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
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	27279	78575	4105872	transposase,tRNA	Synechococcus_phage(25.0%)	48	NA	NA
AUL02627.1|27279_28182_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02628.1|28310_28610_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02629.1|28670_29105_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02630.1|29137_30355_-	thiolase	NA	NA	NA	NA	NA
AUL02631.1|30360_30858_-	dehydratase	NA	NA	NA	NA	NA
AUL02632.1|31065_32001_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05910.1|32210_33002_+	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL02633.1|33044_34466_+	2-methylcitrate dehydratase	NA	NA	NA	NA	NA
AUL02634.1|34669_35572_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02635.1|35568_36759_-	MFS transporter	NA	NA	NA	NA	NA
AUL02636.1|37008_37920_+|tRNA	glycine--tRNA ligase subunit alpha	tRNA	NA	NA	NA	NA
AUL02637.1|37921_40060_+|tRNA	glycine--tRNA ligase subunit beta	tRNA	NA	NA	NA	NA
AUL02638.1|40056_40596_+	D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase	NA	NA	NA	NA	NA
AUL02639.1|40599_41328_+	1-acyl-sn-glycerol-3-phosphate acyltransferase	NA	NA	NA	NA	NA
AUL02640.1|41314_42208_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02641.1|42278_42674_+	lactoylglutathione lyase	NA	NA	NA	NA	NA
AUL02642.1|42683_43214_+	peptide deformylase	NA	E3SLL2	Synechococcus_phage	35.4	3.7e-12
AUL02643.1|43342_43522_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05911.1|45219_45744_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02644.1|45715_45952_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
AUL02645.1|46079_46973_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02646.1|48142_49390_+	homoserine O-acetyltransferase	NA	NA	NA	NA	NA
AUL02647.1|49386_50001_+	methionine biosynthesis protein MetW	NA	NA	NA	NA	NA
AUL02648.1|51128_52385_+	muropeptide transporter AmpG	NA	NA	NA	NA	NA
AUL02649.1|53616_54351_-	glutamate racemase	NA	NA	NA	NA	NA
AUL02650.1|54356_54947_-	arginine transporter ATP-binding subunit	NA	G9BWD6	Planktothrix_phage	33.6	3.2e-20
AUL02651.1|54971_55661_-	amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL02652.1|55657_56419_-	glutamate ABC transporter permease	NA	NA	NA	NA	NA
AUL02653.1|56498_57398_-	amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL02654.1|57491_58442_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02655.1|59242_60469_-	serine kinase HipA	NA	NA	NA	NA	NA
AUL02656.1|60468_60888_-	transcriptional regulator	NA	NA	NA	NA	NA
AUL05912.1|61071_62013_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02657.1|62435_63272_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02658.1|64057_64360_-	ferredoxin	NA	NA	NA	NA	NA
AUL02659.1|64478_65537_-	oxidoreductase	NA	NA	NA	NA	NA
AUL02660.1|65571_66843_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02661.1|66873_67128_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02662.1|67472_68654_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02663.1|69123_70026_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02664.1|70119_70434_+|transposase	transposase	transposase	NA	NA	NA	NA
AUL02665.1|71626_73534_+	molecular chaperone HtpG	NA	A0A1B1ISV4	uncultured_Mediterranean_phage	37.2	1.1e-117
AUL02666.1|73695_74316_-	glutathione S-transferase	NA	NA	NA	NA	NA
AUL02667.1|74347_74929_-	N-acetylmuramoyl-L-alanine amidase	NA	A0A1W6DX33	Sphingobium_phage	54.3	1.7e-05
AUL02668.1|75017_75269_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02669.1|75270_76113_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02670.1|76218_77628_+	signal recognition particle protein	NA	NA	NA	NA	NA
AUL02671.1|77624_78575_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 2
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	107417	175239	4105872	transposase,tRNA	Bacillus_phage(22.22%)	60	NA	NA
AUL02700.1|107417_108320_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02701.1|109266_110460_+	cystathionine beta-lyase	NA	NA	NA	NA	NA
AUL02702.1|110541_111171_-	thiol:disulfide interchange protein	NA	NA	NA	NA	NA
AUL02703.1|111232_111916_-	cell division protein	NA	NA	NA	NA	NA
AUL02704.1|111925_113608_-|tRNA	arginine--tRNA ligase	tRNA	NA	NA	NA	NA
AUL05915.1|113895_114243_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02705.1|114333_114651_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05916.1|114933_115950_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL02706.1|116025_116826_-	ABC transporter permease	NA	NA	NA	NA	NA
AUL02707.1|116822_117698_-	ABC transporter permease	NA	NA	NA	NA	NA
AUL02708.1|117708_119001_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL02709.1|119043_120084_-	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	33.7	6.0e-22
AUL02710.1|120189_121011_-	phosphodiesterase	NA	NA	NA	NA	NA
AUL02711.1|121111_122014_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02712.1|122159_123065_-	ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	31.7	9.8e-21
AUL02713.1|123061_123895_-	ABC transporter permease	NA	NA	NA	NA	NA
AUL02714.1|124731_125742_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL02715.1|125738_126128_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02716.1|126111_126723_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02717.1|127009_128275_+	amidase	NA	NA	NA	NA	NA
AUL02718.1|128365_130066_-	2-isopropylmalate synthase	NA	NA	NA	NA	NA
AUL02719.1|130492_131140_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02720.1|131138_132578_+	RNA polymerase sigma-54 factor	NA	NA	NA	NA	NA
AUL02721.1|132688_132973_+	bacterioferritin	NA	NA	NA	NA	NA
AUL02722.1|133000_133879_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02723.1|135145_136096_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02724.1|136224_136467_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02725.1|136514_138023_-	PLP-dependent threonine dehydratase	NA	NA	NA	NA	NA
AUL02726.1|138769_142732_+	FAD-linked oxidase	NA	NA	NA	NA	NA
AUL02727.1|142784_143567_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02728.1|143654_144878_-	CoA transferase	NA	NA	NA	NA	NA
AUL05917.1|144861_145794_-	lipase	NA	NA	NA	NA	NA
AUL02729.1|145799_146612_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL02730.1|146632_147076_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02731.1|147094_147853_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02732.1|147924_148896_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02733.1|149014_149797_+	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02734.1|150563_151544_-	carboxylase	NA	NA	NA	NA	NA
AUL02735.1|151540_152269_-	allophanate hydrolase	NA	NA	NA	NA	NA
AUL02736.1|152293_152725_-	glyoxalase	NA	NA	NA	NA	NA
AUL02737.1|152826_153702_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02738.1|153753_154953_-	D-3-phosphoglycerate dehydrogenase	NA	A0A1V0SBV6	Catovirus	42.6	3.1e-91
AUL02739.1|155056_155518_-	metal-binding protein	NA	NA	NA	NA	NA
AUL02740.1|155623_157021_-	two-component sensor histidine kinase	NA	NA	NA	NA	NA
AUL02741.1|157017_157695_-	DNA-binding response regulator	NA	W8CYM9	Bacillus_phage	35.2	1.5e-29
AUL02742.1|157750_159061_-	phosphate regulon sensor histidine kinase PhoR	NA	A0A1V0SGX0	Hokovirus	25.5	6.2e-16
AUL02743.1|159072_159771_-	phosphate regulon transcriptional regulatory protein PhoB	NA	W8CYM9	Bacillus_phage	37.1	8.6e-33
AUL02744.1|159934_160711_+	bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase	NA	NA	NA	NA	NA
AUL02745.1|160876_161899_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02746.1|162127_162763_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02747.1|162768_164322_+	ubiquinone biosynthesis regulatory protein kinase UbiB	NA	A0A2N9QVT9	Dishui_lake_phycodnavirus	28.7	1.0e-33
AUL02748.1|164880_165831_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02749.1|167274_168177_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02750.1|168154_168784_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02751.1|169066_170497_+	RNA helicase	NA	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	29.8	5.8e-44
AUL02752.1|170530_171160_+	threonine transporter RhtB	NA	NA	NA	NA	NA
AUL02753.1|171208_172816_+	peptide chain release factor 3	NA	A0A2K9L6L3	Tupanvirus	37.8	9.3e-14
AUL02754.1|172852_173524_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05918.1|173605_174082_-	bacterioferritin	NA	NA	NA	NA	NA
AUL02755.1|174336_175239_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 3
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	224436	278073	4105872	transposase,tRNA	Bacillus_phage(25.0%)	45	NA	NA
AUL02790.1|224436_225387_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02791.1|225605_226301_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02792.1|226317_227730_+	hydroxyacid dehydrogenase	NA	NA	NA	NA	NA
AUL02793.1|227842_229273_+	aldehyde dehydrogenase family protein	NA	NA	NA	NA	NA
AUL02794.1|229314_231228_-	phosphomethylpyrimidine synthase ThiC	NA	NA	NA	NA	NA
AUL02795.1|231546_232113_+	preprotein translocase subunit SecD	NA	NA	NA	NA	NA
AUL02796.1|232203_233205_+	restriction endonuclease	NA	NA	NA	NA	NA
AUL02797.1|233319_234270_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02798.1|234356_235307_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02799.1|235303_236254_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02800.1|236352_237150_-	beta-D-hydroxybutyrate dehydrogenase	NA	NA	NA	NA	NA
AUL02801.1|238099_238510_+	4-carboxymuconolactone decarboxylase	NA	NA	NA	NA	NA
AUL02802.1|238759_239515_+	gamma-hydroxybutyrate dehydrogenase	NA	D2K0C8	Staphylococcus_phage	55.0	4.6e-32
AUL02803.1|239531_240275_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02804.1|240318_241362_-	C4-dicarboxylate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL05922.1|242375_243635_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02805.1|245045_246002_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02806.1|246020_246512_-	2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase	NA	NA	NA	NA	NA
AUL02807.1|246508_247864_-	poly(A) polymerase	NA	A0A1B1IVF3	uncultured_Mediterranean_phage	36.8	3.4e-25
AUL02808.1|247864_248563_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02809.1|248559_249261_-	DnaA regulatory inactivator Hda	NA	NA	NA	NA	NA
AUL02810.1|249513_250563_+	phosphoribosylformylglycinamidine cyclo-ligase	NA	Q58MH8	Prochlorococcus_phage	43.6	5.6e-68
AUL02811.1|250668_251610_-|tRNA	tRNA (adenosine(37)-N6)-dimethylallyltransferase MiaA	tRNA	NA	NA	NA	NA
AUL02812.1|251606_253496_-	DNA mismatch repair protein MutL	NA	A0A1B2LRQ5	Wolbachia_phage	32.8	3.3e-79
AUL05923.1|253600_254221_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02813.1|254363_255749_-	N-acetylmuramoyl-L-alanine amidase	NA	A0A2H4JCM7	uncultured_Caudovirales_phage	30.3	4.5e-17
AUL02814.1|255679_256216_-|tRNA	tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE	tRNA	NA	NA	NA	NA
AUL02815.1|256367_257759_+	fumarate hydratase, class II	NA	NA	NA	NA	NA
AUL02816.1|257775_258756_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02817.1|258891_259875_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL02818.1|259939_260839_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02819.1|260945_262700_+	gamma-glutamyltransferase	NA	NA	NA	NA	NA
AUL02820.1|262707_263817_-	carnitine dehydratase	NA	NA	NA	NA	NA
AUL02821.1|263844_264825_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL02822.1|265555_266506_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02823.1|266520_266892_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02824.1|267065_267611_+	ArsR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02825.1|267736_269314_+	cytochrome d terminal oxidase subunit 1	NA	NA	NA	NA	NA
AUL02826.1|269329_270484_+	cytochrome d ubiquinol oxidase subunit II	NA	NA	NA	NA	NA
AUL02827.1|270497_270623_+	cyd operon protein YbgT	NA	NA	NA	NA	NA
AUL02828.1|270619_272371_+	thiol reductant ABC exporter subunit CydD	NA	W8CYL7	Bacillus_phage	23.8	3.4e-09
AUL02829.1|272367_274047_+	thiol reductant ABC exporter subunit CydC	NA	W8CYL7	Bacillus_phage	27.6	3.6e-16
AUL02830.1|274109_274658_+	adenine phosphoribosyltransferase	NA	A0A1V0SKE5	Klosneuvirus	43.1	1.3e-28
AUL02831.1|275800_276079_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02832.1|277122_278073_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 4
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	390835	448344	4105872	transposase	Orpheovirus(14.29%)	50	NA	NA
AUL02939.1|390835_391786_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02940.1|391928_392840_+	reductase	NA	NA	NA	NA	NA
AUL02941.1|392836_393085_+	NrdH-redoxin	NA	NA	NA	NA	NA
AUL02942.1|393081_394287_+	CoA transferase	NA	NA	NA	NA	NA
AUL02943.1|394359_395355_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02944.1|395377_396598_-	acyl-CoA transferase	NA	NA	NA	NA	NA
AUL02945.1|396594_397239_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02946.1|397235_397628_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02947.1|397516_398869_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02948.1|398969_399779_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05931.1|400083_401037_+	thioredoxin-disulfide reductase	NA	A0A2I2L5E1	Orpheovirus	42.5	5.6e-59
AUL02949.1|401135_402119_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02950.1|402795_403566_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL02951.1|403562_404741_-	carnitine dehydratase	NA	NA	NA	NA	NA
AUL02952.1|404908_406615_-	thiamine pyrophosphate-binding protein	NA	NA	NA	NA	NA
AUL02953.1|406611_407508_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02954.1|407548_409138_-	sulfurtransferase	NA	NA	NA	NA	NA
AUL02955.1|409187_410180_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02956.1|410248_410848_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02957.1|411308_412289_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02958.1|412364_413267_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02959.1|413403_414318_+	EamA family transporter	NA	NA	NA	NA	NA
AUL02960.1|414314_414974_+	hypothetical protein	NA	NA	NA	NA	NA
AUL02961.1|415063_415987_+	alpha/beta hydrolase	NA	A0A1C9C5K3	Heterosigma_akashiwo_virus	27.2	4.8e-07
AUL02962.1|415992_416448_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02963.1|416444_417548_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02964.1|417735_419355_-	dolichyl-phosphate-mannose--protein mannosyltransferase	NA	NA	NA	NA	NA
AUL02965.1|419351_420410_-	glycosyltransferase	NA	I1TED8	Salmonella_phage	40.5	2.8e-59
AUL02966.1|420539_421034_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL02967.1|421126_422104_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02968.1|422299_423505_+	sodium/glutamate symporter	NA	NA	NA	NA	NA
AUL02969.1|423501_425013_+	TRAP ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL05932.1|425028_426342_-	short-chain fatty acid transporter	NA	NA	NA	NA	NA
AUL02970.1|426532_426712_-	hypothetical protein	NA	NA	NA	NA	NA
AUL02971.1|427121_427856_-	DNA polymerase III subunit epsilon	NA	A0A1X9SH08	Bradyrhizobium_phage	43.8	1.4e-41
AUL02972.1|430348_431251_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL02973.1|431382_431781_-	elongation factor G	NA	E4ZFJ7	Streptococcus_phage	44.3	9.0e-19
AUL02974.1|432191_432662_-	universal stress protein	NA	NA	NA	NA	NA
AUL02975.1|432750_433095_-	TIGR01244 family protein	NA	NA	NA	NA	NA
AUL02976.1|433194_434595_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02977.1|436383_436902_-	methyltransferase	NA	G3MA03	Bacillus_virus	38.9	2.1e-12
AUL02978.1|437012_437768_+	hypothetical protein	NA	A0A0R6PEZ3	Moraxella_phage	40.8	2.9e-42
AUL02979.1|437963_439196_+	CoA transferase	NA	NA	NA	NA	NA
AUL02980.1|439188_439974_+	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL02981.1|440040_441012_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL02982.1|441022_442000_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL02983.1|442125_443298_+	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL02984.1|443324_444353_+	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL02985.1|444418_445612_+	acetyl-CoA acetyltransferase	NA	NA	NA	NA	NA
AUL02986.1|447393_448344_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 5
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	619725	720183	4105872	transposase,terminase,tRNA,tail	Pseudomonas_phage(11.54%)	108	NA	NA
AUL03136.1|619725_620676_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03137.1|621374_621758_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03138.1|621815_622418_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05939.1|622435_622837_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03139.1|622952_623864_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03140.1|623860_624442_+	NUDIX hydrolase	NA	NA	NA	NA	NA
AUL05940.1|625245_625971_+	arginyltransferase	NA	NA	NA	NA	NA
AUL03141.1|626011_627061_+	dihydroorotate dehydrogenase (quinone)	NA	NA	NA	NA	NA
AUL03142.1|627208_627787_-	Phasin (PHA-granule associated protein)	NA	NA	NA	NA	NA
AUL03143.1|628173_629151_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL03144.1|629244_633639_-	dermonecrotic toxin	NA	NA	NA	NA	NA
AUL03145.1|633839_634688_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03146.1|634846_635659_-	competence/damage-inducible protein A	NA	NA	NA	NA	NA
AUL03147.1|635712_636663_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03148.1|636760_637561_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03149.1|637622_638006_+	thiol reductase thioredoxin	NA	NA	NA	NA	NA
AUL03150.1|638017_639451_-	ATP-dependent RNA helicase	NA	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	34.4	1.5e-52
AUL03151.1|639656_639986_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03152.1|639988_640738_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03153.1|640920_641841_+	branched chain amino acid aminotransferase	NA	NA	NA	NA	NA
AUL03154.1|641887_642100_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03155.1|642122_642545_+	DUF4440 domain-containing protein	NA	NA	NA	NA	NA
AUL03156.1|642561_643662_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL03157.1|643758_645276_-	peptidase	NA	NA	NA	NA	NA
AUL05941.1|646211_647084_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03158.1|647174_648269_-	porin	NA	NA	NA	NA	NA
AUL03159.1|648562_649465_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05942.1|649587_650529_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03160.1|650612_650972_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03161.1|651353_652391_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03162.1|652707_654048_+	Xaa-Pro aminopeptidase	NA	NA	NA	NA	NA
AUL03163.1|654057_654510_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03164.1|654615_655788_+	monooxygenase	NA	NA	NA	NA	NA
AUL03165.1|655853_656879_+|tRNA	tRNA dihydrouridine synthase DusB	tRNA	NA	NA	NA	NA
AUL03166.1|656919_657159_+	Fis family transcriptional regulator	NA	NA	NA	NA	NA
AUL03167.1|657228_658818_+	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase	NA	Q58MG4	Prochlorococcus_phage	47.2	8.7e-65
AUL03168.1|658817_659366_+	crossover junction endodeoxyribonuclease RuvC	NA	NA	NA	NA	NA
AUL03169.1|659446_660019_+	Holliday junction DNA helicase RuvA	NA	NA	NA	NA	NA
AUL03170.1|660037_660949_-	NAD-dependent dehydratase	NA	NA	NA	NA	NA
AUL03171.1|661022_661991_-	serine dehydratase	NA	NA	NA	NA	NA
AUL03172.1|662113_663187_+	Holliday junction DNA helicase RuvB	NA	A0A127AWE7	Bacillus_phage	25.7	2.3e-08
AUL03173.1|663191_665012_-	ATP-dependent DNA helicase RecQ	NA	L7RCS0	Acanthamoeba_polyphaga_moumouvirus	35.3	3.1e-74
AUL03174.1|665088_665991_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03175.1|666127_666463_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03176.1|666596_667247_+	carbonate dehydratase	NA	NA	NA	NA	NA
AUL03177.1|667268_668687_-	amidase	NA	NA	NA	NA	NA
AUL03178.1|668756_669512_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05943.1|669480_670239_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL03179.1|670249_671131_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL03180.1|671147_671855_+	ABC transporter ATP-binding protein	NA	W8CYL7	Bacillus_phage	25.4	8.2e-07
AUL03181.1|671857_672616_+	ABC transporter ATP-binding protein	NA	W6JKT0	Anomala_cuprea_entomopoxvirus	24.4	4.4e-14
AUL03182.1|672825_674568_+	sulfite reductase	NA	NA	NA	NA	NA
AUL03183.1|674560_675085_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03184.1|675124_675919_-	metal ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL03185.1|676086_677160_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03186.1|677258_678209_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03187.1|678460_678667_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05944.1|678738_679350_-	LexA family transcriptional repressor	NA	NA	NA	NA	NA
AUL03188.1|679829_680150_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03189.1|680142_680841_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03190.1|680855_681077_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03191.1|681094_682045_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03192.1|682684_683170_+|terminase	terminase	terminase	C7U0W1	Enterobacteria_phage	61.5	7.3e-39
AUL03193.1|683156_684434_+|terminase	terminase	terminase	A0A1B1P9C9	Acinetobacter_phage	64.7	2.4e-150
AUL03194.1|684436_685855_+	hypothetical protein	NA	R9TF43	Synechococcus_phage	42.1	2.2e-99
AUL03195.1|685826_686939_+	hypothetical protein	NA	A0A0H5BBX3	Pseudomonas_phage	49.7	2.1e-102
AUL03196.1|686944_687187_+	hypothetical protein	NA	A0A0H5AUE5	Pseudomonas_phage	53.2	5.6e-16
AUL03197.1|687309_687912_+	hypothetical protein	NA	R9TF81	Synechococcus_phage	43.6	7.9e-27
AUL03198.1|688340_689291_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03199.1|689965_690217_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03200.1|690279_690762_+	hypothetical protein	NA	A0A2H4JE38	uncultured_Caudovirales_phage	37.1	1.8e-13
AUL03201.1|690763_690964_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03202.1|690963_691359_+	hypothetical protein	NA	A0A2D2W284	Stenotrophomonas_phage	35.0	7.8e-07
AUL03203.1|691355_691754_+	hypothetical protein	NA	I6PCW1	Cronobacter_phage	38.0	4.2e-16
AUL03204.1|691750_692173_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03205.1|692180_692681_+	HNH endonuclease	NA	A0A1I9SEX5	Klebsiella_phage	45.1	4.4e-31
AUL03206.1|692935_693454_+|tail	phage tail protein	tail	A0A1S5R1H0	Pseudomonas_phage	38.3	5.4e-24
AUL03207.1|693463_693793_+	hypothetical protein	NA	A0A2H4J121	uncultured_Caudovirales_phage	44.0	2.9e-15
AUL03208.1|693810_694101_+	hypothetical protein	NA	A0A2H4JBP7	uncultured_Caudovirales_phage	45.2	3.7e-14
AUL03209.1|696747_697107_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03210.1|697174_697708_+	hypothetical protein	NA	A5A3Q9	Burkholderia_phage	46.9	1.1e-40
AUL03211.1|697704_698094_+	hypothetical protein	NA	A0A0G3EYJ9	Achromobacter_phage	50.0	3.0e-35
AUL03212.1|698086_702043_+	hypothetical protein	NA	A0A0B5A1N2	Achromobacter_phage	40.8	3.9e-215
AUL03213.1|702047_702464_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03214.1|702682_702946_+	hypothetical protein	NA	A0A1B0V3F2	Roseobacter_phage	41.8	7.2e-09
AUL03215.1|702945_703758_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03216.1|703762_704005_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03217.1|703983_704535_+	lysozyme	NA	NA	NA	NA	NA
AUL03218.1|704534_705050_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03219.1|705046_705328_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03220.1|705327_705549_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03221.1|705877_706549_-	hypothetical protein	NA	Q5QF62	Pseudomonas_virus	39.9	4.7e-36
AUL03222.1|706476_706845_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03223.1|706904_707591_-	DNA-binding response regulator	NA	NA	NA	NA	NA
AUL03224.1|707571_708144_-	RNA pyrophosphohydrolase	NA	NA	NA	NA	NA
AUL03225.1|708209_709940_+|tRNA	proline--tRNA ligase	tRNA	A0A2K9L3R9	Tupanvirus	29.4	4.6e-11
AUL03226.1|709992_710421_+	tol-pal system-associated acyl-CoA thioesterase	NA	NA	NA	NA	NA
AUL03227.1|710423_711104_+	protein TolQ	NA	NA	NA	NA	NA
AUL03228.1|711103_711562_+	protein TolR	NA	NA	NA	NA	NA
AUL03229.1|711598_712573_+	protein TolA	NA	NA	NA	NA	NA
AUL03230.1|712589_713906_+	Tol-Pal system beta propeller repeat protein TolB	NA	NA	NA	NA	NA
AUL03231.1|713937_714435_+	peptidoglycan-associated lipoprotein	NA	NA	NA	NA	NA
AUL03232.1|714521_715211_+	tol-pal system protein YbgF	NA	NA	NA	NA	NA
AUL03233.1|715210_716260_+	iron-siderophore ABC transporter permease	NA	NA	NA	NA	NA
AUL03234.1|716256_717051_+	iron ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	30.6	2.4e-15
AUL03235.1|717219_717570_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03236.1|717545_718103_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03237.1|719232_720183_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 6
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	860745	999478	4105872	transposase,holin	Bacillus_phage(11.76%)	119	NA	NA
AUL03339.1|860745_861696_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03340.1|861916_862585_+	transcriptional regulator	NA	NA	NA	NA	NA
AUL03341.1|862708_863815_+	efflux transporter periplasmic adaptor subunit	NA	NA	NA	NA	NA
AUL03342.1|863827_866941_+	multidrug efflux protein	NA	S5VTK5	Leptospira_phage	21.5	4.5e-57
AUL03343.1|866937_868431_+	RND transporter	NA	NA	NA	NA	NA
AUL03344.1|868445_869117_+	MarR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05954.1|869160_869613_-	azurin	NA	NA	NA	NA	NA
AUL03345.1|869795_870443_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05955.1|870546_872595_+	hydantoinase	NA	NA	NA	NA	NA
AUL03346.1|872591_874604_+	hydantoin utilization protein B	NA	NA	NA	NA	NA
AUL03347.1|874629_875964_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03348.1|876072_877065_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03349.1|877131_879216_-	rhodanese-like domain-containing protein	NA	NA	NA	NA	NA
AUL03350.1|879240_880212_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03351.1|880340_881342_-	peptidase M14	NA	NA	NA	NA	NA
AUL03352.1|881375_882527_-	cystathionine beta-lyase	NA	NA	NA	NA	NA
AUL03353.1|882730_883621_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03354.1|883698_884523_+	3-oxoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL05956.1|884719_885736_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL03355.1|886973_888101_-	argininosuccinate lyase	NA	NA	NA	NA	NA
AUL03356.1|888091_888466_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03357.1|888513_889902_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03358.1|889932_890922_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03359.1|891032_892265_-	methylaspartate ammonia-lyase	NA	NA	NA	NA	NA
AUL03360.1|892546_893347_+	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03361.1|893369_895601_-|holin	high-affinity choline transporter BetT	holin	NA	NA	NA	NA
AUL03362.1|896388_896835_-	preprotein translocase subunit SecG	NA	NA	NA	NA	NA
AUL03363.1|896856_897603_-	triose-phosphate isomerase	NA	NA	NA	NA	NA
AUL03364.1|897746_898724_-	NAD(P)H-quinone oxidoreductase	NA	NA	NA	NA	NA
AUL03365.1|899357_899969_+	PIN domain-containing protein	NA	K4HZX4	Acidithiobacillus_phage	32.5	3.3e-12
AUL03366.1|899962_901180_-	threonine ammonia-lyase	NA	NA	NA	NA	NA
AUL03367.1|901320_902271_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03368.1|902267_902987_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03369.1|903107_905267_-	polyribonucleotide nucleotidyltransferase	NA	NA	NA	NA	NA
AUL03370.1|905357_905627_-	30S ribosomal protein S15	NA	NA	NA	NA	NA
AUL05957.1|905920_906448_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03371.1|906466_907246_-	CDP-diacylglycerol--serine O-phosphatidyltransferase	NA	NA	NA	NA	NA
AUL03372.1|907413_908430_-	ketol-acid reductoisomerase	NA	NA	NA	NA	NA
AUL03373.1|908502_908994_-	acetolactate synthase small subunit	NA	NA	NA	NA	NA
AUL03374.1|909004_910720_-	acetolactate synthase, large subunit, biosynthetic type	NA	A0A0P0CDR3	Ostreococcus_lucimarinus_virus	30.3	3.1e-60
AUL03375.1|911190_911802_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03376.1|911883_912834_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03377.1|912830_914663_-	multidrug ABC transporter ATP-binding protein	NA	W8CYL7	Bacillus_phage	26.4	1.3e-27
AUL03378.1|915061_915721_+	thiopurine S-methyltransferase	NA	NA	NA	NA	NA
AUL03379.1|916069_916237_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03380.1|916248_916929_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03381.1|917210_917927_+	flagellar brake protein	NA	NA	NA	NA	NA
AUL03382.1|917941_919243_-	phospholipase	NA	NA	NA	NA	NA
AUL03383.1|921387_924276_+	metal-dependent phosphohydrolase	NA	NA	NA	NA	NA
AUL03384.1|924499_925852_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03385.1|925880_926402_+	acetyl-CoA carboxylase, biotin carboxyl carrier protein	NA	NA	NA	NA	NA
AUL03386.1|926398_927853_+	carboxylase	NA	NA	NA	NA	NA
AUL03387.1|927887_928136_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03388.1|928241_929117_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03389.1|929142_930198_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03390.1|930210_931002_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03391.1|931034_932405_+	acetyl-CoA carboxylase biotin carboxylase subunit	NA	NA	NA	NA	NA
AUL03392.1|933581_934532_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03393.1|934596_934806_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03394.1|934965_935178_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03395.1|935297_936416_+	N-acylglucosamine 2-epimerase	NA	NA	NA	NA	NA
AUL03396.1|936512_936728_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03397.1|936921_937173_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03398.1|937333_938236_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03399.1|938232_938616_-	Rieske (2Fe-2S) protein	NA	NA	NA	NA	NA
AUL03400.1|938670_940485_-	metal ABC transporter permease	NA	W8CYL7	Bacillus_phage	27.9	5.7e-44
AUL05958.1|940634_941462_+	oxidoreductase	NA	A0A2H4PQR8	Staphylococcus_phage	47.4	1.7e-67
AUL03401.1|941507_942488_+	alcohol dehydrogenase	NA	NA	NA	NA	NA
AUL03402.1|942484_942697_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03403.1|942693_943875_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03404.1|944038_944773_+	serine/threonine protein phosphatase	NA	A0A2H4J0P0	uncultured_Caudovirales_phage	49.2	1.9e-62
AUL03405.1|944774_947387_-	penicillin-binding protein	NA	NA	NA	NA	NA
AUL03406.1|947522_949436_-	S9 family peptidase	NA	NA	NA	NA	NA
AUL03407.1|950051_950462_-	phenylacetic acid degradation protein	NA	NA	NA	NA	NA
AUL03408.1|951741_952692_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03409.1|952688_953663_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03410.1|953808_954699_+	LysR family transcriptional regulator	NA	Q6JIH3	Burkholderia_virus	27.6	4.3e-05
AUL03411.1|954975_955368_-	hypothetical protein	NA	A0A0R6PJ17	Moraxella_phage	45.0	4.8e-25
AUL03412.1|955497_956448_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03413.1|956477_956660_-	addiction module toxin, HicA family	NA	A0A1L2JY37	Aeribacillus_phage	56.1	3.7e-12
AUL03414.1|957431_958613_-	MFS transporter	NA	NA	NA	NA	NA
AUL03415.1|958827_959505_-	phosphoglycolate phosphatase	NA	NA	NA	NA	NA
AUL03416.1|959501_960227_-	bifunctional 3-demethylubiquinol 3-O-methyltransferase/2-polyprenyl-6-hydroxyphenol methylase	NA	NA	NA	NA	NA
AUL03417.1|960352_960934_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03418.1|961304_963986_+	DNA gyrase subunit A	NA	G3M9Z5	Bacillus_virus	33.5	3.2e-104
AUL05959.1|963988_965119_+	phosphoserine transaminase	NA	M1Q1P2	Streptococcus_phage	44.0	4.9e-78
AUL03419.1|965111_966197_+	chorismate mutase	NA	NA	NA	NA	NA
AUL03420.1|966283_967183_+	prephenate dehydrogenase	NA	NA	NA	NA	NA
AUL03421.1|967179_968508_+	3-phosphoshikimate 1-carboxyvinyltransferase	NA	NA	NA	NA	NA
AUL03422.1|968522_969194_+	cytidylate kinase	NA	NA	NA	NA	NA
AUL03423.1|969381_971097_+	30S ribosomal protein S1	NA	NA	NA	NA	NA
AUL03424.1|971098_971458_+	integration host factor subunit beta	NA	NA	NA	NA	NA
AUL03425.1|971649_971964_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03426.1|972006_973227_+	lipopolysaccharide assembly protein LapB	NA	NA	NA	NA	NA
AUL03427.1|973223_974165_+	hypothetical protein	NA	A0A2H4N7X4	Lake_Baikal_phage	28.1	1.5e-16
AUL03428.1|974161_975151_+	ADP-glyceromanno-heptose 6-epimerase	NA	E3SJ87	Synechococcus_phage	34.4	2.2e-26
AUL05960.1|975440_975770_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03429.1|975868_976819_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03430.1|976899_977811_+	cysteine synthase B	NA	A0A1X9I5K7	Streptococcus_phage	38.8	8.0e-47
AUL03431.1|977871_979017_-	lytic murein transglycosylase B	NA	NA	NA	NA	NA
AUL03432.1|979036_979951_+	deacetylase	NA	A0A2K9KZC4	Tupanvirus	34.7	9.8e-45
AUL03433.1|980022_980772_+	electron transporter RnfB	NA	NA	NA	NA	NA
AUL03434.1|980771_981701_+	electron transfer flavoprotein subunit alpha	NA	NA	NA	NA	NA
AUL03435.1|981944_983771_+	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL03436.1|983853_984495_+	peroxidase	NA	NA	NA	NA	NA
AUL03437.1|984684_985719_+	sulfate transporter subunit	NA	NA	NA	NA	NA
AUL03438.1|985734_985938_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03439.1|985959_986634_+	sulfate ABC transporter permease subunit CysT	NA	NA	NA	NA	NA
AUL03440.1|986748_987531_+	sulfate ABC transporter permease subunit CysW	NA	NA	NA	NA	NA
AUL03441.1|987555_988620_+	sulfate ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	30.3	3.8e-24
AUL05961.1|989417_990326_+	sulfate adenylyltransferase small subunit	NA	NA	NA	NA	NA
AUL03442.1|991813_993088_+	radical SAM protein	NA	NA	NA	NA	NA
AUL03443.1|993241_993622_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03444.1|993629_994502_-	multidrug DMT transporter permease	NA	NA	NA	NA	NA
AUL03445.1|994807_995188_+	50S ribosomal protein L19	NA	NA	NA	NA	NA
AUL03446.1|995437_996124_+	coenzyme A pyrophosphatase	NA	NA	NA	NA	NA
AUL03447.1|996219_997170_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03448.1|997274_998324_+	aldo/keto reductase	NA	NA	NA	NA	NA
AUL05962.1|998461_999478_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
>prophage 7
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	1023281	1079418	4105872	transposase,tRNA	uncultured_Mediterranean_phage(37.5%)	49	NA	NA
AUL03463.1|1023281_1024184_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03464.1|1024329_1025280_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03465.1|1026312_1028349_+	transketolase	NA	NA	NA	NA	NA
AUL03466.1|1028366_1029377_+	type I glyceraldehyde-3-phosphate dehydrogenase	NA	NA	NA	NA	NA
AUL03467.1|1029494_1030688_+	phosphoglycerate kinase	NA	NA	NA	NA	NA
AUL03468.1|1030717_1031491_-	enoyl-[acyl-carrier-protein] reductase	NA	NA	NA	NA	NA
AUL03469.1|1031487_1032678_-	acetate kinase	NA	NA	NA	NA	NA
AUL03470.1|1032703_1033642_-	phosphate acetyltransferase	NA	NA	NA	NA	NA
AUL05964.1|1033638_1035987_-	3-hydroxyalkanoate synthetase	NA	NA	NA	NA	NA
AUL03471.1|1036141_1036783_-	glutathione S-transferase	NA	NA	NA	NA	NA
AUL03472.1|1038296_1038845_-	damage-inducible protein DinB	NA	NA	NA	NA	NA
AUL03473.1|1038863_1039349_-	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL03474.1|1039526_1040465_+	cytochrome C biogenesis protein	NA	A0A0P0YMJ9	Yellowstone_lake_phycodnavirus	24.1	5.6e-11
AUL03475.1|1040467_1040785_+	MerR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03476.1|1040830_1041775_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03477.1|1043455_1044106_+	molybdopterin adenylyltransferase	NA	NA	NA	NA	NA
AUL03478.1|1044159_1044495_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05965.1|1044509_1045352_+	peptidase	NA	A0A292GJG6	Xanthomonas_phage	36.1	2.6e-15
AUL03479.1|1045368_1045650_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03480.1|1045723_1045987_-	translation initiation factor IF-1	NA	NA	NA	NA	NA
AUL03481.1|1046230_1047181_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05966.1|1047479_1048220_-	RNA polymerase sigma factor FliA	NA	NA	NA	NA	NA
AUL03482.1|1048651_1048975_+	flagellar transcriptional activator FlhD	NA	NA	NA	NA	NA
AUL03483.1|1049009_1049570_+	transcriptional regulator FlhC	NA	NA	NA	NA	NA
AUL03484.1|1049690_1050566_+	flagellar motor stator protein MotA	NA	NA	NA	NA	NA
AUL03485.1|1050578_1051526_+	flagellar motor protein MotB	NA	NA	NA	NA	NA
AUL03486.1|1051626_1051920_+	two-component system response regulator	NA	NA	NA	NA	NA
AUL03487.1|1051946_1054004_+	chemotaxis protein CheA	NA	NA	NA	NA	NA
AUL03488.1|1054018_1054519_+	chemotaxis protein CheW	NA	NA	NA	NA	NA
AUL03489.1|1054592_1056299_+	chemotaxis protein	NA	A0A2H4J162	uncultured_Caudovirales_phage	41.7	1.4e-12
AUL03490.1|1057162_1058215_+	chemotaxis response regulator protein-glutamate methylesterase	NA	NA	NA	NA	NA
AUL03491.1|1058267_1058657_+	two-component system response regulator	NA	Q56AR1	Bacillus_thuringiensis_phage	33.3	5.7e-10
AUL03492.1|1058665_1059298_+	protein phosphatase CheZ	NA	NA	NA	NA	NA
AUL05967.1|1059397_1060414_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL05968.1|1061244_1062252_+	aldo/keto reductase	NA	NA	NA	NA	NA
AUL03493.1|1062248_1063892_-	apolipoprotein N-acyltransferase	NA	NA	NA	NA	NA
AUL03494.1|1063888_1064776_-	magnesium/cobalt efflux protein	NA	NA	NA	NA	NA
AUL03495.1|1064916_1065390_-	rRNA maturation RNase YbeY	NA	NA	NA	NA	NA
AUL03496.1|1065379_1066402_-	phosphate starvation-inducible protein PhoH	NA	A0A0S0MVD6	Pseudomonas_phage	45.4	8.7e-50
AUL03497.1|1066398_1067826_-|tRNA	tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB	tRNA	NA	NA	NA	NA
AUL05969.1|1068763_1069780_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL03498.1|1070112_1071048_-	protein-export membrane protein SecF	NA	A0A1B1IVP7	uncultured_Mediterranean_phage	35.5	3.0e-41
AUL03499.1|1071097_1072978_-	protein-export membrane protein SecD	NA	NA	NA	NA	NA
AUL03500.1|1073044_1073389_-	preprotein translocase subunit YajC	NA	A0A1B1IVR5	uncultured_Mediterranean_phage	40.4	1.0e-10
AUL03501.1|1073533_1074670_-|tRNA	tRNA guanosine(34) transglycosylase Tgt	tRNA	A0A1B1IVQ4	uncultured_Mediterranean_phage	44.4	1.9e-85
AUL03502.1|1074666_1075740_-|tRNA	tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA	tRNA	NA	NA	NA	NA
AUL03503.1|1075897_1077334_+	D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase	NA	NA	NA	NA	NA
AUL05970.1|1077424_1078066_+	uracil phosphoribosyltransferase	NA	NA	NA	NA	NA
AUL05971.1|1078401_1079418_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
>prophage 8
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	1157520	1219641	4105872	transposase,tRNA	Erysipelothrix_phage(33.33%)	50	NA	NA
AUL03556.1|1157520_1158423_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03557.1|1158569_1159193_-	fimbrial protein	NA	NA	NA	NA	NA
AUL03558.1|1159366_1161649_-	NADP-dependent malic enzyme	NA	NA	NA	NA	NA
AUL03559.1|1161803_1164500_-	pyruvate dehydrogenase (acetyl-transferring), homodimeric type	NA	NA	NA	NA	NA
AUL03560.1|1164625_1165114_+	ArsR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03561.1|1165149_1167012_+	oligopeptide transporter, OPT family	NA	NA	NA	NA	NA
AUL03562.1|1166990_1167200_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03563.1|1167524_1170395_+	2-oxoglutarate dehydrogenase E1 component	NA	NA	NA	NA	NA
AUL03564.1|1170440_1171655_+	dihydrolipoamide succinyltransferase	NA	NA	NA	NA	NA
AUL03565.1|1171884_1173312_+	dihydrolipoyl dehydrogenase	NA	A0A2K5B2C5	Erysipelothrix_phage	28.1	2.1e-41
AUL03566.1|1173409_1174501_+	cell division protein ZapE	NA	NA	NA	NA	NA
AUL03567.1|1174513_1175272_-	3-oxoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL03568.1|1175359_1176262_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03569.1|1176258_1177209_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03570.1|1177338_1178322_-	LacI family transcriptional regulator	NA	NA	NA	NA	NA
AUL03571.1|1178376_1179099_-	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL03572.1|1180577_1181933_+|tRNA	tryptophan--tRNA ligase	tRNA	NA	NA	NA	NA
AUL03573.1|1182013_1184389_-	RNA-binding transcriptional accessory protein	NA	NA	NA	NA	NA
AUL03574.1|1184553_1186629_+	helicase	NA	A0A127AW80	Bacillus_phage	30.0	2.4e-75
AUL05977.1|1186690_1187485_-	outer membrane protein assembly factor BamD	NA	NA	NA	NA	NA
AUL03575.1|1187592_1188555_+	RNA pseudouridine synthase	NA	NA	NA	NA	NA
AUL03576.1|1188542_1189298_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03577.1|1189405_1191043_+	class I poly(R)-hydroxyalkanoic acid synthase	NA	NA	NA	NA	NA
AUL03578.1|1191110_1191848_+	beta-ketoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL03579.1|1191950_1192526_+	polyhydroxyalkanoate synthesis repressor PhaR	NA	NA	NA	NA	NA
AUL05978.1|1193266_1193581_+	periplasmic lipoprotein involved in iron transport	NA	NA	NA	NA	NA
AUL03580.1|1193596_1194442_+	FTR1 family iron permease	NA	NA	NA	NA	NA
AUL03581.1|1194480_1195860_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03582.1|1195937_1196819_+	phenazine biosynthesis protein PhzC/PhzF	NA	NA	NA	NA	NA
AUL03583.1|1196965_1197868_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03584.1|1197864_1198275_-	lactoylglutathione lyase	NA	NA	NA	NA	NA
AUL03585.1|1198382_1199237_-	2-pyrone-4,6-dicarboxylate hydrolase	NA	NA	NA	NA	NA
AUL03586.1|1200236_1201361_-	racemase	NA	Q6A202	Oenococcus_phage	28.3	1.5e-31
AUL03587.1|1201466_1202345_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03588.1|1202469_1203249_+	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL03589.1|1203402_1204824_+	MFS transporter	NA	NA	NA	NA	NA
AUL03590.1|1205258_1206956_+	sodium:proline symporter	NA	NA	NA	NA	NA
AUL03591.1|1206984_1207107_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05979.1|1207182_1208124_-	LD-carboxypeptidase	NA	NA	NA	NA	NA
AUL03592.1|1208450_1209197_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03593.1|1209204_1210131_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03594.1|1210252_1211170_+	oxidoreductase	NA	NA	NA	NA	NA
AUL03595.1|1211209_1212163_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL03596.1|1212187_1212766_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03597.1|1214439_1215048_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03598.1|1215125_1215479_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05980.1|1215562_1216495_-	succinylglutamate desuccinylase	NA	NA	NA	NA	NA
AUL03599.1|1216802_1217705_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03600.1|1217791_1218742_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03601.1|1218738_1219641_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 9
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	1292650	1329415	4105872	transposase	Salmonella_phage(50.0%)	36	NA	NA
AUL03652.1|1292650_1293601_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03653.1|1293580_1294162_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03654.1|1294222_1295950_-	sodium-independent anion transporter	NA	NA	NA	NA	NA
AUL03655.1|1296061_1297420_+	MBL fold metallo-hydrolase	NA	NA	NA	NA	NA
AUL03656.1|1297712_1298663_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03657.1|1298703_1299774_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05986.1|1299796_1300675_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03658.1|1300846_1301818_+	AraC family transcriptional regulator	NA	NA	NA	NA	NA
AUL03659.1|1301980_1302823_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03660.1|1302984_1303665_+	anti-sigma factor	NA	NA	NA	NA	NA
AUL03661.1|1303658_1304828_+	amine oxidase	NA	NA	NA	NA	NA
AUL03662.1|1304824_1305856_+	alcohol dehydrogenase	NA	A0A2K9L339	Tupanvirus	27.8	1.8e-26
AUL03663.1|1305923_1307141_+	MFS transporter	NA	NA	NA	NA	NA
AUL03664.1|1307175_1308708_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03665.1|1308788_1309412_+	transcriptional regulator	NA	NA	NA	NA	NA
AUL03666.1|1309442_1310054_+	RhtB family transporter	NA	NA	NA	NA	NA
AUL03667.1|1310089_1310560_+	histidine kinase	NA	NA	NA	NA	NA
AUL03668.1|1310734_1310983_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03669.1|1310990_1311995_+	peptidase M20	NA	NA	NA	NA	NA
AUL03670.1|1312031_1313546_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL03671.1|1313549_1314509_+	ABC transporter	NA	NA	NA	NA	NA
AUL03672.1|1314537_1315341_+	peptide ABC transporter permease	NA	NA	NA	NA	NA
AUL03673.1|1315342_1316977_+	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	31.1	2.9e-15
AUL03674.1|1317060_1318122_+	LacI family transcriptional regulator	NA	NA	NA	NA	NA
AUL03675.1|1318593_1319118_+	DNA-binding protein	NA	J9Q7G7	Salmonella_phage	32.9	6.5e-09
AUL03676.1|1319581_1320484_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03677.1|1320480_1321515_-	hydrolase	NA	NA	NA	NA	NA
AUL03678.1|1321623_1322262_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03679.1|1322556_1322784_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL03680.1|1322906_1323620_+	SAM-dependent methyltransferase	NA	NA	NA	NA	NA
AUL03681.1|1323864_1324815_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03682.1|1324954_1325200_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03683.1|1325314_1326763_-	2-aminoadipate aminotransferase	NA	NA	NA	NA	NA
AUL03684.1|1326873_1327824_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03685.1|1327820_1328270_-	deoxyuridine 5'-triphosphate nucleotidohydrolase	NA	S4TNT3	Salmonella_phage	67.2	3.7e-45
AUL03686.1|1328512_1329415_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 10
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	1418051	1472261	4105872	transposase,tRNA	Salmonella_phage(22.22%)	44	NA	NA
AUL03762.1|1418051_1419002_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03763.1|1419168_1419522_+	cytochrome C	NA	NA	NA	NA	NA
AUL03764.1|1419534_1419897_+	cytochrome	NA	NA	NA	NA	NA
AUL03765.1|1419938_1420364_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03766.1|1420566_1421823_+	NADP-dependent isocitrate dehydrogenase	NA	Q77Z09	Phage_21	64.8	1.2e-11
AUL03767.1|1422021_1423002_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03768.1|1423151_1424393_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03769.1|1424491_1425442_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03770.1|1425450_1426146_-	two-component system response regulator KdpE	NA	NA	NA	NA	NA
AUL03771.1|1428966_1429566_-	potassium-transporting ATPase subunit C	NA	NA	NA	NA	NA
AUL03772.1|1429576_1431742_-	potassium-transporting ATPase subunit B	NA	M1HBF8	Paramecium_bursaria_Chlorella_virus	27.1	1.2e-24
AUL03773.1|1431765_1433550_-	potassium-transporting ATPase subunit KdpA	NA	NA	NA	NA	NA
AUL03774.1|1433549_1433639_-	potassium-transporting ATPase subunit F	NA	NA	NA	NA	NA
AUL03775.1|1434333_1434606_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03776.1|1434605_1436672_+	cation acetate symporter	NA	NA	NA	NA	NA
AUL03777.1|1436668_1437571_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03778.1|1437717_1438620_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03779.1|1438783_1439116_-	QacE family quaternary ammonium compound efflux SMR transporter	NA	NA	NA	NA	NA
AUL03780.1|1439112_1439799_-	DNA mismatch repair protein MutS	NA	NA	NA	NA	NA
AUL03781.1|1439785_1440745_-	thioredoxin-disulfide reductase	NA	A0A2I2L5E1	Orpheovirus	40.2	3.1e-57
AUL03782.1|1440777_1443147_+	cell division protein FtsK	NA	S5VNE3	Mycobacterium_phage	48.0	7.6e-81
AUL03783.1|1443146_1443779_+	outer membrane lipoprotein carrier protein LolA	NA	NA	NA	NA	NA
AUL03784.1|1443880_1445221_+	recombination factor protein RarA	NA	G3MBE0	Bacillus_virus	38.9	1.6e-75
AUL03785.1|1445267_1446623_+|tRNA	serine--tRNA ligase	tRNA	A0A1B1IVT2	uncultured_Mediterranean_phage	47.5	1.6e-83
AUL03786.1|1446913_1447150_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03787.1|1447337_1447655_-	virulence factor	NA	NA	NA	NA	NA
AUL03788.1|1447927_1448443_-	hypothetical protein	NA	T1SAR8	Salmonella_phage	44.6	5.1e-06
AUL03789.1|1448536_1448698_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03790.1|1448713_1449469_-	GGDEF domain-containing protein	NA	NA	NA	NA	NA
AUL03791.1|1449807_1450014_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03792.1|1450021_1450681_-	antibiotic resistance protein	NA	NA	NA	NA	NA
AUL03793.1|1450975_1453180_-	porin	NA	NA	NA	NA	NA
AUL03794.1|1453290_1454514_-	multidrug transporter	NA	S4TR35	Salmonella_phage	29.4	9.8e-24
AUL03795.1|1454636_1455548_-	AraC family transcriptional regulator	NA	NA	NA	NA	NA
AUL03796.1|1455677_1456871_-	Rieske (2Fe-2S) protein	NA	NA	NA	NA	NA
AUL03797.1|1456885_1457686_-	siderophore ferric iron reductase	NA	NA	NA	NA	NA
AUL03798.1|1457682_1459539_-	IucA/IucC family protein	NA	NA	NA	NA	NA
AUL03799.1|1459535_1460141_-	siderophore biosynthesis protein	NA	NA	NA	NA	NA
AUL03800.1|1460159_1461545_-	alcaligin biosynthesis protein	NA	NA	NA	NA	NA
AUL03801.1|1465426_1466200_+	peroxide stress protein YaaA	NA	NA	NA	NA	NA
AUL03802.1|1466211_1467453_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03803.1|1469282_1470185_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03804.1|1470216_1471314_+	GGDEF domain-containing protein	NA	A0A127AWB9	Bacillus_phage	37.3	3.5e-20
AUL03805.1|1471310_1472261_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 12
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	1618143	1681944	4105872	transposase	Tetraselmis_virus(100.0%)	50	NA	NA
AUL03926.1|1618143_1619094_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03927.1|1619152_1619926_+	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL03928.1|1619918_1621475_+	capsular biosynthesis protein	NA	NA	NA	NA	NA
AUL03929.1|1621471_1622422_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03930.1|1628193_1628952_-	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL03931.1|1628998_1630000_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL03932.1|1630165_1631134_-	phenol degradation protein meta	NA	NA	NA	NA	NA
AUL03933.1|1632673_1633642_+	AAA family ATPase	NA	NA	NA	NA	NA
AUL03934.1|1633650_1634592_+	MoxR protein	NA	NA	NA	NA	NA
AUL06003.1|1635065_1636076_+	hypothetical protein	NA	NA	NA	NA	NA
AUL06005.1|1636066_1637581_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03935.1|1637577_1638924_+	hypothetical protein	NA	NA	NA	NA	NA
AUL06004.1|1638926_1639961_+	haloacid dehalogenase	NA	NA	NA	NA	NA
AUL03936.1|1640010_1641636_+	arylsulfatase	NA	A0A2P0VMN7	Tetraselmis_virus	52.2	2.0e-149
AUL03937.1|1641729_1642209_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03938.1|1642188_1643091_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03939.1|1643243_1644191_+	hypothetical protein	NA	NA	NA	NA	NA
AUL06006.1|1644244_1646059_-	histidine kinase	NA	NA	NA	NA	NA
AUL03940.1|1646051_1646726_-	DNA-binding response regulator	NA	NA	NA	NA	NA
AUL03941.1|1646855_1649930_+	autotransporter outer membrane beta-barrel domain-containing protein	NA	NA	NA	NA	NA
AUL03942.1|1649943_1650243_-	transcriptional regulator	NA	NA	NA	NA	NA
AUL06007.1|1650557_1651181_-	glutathione S-transferase	NA	NA	NA	NA	NA
AUL03943.1|1651424_1652294_+	2,4-dichlorophenoxyacetate dioxygenase	NA	NA	NA	NA	NA
AUL03944.1|1652271_1653084_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03945.1|1653301_1654228_-	hypothetical protein	NA	NA	NA	NA	NA
AUL03946.1|1654340_1655120_-	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL03947.1|1655110_1656307_-	alpha-hydroxy-acid oxidizing enzyme	NA	NA	NA	NA	NA
AUL03948.1|1656337_1657288_-	hydrolase	NA	NA	NA	NA	NA
AUL03949.1|1657509_1658199_+	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL03950.1|1658263_1659019_+	3-oxoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL03951.1|1659070_1660063_+	MFS transporter	NA	NA	NA	NA	NA
AUL03952.1|1660072_1661026_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03953.1|1661141_1662104_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03954.1|1663505_1663934_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03955.1|1663930_1664881_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03956.1|1664989_1665178_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03957.1|1666334_1667522_-	hypothetical protein	NA	NA	NA	NA	NA
AUL06008.1|1667525_1667876_-	transcriptional regulator	NA	NA	NA	NA	NA
AUL06009.1|1669624_1670596_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL03958.1|1670609_1671323_+	3-oxoacyl-[acyl-carrier-protein] reductase	NA	NA	NA	NA	NA
AUL03959.1|1671327_1672245_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03960.1|1672351_1672648_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03961.1|1672746_1673697_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03962.1|1674855_1677789_+	monovalent cation/H+ antiporter subunit A	NA	NA	NA	NA	NA
AUL03963.1|1677788_1678133_+	Na+/H+ antiporter subunit C	NA	NA	NA	NA	NA
AUL03964.1|1678129_1679758_+	monovalent cation/H+ antiporter subunit D	NA	NA	NA	NA	NA
AUL03965.1|1679757_1680234_+	Na+/H+ antiporter subunit E	NA	NA	NA	NA	NA
AUL03966.1|1680233_1680515_+	K+/H+ antiporter subunit F	NA	NA	NA	NA	NA
AUL03967.1|1680511_1680838_+	cation:proton antiporter	NA	NA	NA	NA	NA
AUL03968.1|1680993_1681944_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 13
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	1695355	1787324	4105872	transposase,tRNA	Brevibacillus_phage(14.29%)	60	NA	NA
AUL03980.1|1695355_1696306_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03981.1|1696329_1696794_-|tRNA	glutamyl-tRNA amidotransferase	tRNA	A0A0K2FLI9	Brevibacillus_phage	32.4	3.9e-05
AUL03982.1|1696940_1698149_+	nitric oxide dioxygenase	NA	NA	NA	NA	NA
AUL03983.1|1698192_1698630_+	BadM/Rrf2 family transcriptional regulator	NA	NA	NA	NA	NA
AUL03984.1|1698748_1700038_+	D-amino acid dehydrogenase small subunit	NA	NA	NA	NA	NA
AUL03985.1|1702778_1703681_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL03986.1|1703827_1704844_-	folate-binding protein YgfZ	NA	NA	NA	NA	NA
AUL03987.1|1705022_1706057_+	aminodeoxychorismate lyase	NA	NA	NA	NA	NA
AUL03988.1|1706053_1706680_+	dTMP kinase	NA	A0A1L2BX49	Bacteriophage	35.1	1.6e-22
AUL03989.1|1706676_1707729_+	DNA polymerase III subunit delta'	NA	NA	NA	NA	NA
AUL03990.1|1707778_1708549_+	DNAase	NA	NA	NA	NA	NA
AUL03991.1|1708599_1709436_+	hypothetical protein	NA	NA	NA	NA	NA
AUL03992.1|1709631_1710372_+	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL03993.1|1710446_1711190_+	glutamine ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL03994.1|1711851_1712625_+	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	37.7	3.1e-31
AUL03995.1|1713762_1715052_+	glutamate dehydrogenase	NA	NA	NA	NA	NA
AUL03996.1|1716662_1717910_-	Zn-dependent hydrolase	NA	NA	NA	NA	NA
AUL03997.1|1717919_1719629_-	thiamine pyrophosphate-binding protein	NA	A0A0P0YLY7	Yellowstone_lake_phycodnavirus	27.3	5.9e-35
AUL03998.1|1719625_1720564_-	CoA ester lyase	NA	NA	NA	NA	NA
AUL03999.1|1720560_1721844_-	C4-dicarboxylate ABC transporter permease	NA	NA	NA	NA	NA
AUL04000.1|1721847_1722330_-	TRAP transporter small permease protein	NA	NA	NA	NA	NA
AUL04001.1|1722330_1723317_-	C4-dicarboxylate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04002.1|1723489_1724209_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04003.1|1724325_1725276_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04004.1|1728461_1729811_+	amidase	NA	NA	NA	NA	NA
AUL04005.1|1729868_1730663_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04006.1|1730796_1731672_+	diguanylate phosphodiesterase	NA	NA	NA	NA	NA
AUL04007.1|1731715_1735432_-	hybrid sensor histidine kinase/response regulator	NA	A0A1V0SGX0	Hokovirus	32.0	4.2e-33
AUL04008.1|1735440_1736070_-	DNA-binding response regulator	NA	NA	NA	NA	NA
AUL04009.1|1747342_1747780_+	protein fimA	NA	NA	NA	NA	NA
AUL04010.1|1747939_1748764_+	molecular chaperone	NA	NA	NA	NA	NA
AUL04011.1|1748826_1751448_+	usher protein	NA	NA	NA	NA	NA
AUL06011.1|1751461_1752559_+	protein fhaE	NA	NA	NA	NA	NA
AUL04012.1|1752551_1754306_+	filamentous hemagglutinin	NA	NA	NA	NA	NA
AUL04013.1|1755623_1756124_-	TRAP transporter small permease protein	NA	NA	NA	NA	NA
AUL06012.1|1756130_1757105_-	C4-dicarboxylate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04014.1|1758661_1759153_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04015.1|1759166_1760132_-	C4-dicarboxylate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04016.1|1760152_1760854_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04017.1|1762028_1762541_+	transcriptional regulator	NA	NA	NA	NA	NA
AUL04018.1|1762619_1766243_+	5-oxoprolinase	NA	NA	NA	NA	NA
AUL04019.1|1766256_1767288_-	peptidase C45	NA	NA	NA	NA	NA
AUL04020.1|1768447_1769281_+	mechanosensitive ion channel protein MscS	NA	NA	NA	NA	NA
AUL04021.1|1769294_1770053_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04022.1|1770214_1771207_+	MFS transporter	NA	NA	NA	NA	NA
AUL04023.1|1771424_1772168_-	RNA methyltransferase	NA	NA	NA	NA	NA
AUL04024.1|1772308_1773091_+	inositol monophosphatase	NA	NA	NA	NA	NA
AUL04025.1|1773217_1774804_+	hypothetical protein	NA	A0A0R6PEZ3	Moraxella_phage	42.0	1.9e-35
AUL04026.1|1774828_1775692_+	undecaprenyl-diphosphatase	NA	NA	NA	NA	NA
AUL04027.1|1775899_1776676_-	UDP-2,3-diacylglucosamine diphosphatase	NA	NA	NA	NA	NA
AUL06013.1|1776668_1777178_-	cyclophilin	NA	NA	NA	NA	NA
AUL04028.1|1777306_1777990_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04029.1|1778229_1779690_+|tRNA	cysteine--tRNA ligase	tRNA	A0A2K9L6B7	Tupanvirus	27.9	2.5e-34
AUL04030.1|1779709_1780354_+	DNA-3-methyladenine glycosylase	NA	NA	NA	NA	NA
AUL04031.1|1780390_1781356_+	acetyl-CoA carboxylase carboxyltransferase subunit alpha	NA	NA	NA	NA	NA
AUL04032.1|1781454_1782405_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04033.1|1782551_1783454_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04034.1|1783514_1784549_+|tRNA	tRNA lysidine(34) synthetase TilS	tRNA	NA	NA	NA	NA
AUL04035.1|1784648_1785914_+	aspartate kinase	NA	NA	NA	NA	NA
AUL06014.1|1786307_1787324_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
>prophage 14
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	1832508	1904017	4105872	transposase,tRNA	Klosneuvirus(22.22%)	60	NA	NA
AUL04081.1|1832508_1833459_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04082.1|1833583_1834393_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL04083.1|1834641_1835544_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04084.1|1836817_1838035_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04085.1|1838031_1839087_+	4-hydroxythreonine-4-phosphate dehydrogenase PdxA	NA	NA	NA	NA	NA
AUL04086.1|1839091_1839994_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04087.1|1840070_1840943_+	MOSC domain-containing protein	NA	NA	NA	NA	NA
AUL04088.1|1841073_1841442_+	aspartate 1-decarboxylase	NA	NA	NA	NA	NA
AUL04089.1|1841499_1842546_+	CDP-6-deoxy-delta-3,4-glucoseen reductase	NA	NA	NA	NA	NA
AUL04090.1|1842741_1843998_+	amino acid dehydrogenase	NA	NA	NA	NA	NA
AUL04091.1|1844002_1845340_+	glycerol-3-phosphate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04092.1|1845489_1846446_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04093.1|1847903_1848269_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04094.1|1848316_1849891_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04095.1|1849943_1850888_+	peptide ABC transporter	NA	NA	NA	NA	NA
AUL06018.1|1850815_1851736_+	peptide ABC transporter permease	NA	NA	NA	NA	NA
AUL04096.1|1851728_1853363_+	microcin ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	32.7	8.2e-18
AUL04097.1|1853359_1854715_+	amidase	NA	NA	NA	NA	NA
AUL04098.1|1855621_1857199_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04099.1|1857202_1858477_+	hypothetical protein	NA	NA	NA	NA	NA
AUL06019.1|1858574_1858949_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04100.1|1860664_1861798_+	general secretion pathway protein	NA	NA	NA	NA	NA
AUL04101.1|1861835_1862441_+	prepilin-type N-terminal cleavage/methylation domain-containing protein	NA	NA	NA	NA	NA
AUL04102.1|1862437_1863256_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04103.1|1863327_1865952_+|tRNA	alanine--tRNA ligase	tRNA	A0A1V0SK38	Klosneuvirus	39.4	1.7e-81
AUL04104.1|1865938_1866193_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04105.1|1866259_1866841_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04106.1|1867144_1867405_+	30S ribosomal protein S16	NA	NA	NA	NA	NA
AUL04107.1|1867570_1868194_+	ribosome maturation factor RimM	NA	NA	NA	NA	NA
AUL04108.1|1868193_1868967_+|tRNA	tRNA (guanosine(37)-N1)-methyltransferase TrmD	tRNA	NA	NA	NA	NA
AUL04109.1|1868963_1870172_-	class V aminotransferase	NA	NA	NA	NA	NA
AUL04110.1|1870197_1870671_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04111.1|1870744_1871695_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04112.1|1871793_1872696_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04113.1|1872842_1874192_-	two-component sensor histidine kinase	NA	NA	NA	NA	NA
AUL04114.1|1874957_1875713_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04115.1|1875805_1878688_-|tRNA	valine--tRNA ligase	tRNA	A0A1V0SK04	Klosneuvirus	37.1	3.7e-138
AUL04116.1|1879010_1879436_+	nucleoside-diphosphate kinase	NA	D2E8E1	Anguillid_herpesvirus	43.2	2.1e-21
AUL04117.1|1879463_1880612_+	23S rRNA (adenine(2503)-C(2))-methyltransferase	NA	NA	NA	NA	NA
AUL04118.1|1880608_1881115_+	transcriptional regulator	NA	NA	NA	NA	NA
AUL04119.1|1881130_1882417_+	4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase	NA	NA	NA	NA	NA
AUL06020.1|1882466_1883762_+|tRNA	histidine--tRNA ligase	tRNA	NA	NA	NA	NA
AUL04120.1|1883763_1884402_+	hypothetical protein	NA	NA	NA	NA	NA
AUL06021.1|1884407_1885565_+	outer membrane protein assembly factor BamB	NA	NA	NA	NA	NA
AUL04121.1|1885591_1886947_+	ribosome biogenesis GTPase Der	NA	NA	NA	NA	NA
AUL04122.1|1886950_1888021_+	histidinol-phosphate transaminase	NA	A0A1X6WGT4	Pacmanvirus	25.7	2.5e-15
AUL04123.1|1888159_1888396_+	RNA chaperone Hfq	NA	NA	NA	NA	NA
AUL04124.1|1888483_1889590_+	GTPase HflX	NA	NA	NA	NA	NA
AUL04125.1|1889555_1890860_+	HflK protein	NA	NA	NA	NA	NA
AUL04126.1|1890878_1891778_+	HflC protein	NA	NA	NA	NA	NA
AUL04127.1|1891961_1893119_+	ATP phosphoribosyltransferase regulatory subunit	NA	NA	NA	NA	NA
AUL04128.1|1893195_1894491_+	adenylosuccinate synthase	NA	A0A160ER07	Powai_lake_megavirus	33.5	3.0e-63
AUL04129.1|1894604_1895144_+	nicotinate phosphoribosyltransferase	NA	NA	NA	NA	NA
AUL04130.1|1895421_1895634_+	30S ribosomal protein S21	NA	NA	NA	NA	NA
AUL04131.1|1895653_1897684_+	DNA primase	NA	A0A0K1LMQ9	Caulobacter_phage	41.9	1.0e-65
AUL04132.1|1898369_1900652_+	RNA polymerase sigma factor RpoD	NA	A0A2I7SAT0	Vibrio_phage	30.1	3.2e-36
AUL04133.1|1901060_1901360_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04134.1|1901644_1902058_+	transcriptional regulator	NA	A0A222YXG1	Escherichia_phage	59.0	3.8e-36
AUL04135.1|1902017_1902968_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04136.1|1903066_1904017_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 15
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	1915269	1963568	4105872	transposase	Klosneuvirus(16.67%)	47	NA	NA
AUL04147.1|1915269_1916172_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04148.1|1916168_1917443_-	adenosylmethionine--8-amino-7-oxononanoate transaminase	NA	A0A1V0SKB7	Klosneuvirus	28.9	9.6e-14
AUL04149.1|1917546_1918740_+	8-amino-7-oxononanoate synthase	NA	NA	NA	NA	NA
AUL04150.1|1918736_1919390_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL04151.1|1919386_1920823_+	dethiobiotin synthase	NA	NA	NA	NA	NA
AUL04152.1|1920810_1921170_+	CidA/LrgA family protein	NA	NA	NA	NA	NA
AUL04153.1|1921255_1921906_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04154.1|1922142_1923006_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04155.1|1923089_1924955_-	sigma-54-dependent Fis family transcriptional regulator	NA	NA	NA	NA	NA
AUL06025.1|1925212_1926733_+	aldehyde dehydrogenase	NA	NA	NA	NA	NA
AUL04156.1|1926820_1927471_-	NAD(P)H dehydrogenase	NA	NA	NA	NA	NA
AUL04157.1|1928419_1929715_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04158.1|1929736_1930621_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL06026.1|1930719_1931595_+	PhzF family phenazine biosynthesis protein	NA	NA	NA	NA	NA
AUL04159.1|1931584_1931941_-	RNA signal recognition particle	NA	NA	NA	NA	NA
AUL04160.1|1932071_1933046_+	AraC family transcriptional regulator	NA	NA	NA	NA	NA
AUL04161.1|1933175_1933355_-	DUF3008 domain-containing protein	NA	NA	NA	NA	NA
AUL04162.1|1933497_1933977_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04163.1|1933987_1934824_-	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL04164.1|1934936_1935308_+	transcriptional regulator	NA	NA	NA	NA	NA
AUL04165.1|1935304_1935856_+	ATPase	NA	NA	NA	NA	NA
AUL04166.1|1935871_1937563_-	sodium-independent anion transporter	NA	A0A2H4J153	uncultured_Caudovirales_phage	27.3	5.0e-42
AUL04167.1|1937611_1938292_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04168.1|1938539_1939004_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04169.1|1939173_1940103_+	hypothetical protein	NA	NA	NA	NA	NA
AUL06027.1|1940115_1940709_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04170.1|1940836_1942654_-	ABC transporter ATP-binding protein	NA	W8CYL7	Bacillus_phage	27.4	2.3e-37
AUL04171.1|1942737_1943688_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL06028.1|1943786_1944266_-	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL04172.1|1944388_1945291_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04173.1|1945309_1945657_-	aldehyde-activating protein	NA	NA	NA	NA	NA
AUL04174.1|1945685_1947125_-	MFS transporter	NA	A0A0M3UL24	Mycobacterium_phage	37.4	7.4e-55
AUL04175.1|1947143_1947539_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04176.1|1947713_1948322_+	peptidase S16	NA	NA	NA	NA	NA
AUL04177.1|1948334_1949153_+	hypothetical protein	NA	A0A1B1INV8	uncultured_Mediterranean_phage	28.8	2.3e-16
AUL04178.1|1949104_1950079_-	AraC family transcriptional regulator	NA	NA	NA	NA	NA
AUL04179.1|1950107_1951169_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04180.1|1951165_1953382_-	aldehyde oxidase	NA	NA	NA	NA	NA
AUL04181.1|1953395_1953854_-	(2Fe-2S)-binding protein	NA	NA	NA	NA	NA
AUL04182.1|1954011_1954356_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04183.1|1954512_1955418_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL06029.1|1955504_1956518_+	pyridoxamine 5'-phosphate oxidase	NA	NA	NA	NA	NA
AUL06030.1|1958497_1959514_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL04184.1|1959656_1961009_-	glutathione-disulfide reductase	NA	A0A2K5B2C5	Erysipelothrix_phage	27.6	2.9e-45
AUL04185.1|1961183_1961480_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04186.1|1961626_1962631_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04187.1|1962665_1963568_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 16
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	1975064	2039384	4105872	transposase	Vibrio_phage(20.0%)	54	NA	NA
AUL04200.1|1975064_1976015_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04201.1|1976236_1977187_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04202.1|1977285_1978251_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04203.1|1978388_1979288_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04204.1|1979815_1981642_+	DUF3604 domain-containing protein	NA	NA	NA	NA	NA
AUL04205.1|1981999_1983370_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04206.1|1983380_1984577_+	acetyl-CoA acetyltransferase	NA	NA	NA	NA	NA
AUL04207.1|1984649_1985969_+	acyl--CoA ligase	NA	NA	NA	NA	NA
AUL04208.1|1985965_1986841_+	esterase	NA	NA	NA	NA	NA
AUL04209.1|1986871_1988020_-	carnitine dehydratase	NA	NA	NA	NA	NA
AUL04210.1|1988037_1988352_-	2Fe-2S ferredoxin	NA	NA	NA	NA	NA
AUL04211.1|1988373_1989096_-	3-oxoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL04212.1|1989095_1989914_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL04213.1|1989918_1990446_-	ring-hydroxylating dioxygenase subunit beta	NA	NA	NA	NA	NA
AUL04214.1|1990451_1991708_-	ring-hydroxylating oxygenase subunit alpha	NA	NA	NA	NA	NA
AUL04215.1|1992066_1993206_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04216.1|1993283_1994156_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL04217.1|1995074_1995977_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04218.1|1995936_1996572_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04219.1|1996931_1998254_-	isocitrate lyase	NA	NA	NA	NA	NA
AUL04220.1|1998572_1999394_+	NADPH-dependent 7-cyano-7-deazaguanine reductase QueF	NA	A0A2I7SAX1	Vibrio_phage	37.6	4.1e-42
AUL04221.1|1999329_1999671_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04222.1|1999680_2000649_-	MFS transporter	NA	NA	NA	NA	NA
AUL04223.1|2000818_2001391_-	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase	NA	NA	NA	NA	NA
AUL04224.1|2001430_2003260_-	excinuclease ABC subunit C	NA	NA	NA	NA	NA
AUL04225.1|2003222_2004281_-	beta-N-acetylhexosaminidase	NA	NA	NA	NA	NA
AUL04226.1|2004318_2004780_-	holo-ACP synthase	NA	NA	NA	NA	NA
AUL04227.1|2004864_2005611_-	pyridoxine 5'-phosphate synthase	NA	NA	NA	NA	NA
AUL04228.1|2007101_2010332_-	multidrug efflux RND transporter permease subunit	NA	NA	NA	NA	NA
AUL04229.1|2010398_2011730_-	efflux transporter periplasmic adaptor subunit	NA	NA	NA	NA	NA
AUL04230.1|2011982_2012357_-	DNA-binding protein	NA	NA	NA	NA	NA
AUL04231.1|2012459_2013638_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04232.1|2013648_2014239_-	hypothetical protein	NA	NA	NA	NA	NA
AUL06032.1|2014349_2015156_+	molybdenum-dependent transcriptional regulator	NA	NA	NA	NA	NA
AUL04233.1|2015181_2015976_-	ABC transporter ATP-binding protein	NA	A0A1V0SE00	Indivirus	25.7	5.1e-05
AUL04234.1|2016976_2017951_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04235.1|2018109_2018622_-	superoxide dismutase	NA	Q9MC02	Salmonella_phage	52.3	1.8e-43
AUL04236.1|2018778_2019750_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04237.1|2021493_2022300_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL04238.1|2022296_2023598_-	malonyl-CoA decarboxylase	NA	NA	NA	NA	NA
AUL04239.1|2023548_2024313_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04240.1|2024426_2025197_-	spermidine synthase	NA	NA	NA	NA	NA
AUL04241.1|2025281_2026469_-	acetyl-CoA acetyltransferase	NA	NA	NA	NA	NA
AUL04242.1|2026541_2026916_-	4-oxalocrotonate tautomerase	NA	NA	NA	NA	NA
AUL04243.1|2027016_2028279_-	glycine/betaine ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	36.6	6.8e-28
AUL04244.1|2028275_2029133_-	ABC transporter permease	NA	NA	NA	NA	NA
AUL04245.1|2029305_2030307_-	glycine/betaine ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04246.1|2030758_2031661_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL06033.1|2033272_2034424_+	Bcr/CflA family drug resistance efflux transporter	NA	NA	NA	NA	NA
AUL04247.1|2034792_2035029_+	50S ribosomal protein L28	NA	NA	NA	NA	NA
AUL04248.1|2035092_2035260_+	50S ribosomal protein L33	NA	NA	NA	NA	NA
AUL04249.1|2035373_2037179_-	sulfate transporter	NA	A0A2H4J153	uncultured_Caudovirales_phage	27.5	2.2e-19
AUL04250.1|2037432_2038335_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04251.1|2038481_2039384_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 17
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	2170964	2220615	4105872	transposase,tRNA	uncultured_Mediterranean_phage(16.67%)	43	NA	NA
AUL04346.1|2170964_2171915_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL06044.1|2172013_2173411_-	rRNA methyltransferase	NA	NA	NA	NA	NA
AUL04347.1|2174067_2175033_+	riboflavin biosynthesis protein RibF	NA	NA	NA	NA	NA
AUL04348.1|2175022_2177884_+|tRNA	isoleucine--tRNA ligase	tRNA	A0A1V0SJ93	Klosneuvirus	25.5	1.0e-71
AUL04349.1|2177886_2178393_+	signal peptidase II	NA	NA	NA	NA	NA
AUL04350.1|2178497_2179706_+	phosphopantothenate synthase	NA	Q9HH70	Methanothermobacter_phage	30.0	3.8e-36
AUL04351.1|2179707_2180646_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04352.1|2180807_2181281_+	AsnC family transcriptional regulator	NA	NA	NA	NA	NA
AUL04353.1|2181277_2182228_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04354.1|2182338_2182779_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04355.1|2182907_2184137_-	lytic transglycosylase	NA	NA	NA	NA	NA
AUL04356.1|2184175_2184997_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04357.1|2185050_2186202_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL04358.1|2186293_2186764_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04359.1|2189332_2191882_+	cyanophycin synthetase	NA	NA	NA	NA	NA
AUL04360.1|2191952_2194526_+	cyanophycin synthetase	NA	NA	NA	NA	NA
AUL04361.1|2194791_2194992_+	general stress protein CsbD	NA	NA	NA	NA	NA
AUL04362.1|2195023_2195185_+	DUF1328 domain-containing protein	NA	NA	NA	NA	NA
AUL04363.1|2195242_2195581_+	phospholipid-binding protein	NA	NA	NA	NA	NA
AUL04364.1|2195729_2196632_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04365.1|2197453_2198122_+	arylesterase	NA	NA	NA	NA	NA
AUL06045.1|2198103_2200059_-	peptidylprolyl isomerase	NA	NA	NA	NA	NA
AUL04366.1|2200301_2201051_+	glycerophosphodiester phosphodiesterase	NA	A0A2H4PGQ5	Escherichia_phage	27.8	1.5e-14
AUL04367.1|2201063_2201927_+	23S rRNA (adenine(2030)-N(6))-methyltransferase RlmJ	NA	NA	NA	NA	NA
AUL04368.1|2201930_2203346_-	dihydrolipoyl dehydrogenase	NA	NA	NA	NA	NA
AUL04369.1|2203479_2204208_-	glutathione peroxidase	NA	A0A1D8KSL1	Synechococcus_phage	56.8	9.6e-43
AUL04370.1|2204346_2204547_-	heavy metal transporter	NA	NA	NA	NA	NA
AUL04371.1|2204722_2205121_+	Cu(I)-responsive transcriptional regulator	NA	NA	NA	NA	NA
AUL04372.1|2205144_2206545_-	23S rRNA (uracil(1939)-C(5))-methyltransferase	NA	A0A2K5B251	Erysipelothrix_phage	26.5	7.3e-31
AUL04373.1|2206663_2207416_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04374.1|2207704_2208304_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04375.1|2208408_2209188_-	3'-5' exonuclease	NA	NA	NA	NA	NA
AUL04376.1|2209184_2210069_-	peptidase	NA	A0A292GJG6	Xanthomonas_phage	49.5	4.6e-15
AUL04377.1|2210086_2210866_-	protein-L-isoaspartate O-methyltransferase	NA	A0A1B1IU40	uncultured_Mediterranean_phage	46.9	4.8e-32
AUL04378.1|2210850_2211609_-	5'/3'-nucleotidase SurE	NA	A0A1B1ITZ2	uncultured_Mediterranean_phage	51.2	1.4e-68
AUL06046.1|2211746_2212382_+	glycerol-3-phosphate acyltransferase	NA	NA	NA	NA	NA
AUL06047.1|2212649_2213666_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL04379.1|2213763_2214804_-|tRNA	tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD	tRNA	A0A0R6PI74	Moraxella_phage	51.3	6.1e-91
AUL04380.1|2214938_2216231_+	guanine permease	NA	A0A0R6PHV4	Moraxella_phage	36.0	1.7e-66
AUL04381.1|2217590_2217974_+	thiol reductase thioredoxin	NA	V9SJ74	Achromobacter_phage	25.8	8.1e-09
AUL04382.1|2217991_2218579_-	thymidylate synthase	NA	A0A1X9I5T8	Streptococcus_phage	35.8	4.7e-16
AUL04383.1|2218616_2219519_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04384.1|2219664_2220615_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 18
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	2577480	2643932	4105872	transposase	uncultured_Caudovirales_phage(40.0%)	58	NA	NA
AUL04674.1|2577480_2578383_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04675.1|2578398_2578611_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04676.1|2578752_2579325_+	flagellar basal body protein FliL	NA	NA	NA	NA	NA
AUL04677.1|2579327_2580338_+	flagellar motor switch protein FliM	NA	NA	NA	NA	NA
AUL04678.1|2580330_2580831_+	flagellar motor switch protein FliN	NA	NA	NA	NA	NA
AUL04679.1|2580841_2581183_+	flagellar biosynthetic protein FliO	NA	NA	NA	NA	NA
AUL06074.1|2581251_2581986_+	flagellar biosynthetic protein FliP	NA	NA	NA	NA	NA
AUL04680.1|2582002_2582272_+	EscS/YscS/HrcS family type III secretion system export apparatus protein	NA	NA	NA	NA	NA
AUL04681.1|2582294_2583083_+	flagellar biosynthetic protein FliR	NA	NA	NA	NA	NA
AUL06075.1|2583129_2584146_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL04682.1|2584362_2585805_-	chemotaxis protein	NA	A0A1B0V854	Salmonella_phage	41.8	1.0e-35
AUL04683.1|2585983_2587603_-	methyl-accepting chemotaxis protein	NA	A0A2H4J162	uncultured_Caudovirales_phage	45.3	1.5e-08
AUL04684.1|2587723_2589544_-	methyl-accepting chemotaxis protein	NA	A0A2H4J162	uncultured_Caudovirales_phage	52.6	6.4e-11
AUL04685.1|2589622_2591155_-	flagellar hook-associated protein 3	NA	NA	NA	NA	NA
AUL04686.1|2591188_2592835_-	flagellar hook-associated protein FlgK	NA	NA	NA	NA	NA
AUL04687.1|2592904_2593927_-	flagellar rod assembly protein/muramidase FlgJ	NA	A0A088F6W1	Sulfitobacter_phage	31.4	1.9e-12
AUL04688.1|2593944_2595078_-	flagellar biosynthesis protein FlgI	NA	NA	NA	NA	NA
AUL04689.1|2595080_2595770_-	flagellar basal body L-ring protein	NA	NA	NA	NA	NA
AUL04690.1|2595769_2596555_-	flagellar basal-body rod protein FlgG	NA	NA	NA	NA	NA
AUL04691.1|2596598_2597363_-	flagellar biosynthesis protein FlgF	NA	NA	NA	NA	NA
AUL04692.1|2597401_2598823_-	flagellar hook protein FlgE	NA	NA	NA	NA	NA
AUL04693.1|2598888_2599593_-	flagellar basal body rod modification protein	NA	NA	NA	NA	NA
AUL04694.1|2599640_2600060_-	flagellar basal body rod protein FlgC	NA	NA	NA	NA	NA
AUL04695.1|2600072_2600480_-	flagellar basal body rod protein FlgB	NA	NA	NA	NA	NA
AUL06076.1|2600663_2601374_+	flagella basal body P-ring formation protein FlgA	NA	NA	NA	NA	NA
AUL04696.1|2601500_2601791_+	flagellar biosynthesis anti-sigma factor FlgM	NA	NA	NA	NA	NA
AUL04697.1|2601808_2602291_+	flagellar protein FlgN	NA	NA	NA	NA	NA
AUL04698.1|2606796_2607951_-	flagellar biosynthesis protein FlhB	NA	NA	NA	NA	NA
AUL06077.1|2608256_2609273_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL04699.1|2609519_2610308_+	amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04700.1|2610374_2611055_+	cysteine ABC transporter permease	NA	NA	NA	NA	NA
AUL04701.1|2611051_2611822_+	ATP-binding protein	NA	G9BWD6	Planktothrix_phage	39.1	9.8e-30
AUL04702.1|2611920_2612871_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04703.1|2612926_2613844_-	2-dehydropantoate 2-reductase	NA	NA	NA	NA	NA
AUL04704.1|2613854_2615033_-	mandelate racemase	NA	NA	NA	NA	NA
AUL04705.1|2615052_2616048_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04706.1|2617636_2618245_+	3-isopropylmalate dehydratase small subunit	NA	NA	NA	NA	NA
AUL04707.1|2618232_2619273_+	LacI family transcriptional regulator	NA	NA	NA	NA	NA
AUL04708.1|2619290_2620253_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04709.1|2620249_2621443_-	CoA transferase	NA	NA	NA	NA	NA
AUL04710.1|2621439_2622237_-	citryl-CoA lyase	NA	NA	NA	NA	NA
AUL04711.1|2622262_2623249_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04712.1|2623267_2625307_-	acetyl-CoA synthetase	NA	NA	NA	NA	NA
AUL06078.1|2625508_2626189_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04713.1|2626202_2627114_-	CoA ester lyase	NA	NA	NA	NA	NA
AUL04714.1|2627110_2627689_-	NADPH-dependent FMN reductase	NA	NA	NA	NA	NA
AUL04715.1|2627827_2628733_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04716.1|2628740_2632160_+	nuclease	NA	NA	NA	NA	NA
AUL04717.1|2632147_2634748_-	autotransporter outer membrane beta-barrel domain-containing protein	NA	NA	NA	NA	NA
AUL04718.1|2635703_2636336_-	PadR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04719.1|2636729_2637488_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04720.1|2637484_2638687_+	cardiolipin synthase B	NA	NA	NA	NA	NA
AUL04721.1|2638683_2638884_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04722.1|2638874_2639825_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04723.1|2640732_2641878_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04724.1|2641864_2642620_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL04725.1|2642736_2642916_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04726.1|2642981_2643932_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 19
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	2672094	2709458	4105872	transposase	Planktothrix_phage(33.33%)	40	NA	NA
AUL04744.1|2672094_2672997_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04745.1|2673143_2674046_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04746.1|2674138_2674678_+	peroxiredoxin	NA	NA	NA	NA	NA
AUL04747.1|2674784_2675129_-	arsenate reductase (glutaredoxin)	NA	A0A2H4J8T1	uncultured_Caudovirales_phage	58.4	3.0e-31
AUL04748.1|2675186_2676635_-	carnitine dehydratase	NA	NA	NA	NA	NA
AUL06081.1|2676822_2677149_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04749.1|2678785_2679964_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04750.1|2680046_2680547_+	glutathione peroxidase	NA	Q6VZR0	Canarypox_virus	38.4	4.7e-25
AUL04751.1|2680656_2681358_+	thiol:disulfide oxidoreductase	NA	NA	NA	NA	NA
AUL04752.1|2681369_2681834_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL04753.1|2681848_2682124_+	biotin--protein ligase	NA	NA	NA	NA	NA
AUL04754.1|2682120_2682897_+	lipoate--protein ligase	NA	NA	NA	NA	NA
AUL04755.1|2682925_2683753_+	hypothetical protein	NA	NA	NA	NA	NA
AUL06082.1|2683878_2684349_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04756.1|2684475_2685369_+	phosphatidylserine decarboxylase	NA	NA	NA	NA	NA
AUL04757.1|2685416_2686598_+	alpha-hydroxy-acid oxidizing enzyme	NA	NA	NA	NA	NA
AUL04758.1|2686610_2687426_-	iron ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04759.1|2687559_2688087_-	hypothetical protein	NA	NA	NA	NA	NA
AUL06083.1|2688083_2688581_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04760.1|2688728_2689106_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04761.1|2689063_2689348_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04762.1|2689327_2690230_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL06084.1|2690376_2690988_-	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL04763.1|2691222_2692350_+	leucine ABC transporter subunit substrate-binding protein LivK	NA	NA	NA	NA	NA
AUL04764.1|2692460_2693549_-	sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC	NA	G9BWD6	Planktothrix_phage	31.2	2.2e-19
AUL04765.1|2693601_2694453_-	glycerol-3-phosphate transporter	NA	NA	NA	NA	NA
AUL04766.1|2694472_2695354_-	glycerol-3-phosphate transporter permease	NA	NA	NA	NA	NA
AUL06085.1|2695530_2696844_-	sn-glycerol-3-phosphate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04767.1|2697054_2697888_+	pyrroline-5-carboxylate reductase	NA	NA	NA	NA	NA
AUL04768.1|2697884_2698466_+	hypothetical protein	NA	A0A2I7SAW6	Vibrio_phage	37.3	9.4e-17
AUL04769.1|2698819_2699770_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04770.1|2699785_2700901_+	leucine ABC transporter subunit substrate-binding protein LivK	NA	NA	NA	NA	NA
AUL04771.1|2701003_2701930_+	branched-chain amino acid ABC transporter permease LivH	NA	NA	NA	NA	NA
AUL04772.1|2701929_2703168_+	high-affinity branched-chain amino acid ABC transporter permease LivM	NA	NA	NA	NA	NA
AUL04773.1|2703164_2703932_+	high-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG	NA	A0A2H4PQG7	Staphylococcus_phage	26.4	1.2e-14
AUL04774.1|2703932_2704634_+	branched-chain amino acid ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	30.4	1.3e-17
AUL06086.1|2704715_2705162_-	glutamate racemase	NA	NA	NA	NA	NA
AUL04775.1|2706051_2706690_+	glutathione S-transferase	NA	NA	NA	NA	NA
AUL04776.1|2707458_2708409_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04777.1|2708507_2709458_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 20
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	2814916	2872026	4105872	transposase	Diachasmimorpha_longicaudata_entomopoxvirus(20.0%)	51	NA	NA
AUL04862.1|2814916_2815819_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL06095.1|2817028_2817535_-	phenylacetate-CoA oxygenase subunit PaaJ	NA	NA	NA	NA	NA
AUL04863.1|2817531_2818296_-	phenylacetate-CoA oxygenase subunit PaaI	NA	NA	NA	NA	NA
AUL04864.1|2818311_2818596_-	1,2-phenylacetyl-CoA epoxidase subunit B	NA	NA	NA	NA	NA
AUL04865.1|2818660_2819650_-	1,2-phenylacetyl-CoA epoxidase subunit A	NA	NA	NA	NA	NA
AUL04866.1|2819821_2820751_+	phenylacetic acid degradation operon negative regulatory protein PaaX	NA	NA	NA	NA	NA
AUL04867.1|2820722_2821409_-	NAD(P)H-hydrate epimerase	NA	NA	NA	NA	NA
AUL04868.1|2821442_2821988_-	oligoribonuclease	NA	Q8B5Y0	Diachasmimorpha_longicaudata_entomopoxvirus	37.7	2.1e-26
AUL04869.1|2822032_2823298_+	peptidase M48	NA	NA	NA	NA	NA
AUL04870.1|2823294_2824197_+	ribosome small subunit-dependent GTPase A	NA	NA	NA	NA	NA
AUL04871.1|2825378_2826323_-	peptide ABC transporter	NA	NA	NA	NA	NA
AUL04872.1|2826417_2827935_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04873.1|2827976_2829605_-	gamma-glutamyltransferase	NA	NA	NA	NA	NA
AUL04874.1|2829712_2830594_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04875.1|2830854_2831082_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04876.1|2833706_2834081_+	endonuclease	NA	F4YXR7	Roseobacter_phage	54.4	2.1e-25
AUL04877.1|2834105_2834444_-	transcriptional regulator	NA	NA	NA	NA	NA
AUL04878.1|2834487_2836122_-	NAD+ synthase	NA	A0A2L0UZF5	Agrobacterium_phage	36.6	8.3e-87
AUL04879.1|2836160_2837507_-	mechanosensitive ion channel protein MscS	NA	NA	NA	NA	NA
AUL06096.1|2837614_2839036_+	argininosuccinate lyase	NA	NA	NA	NA	NA
AUL04880.1|2839105_2839690_-	nitroreductase	NA	NA	NA	NA	NA
AUL04881.1|2839792_2840743_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04882.1|2840877_2841984_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04883.1|2841994_2843092_+	cyclic pyranopterin phosphate synthase	NA	NA	NA	NA	NA
AUL04884.1|2843236_2844442_-	molybdopterin molybdenumtransferase MoeA	NA	NA	NA	NA	NA
AUL04885.1|2844448_2844970_-	molybdenum cofactor biosynthesis protein B	NA	NA	NA	NA	NA
AUL06097.1|2844966_2845449_-	molybdenum cofactor biosynthesis protein MoaE	NA	NA	NA	NA	NA
AUL04886.1|2845454_2845706_-	molybdopterin synthase sulfur carrier subunit	NA	NA	NA	NA	NA
AUL04887.1|2845686_2846172_-	molybdenum cofactor biosynthesis protein C	NA	NA	NA	NA	NA
AUL04888.1|2846307_2849769_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04889.1|2849786_2850671_+	carboxymethylenebutenolidase	NA	NA	NA	NA	NA
AUL04890.1|2850680_2851112_-	hypothetical protein	NA	NA	NA	NA	NA
AUL06098.1|2851358_2851862_+	peroxiredoxin	NA	M1I839	Pelagibacter_phage	44.1	1.8e-24
AUL04891.1|2851939_2853340_+	MFS transporter	NA	NA	NA	NA	NA
AUL04892.1|2853414_2854290_-	hypothetical protein	NA	NA	NA	NA	NA
AUL06099.1|2854286_2855294_-	biotin synthase BioB	NA	NA	NA	NA	NA
AUL04893.1|2855761_2856067_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04894.1|2856157_2856748_+	TetR family transcriptional regulator	NA	NA	NA	NA	NA
AUL06100.1|2856938_2857955_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL04895.1|2858146_2860483_-	copper-translocating P-type ATPase	NA	E4ZFI9	Streptococcus_phage	42.8	3.2e-124
AUL04896.1|2860565_2861000_+	Cd(II)/Pb(II)-responsive transcriptional regulator	NA	NA	NA	NA	NA
AUL04897.1|2861146_2862049_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04898.1|2862147_2863098_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04899.1|2863094_2863889_-	N-formylglutamate deformylase	NA	NA	NA	NA	NA
AUL04900.1|2863920_2864625_-	3-oxoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL04901.1|2864699_2865500_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04902.1|2865496_2865904_-	cytochrome o ubiquinol oxidase subunit IV	NA	NA	NA	NA	NA
AUL04903.1|2865900_2866542_-	cytochrome o ubiquinol oxidase subunit III	NA	NA	NA	NA	NA
AUL06101.1|2866534_2868535_-	cytochrome o ubiquinol oxidase subunit I	NA	NA	NA	NA	NA
AUL04904.1|2869795_2871127_+	arabinose ABC transporter permease	NA	NA	NA	NA	NA
AUL04905.1|2871123_2872026_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 21
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	2886548	2927906	4105872	transposase,protease	uncultured_Mediterranean_phage(40.0%)	29	NA	NA
AUL04915.1|2886548_2887451_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04916.1|2887829_2891651_-	trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase	NA	NA	NA	NA	NA
AUL04917.1|2891807_2892476_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04918.1|2892480_2894154_-	paraquat-inducible protein B	NA	NA	NA	NA	NA
AUL04919.1|2894172_2895492_-	paraquat-inducible membrane protein A	NA	NA	NA	NA	NA
AUL04920.1|2895496_2897812_-|protease	ATP-dependent Clp protease ATP-binding subunit ClpA	protease	A0A223W0B1	Agrobacterium_phage	41.9	4.1e-164
AUL06103.1|2897867_2900036_-	penicillin-binding protein 1C	NA	NA	NA	NA	NA
AUL06104.1|2900032_2904598_-	alpha-2-macroglobulin	NA	NA	NA	NA	NA
AUL04921.1|2905311_2905626_-|protease	ATP-dependent Clp protease adapter ClpS	protease	A0A1B1IT64	uncultured_Mediterranean_phage	43.8	1.2e-10
AUL04922.1|2905853_2906099_+	cold-shock protein	NA	A0A2H4N7Y6	Lake_Baikal_phage	76.6	1.3e-20
AUL04923.1|2906220_2906712_+	hypothetical protein	NA	A0A1B1IUW8	uncultured_Mediterranean_phage	42.2	4.8e-14
AUL04924.1|2906811_2908017_-	3-oxoadipyl-CoA thiolase	NA	NA	NA	NA	NA
AUL04925.1|2908132_2909530_-	chloride channel protein EriC	NA	NA	NA	NA	NA
AUL04926.1|2910296_2911688_-	exodeoxyribonuclease VII large subunit	NA	A0A1V0SD82	Indivirus	32.0	1.4e-29
AUL04927.1|2911855_2912806_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04928.1|2913086_2913707_+	flagellar motor protein MotA	NA	NA	NA	NA	NA
AUL04929.1|2913703_2914117_+	biopolymer transporter ExbD	NA	NA	NA	NA	NA
AUL04930.1|2914113_2915157_+	tetraacyldisaccharide 4'-kinase	NA	NA	NA	NA	NA
AUL04931.1|2915212_2915401_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04932.1|2915410_2916175_+	3-deoxy-manno-octulosonate cytidylyltransferase	NA	NA	NA	NA	NA
AUL04933.1|2916265_2916922_+	adenylate kinase	NA	NA	NA	NA	NA
AUL04934.1|2917013_2917772_+	3-hydroxyacyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL04935.1|2917797_2919399_+	murein biosynthesis integral membrane protein MurJ	NA	NA	NA	NA	NA
AUL04936.1|2919599_2920604_+	iron dicitrate transport regulator FecR	NA	NA	NA	NA	NA
AUL04937.1|2920704_2920968_+	30S ribosomal protein S20	NA	NA	NA	NA	NA
AUL04938.1|2921085_2921862_-	2-dehydro-3-deoxyglucarate aldolase	NA	NA	NA	NA	NA
AUL04939.1|2922452_2923403_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04940.1|2925786_2926899_-	malate dehydrogenase	NA	NA	NA	NA	NA
AUL04941.1|2926955_2927906_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 22
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	2950283	3001932	4105872	transposase	Staphylococcus_phage(25.0%)	45	NA	NA
AUL04965.1|2950283_2951147_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04966.1|2951342_2952815_-	magnesium transporter	NA	NA	NA	NA	NA
AUL04967.1|2952825_2953236_-	acyl-CoA thioesterase	NA	NA	NA	NA	NA
AUL04968.1|2953299_2954346_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04969.1|2954452_2955331_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL04970.1|2955344_2956541_-	amidohydrolase	NA	NA	NA	NA	NA
AUL04971.1|2956602_2958294_+	long-chain fatty acid--CoA ligase	NA	A0A2H4PQU7	Staphylococcus_phage	28.1	9.4e-33
AUL04972.1|2958290_2959193_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04973.1|2959361_2960258_-	inositol monophosphatase	NA	NA	NA	NA	NA
AUL04974.1|2962535_2964761_+	glycosyl hydrolase	NA	NA	NA	NA	NA
AUL04975.1|2964925_2966014_+	phosphate ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	36.4	8.7e-32
AUL04976.1|2965970_2966624_+	DL-methionine transporter permease subunit	NA	NA	NA	NA	NA
AUL04977.1|2966671_2967469_+	metal ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04978.1|2968048_2968951_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04979.1|2969031_2970180_+	alcohol dehydrogenase	NA	NA	NA	NA	NA
AUL04980.1|2970236_2971187_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04981.1|2971285_2971591_-	antibiotic biosynthesis monooxygenase	NA	NA	NA	NA	NA
AUL04982.1|2971619_2972054_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04983.1|2972055_2973300_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04984.1|2973296_2974007_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL06105.1|2974021_2974933_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04985.1|2975295_2975700_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04986.1|2975696_2976155_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04987.1|2976161_2977070_+	hypothetical protein	NA	NA	NA	NA	NA
AUL06106.1|2977066_2977933_+	ABC transporter permease	NA	NA	NA	NA	NA
AUL04988.1|2977919_2978747_+	sugar ABC transporter permease	NA	NA	NA	NA	NA
AUL04989.1|2978757_2979885_+	phosphate ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	32.3	1.2e-23
AUL04990.1|2982242_2983505_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL04991.1|2983511_2984264_+	DNA-binding protein	NA	NA	NA	NA	NA
AUL04992.1|2984315_2984501_-	hypothetical protein	NA	NA	NA	NA	NA
AUL06107.1|2984776_2985241_+	redox-sensitive transcriptional activator SoxR	NA	NA	NA	NA	NA
AUL04993.1|2985320_2985932_+	3-methyladenine DNA glycosylase	NA	NA	NA	NA	NA
AUL04994.1|2986076_2988185_+	hypothetical protein	NA	NA	NA	NA	NA
AUL04995.1|2988181_2989084_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL04996.1|2989234_2989855_-	TetR family transcriptional regulator	NA	NA	NA	NA	NA
AUL06108.1|2989958_2990699_+	oxidoreductase	NA	NA	NA	NA	NA
AUL04997.1|2991833_2992958_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04998.1|2993003_2993372_-	hypothetical protein	NA	NA	NA	NA	NA
AUL04999.1|2993613_2994516_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05000.1|2995599_2996142_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05001.1|2996527_2997478_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05002.1|2997474_2998383_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05003.1|2998509_2999346_+	3-methyl-2-oxobutanoate hydroxymethyltransferase	NA	A0A0P0BXC9	Ostreococcus_lucimarinus_virus	33.3	1.6e-33
AUL05004.1|2999858_3000968_+	porin	NA	NA	NA	NA	NA
AUL05005.1|3001029_3001932_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 24
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	3401467	3465296	4105872	transposase,tRNA	Staphylococcus_phage(11.11%)	49	NA	NA
AUL05315.1|3401467_3402370_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05316.1|3403183_3404278_-	CoA transferase	NA	NA	NA	NA	NA
AUL05317.1|3404270_3405605_-	CoA ligase	NA	NA	NA	NA	NA
AUL05318.1|3405558_3406242_-	TetR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05319.1|3406267_3407431_-	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL05320.1|3407427_3408429_-	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL05321.1|3408428_3409301_-	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL05322.1|3409297_3410047_-	ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	27.8	1.9e-09
AUL05323.1|3410043_3410835_-	ABC transporter ATP-binding protein	NA	A0A1M7XV31	Cedratvirus	29.4	1.7e-08
AUL05324.1|3410831_3411971_-	ABC transporter	NA	NA	NA	NA	NA
AUL05325.1|3412246_3413032_+	3-hydroxyacyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL05326.1|3413065_3413848_+	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL05327.1|3413851_3414241_+	DNA-binding protein	NA	NA	NA	NA	NA
AUL05328.1|3415380_3416244_+	3-alpha,7-alpha, 12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL05329.1|3416279_3417368_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05330.1|3418667_3421646_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05331.1|3422572_3423451_+	fatty acid desaturase	NA	NA	NA	NA	NA
AUL05332.1|3423486_3423819_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05333.1|3423797_3425318_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05334.1|3425399_3426350_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05335.1|3426346_3426814_-	ribonuclease HI	NA	J9Q745	Salmonella_phage	50.7	5.6e-36
AUL05336.1|3426856_3427627_-	SAM-dependent methyltransferase	NA	NA	NA	NA	NA
AUL05337.1|3427647_3428448_+	hydroxyacylglutathione hydrolase	NA	NA	NA	NA	NA
AUL05338.1|3429961_3430747_+	enoyl-[acyl-carrier-protein] reductase	NA	NA	NA	NA	NA
AUL06129.1|3430986_3432003_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL05339.1|3432110_3432503_-	osmotically inducible protein OsmC	NA	NA	NA	NA	NA
AUL05340.1|3432640_3433321_+	hypothetical protein	NA	NA	NA	NA	NA
AUL06130.1|3433325_3434297_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL05341.1|3434392_3435295_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05342.1|3436847_3437549_+	two-component system response regulator OmpR	NA	W8CYM9	Bacillus_phage	36.6	5.6e-32
AUL05343.1|3437548_3438973_+	ATPase	NA	NA	NA	NA	NA
AUL05344.1|3440042_3441383_-	cytochrome ubiquinol oxidase subunit I	NA	NA	NA	NA	NA
AUL05345.1|3441498_3443262_+|tRNA	glutamine--tRNA ligase	tRNA	A0A222YZ70	Escherichia_phage	50.0	5.0e-162
AUL05346.1|3443373_3444252_+	septum site-determining protein MinC	NA	NA	NA	NA	NA
AUL05347.1|3444364_3445180_+	septum site-determining protein MinD	NA	NA	NA	NA	NA
AUL05348.1|3445183_3445435_+	cell division topological specificity factor MinE	NA	NA	NA	NA	NA
AUL06131.1|3445519_3446536_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL05349.1|3446866_3447088_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05350.1|3447733_3449353_-	energy-dependent translational throttle protein EttA	NA	A0A2K9L3Z8	Tupanvirus	28.0	5.4e-38
AUL06132.1|3449447_3450314_-	EamA family transporter	NA	NA	NA	NA	NA
AUL05351.1|3450862_3452071_-	ABC transporter permease	NA	NA	NA	NA	NA
AUL05352.1|3452150_3453722_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL05353.1|3453839_3454775_-	glycosyl transferase	NA	NA	NA	NA	NA
AUL05354.1|3454963_3455908_+	LysR family transcriptional regulator	NA	A0A2P0ZL89	Lactobacillus_phage	23.2	8.4e-07
AUL05355.1|3455976_3456147_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05356.1|3456475_3462193_+	excinuclease ABC subunit A	NA	A0A1B1IVR3	uncultured_Mediterranean_phage	39.5	1.0e-195
AUL05357.1|3462198_3463326_+	aminodeoxychorismate synthase, component I	NA	S4VT78	Pandoravirus	37.8	3.8e-38
AUL05358.1|3463381_3464008_+	aminotransferase	NA	NA	NA	NA	NA
AUL06133.1|3464279_3465296_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
>prophage 25
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	3469710	3587549	4105872	transposase,tRNA,holin	Acinetobacter_phage(22.22%)	105	NA	NA
AUL05362.1|3469710_3470583_-|tRNA	tRNA threonylcarbamoyladenosine dehydratase	tRNA	NA	NA	NA	NA
AUL05363.1|3470932_3472072_+	MFS transporter	NA	NA	NA	NA	NA
AUL05364.1|3472068_3472728_+	gamma-glutamylcyclotransferase	NA	NA	NA	NA	NA
AUL05365.1|3472799_3473432_+	pyridoxamine 5'-phosphate oxidase	NA	NA	NA	NA	NA
AUL05366.1|3473461_3473980_+	flavin reductase	NA	NA	NA	NA	NA
AUL05367.1|3473990_3475100_+	FAD-dependent oxidoreductase	NA	NA	NA	NA	NA
AUL05368.1|3475146_3476001_+	formyltetrahydrofolate deformylase	NA	NA	NA	NA	NA
AUL05369.1|3476002_3476905_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05370.1|3478127_3479078_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05371.1|3479174_3480308_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05372.1|3480344_3480593_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05373.1|3480832_3481822_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05374.1|3481997_3482786_-	indole-3-glycerol-phosphate synthase	NA	A0A0P0IR83	Acinetobacter_phage	53.0	5.1e-66
AUL05375.1|3482782_3483814_-	anthranilate phosphoribosyltransferase	NA	A0A0N7IRD9	Acinetobacter_phage	42.7	7.4e-73
AUL05376.1|3483832_3484396_-	anthranilate/aminodeoxychorismate synthase component II	NA	A0A0P0IKJ1	Acinetobacter_phage	62.1	1.1e-65
AUL05377.1|3484450_3485971_-	anthranilate synthase component I	NA	S4VT78	Pandoravirus	32.1	9.0e-43
AUL05378.1|3486234_3486939_-	phosphoglycolate phosphatase	NA	NA	NA	NA	NA
AUL05379.1|3486946_3487675_-	ribulose-phosphate 3-epimerase	NA	NA	NA	NA	NA
AUL05380.1|3487789_3488164_+	Co2+/Mg2+ efflux protein ApaG	NA	NA	NA	NA	NA
AUL05381.1|3488206_3489496_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05382.1|3489492_3490662_+	ubiquinone biosynthesis protein UbiH	NA	NA	NA	NA	NA
AUL05383.1|3490688_3491498_+	disulfide bond formation protein DsbC	NA	NA	NA	NA	NA
AUL05384.1|3491557_3492493_+	hydroxyacid dehydrogenase	NA	A0A1J0F959	Only_Syngen_Nebraska_virus	27.7	6.4e-15
AUL05385.1|3492505_3493456_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05386.1|3493554_3494517_-|tRNA	tRNA 2-thiocytidine(32) synthetase TtcA	tRNA	A0A0U2S5Z2	Escherichia_phage	64.5	4.6e-93
AUL05387.1|3494548_3494908_-	dihydroneopterin aldolase	NA	NA	NA	NA	NA
AUL05388.1|3495032_3495935_+	oxidoreductase	NA	G3MA85	Bacillus_virus	24.0	1.9e-08
AUL06135.1|3495936_3497703_-	peptidase M61	NA	NA	NA	NA	NA
AUL05389.1|3497743_3498520_+	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL05390.1|3499843_3500746_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05391.1|3500960_3501374_+	hypothetical protein	NA	NA	NA	NA	NA
AUL06136.1|3501645_3501966_+	ABC transporter permease	NA	NA	NA	NA	NA
AUL05392.1|3502038_3502920_+	F0F1 ATP synthase subunit A	NA	NA	NA	NA	NA
AUL05393.1|3503036_3503279_+	F0F1 ATP synthase subunit C	NA	NA	NA	NA	NA
AUL05394.1|3503416_3503887_+	F0F1 ATP synthase subunit B	NA	NA	NA	NA	NA
AUL05395.1|3503899_3504439_+	F0F1 ATP synthase subunit delta	NA	NA	NA	NA	NA
AUL05396.1|3504473_3506015_+	F0F1 ATP synthase subunit alpha	NA	NA	NA	NA	NA
AUL05397.1|3506113_3507019_+	F0F1 ATP synthase subunit gamma	NA	NA	NA	NA	NA
AUL05398.1|3507061_3508462_+	F0F1 ATP synthase subunit beta	NA	NA	NA	NA	NA
AUL05399.1|3508471_3508894_+	F0F1 ATP synthase subunit epsilon	NA	NA	NA	NA	NA
AUL06137.1|3509076_3509961_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05400.1|3510036_3511113_+	uroporphyrinogen decarboxylase	NA	NA	NA	NA	NA
AUL05401.1|3511419_3513522_+	primosomal protein N'	NA	NA	NA	NA	NA
AUL05402.1|3513564_3515634_+	ATP-dependent DNA helicase Rep	NA	A7KV33	Bacillus_phage	37.3	2.6e-101
AUL05403.1|3515732_3516683_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05404.1|3516811_3517945_-	peptidase	NA	NA	NA	NA	NA
AUL05405.1|3517988_3518894_-	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL05406.1|3520593_3521514_-	peptide ABC transporter permease	NA	NA	NA	NA	NA
AUL05407.1|3521521_3522499_-	ABC transporter permease	NA	NA	NA	NA	NA
AUL05408.1|3522557_3523517_-	succinylglutamate desuccinylase	NA	NA	NA	NA	NA
AUL05409.1|3525566_3525803_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05410.1|3525929_3526793_-	NAD(P)H-hydrate dehydratase	NA	NA	NA	NA	NA
AUL05411.1|3526881_3527703_+	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL05412.1|3527782_3528520_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL05413.1|3528516_3529509_-	2-nitropropane dioxygenase	NA	NA	NA	NA	NA
AUL06138.1|3529661_3530285_+	TetR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05414.1|3530329_3531478_+	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL05415.1|3533849_3534752_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05416.1|3535092_3536043_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05417.1|3536188_3537091_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05418.1|3537387_3537885_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05419.1|3537927_3539703_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05420.1|3539710_3540577_+	copper resistance protein	NA	NA	NA	NA	NA
AUL05421.1|3540583_3541309_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL05422.1|3541478_3541709_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05423.1|3541773_3541968_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05424.1|3542487_3543258_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05425.1|3543571_3544162_+	cysteine dioxygenase	NA	NA	NA	NA	NA
AUL05426.1|3544195_3545524_-	amidase	NA	NA	NA	NA	NA
AUL05427.1|3545598_3546744_-	transporter	NA	NA	NA	NA	NA
AUL05428.1|3546855_3547854_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05429.1|3547816_3548251_+	carbon monoxide dehydrogenase	NA	NA	NA	NA	NA
AUL05430.1|3549766_3550651_+	EamA family transporter	NA	NA	NA	NA	NA
AUL05431.1|3550647_3551853_-	cardiolipin synthase B	NA	NA	NA	NA	NA
AUL05432.1|3551849_3552710_-	endonuclease	NA	NA	NA	NA	NA
AUL05433.1|3552822_3554613_-|tRNA	aspartate--tRNA ligase	tRNA	A0A1V0SAC0	Catovirus	25.5	6.5e-08
AUL06139.1|3554653_3555298_-	hypothetical protein	NA	A0A2I7S9X1	Vibrio_phage	28.4	8.5e-11
AUL05434.1|3555319_3555628_-	FmdB family transcriptional regulator	NA	NA	NA	NA	NA
AUL06140.1|3555793_3557080_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05435.1|3557206_3558466_-|holin	choline dehydrogenase	holin	A0A2I2L3D3	Orpheovirus	27.6	6.1e-13
AUL05436.1|3558513_3559464_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05437.1|3561415_3562630_-	phosphoribosylglycinamide formyltransferase 2	NA	NA	NA	NA	NA
AUL05438.1|3562735_3563725_+	D-arabinose 5-phosphate isomerase	NA	A0A2P0VNK5	Tetraselmis_virus	37.7	4.3e-38
AUL05439.1|3563721_3564330_+	phenylphosphate carboxylase subunit delta	NA	E3T535	Cafeteria_roenbergensis_virus	26.1	5.2e-10
AUL05440.1|3564342_3564972_+	LPS export ABC transporter periplasmic protein LptC	NA	NA	NA	NA	NA
AUL05441.1|3564968_3565589_+	lipopolysaccharide transport periplasmic protein LptA	NA	NA	NA	NA	NA
AUL05442.1|3565620_3566412_+	LPS export ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	27.4	9.5e-20
AUL05443.1|3566765_3566987_+	ribosomal subunit interface protein	NA	NA	NA	NA	NA
AUL05444.1|3567263_3567719_+	PTS sugar transporter subunit IIA	NA	NA	NA	NA	NA
AUL05445.1|3567737_3568664_+	HPr kinase/phosphorylase	NA	NA	NA	NA	NA
AUL05446.1|3568717_3570004_-	alcohol dehydrogenase	NA	NA	NA	NA	NA
AUL05447.1|3570934_3571807_+	RNase adaptor protein RapZ	NA	A0A1P8D5W0	Corynebacterium_phage	34.5	2.4e-08
AUL05448.1|3571803_3572754_+	hypothetical protein	NA	F5B3X9	Synechococcus_phage	47.2	6.9e-17
AUL05449.1|3572899_3573802_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05450.1|3574262_3574682_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05451.1|3574668_3577050_-	dehydrogenase	NA	NA	NA	NA	NA
AUL05452.1|3577042_3577552_-	4-hydroxybenzoyl-CoA reductase subunit gamma	NA	A0A0P0IVM8	Acinetobacter_phage	37.3	8.8e-19
AUL05453.1|3578434_3579430_-	4,5-dihydroxyphthalate decarboxylase	NA	NA	NA	NA	NA
AUL05454.1|3580680_3581241_-	3-octaprenyl-4-hydroxybenzoate carboxy-lyase	NA	NA	NA	NA	NA
AUL05455.1|3581245_3581572_-	monothiol glutaredoxin, Grx4 family	NA	NA	NA	NA	NA
AUL05456.1|3581608_3582421_-	protein-(glutamine-N5) methyltransferase, release factor-specific	NA	NA	NA	NA	NA
AUL05457.1|3582431_3583514_-	peptide chain release factor 1	NA	A0A0S4KWG0	Pseudomonas_phage	40.7	3.3e-07
AUL05458.1|3583600_3584875_-|tRNA	glutamyl-tRNA reductase	tRNA	NA	NA	NA	NA
AUL05459.1|3585597_3586548_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05460.1|3586646_3587549_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 26
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	3705965	3749135	4105872	transposase,tRNA,integrase	Streptococcus_phage(11.11%)	41	3743974:3743992	3749758:3749776
AUL05554.1|3705965_3706868_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05555.1|3707014_3707917_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05556.1|3707913_3708549_-	lysine transporter LysE	NA	NA	NA	NA	NA
AUL05557.1|3708678_3709578_+	transcriptional regulator ArgP	NA	NA	NA	NA	NA
AUL05558.1|3709673_3710165_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05559.1|3710211_3711177_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL05560.1|3712310_3713552_+	2-aminoadipate aminotransferase	NA	A0A1X9I5H2	Streptococcus_phage	24.9	1.9e-14
AUL05561.1|3713665_3714682_+	amino acid ABC transporter substrate-binding protein	NA	A0A1B1IT51	uncultured_Mediterranean_phage	43.8	3.5e-75
AUL05562.1|3714716_3715193_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05563.1|3715335_3716244_-	hydroxymethylglutaryl-CoA lyase	NA	NA	NA	NA	NA
AUL05564.1|3716357_3717470_-	DNA protecting protein DprA	NA	S6BFL3	Thermus_phage	35.0	1.9e-21
AUL06149.1|3717570_3718056_-	AsnC family transcriptional regulator	NA	NA	NA	NA	NA
AUL05565.1|3718192_3719443_+	kynureninase	NA	NA	NA	NA	NA
AUL05566.1|3719544_3720057_+	peptide deformylase	NA	E3SLL2	Synechococcus_phage	43.3	8.5e-22
AUL05567.1|3720155_3721106_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05568.1|3721171_3722110_+|tRNA	methionyl-tRNA formyltransferase	tRNA	E3SNR5	Prochlorococcus_phage	35.7	1.4e-09
AUL05569.1|3722132_3722759_-	flavin-nucleotide-binding protein	NA	NA	NA	NA	NA
AUL05570.1|3722755_3723412_-	HAD family hydrolase	NA	NA	NA	NA	NA
AUL05571.1|3723408_3724011_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05572.1|3724017_3724605_-	Rossman fold protein, TIGR00730 family	NA	A0A2I2L3F0	Orpheovirus	23.3	1.1e-07
AUL05573.1|3724785_3725355_+	bacterioferritin	NA	NA	NA	NA	NA
AUL05574.1|3725425_3726745_-	ribosomal protein S12 methylthiotransferase	NA	NA	NA	NA	NA
AUL05575.1|3726851_3727043_-	4-oxalocrotonate tautomerase	NA	NA	NA	NA	NA
AUL05576.1|3727294_3728584_+	glycine/D-amino acid oxidase	NA	NA	NA	NA	NA
AUL05577.1|3728738_3729734_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05578.1|3729818_3730493_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05579.1|3730489_3731392_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05580.1|3731601_3732843_+	ornithine--oxo-acid transaminase	NA	A0A1V0SKB7	Klosneuvirus	25.2	4.0e-25
AUL05581.1|3732839_3733784_+	arginase	NA	A0A0N9R043	Chrysochromulina_ericina_virus	33.3	9.5e-27
AUL05582.1|3733950_3734853_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05583.1|3734812_3735742_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05584.1|3735795_3736131_-	alkylhydroperoxidase	NA	NA	NA	NA	NA
AUL05585.1|3736175_3736940_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL05586.1|3736963_3737704_-	transcriptional regulator	NA	NA	NA	NA	NA
AUL05587.1|3737711_3739265_-	long-chain fatty acid--CoA ligase	NA	A0A2K9L3I8	Tupanvirus	22.6	1.5e-13
AUL05588.1|3739299_3740277_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05589.1|3740549_3741131_-	ureidoglycolate hydrolase	NA	NA	NA	NA	NA
AUL05590.1|3741182_3748316_-	autotransporter outer membrane beta-barrel domain-containing protein	NA	NA	NA	NA	NA
3743974:3743992	attL	GCGACCCGCAGCGTGCCGG	NA	NA	NA	NA
AUL05591.1|3748531_3748663_-	entericidin	NA	NA	NA	NA	NA
AUL06150.1|3748694_3748820_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05592.1|3748928_3749135_-|integrase	integrase	integrase	NA	NA	NA	NA
3749758:3749776	attR	GCGACCCGCAGCGTGCCGG	NA	NA	NA	NA
>prophage 27
CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4105872	3755070	3790744	4105872	transposase,integrase	Burkholderia_phage(11.11%)	37	3751609:3751626	3796248:3796265
3751609:3751626	attL	CAGCGTGCTGGCCACCGT	NA	NA	NA	NA
AUL05599.1|3755070_3755973_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05600.1|3755983_3756625_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05601.1|3756791_3757034_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05602.1|3757179_3758082_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05603.1|3758117_3758585_+	hypothetical protein	NA	Q3HQX1	Burkholderia_phage	71.3	2.1e-43
AUL05604.1|3758818_3759196_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05605.1|3759192_3759375_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05606.1|3759378_3760365_+	DNA recombinase	NA	H9C0R8	Aeromonas_phage	57.3	2.0e-67
AUL05607.1|3760361_3761009_+	exonuclease	NA	A0A0U2BXF3	Paracoccus_phage	41.4	2.0e-31
AUL05608.1|3761066_3761594_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05609.1|3761630_3762815_+	hypothetical protein	NA	A0A291L9X3	Bordetella_phage	37.8	1.5e-24
AUL05610.1|3762825_3763167_+	hypothetical protein	NA	A0A0H5ARN8	Pseudomonas_phage	45.3	1.0e-10
AUL05611.1|3763159_3763279_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05612.1|3763279_3763480_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05613.1|3763476_3764466_-|integrase	integrase	integrase	A0A1B1P9F9	Acinetobacter_phage	44.4	4.4e-75
AUL05614.1|3765952_3767923_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05615.1|3768164_3768563_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05616.1|3768571_3769495_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05617.1|3770000_3770903_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05618.1|3771133_3772825_-	membrane protein insertase YidC	NA	NA	NA	NA	NA
AUL05619.1|3772873_3773146_-	membrane protein insertion efficiency factor YidD	NA	A0A2H4PQM5	Staphylococcus_phage	52.2	7.0e-15
AUL05620.1|3773142_3773514_-	ribonuclease P protein component	NA	NA	NA	NA	NA
AUL05621.1|3773609_3773744_-	50S ribosomal protein L34	NA	NA	NA	NA	NA
AUL05622.1|3774149_3775559_+	chromosomal replication initiation protein DnaA	NA	NA	NA	NA	NA
AUL05623.1|3775561_3776671_+	DNA polymerase III subunit beta	NA	B4UTW9	Rhizobium_phage	32.6	1.2e-41
AUL05624.1|3776765_3779219_+	DNA gyrase subunit B	NA	G3M9Z3	Bacillus_virus	34.8	2.3e-112
AUL05625.1|3779337_3780129_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05626.1|3780248_3781676_+	amidase	NA	NA	NA	NA	NA
AUL06151.1|3781714_3782686_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL06152.1|3782770_3782974_+	hypothetical protein	NA	NA	NA	NA	NA
AUL05627.1|3783104_3784268_+	alpha-hydroxy-acid oxidizing enzyme	NA	NA	NA	NA	NA
AUL05628.1|3784355_3785201_+	AraC family transcriptional regulator	NA	NA	NA	NA	NA
AUL05629.1|3786805_3787708_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL05630.1|3787704_3788049_-	hypothetical protein	NA	NA	NA	NA	NA
AUL05631.1|3788262_3788637_-	MerR family transcriptional regulator	NA	NA	NA	NA	NA
AUL05632.1|3788711_3789770_+	Zn-dependent hydrolase	NA	NA	NA	NA	NA
AUL05633.1|3789793_3790744_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
3796248:3796265	attR	CAGCGTGCTGGCCACCGT	NA	NA	NA	NA
