078813_-	DUF987 domain-containing protein	NA	A0A142F0X9	Klebsiella_phage	44.4	3.2e-10
AZG51539.1|3078875_3079352_-	DNA repair protein RadC	NA	NA	NA	NA	NA
AZG51540.1|3079367_3079841_-	antirestriction protein	NA	A9J566	Pseudomonas_phage	30.5	1.9e-12
AZG51541.1|3080182_3081004_-	DUF945 domain-containing protein	NA	A0A2C9CX26	Yersinia_phage	38.3	7.2e-47
AZG51542.1|3081103_3081277_-	DUF905 domain-containing protein	NA	NA	NA	NA	NA
AZG51543.1|3081396_3081846_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51544.1|3083820_3084726_-	chemotaxis protein	NA	NA	NA	NA	NA
AZG51545.1|3084722_3087107_-	dGTPase	NA	NA	NA	NA	NA
AZG51546.1|3087324_3088197_-	GTPase family protein	NA	NA	NA	NA	NA
AZG51547.1|3088281_3089199_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51548.1|3089331_3089547_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51549.1|3090030_3090228_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51550.1|3090398_3091001_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51551.1|3091095_3091374_-	AlpA family transcriptional regulator	NA	NA	NA	NA	NA
AZG52879.1|3091342_3091501_-	transcriptional regulator	NA	NA	NA	NA	NA
AZG51552.1|3091442_3091709_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51553.1|3092045_3092186_+	hemolysin activation protein	NA	NA	NA	NA	NA
AZG51554.1|3092531_3092732_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51555.1|3092930_3093500_+	inovirus Gp2 family protein	NA	NA	NA	NA	NA
AZG52880.1|3093759_3094161_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51556.1|3094148_3094583_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51557.1|3094582_3094819_+	hypothetical protein	NA	NA	NA	NA	NA
AZG52881.1|3094937_3095318_+	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZBP6	Stx2-converting_phage	99.2	7.1e-66
AZG51558.1|3095314_3095662_+	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZBY2	Stx2-converting_phage	98.3	1.4e-60
AZG51559.1|3095711_3097097_+|transposase	IS66 family transposase	transposase	A0A0P0ZBS5	Stx2-converting_phage	89.1	1.0e-258
>prophage 15
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	3122799	3172554	4586233	integrase,transposase	Salmonella_phage(22.22%)	31	3120505:3120564	3130754:3131521
3120505:3120564	attL	GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTC	NA	NA	NA	NA
AZG51581.1|3122799_3125766_-|transposase	Tn3-like element TnAs3 family transposase	transposase	A0A1B0V7H9	Salmonella_phage	73.6	0.0e+00
AZG51582.1|3125768_3126329_-	recombinase family protein	NA	A0A1B0V7I5	Salmonella_phage	86.2	4.0e-49
AZG52883.1|3126454_3126805_-	DUF3330 domain-containing protein	NA	NA	NA	NA	NA
AZG51583.1|3127007_3128021_-|integrase	class 1 integron integrase IntI1	integrase	A0A1P8DJJ6	Virus_Rctr41k	45.5	1.0e-71
AZG52884.1|3128230_3129061_+	oxacillin-hydrolyzing class D beta-lactamase OXA-1	NA	NA	NA	NA	NA
AZG51584.1|3129173_3129965_+	ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1	NA	NA	NA	NA	NA
AZG51585.1|3130820_3131303_+	glycosyltransferase	NA	NA	NA	NA	NA
AZG51586.1|3131307_3132258_+	DUF535 domain-containing protein	NA	NA	NA	NA	NA
3130754:3131521	attR	GACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGAATTTATGTTGAATTTACTGTTCCATTTAAAAATGAATGGACGACAGTTCTGTTGGTTGATTGTGGGGTCTGGTTCACCTGAACTGCGGGAACATTTACAGTATCAGATTGACAGTATGGGCATGCATGATGATGTTTTTATTGCTGACAATGTTTTTCCTGCCGCCCCCGTATATCGGGTTGCCAGTCTGGTGGTTCTGCCTTCAGAAAACGAATCTTTTGGTATGGTGCTGGCAGAAGCATCGGCATTTTCTGTGCCTGTAGTGGCCACTCAGATTGGTGGAATCCCTGAGGTTATTCAGAACAACCAGACCGGGACATTGTTACCAGCAAGTAATAAGCACGCATGGATGTGCGCCCTGAATGATTTTTTTAATGACCCTGGGCGTTTTTATCAGATGGCTCGCCTGGCAAAACAGGATATAGAAGAGCGGTTTGATATTAATAAAACTGCGTTAAAAATACTCACATTAGCGAAGCAAAAGTAACAATATGTTTTCTATAAGTAACTTATCATTTATCGGTTTCCTTAAAAGGATTATTTTTTCCTCAGATTCACTACCGGGGAAGTGGGAACACAGAAAATTTCGGTTCATGTACATTTTGCGATGTTCTATAAATCCGGTTGTCAGTATTCGATATTATTATGAACTGCGTTCCTTGCCGTGCATTGAGGATATTCTGGCAATACACCCCACGTTGCCAG	NA	NA	NA	NA
AZG51587.1|3132322_3133267_+	lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase	NA	NA	NA	NA	NA
AZG51588.1|3133447_3134587_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.0	4.3e-66
AZG51589.1|3134830_3136129_-	anaerobic C4-dicarboxylate transporter	NA	NA	NA	NA	NA
AZG51590.1|3136194_3136914_-	amino acid racemase	NA	NA	NA	NA	NA
AZG51591.1|3137258_3138203_+	HTH-type transcriptional regulator	NA	NA	NA	NA	NA
AZG51592.1|3138815_3140028_+|transposase	IS3 family transposase	transposase	Q6H9S3	Enterobacteria_phage	99.0	3.2e-168
AZG51593.1|3141203_3141410_-	helicase	NA	NA	NA	NA	NA
AZG51594.1|3141516_3142080_-	inovirus Gp2 family protein	NA	NA	NA	NA	NA
AZG51595.1|3143166_3144440_-|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	99.0	3.0e-177
AZG51596.1|3144790_3146626_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51597.1|3146726_3147014_+	AlpA family transcriptional regulator	NA	NA	NA	NA	NA
AZG51598.1|3146985_3148515_+	DUF3987 domain-containing protein	NA	NA	NA	NA	NA
AZG51599.1|3148684_3149902_-	DUF4102 domain-containing protein	NA	A0A1B0VMI6	Pseudomonas_phage	34.4	1.7e-44
AZG51600.1|3150268_3151255_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51601.1|3151846_3153008_+|transposase	IS3-like element IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	40.6	5.2e-51
AZG52885.1|3153397_3153574_+	transcriptional regulator	NA	NA	NA	NA	NA
AZG52886.1|3155021_3156461_-	EAL domain-containing protein	NA	NA	NA	NA	NA
AZG51602.1|3157523_3158084_-	diguanylate cyclase	NA	NA	NA	NA	NA
AZG51603.1|3166386_3167310_-	phosphate starvation-inducible protein PhoH	NA	R4II13	Cronobacter_phage	75.7	1.0e-89
AZG51604.1|3167782_3169048_-	deferrochelatase/peroxidase EfeB	NA	NA	NA	NA	NA
AZG51605.1|3169053_3170181_-	iron uptake system component EfeO	NA	NA	NA	NA	NA
AZG51606.1|3171001_3171367_+|transposase	transposase	transposase	NA	NA	NA	NA
AZG51607.1|3171366_3172554_+|transposase	IS91 family transposase	transposase	NA	NA	NA	NA
>prophage 16
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	3190201	3229467	4586233	tail,plate,protease,terminase,head,transposase	Salmonella_phage(57.14%)	41	NA	NA
AZG51624.1|3190201_3190894_+	two-component system response regulator TorR	NA	W8CYM9	Bacillus_phage	28.0	1.0e-17
AZG51625.1|3190866_3191895_-	TMAO reductase system periplasmic protein TorT	NA	NA	NA	NA	NA
AZG51626.1|3193107_3194109_+	acyltransferase	NA	Q716G0	Shigella_phage	90.7	1.0e-172
AZG51627.1|3194399_3194849_-|tail	tail fiber assembly protein	tail	S5FXM8	Shigella_phage	98.6	2.1e-77
AZG51628.1|3194805_3195597_-|tail	phage tail protein	tail	A0A0M3ULD8	Salmonella_phage	80.6	2.2e-61
AZG51629.1|3195596_3196277_-	DUF2612 domain-containing protein	NA	A0A0M5M1K4	Salmonella_phage	81.0	1.1e-109
AZG51630.1|3196273_3197473_-|plate	baseplate J/gp47 family protein	plate	A0A0M4RD32	Salmonella_phage	82.5	1.2e-178
AZG51631.1|3198643_3198934_+	DUF4236 domain-containing protein	NA	NA	NA	NA	NA
AZG51632.1|3198957_3199302_-	hypothetical protein	NA	A0A2H4J1A5	uncultured_Caudovirales_phage	42.1	1.1e-17
AZG51633.1|3199314_3200379_-	hypothetical protein	NA	A0A2H4J1B2	uncultured_Caudovirales_phage	66.8	8.8e-138
AZG51634.1|3200381_3200687_-	hypothetical protein	NA	A0A2H4J495	uncultured_Caudovirales_phage	53.5	9.2e-24
AZG51635.1|3200896_3202064_+|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51636.1|3202542_3204558_-	lytic transglycosylase domain-containing protein	NA	A0A0M4REK7	Salmonella_phage	73.4	6.5e-283
AZG52889.1|3204547_3204676_-	lytic transglycosylase	NA	NA	NA	NA	NA
AZG51637.1|3204735_3205161_-	hypothetical protein	NA	A0A2H4J2V6	uncultured_Caudovirales_phage	57.5	2.1e-37
AZG51638.1|3205164_3205605_-	DUF3277 family protein	NA	A0A0M5M1K6	Salmonella_phage	77.4	7.5e-59
AZG51639.1|3205615_3206761_-	DUF3383 domain-containing protein	NA	A0A2H4J8G4	uncultured_Caudovirales_phage	73.5	5.2e-160
AZG51640.1|3206764_3207322_-	hypothetical protein	NA	A0A0M4R331	Salmonella_phage	75.1	2.7e-77
AZG51641.1|3207296_3207686_-|head,tail	head-tail adaptor	head,tail	A0A0M3ULK0	Salmonella_phage	96.1	1.1e-66
AZG51642.1|3207672_3208227_-	hypothetical protein	NA	A0A0M4S631	Salmonella_phage	84.8	1.4e-81
AZG51643.1|3208223_3208631_-	DUF4054 domain-containing protein	NA	A0A0M5M3S2	Salmonella_phage	95.6	8.7e-70
AZG51644.1|3208596_3208818_-	hypothetical protein	NA	A0A0M4RTX5	Salmonella_phage	68.6	7.7e-12
AZG51645.1|3208860_3209802_-	DUF2184 domain-containing protein	NA	A0A0M3ULD3	Salmonella_phage	87.2	1.7e-156
AZG51646.1|3209813_3210317_-	hypothetical protein	NA	A0A0M4QWZ6	Salmonella_phage	82.6	1.2e-73
AZG51647.1|3210321_3211542_-	DUF2213 domain-containing protein	NA	A0A0M4R5A6	Salmonella_phage	90.7	8.7e-206
AZG51648.1|3211556_3212294_-|head	phage head morphogenesis protein	head	A0A0M4REK0	Salmonella_phage	95.0	6.6e-108
AZG51649.1|3212181_3213648_-	DUF1073 domain-containing protein	NA	A0A0M4S6U1	Salmonella_phage	95.1	1.0e-269
AZG51650.1|3213647_3215270_-	TerL protein	NA	A0A0M5M1R6	Salmonella_phage	95.2	3.0e-312
AZG51651.1|3215272_3215827_-|terminase	terminase small subunit	terminase	G0ZND3	Cronobacter_phage	69.4	2.0e-64
AZG51652.1|3215828_3216155_-	HNH endonuclease	NA	E5KJN2	Acinetobacter_phage	48.0	2.4e-17
AZG51653.1|3216216_3217384_+|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51654.1|3218189_3219389_+	porin	NA	NA	NA	NA	NA
AZG51655.1|3220561_3221008_+	protein-tyrosine-phosphatase	NA	NA	NA	NA	NA
AZG51656.1|3221027_3223208_+	tyrosine-protein kinase	NA	NA	NA	NA	NA
AZG52890.1|3223322_3224621_-	phytase AppA	NA	NA	NA	NA	NA
AZG51657.1|3224700_3224793_-	cytochrome bd-II oxidase subunit CbdX	NA	NA	NA	NA	NA
AZG51658.1|3224804_3225941_-	cytochrome bd-II ubiquinol oxidase subunit 2	NA	NA	NA	NA	NA
AZG51659.1|3225952_3227497_-	cytochrome bd-II oxidase subunit 1	NA	NA	NA	NA	NA
AZG51660.1|3227630_3228488_-	hydrogenase expression/formation protein	NA	NA	NA	NA	NA
AZG51661.1|3228484_3228883_-	hydrogenase-1 operon protein HyaE	NA	NA	NA	NA	NA
AZG51662.1|3228879_3229467_-|protease	hydrogenase 1 maturation protease	protease	NA	NA	NA	NA
>prophage 17
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	3247788	3323428	4586233	transposase,tRNA,protease	Acinetobacter_phage(15.38%)	56	NA	NA
AZG51680.1|3247788_3249549_+|protease	Lon protease family protein	protease	NA	NA	NA	NA
AZG52892.1|3249617_3250136_+	bifunctional 3-hydroxydecanoyl-ACP dehydratase/trans-2-decenoyl-ACP isomerase	NA	NA	NA	NA	NA
AZG51681.1|3250205_3250373_-	ribosome modulation factor	NA	NA	NA	NA	NA
AZG51682.1|3250628_3251192_-	membrane integrity-associated transporter subunit PqiC	NA	NA	NA	NA	NA
AZG51683.1|3251188_3252829_-	intermembrane transport protein PqiB	NA	NA	NA	NA	NA
AZG51684.1|3252833_3254087_-	membrane integrity-associated transporter subunit PqiA	NA	NA	NA	NA	NA
AZG51685.1|3254216_3256124_-	ABC transporter ATP-binding protein	NA	A0A2K9L3Z8	Tupanvirus	29.5	8.3e-54
AZG51686.1|3256135_3258244_-	bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2))-methyltransferase RlmL	NA	NA	NA	NA	NA
AZG51687.1|3258487_3259597_+	MOSC domain-containing protein	NA	NA	NA	NA	NA
AZG51688.1|3259593_3260136_-	cell division protein ZapC	NA	NA	NA	NA	NA
AZG51689.1|3260309_3261320_-	quinone-dependent dihydroorotate dehydrogenase	NA	NA	NA	NA	NA
AZG51690.1|3261430_3262144_-	fimbrial chaperone	NA	NA	NA	NA	NA
AZG51691.1|3262136_3262652_-	type 1 fimbrial protein	NA	NA	NA	NA	NA
AZG51692.1|3262659_3263202_-	fimbrial protein	NA	NA	NA	NA	NA
AZG51693.1|3263299_3264283_-	fimbrial protein	NA	NA	NA	NA	NA
AZG51694.1|3264273_3266652_-	outer membrane usher protein	NA	NA	NA	NA	NA
AZG51695.1|3267400_3267526_+	FMN reductase	NA	NA	NA	NA	NA
AZG51696.1|3267518_3268478_+	sulfonate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AZG51697.1|3268474_3269620_+	alkanesulfonate monooxygenase, FMNH(2)-dependent	NA	NA	NA	NA	NA
AZG51698.1|3269631_3269814_+	aliphatic sulfonate ABC transporter	NA	NA	NA	NA	NA
AZG51699.1|3271755_3272523_+	aliphatic sulfonates ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	36.6	4.1e-28
AZG51700.1|3272729_3275345_-	aminopeptidase N	NA	A0A0P0IY26	Acinetobacter_phage	22.6	2.4e-19
AZG51701.1|3275610_3276813_+	nicotinate phosphoribosyltransferase	NA	NA	NA	NA	NA
AZG51702.1|3276981_3278382_+|tRNA	asparagine--tRNA ligase	tRNA	A0A2K9V902	Bandra_megavirus	36.1	5.3e-82
AZG51703.1|3278982_3280071_+	porin OmpF	NA	Q1MVN1	Enterobacteria_phage	54.3	1.8e-98
AZG51704.1|3280255_3281446_+	aspartate/tyrosine/aromatic aminotransferase	NA	NA	NA	NA	NA
AZG51705.1|3281668_3282316_-	MBL fold metallo-hydrolase	NA	NA	NA	NA	NA
AZG52893.1|3282342_3282891_-	DUF882 domain-containing protein	NA	A0A0K1LKR7	Rhodobacter_phage	33.7	7.0e-06
AZG51706.1|3283071_3284919_-	L,D-transpeptidase	NA	NA	NA	NA	NA
AZG51707.1|3285126_3286455_-|transposase	IS4 family transposase	transposase	NA	NA	NA	NA
AZG51708.1|3286617_3291078_-	chromosome partition protein MukB	NA	NA	NA	NA	NA
AZG51709.1|3291077_3291782_-	chromosome partition protein MukE	NA	NA	NA	NA	NA
AZG51710.1|3291762_3293085_-	chromosome partition protein MukF	NA	NA	NA	NA	NA
AZG51711.1|3293081_3293867_-|tRNA	tRNA uridine 5-oxyacetic acid(34) methyltransferase CmoM	tRNA	NA	NA	NA	NA
AZG51712.1|3294002_3294782_+	envelope biogenesis factor ElyC	NA	NA	NA	NA	NA
AZG51713.1|3294758_3295652_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51714.1|3295805_3296552_-	3-deoxy-manno-octulosonate cytidylyltransferase	NA	NA	NA	NA	NA
AZG51715.1|3296548_3296731_-	protein YcaR	NA	NA	NA	NA	NA
AZG51716.1|3296782_3298015_-	winged helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
AZG51717.1|3298051_3299038_-	tetraacyldisaccharide 4'-kinase	NA	NA	NA	NA	NA
AZG51718.1|3299034_3300783_-	lipid A export ATP-binding/permease MsbA	NA	W8CYL7	Bacillus_phage	29.8	3.3e-57
AZG51719.1|3303285_3303570_-	integration host factor subunit beta	NA	A7KV42	Bacillus_phage	40.2	3.2e-10
AZG51720.1|3303729_3305403_-	30S ribosomal protein S1	NA	NA	NA	NA	NA
AZG51721.1|3305513_3306197_-	(d)CMP kinase	NA	NA	NA	NA	NA
AZG51722.1|3306373_3307135_-|protease	metalloprotease	protease	NA	NA	NA	NA
AZG51723.1|3307270_3308599_-|transposase	IS4 family transposase	transposase	NA	NA	NA	NA
AZG51724.1|3308742_3310026_-	3-phosphoshikimate 1-carboxyvinyltransferase	NA	NA	NA	NA	NA
AZG51725.1|3310096_3311185_-	3-phosphoserine/phosphohydroxythreonine aminotransferase	NA	M1Q1P2	Streptococcus_phage	46.8	3.5e-81
AZG52894.1|3312139_3313900_+	30S ribosomal protein S12 methylthiotransferase accessory protein YcaO	NA	NA	NA	NA	NA
AZG51726.1|3314305_3315163_+	formate transporter FocA	NA	NA	NA	NA	NA
AZG51727.1|3315217_3317500_+	formate C-acetyltransferase	NA	A0A2P0VNR5	Tetraselmis_virus	41.2	4.9e-162
AZG51728.1|3317691_3318432_+	pyruvate formate lyase 1-activating protein	NA	A0A2P0VNQ0	Tetraselmis_virus	26.5	8.0e-21
AZG51729.1|3319358_3319685_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51730.1|3319590_3320747_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	8.9e-67
AZG52895.1|3321200_3321845_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AZG51731.1|3323221_3323428_-|transposase	transposase domain-containing protein	transposase	A0A0N7BTS3	Escherichia_phage	96.2	2.6e-06
>prophage 18
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	3437664	3602753	4586233	integrase,tail,holin,tRNA,terminase,head,capsid,transposase	Enterobacteria_phage(23.17%)	156	3514568:3514627	3548271:3549519
AZG51825.1|3437664_3438993_-|transposase	IS4 family transposase	transposase	NA	NA	NA	NA
AZG51826.1|3441108_3441786_+	Fe2+-dependent dioxygenase	NA	Q5GQB0	Synechococcus_phage	29.7	3.4e-18
AZG51827.1|3441859_3442126_+	DksA/TraR family C4-type zinc finger protein	NA	E5G6L7	Salmonella_phage	45.6	4.0e-07
AZG51828.1|3442390_3442651_+	DUF1471 domain-containing protein	NA	NA	NA	NA	NA
AZG51829.1|3442879_3443965_-	malate/lactate/ureidoglycolate dehydrogenase	NA	NA	NA	NA	NA
AZG51830.1|3444105_3445068_-	DNA-binding protein YbiB	NA	NA	NA	NA	NA
AZG52901.1|3445095_3447246_-	ATP-dependent DNA helicase DinG	NA	A0A127AW80	Bacillus_phage	25.6	3.1e-41
AZG51831.1|3447365_3447848_+	NADAR family protein	NA	A0A0H3TLU0	Faustovirus	52.0	1.3e-35
AZG52902.1|3449470_3450142_+	transcriptional regulator	NA	NA	NA	NA	NA
AZG51832.1|3450144_3451140_+	secretion protein HlyD	NA	NA	NA	NA	NA
AZG51833.1|3451132_3452869_+	ABC transporter ATP-binding protein	NA	W6JKT0	Anomala_cuprea_entomopoxvirus	29.8	2.3e-18
AZG51834.1|3452861_3453995_+	ABC transporter permease	NA	NA	NA	NA	NA
AZG51835.1|3454005_3455112_+	inner membrane transport permease YbhR	NA	NA	NA	NA	NA
AZG51836.1|3455073_3455484_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51837.1|3455616_3456378_+	endonuclease/exonuclease/phosphatase family protein	NA	NA	NA	NA	NA
AZG51838.1|3456374_3457616_+	cardiolipin synthase ClsB	NA	NA	NA	NA	NA
AZG51839.1|3457615_3458572_+	UPF0104 family protein	NA	NA	NA	NA	NA
AZG51840.1|3458607_3459321_-	Bax inhibitor-1/YccA family protein	NA	NA	NA	NA	NA
AZG51841.1|3459525_3460230_-	Bax inhibitor-1/YccA family protein	NA	NA	NA	NA	NA
AZG51842.1|3460366_3460819_-	molybdopterin synthase catalytic subunit MoaE	NA	NA	NA	NA	NA
AZG51843.1|3460820_3461066_-	molybdopterin synthase sulfur carrier subunit	NA	NA	NA	NA	NA
AZG51844.1|3461058_3461544_-	cyclic pyranopterin monophosphate synthase MoaC	NA	NA	NA	NA	NA
AZG51845.1|3461546_3462059_-	molybdenum cofactor biosynthesis protein B	NA	NA	NA	NA	NA
AZG51846.1|3462080_3463070_-	GTP 3',8-cyclase MoaA	NA	NA	NA	NA	NA
AZG51847.1|3463466_3464375_+	uridine diphosphate-N-acetylglucosamine-binding protein YvcK	NA	A1IMD5	Streptococcus_phage	31.1	1.4e-27
AZG51848.1|3464566_3466588_-	excinuclease ABC subunit B	NA	NA	NA	NA	NA
AZG51849.1|3467166_3467844_-	ATP-dependent dethiobiotin synthetase BioD	NA	NA	NA	NA	NA
AZG51850.1|3467836_3468592_-	malonyl-ACP O-methyltransferase BioC	NA	NA	NA	NA	NA
AZG51851.1|3468578_3469733_-	8-amino-7-oxononanoate synthase	NA	NA	NA	NA	NA
AZG51852.1|3469729_3470770_-	biotin synthase	NA	NA	NA	NA	NA
AZG51853.1|3470856_3472146_+	adenosylmethionine--8-amino-7-oxononanoate transaminase	NA	A0A1V0SKB7	Klosneuvirus	28.6	6.5e-18
AZG51854.1|3472204_3472681_+	kinase inhibitor	NA	NA	NA	NA	NA
AZG51855.1|3473263_3475027_+	E3 ubiquitin--protein ligase	NA	NA	NA	NA	NA
AZG51856.1|3475027_3475207_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51857.1|3475206_3475830_-	DUF4376 domain-containing protein	NA	A0A0U2QQK4	Escherichia_phage	75.9	5.1e-77
AZG51858.1|3477258_3477858_-	Ail/Lom family protein	NA	H6WZM8	Escherichia_phage	93.5	6.1e-104
AZG51859.1|3481466_3482069_-|tail	tail assembly protein	tail	A5LH42	Enterobacteria_phage	85.6	8.1e-88
AZG51860.1|3482005_3482749_-|tail	phage tail protein	tail	K7PLW1	Enterobacteria_phage	94.7	6.8e-145
AZG51861.1|3482753_3483452_-|tail	phage minor tail protein L	tail	A0A0K2FJ01	Enterobacteria_phage	89.7	8.4e-121
AZG51862.1|3483451_3483781_-|tail	phage tail protein	tail	A5LH39	Enterobacteria_phage	97.2	2.4e-57
AZG52903.1|3484574_3484766_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51863.1|3486488_3486818_-|tail	phage tail assembly protein T	tail	A5LH37	Enterobacteria_phage	99.1	1.3e-55
AZG51864.1|3487270_3488011_-|tail	phage tail protein	tail	A5LH35	Enterobacteria_phage	96.7	1.5e-128
AZG51865.1|3488021_3488423_-|tail	phage tail protein	tail	A0A291AWY2	Escherichia_phage	97.7	1.6e-71
AZG51866.1|3488419_3489004_-|tail	phage tail protein	tail	A5LH33	Enterobacteria_phage	87.6	6.0e-88
AZG51867.1|3488990_3489368_-|tail	phage tail protein	tail	A0A2R9YJJ5	Escherichia_phage	57.3	2.5e-31
AZG51868.1|3489379_3489766_-	DNA-packaging protein FI	NA	NA	NA	NA	NA
AZG51869.1|3489817_3490846_-|capsid	major capsid protein	capsid	C6ZCY2	Enterobacteria_phage	62.8	1.4e-116
AZG51870.1|3490903_3491251_-|head	head decoration protein	head	A0A2R9YJN3	Escherichia_phage	55.9	6.4e-21
AZG51871.1|3491287_3492793_-	S49 family peptidase	NA	A0A2I6TC87	Escherichia_phage	53.2	3.0e-99
AZG51872.1|3494372_3494576_-|tail	phage tail protein	tail	K7PM10	Enterobacteria_phage	57.4	8.6e-10
AZG51873.1|3494559_3496488_-|terminase	phage terminase large subunit family protein	terminase	A0A0K2FJ14	Enterobacteria_phage	66.0	1.8e-258
AZG52904.1|3496459_3496744_-	DNA packaging protein	NA	NA	NA	NA	NA
AZG51874.1|3500639_3500846_-	hypothetical protein	NA	H6WRZ6	Salmonella_phage	98.5	4.0e-31
AZG51875.1|3501062_3501596_-	lysozyme	NA	K7PLY1	Enterobacteria_phage	98.3	1.6e-100
AZG52905.1|3501661_3502276_-	hypothetical protein	NA	Q08JA0	Stx2-converting_phage	56.9	1.0e-29
AZG51876.1|3502294_3502510_-|holin	holin	holin	M1FN85	Enterobacteria_phage	94.4	2.2e-32
AZG51877.1|3503312_3503693_-	antitermination protein	NA	A0A088CD47	Shigella_phage	87.9	8.2e-62
AZG51878.1|3503685_3503886_-	protein ninH	NA	A0A088CC23	Shigella_phage	74.2	1.1e-20
AZG52906.1|3503980_3504223_-	hypothetical protein	NA	Q8W639	Enterobacteria_phage	93.8	7.8e-34
AZG51879.1|3504234_3505626_-	replicative DNA helicase	NA	Q8W640	Enterobacteria_phage	95.7	3.6e-256
AZG51880.1|3505622_3506501_-	AAA family ATPase	NA	Q8W641	Enterobacteria_phage	95.6	3.0e-139
AZG51881.1|3506511_3507420_-	DNA-binding protein	NA	Q8W642	Enterobacteria_phage	96.6	1.3e-60
AZG51882.1|3507406_3507640_-	hypothetical protein	NA	A0A1C9II64	Salmonella_phage	51.4	5.1e-14
AZG51883.1|3508584_3508848_+	type II toxin-antitoxin system RelE/ParE family toxin	NA	A0A088CBP5	Shigella_phage	93.1	2.9e-42
AZG51884.1|3508837_3509146_+	XRE family transcriptional regulator	NA	A0A088CD40	Shigella_phage	98.0	3.5e-47
AZG51885.1|3509187_3509364_-	NinE family protein	NA	K7PHE6	Enterobacteria_phage	96.6	3.0e-27
AZG51886.1|3509360_3509771_-	recombination protein NinB	NA	A0A0P0ZCW6	Stx2-converting_phage	98.5	8.0e-71
AZG52907.1|3509767_3510046_-	hypothetical protein	NA	Q9ZWY1	Enterobacteria_phage	96.7	5.4e-47
AZG51887.1|3510384_3511552_+|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51888.1|3511487_3511667_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51889.1|3511682_3512811_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	42.3	4.6e-60
AZG51890.1|3514124_3514547_-	DUF1133 family protein	NA	A0A0U2S606	Escherichia_phage	63.4	9.4e-43
3514568:3514627	attL	TGAAGTGGTCAACAAAAACTGGCCACCGAGTTAGAGTTTTTCCAGTATCGATTTTCCGAT	NA	NA	NA	NA
AZG51891.1|3514575_3515744_-|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51892.1|3515914_3516580_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51893.1|3516748_3517162_-	hypothetical protein	NA	A0A2R2Z307	Escherichia_phage	97.5	4.6e-58
AZG51894.1|3517162_3517585_-	DUF977 family protein	NA	A0A2I6TCA7	Escherichia_phage	76.6	5.9e-53
AZG51895.1|3519213_3519636_-	hypothetical protein	NA	A0A0U2RXZ9	Escherichia_phage	93.6	3.8e-68
AZG51896.1|3519619_3519847_-	transcriptional regulator	NA	NA	NA	NA	NA
AZG51897.1|3519923_3520331_+	helix-turn-helix domain-containing protein	NA	I6PD69	Cronobacter_phage	49.6	1.7e-28
AZG51898.1|3520533_3520689_+	DUF1391 domain-containing protein	NA	M4QQ57	Salicola_phage	53.2	5.2e-07
AZG51899.1|3520690_3520894_+	hypothetical protein	NA	I6PDF6	Cronobacter_phage	82.5	1.0e-10
AZG51900.1|3520870_3521161_-	hypothetical protein	NA	NA	NA	NA	NA
AZG51901.1|3521135_3522409_-|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	99.0	3.0e-177
AZG51902.1|3522911_3523760_+	transcriptional regulator	NA	A0A0P0ZE80	Stx2-converting_phage	57.0	9.7e-55
AZG51903.1|3523776_3524058_+	hypothetical protein	NA	A0A0U2SHB5	Escherichia_phage	55.8	2.0e-09
AZG51904.1|3524273_3525402_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	42.3	4.2e-61
AZG51905.1|3525951_3527119_+|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51906.1|3527666_3528823_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.4	1.2e-66
AZG51907.1|3528888_3529506_+	DUF4376 domain-containing protein	NA	A0A0U2QQK4	Escherichia_phage	76.5	5.7e-81
AZG51908.1|3529505_3529685_+	hypothetical protein	NA	NA	NA	NA	NA
AZG51909.1|3529685_3530639_-	invasion protein	NA	NA	NA	NA	NA
AZG51910.1|3532001_3532133_+	DNA invertase	NA	A0A0C4UR34	Shigella_phage	86.7	2.6e-07
AZG51911.1|3532392_3533388_+	6-phosphogluconolactonase	NA	NA	NA	NA	NA
AZG51912.1|3534565_3535618_+	4-oxalomesaconate tautomerase	NA	NA	NA	NA	NA
AZG51913.1|3535693_3537127_+	anion permease	NA	NA	NA	NA	NA
AZG51914.1|3537309_3539490_+	hydratase	NA	NA	NA	NA	NA
AZG51915.1|3539630_3540914_-	putative acyl-CoA thioester hydrolase	NA	NA	NA	NA	NA
AZG51916.1|3541048_3541930_-|integrase	integrase	integrase	K7P6P6	Enterobacteria_phage	99.7	7.2e-162
AZG51917.1|3542030_3543160_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	41.9	1.0e-59
AZG51918.1|3543728_3544403_+	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZCV4	Stx2-converting_phage	30.1	5.8e-10
AZG51919.1|3544399_3544750_+|transposase	transposase	transposase	A0A0P0ZDM8	Stx2-converting_phage	68.7	3.5e-27
AZG51920.1|3545477_3546633_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.4	2.0e-66
AZG51921.1|3547153_3548321_+|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51922.1|3548664_3549174_-	DedA family protein	NA	NA	NA	NA	NA
AZG51923.1|3549371_3550067_+	hypothetical protein	NA	G8C7P2	Escherichia_phage	55.4	6.4e-12
3548271:3549519	attR	ATCGGAAAATCGATACTGGAAAAACTCTAACTCGGTGGCCAGTTTTTGTTGACCACTTCAAAAGCTGAAAATGATGCTCTTCGGCGCAAGCTTGATAATGGTGGTCGGGTGCTCGTCAAAGGAAAATGCCCTGTGCCATCCTCAGCCGAAACCTCCAGCGCCTCCGGCATGGGCAATGATGCCACCGTCGAACTCTCTCCAGTTGCTGGACGAAACGTTCTCGGTATCCGGGACGGAATCATCAGCGACCAGACAGCATTGAGAATGCTTCAGGAGTACATCAGGATCCAATGCCTTGGGGGGTAGCGGTAATTTTACTCATTATCCTTCAAATCAGATTCTGTTGTCAGAGGAATGGGGGAAGCTGGATTCGCAAGAGCTTTTTATGGGCAGTTTAGCTAAAAAAAGGCAACACGAAGCTAAAACTACCAACATAAAGTGCTGACCAGCTAGCAGCTGAAATCAGACTCACTGTATACACTTTCACTGGATGAAGTTGCAACATTCCTGCCACCAAAGGAGCAATGTAACGCAGCACGGCGATAAAGCGCGAAGTGAAAAGTATTGACACAGAGTTATTTTGCAACTGAAGGCGAACCCGTTCTATTGTATTGGAACGGCTCGATATTATACATGCAAGTTGAGGGATATGCCCAATTATTATACCAAGATGGTAATTAACGATAGTACCGCACCATGCGCCACTCATGACCGTGATTCCAGCTTCCCATGGTGAAAGAGTCGTCTTGCTGACTGTAATTACAGTGGCCATCATAATTGATGCTGGTGGCAATATCGCCGAAATGAGTAAAGTGGATTTTGTGAACGCTATTATAAAAAGAAGCCCCCATAGGCGATATGGATGAAGTACAAAATAGTTCATCAAAGCATTTATCCACTCCATCAATGTCTTTCCTTCTGTGAATTTTTCTTTGCTATTTAACCGTGATACGACTTAATTTAGGCTTAAACACCTTACATTTACAAGGTACTCCTGTGGGGGGCCCTGCCACGGAGCGTCGCAGGAGTGAGTGATGAGGAAGAATTAAAGCAACCTATTGTGACAGGCAGCGATAACAGTAAATCACAGGAAGCATAATCATGGCAAAACCGGACTGGGAGGCCATCGAATCGGCATACCGGGCCGGAGTCCTTAGCCTCCGTGATATAGGCGAGAAATACGGCGTTACAGAAGGGGCTATCAGGAAGAGGGCCAAAAAGCTTGATTGGGCACGCAGTGGCGGTACGC	NA	NA	NA	NA
AZG51924.1|3550072_3551241_-|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG51925.1|3551314_3552022_+|terminase	PBSX family phage terminase large subunit	terminase	K4NXU1	Acinetobacter_phage	73.4	9.5e-96
AZG51926.1|3552052_3553324_+|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	99.0	3.0e-177
AZG51927.1|3554069_3555536_+	DUF1073 domain-containing protein	NA	A0A0M4S6U1	Salmonella_phage	91.0	9.6e-260
AZG51928.1|3555426_3556170_+|head	phage head morphogenesis protein	head	A0A0M4REK0	Salmonella_phage	84.4	5.3e-89
AZG51929.1|3556173_3557394_+	DUF2213 domain-containing protein	NA	A0A0M4R5A6	Salmonella_phage	85.4	2.1e-191
AZG51930.1|3557397_3557754_+	hypothetical protein	NA	A0A0M4QWZ6	Salmonella_phage	87.4	4.7e-51
AZG51931.1|3557898_3558840_+	DUF2184 domain-containing protein	NA	A0A0M3ULD3	Salmonella_phage	85.9	7.8e-154
AZG51932.1|3558881_3559127_+	hypothetical protein	NA	A0A0M4RTX5	Salmonella_phage	68.6	1.1e-11
AZG51933.1|3559123_3560280_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	8.9e-67
AZG52908.1|3561950_3562196_-	transcriptional regulator	NA	A0A2I7S995	Vibrio_phage	63.2	6.1e-18
AZG51934.1|3562358_3562868_+	DNA-binding protein	NA	NA	NA	NA	NA
AZG51935.1|3563587_3564973_-	anaerobic C4-dicarboxylate transporter DcuC	NA	NA	NA	NA	NA
AZG51936.1|3565560_3566121_+	phospholipid:lipid A palmitoyltransferase	NA	NA	NA	NA	NA
AZG51937.1|3566295_3566505_+	cold-shock protein CspE	NA	A0A1W6JNX5	Morganella_phage	78.1	2.7e-22
AZG51938.1|3566558_3566942_-	fluoride efflux transporter CrcB	NA	A0A2H4J148	uncultured_Caudovirales_phage	53.6	6.8e-24
AZG51939.1|3567034_3567823_+	deaminated glutathione amidase	NA	NA	NA	NA	NA
AZG51940.1|3567951_3568155_+	twin-arginine translocase subunit TatE	NA	NA	NA	NA	NA
AZG51941.1|3568255_3569221_-	lipoyl synthase	NA	NA	NA	NA	NA
AZG51942.1|3569429_3570383_-	DNA-binding transcriptional regulator	NA	NA	NA	NA	NA
AZG51943.1|3570641_3571283_-	octanoyltransferase	NA	NA	NA	NA	NA
AZG51944.1|3571383_3571647_-	DUF493 family protein	NA	NA	NA	NA	NA
AZG51945.1|3571757_3572969_-	serine-type D-Ala-D-Ala carboxypeptidase	NA	B6DZZ7	Stx2-converting_phage	47.2	7.5e-101
AZG51946.1|3573107_3574196_-	endolytic peptidoglycan transglycosylase RlpA	NA	F5B3X9	Synechococcus_phage	53.2	3.6e-09
AZG51947.1|3574206_3575319_-	rod shape-determining protein RodA	NA	NA	NA	NA	NA
AZG51948.1|3575321_3577223_-	penicillin-binding protein 2	NA	NA	NA	NA	NA
AZG51949.1|3577253_3577721_-	23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH	NA	NA	NA	NA	NA
AZG51950.1|3577724_3578042_-	ribosome silencing factor RsfS	NA	NA	NA	NA	NA
AZG51951.1|3578301_3578913_-	adenosylcobalamin/alpha-ribazole phosphatase	NA	NA	NA	NA	NA
AZG51952.1|3578936_3579578_-	nicotinate-nucleotide adenylyltransferase	NA	NA	NA	NA	NA
AZG51953.1|3579579_3580611_-	DNA polymerase III subunit delta	NA	NA	NA	NA	NA
AZG51954.1|3580610_3581192_-	LPS assembly lipoprotein LptE	NA	NA	NA	NA	NA
AZG51955.1|3581206_3583789_-|tRNA	leucine--tRNA ligase	tRNA	A0A2H4PQS0	Staphylococcus_phage	42.3	1.4e-184
AZG51956.1|3584023_3584506_+	zinc ribbon-containing protein	NA	NA	NA	NA	NA
AZG51957.1|3584575_3585553_-	Sel1 family TPR-like repeat protein YbeQ	NA	NA	NA	NA	NA
AZG51958.1|3585716_3586424_+	DUF1266 domain-containing protein	NA	NA	NA	NA	NA
AZG51959.1|3586420_3587848_+	J domain-containing protein	NA	NA	NA	NA	NA
AZG51960.1|3587857_3588412_-	sel1 repeat family protein	NA	NA	NA	NA	NA
AZG51961.1|3588513_3589221_+	DUF1266 domain-containing protein	NA	NA	NA	NA	NA
AZG51962.1|3589217_3590669_+	J domain-containing protein	NA	NA	NA	NA	NA
AZG51963.1|3592473_3593409_-	pyrimidine-specific ribonucleoside hydrolase RihA	NA	NA	NA	NA	NA
AZG51964.1|3593526_3594252_-	amino acid ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	38.6	1.7e-31
AZG51965.1|3594251_3594926_-	glutamate/aspartate ABC transporter permease GltK	NA	NA	NA	NA	NA
AZG51966.1|3594925_3595666_-	amino acid ABC transporter permease	NA	NA	NA	NA	NA
AZG51967.1|3595835_3596744_-	amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AZG51968.1|3597140_3598679_-	apolipoprotein N-acyltransferase	NA	NA	NA	NA	NA
AZG51969.1|3598703_3599582_-	magnesium and cobalt efflux protein CorC	NA	NA	NA	NA	NA
AZG51970.1|3599671_3600139_-	endoribonuclease YbeY	NA	NA	NA	NA	NA
AZG51971.1|3600135_3601215_-	PhoH family protein	NA	A0A0S0MVD6	Pseudomonas_phage	46.6	4.3e-47
AZG51972.1|3601328_3602753_-|tRNA	tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB	tRNA	NA	NA	NA	NA
>prophage 19
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	3855244	3912316	4586233	integrase,tail,tRNA,coat,transposase	Enterobacteria_phage(20.0%)	51	3897086:3897145	3900093:3900244
AZG52178.1|3855244_3856693_-|tRNA	tRNA 4-thiouridine(8) synthase ThiI	tRNA	NA	NA	NA	NA
AZG52179.1|3856604_3856793_+	hypothetical protein	NA	NA	NA	NA	NA
AZG52180.1|3856898_3857141_+	exodeoxyribonuclease 7 small subunit	NA	NA	NA	NA	NA
AZG52181.1|3857140_3858040_+	(2E,6E)-farnesyl diphosphate synthase	NA	NA	NA	NA	NA
AZG52182.1|3858064_3859927_+	1-deoxy-D-xylulose-5-phosphate synthase	NA	NA	NA	NA	NA
AZG52183.1|3859981_3860899_+	aldo/keto reductase	NA	NA	NA	NA	NA
AZG52184.1|3861009_3861528_-	phosphatidylglycerophosphatase A	NA	NA	NA	NA	NA
AZG52185.1|3861505_3862483_-	thiamine-phosphate kinase	NA	NA	NA	NA	NA
AZG52186.1|3862560_3862980_-	N utilization substance protein B	NA	NA	NA	NA	NA
AZG52187.1|3862999_3863470_-	6,7-dimethyl-8-ribityllumazine synthase	NA	A0A2H4PQS3	Staphylococcus_phage	47.4	1.3e-29
AZG52188.1|3863558_3864662_-	bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD	NA	A0A1V0SE20	Indivirus	35.5	9.1e-53
AZG52189.1|3864665_3865115_-	transcriptional regulator NrdR	NA	NA	NA	NA	NA
AZG52190.1|3865265_3865805_+	DUF3251 domain-containing protein	NA	NA	NA	NA	NA
AZG52191.1|3866102_3866987_+	nucleoside-specific channel-forming protein Tsx	NA	NA	NA	NA	NA
AZG52192.1|3867163_3867511_-	HNH endonuclease	NA	NA	NA	NA	NA
AZG52193.1|3867639_3868611_-	protein translocase subunit SecF	NA	A0A1B1IVP7	uncultured_Mediterranean_phage	37.9	8.0e-45
AZG52194.1|3868621_3870469_-	protein translocase subunit SecD	NA	NA	NA	NA	NA
AZG52195.1|3870496_3870829_-	preprotein translocase subunit YajC	NA	A0A1B1IVR5	uncultured_Mediterranean_phage	33.0	2.8e-10
AZG52196.1|3870851_3871979_-|tRNA	tRNA guanosine(34) transglycosylase Tgt	tRNA	A0A1B1IVQ4	uncultured_Mediterranean_phage	46.3	1.6e-89
AZG52197.1|3872033_3873104_-|tRNA	tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA	tRNA	NA	NA	NA	NA
AZG52198.1|3873774_3875592_-	maltodextrin glucosidase	NA	NA	NA	NA	NA
AZG52199.1|3875747_3877121_-	proline-specific permease ProY	NA	NA	NA	NA	NA
AZG52200.1|3877196_3878516_-	branched-chain amino acid transporter carrier protein BrnQ	NA	NA	NA	NA	NA
AZG52201.1|3878922_3880218_-	phosphate regulon sensor histidine kinase PhoR	NA	W8CYF6	Bacillus_phage	30.8	1.7e-26
AZG52202.1|3881154_3882357_+	exonuclease subunit SbcD	NA	R4JGS2	Bacillus_phage	31.5	2.4e-06
AZG52203.1|3882353_3885497_+	exonuclease subunit SbcC	NA	G3MAB6	Bacillus_virus	26.9	5.8e-12
AZG52916.1|3885622_3886804_+	MFS transporter AraJ	NA	NA	NA	NA	NA
AZG52204.1|3886946_3887855_-	fructokinase	NA	NA	NA	NA	NA
AZG52917.1|3887979_3888891_+	recombination-associated protein RdgC	NA	S4TWL4	Salmonella_phage	63.3	4.6e-103
AZG52205.1|3889910_3890195_-	pyrimidine/purine nucleoside phosphorylase	NA	NA	NA	NA	NA
AZG52206.1|3890266_3890944_-	protein AroM	NA	NA	NA	NA	NA
AZG52207.1|3891204_3891393_-	protein YaiA	NA	NA	NA	NA	NA
AZG52208.1|3891442_3891967_-	shikimate kinase	NA	NA	NA	NA	NA
AZG52209.1|3892149_3892608_-	YaiI/YqxD family protein	NA	NA	NA	NA	NA
AZG52210.1|3892727_3893537_+	pyrroline-5-carboxylate reductase	NA	NA	NA	NA	NA
AZG52211.1|3893553_3894669_-	diguanylate cyclase AdrA	NA	A0A127AWB9	Bacillus_phage	34.5	1.5e-18
AZG52212.1|3895994_3897210_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	5.5e-67
3897086:3897145	attL	GATGAAGCCATCTCAGTAATACGGGAATACATTGAGATTTTCTACAATCGTCAGCGTCGT	NA	NA	NA	NA
AZG52213.1|3897337_3897961_+|tail	phage tail protein	tail	A0A088CQ58	Enterobacteria_phage	76.3	2.9e-72
AZG52214.1|3898014_3899181_-	acyltransferase	NA	A0A088CPR9	Enterobacteria_phage	99.5	3.6e-209
AZG52215.1|3899535_3900000_-|integrase	site-specific integrase	integrase	U5P434	Shigella_phage	96.1	3.5e-83
AZG52216.1|3900893_3901960_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	45.9	8.7e-61
3900093:3900244	attR	ACGACGCTGACGATTGTAGAAAATCTCAATGTATTCCCGTATTACTGAGATGGCTTCATCGGTAATGACTCCAACTTACTGATAGTGTTTTATGTTCAGATAATGCCCGATGACCTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGTG	NA	NA	NA	NA
AZG52217.1|3902820_3903989_-|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG52218.1|3904064_3905216_+|coat	coat protein	coat	A0A2D1GLV2	Escherichia_phage	98.7	1.6e-214
AZG52219.1|3905260_3905485_+	hypothetical protein	NA	A0A2D1GLK1	Escherichia_phage	69.3	1.4e-24
AZG52220.1|3905462_3905963_+	recombinase RmuC	NA	G8EYJ2	Enterobacteria_phage	99.4	6.5e-91
AZG52221.1|3905962_3907381_+	hypothetical protein	NA	Q9AYZ4	Salmonella_phage	98.9	1.9e-273
AZG52222.1|3907380_3908178_+	hypothetical protein	NA	Q716G6	Shigella_phage	92.9	2.3e-90
AZG52223.1|3908177_3908633_+	DUF2824 family protein	NA	A0A2D1GLX4	Escherichia_phage	99.3	8.8e-87
AZG52224.1|3908635_3909244_+	DNA transfer protein	NA	G5DA80	Enterobacteria_phage	85.2	4.8e-96
AZG52225.1|3909253_3910585_+	acyltransferase	NA	A0A2D1GLX5	Escherichia_phage	99.8	3.1e-217
AZG52226.1|3910585_3912316_+	lytic transglycosylase domain-containing protein	NA	A0A088CQ71	Enterobacteria_phage	98.1	3.1e-281
>prophage 20
CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4586233	3926328	3973840	4586233	integrase,tail,plate,transposase	Shigella_phage(25.0%)	39	3928394:3928425	3969681:3969712
AZG52237.1|3926328_3927602_-|transposase	IS3-like element IS2 family transposase	transposase	Q9ZXG3	Shigella_phage	99.0	3.0e-177
3928394:3928425	attL	CTGGTTGTCTGGAGATTCAGGGGGCCAGTCTA	NA	NA	NA	NA
AZG52238.1|3929317_3930292_+	porphobilinogen synthase	NA	NA	NA	NA	NA
AZG52239.1|3930397_3931249_-	taurine dioxygenase	NA	NA	NA	NA	NA
AZG52240.1|3931245_3932073_-	taurine ABC transporter permease TauC	NA	NA	NA	NA	NA
AZG52241.1|3932069_3932837_-	taurine ABC transporter ATP-binding subunit	NA	G9BWD6	Planktothrix_phage	39.8	4.3e-25
AZG52242.1|3932849_3933776_-	taurine ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AZG52243.1|3935118_3935889_-	amidohydrolase	NA	NA	NA	NA	NA
AZG52244.1|3936042_3936516_+	C-lysozyme inhibitor	NA	NA	NA	NA	NA
AZG52245.1|3939242_3939821_+	phosphoheptose isomerase	NA	A0A067XQR2	Caulobacter_phage	32.0	1.1e-14
AZG52246.1|3940026_3940794_+	class II glutamine amidotransferase	NA	NA	NA	NA	NA
AZG52247.1|3940764_3941505_-	transpeptidase	NA	NA	NA	NA	NA
AZG52248.1|3941855_3942410_+	peptidoglycan endopeptidase	NA	A0A0A8WIF2	Clostridium_phage	36.1	1.4e-14
AZG52249.1|3942585_3943083_+|transposase	transposase	transposase	NA	NA	NA	NA
AZG52250.1|3943299_3945039_-	flagellar type III secretion system protein FlhA	NA	NA	NA	NA	NA
AZG52918.1|3944983_3945769_+	putative lateral flagellar export/assembly protein LafU	NA	NA	NA	NA	NA
AZG52251.1|3945839_3946895_+	DNA polymerase IV	NA	NA	NA	NA	NA
AZG52252.1|3946946_3947240_+	type I toxin-antitoxin system antitoxin YafN	NA	NA	NA	NA	NA
AZG52253.1|3947242_3947641_+	type II toxin-antitoxin system YafO family toxin	NA	NA	NA	NA	NA
AZG52254.1|3947650_3948103_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AZG52255.1|3948321_3949392_+	RNA ligase RtcB family protein	NA	A0A059VHB8	Mycobacterium_phage	30.0	7.0e-26
AZG52256.1|3950124_3951582_-	cytosol nonspecific dipeptidase	NA	NA	NA	NA	NA
AZG52257.1|3951843_3952302_+	xanthine phosphoribosyltransferase	NA	NA	NA	NA	NA
AZG52258.1|3952393_3953638_+	esterase	NA	NA	NA	NA	NA
AZG52259.1|3953695_3954097_+	sigma factor-binding protein Crl	NA	NA	NA	NA	NA
AZG52260.1|3954135_3955191_-	phosphoporin PhoE	NA	Q1MVN1	Enterobacteria_phage	60.9	3.5e-118
AZG52261.1|3956254_3957358_+	glutamate 5-kinase	NA	A0A1X9I5D0	Streptococcus_phage	40.1	4.1e-61
AZG52262.1|3957369_3958623_+	gamma-glutamyl-phosphate reductase	NA	A0A1X9I5D4	Streptococcus_phage	47.2	5.8e-96
AZG52919.1|3958827_3959766_-|integrase	site-specific integrase	integrase	U5P434	Shigella_phage	99.7	4.7e-183
AZG52263.1|3959839_3960996_-|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	8.9e-67
AZG52264.1|3961529_3961985_+|tail	tail fiber assembly protein	tail	M1FJ98	Enterobacteria_phage	100.0	3.2e-81
AZG52265.1|3962218_3962524_-	hypothetical protein	NA	M1FPE6	Enterobacteria_phage	100.0	2.8e-52
AZG52266.1|3963741_3964662_-	glycosyltransferase	NA	M1FQW5	Enterobacteria_phage	99.7	6.2e-172
AZG52267.1|3964658_3965021_-	GtrA family protein	NA	U5P0S6	Shigella_phage	99.2	1.1e-58
AZG52268.1|3966784_3967953_-|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG52920.1|3968048_3968336_+	hypothetical protein	NA	A0A1P8DTP0	Salmonella_phage	60.0	1.8e-29
AZG52269.1|3970619_3971252_+	impE family protein	NA	NA	NA	NA	NA
3969681:3969712	attR	CTGGTTGTCTGGAGATTCAGGGGGCCAGTCTA	NA	NA	NA	NA
AZG52270.1|3971252_3971450_+	hypothetical protein	NA	NA	NA	NA	NA
AZG52271.1|3971446_3971941_+|plate	type VI secretion system baseplate subunit TssE	plate	NA	NA	NA	NA
AZG52272.1|3971956_3973840_+|plate	type VI secretion system baseplate subunit TssF	plate	NA	NA	NA	NA
>prophage 1
CP034059	Shigella flexneri strain FDAARGOS_535 plasmid unnamed1, complete sequence	217451	625	71627	217451	transposase,tRNA,protease,integrase	Escherichia_phage(28.57%)	56	2145:2167	70347:70369
AZG48862.1|625_1832_+|transposase	IS91 family transposase	transposase	NA	NA	NA	NA
AZG48863.1|1902_2133_+	hypothetical protein	NA	NA	NA	NA	NA
2145:2167	attL	TAGTCTCCAGGATTCCCGGGGCG	NA	NA	NA	NA
AZG48864.1|2180_2399_+	hypothetical protein	NA	NA	NA	NA	NA
AZG48865.1|2281_3736_-	hypothetical protein	NA	NA	NA	NA	NA
AZG48866.1|6290_6710_-	hypothetical protein	NA	NA	NA	NA	NA
AZG48867.1|6759_7938_+	group II intron reverse transcriptase/maturase	NA	A0A0U4J920	Pseudomonas_phage	32.1	9.7e-29
AZG48868.1|8967_9948_-	ParB/RepB/Spo0J family partition protein	NA	Q38420	Escherichia_phage	58.2	5.0e-95
AZG48869.1|9947_11147_-	ParA family protein	NA	Q71TL9	Escherichia_phage	75.1	2.0e-175
AZG48870.1|11284_11491_-	hypothetical protein	NA	A0A0P0ZEB3	Stx2-converting_phage	57.1	1.0e-05
AZG48871.1|11873_12656_-	AAA family ATPase	NA	A0A2L1IVB6	Escherichia_phage	98.8	8.5e-138
AZG48872.1|13088_14282_+|transposase	IS4-like element ISSfl1 family transposase	transposase	S5FM71	Shigella_phage	62.5	2.0e-138
AZG48873.1|14998_15112_-	glutathione S-transferase	NA	NA	NA	NA	NA
AZG49020.1|16852_17329_-	hypothetical protein	NA	NA	NA	NA	NA
AZG48874.1|17820_18045_+	hypothetical protein	NA	NA	NA	NA	NA
AZG48875.1|18244_18463_+	hypothetical protein	NA	NA	NA	NA	NA
AZG48876.1|18526_19204_-	hypothetical protein	NA	NA	NA	NA	NA
AZG48877.1|22092_22440_-	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZDM8	Stx2-converting_phage	75.7	3.4e-46
AZG49021.1|22901_24230_+|transposase	IS4 family transposase	transposase	NA	NA	NA	NA
AZG48878.1|24240_24525_-	IS66 family insertion sequence hypothetical protein	NA	NA	NA	NA	NA
AZG48879.1|24624_24873_+|transposase	transposase	transposase	NA	NA	NA	NA
AZG48880.1|26194_26773_+	hypothetical protein	NA	NA	NA	NA	NA
AZG48881.1|27804_28524_+	type III secretion system effector phosphothreonine lyase	NA	NA	NA	NA	NA
AZG48882.1|28955_30665_+	ShET2/EspL2 family type III secretion system effector toxin	NA	NA	NA	NA	NA
AZG48883.1|31294_31477_+	hypothetical protein	NA	A0A0N7C1Y0	Escherichia_phage	86.0	5.5e-16
AZG48884.1|31577_32318_-	phosphatase PAP2 family protein	NA	A0A1B1IUP6	uncultured_Mediterranean_phage	28.9	2.6e-11
AZG49022.1|32646_33330_-	OspB	NA	A0A0P0ZCT1	Stx2-converting_phage	34.2	5.8e-26
AZG49023.1|35059_36007_-|protease	omptin family outer membrane protease IcsP	protease	NA	NA	NA	NA
AZG48885.1|36968_37106_+	non-LEE-encoded type III effector F	NA	NA	NA	NA	NA
AZG48886.1|38312_39481_-|transposase	IS3-like element IS911 family transposase	transposase	Q716C2	Shigella_phage	100.0	1.8e-184
AZG48887.1|41297_41564_+	hypothetical protein	NA	NA	NA	NA	NA
AZG48888.1|41954_43682_+	E3 ubiquitin--protein ligase	NA	NA	NA	NA	NA
AZG48889.1|44012_44201_+	hypothetical protein	NA	NA	NA	NA	NA
AZG48890.1|45633_45825_-	hypothetical protein	NA	NA	NA	NA	NA
AZG48891.1|46524_47382_-	incFII family plasmid replication initiator RepA	NA	NA	NA	NA	NA
AZG49024.1|47374_47449_-	positive regulator of RepFIC repA1 expression	NA	NA	NA	NA	NA
AZG48892.1|47495_47621_+	replication protein RepA	NA	NA	NA	NA	NA
AZG48893.1|47672_47933_-	replication regulatory protein repA2	NA	NA	NA	NA	NA
AZG48894.1|48172_48763_-	DUF2726 domain-containing protein	NA	NA	NA	NA	NA
AZG48895.1|48801_49011_-	hemolysin expression modulator Hha	NA	NA	NA	NA	NA
AZG48896.1|49345_50501_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	3.4e-66
AZG48897.1|51016_51229_-	ANR family transcriptional regulator	NA	NA	NA	NA	NA
AZG49025.1|51359_51920_-	fertility inhibition protein FinO	NA	NA	NA	NA	NA
AZG48898.1|51974_52721_-	type-F conjugative transfer system pilin acetylase TraX	NA	A0A077JBM8	Xanthomonas_phage	32.0	5.4e-09
AZG48899.1|57622_58015_-	conjugative relaxase	NA	NA	NA	NA	NA
AZG48900.1|58072_58303_+	antitoxin	NA	NA	NA	NA	NA
AZG48901.1|58302_58701_+|tRNA	tRNA(fMet)-specific endonuclease VapC	tRNA	NA	NA	NA	NA
AZG48902.1|58709_58895_-	conjugal transfer protein TraD	NA	NA	NA	NA	NA
AZG48903.1|58933_60089_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.7	2.0e-66
AZG48904.1|61140_62085_-	lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase	NA	NA	NA	NA	NA
AZG48905.1|62149_63100_-	DUF535 domain-containing protein	NA	NA	NA	NA	NA
AZG48906.1|63104_64193_-	glycosyltransferase family 1 protein	NA	NA	NA	NA	NA
AZG49026.1|64195_65017_-	carbohydrate transporter	NA	NA	NA	NA	NA
AZG48907.1|65401_65518_-|integrase	integrase	integrase	NA	NA	NA	NA
AZG48908.1|65583_68433_+	hypothetical protein	NA	NA	NA	NA	NA
AZG48909.1|68736_68979_+	IS66 family insertion sequence hypothetical protein	NA	NA	NA	NA	NA
AZG48910.1|70325_71627_-|transposase	IS4 family transposase	transposase	NA	NA	NA	NA
70347:70369	attR	TAGTCTCCAGGATTCCCGGGGCG	NA	NA	NA	NA
>prophage 2
CP034059	Shigella flexneri strain FDAARGOS_535 plasmid unnamed1, complete sequence	217451	82046	121378	217451	transposase,protease	Stx2-converting_phage(40.0%)	26	NA	NA
AZG48920.1|82046_82397_-|transposase	transposase	transposase	A0A0P0ZDM8	Stx2-converting_phage	67.5	2.3e-26
AZG48921.1|82393_83068_-	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZCV4	Stx2-converting_phage	30.8	2.0e-10
AZG49029.1|84657_84888_-	hypothetical protein	NA	NA	NA	NA	NA
AZG48922.1|86123_86798_+	IS66 family insertion sequence hypothetical protein	NA	A0A0P0ZCV4	Stx2-converting_phage	30.8	2.0e-10
AZG48923.1|86794_87145_+|transposase	transposase	transposase	A0A0P0ZDM8	Stx2-converting_phage	68.7	3.5e-27
AZG48924.1|87750_88906_+|transposase	IS3 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	44.4	2.0e-66
AZG48925.1|90946_91717_-	hypothetical protein	NA	NA	NA	NA	NA
AZG48926.1|92207_92429_-	hypothetical protein	NA	NA	NA	NA	NA
AZG48927.1|92429_93113_-	DNA methylase	NA	A0A2I7RE86	Vibrio_phage	36.9	2.3e-30
AZG49030.1|93484_94387_-	DUF1281 domain-containing protein	NA	NA	NA	NA	NA
AZG48928.1|94826_95786_+	plasmid stabilization protein	NA	A0A222YXF2	Escherichia_phage	40.9	1.4e-62
AZG48929.1|95785_96181_+	plasmid stabilization protein	NA	NA	NA	NA	NA
AZG48930.1|96369_96744_+	type II toxin-antitoxin system RelB/DinJ family antitoxin	NA	NA	NA	NA	NA
AZG48931.1|96789_97633_+|transposase	IS5 family transposase	transposase	A0A0N9SHJ4	Paenibacillus_phage	49.1	2.2e-22
AZG48932.1|97803_98553_-	phosphatase PAP2 family protein	NA	NA	NA	NA	NA
AZG48933.1|100850_102503_-	bifunctional UDP-sugar hydrolase/5'-nucleotidase	NA	NA	NA	NA	NA
AZG48934.1|104686_107995_-	autotransporter outer membrane beta-barrel domain-containing protein	NA	A0A2L1IV18	Escherichia_phage	28.6	1.9e-74
AZG48935.1|108523_109726_+|protease	cysteine protease	protease	NA	NA	NA	NA
AZG48936.1|110952_111195_-	hypothetical protein	NA	NA	NA	NA	NA
AZG48937.1|111154_111394_+	reverse transcriptase	NA	NA	NA	NA	NA
AZG48938.1|112056_112479_+|transposase	transposase	transposase	NA	NA	NA	NA
AZG49031.1|116044_116761_+	hypothetical protein	NA	NA	NA	NA	NA
AZG49032.1|117312_117717_+	hypothetical protein	NA	NA	NA	NA	NA
AZG48939.1|118454_119653_-|transposase	IS91 family transposase	transposase	NA	NA	NA	NA
AZG48940.1|119662_119851_-	hypothetical protein	NA	NA	NA	NA	NA
AZG48941.1|120315_121378_+|transposase	IS3-like element ISSfl11 family transposase	transposase	A0A0P0I4A4	Acinetobacter_phage	45.2	1.5e-57
