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
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	27282	70442	4109385	protease,tRNA,transposase	Synechococcus_phage(50.0%)	42	NA	NA
AUL09800.1|27282_28185_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09801.1|28314_28614_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09802.1|28674_29109_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09803.1|29141_30359_-	thiolase	NA	NA	NA	NA	NA
AUL09804.1|30364_30862_-	dehydratase	NA	NA	NA	NA	NA
AUL09805.1|31069_32005_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL13099.1|32214_33006_+	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL09806.1|33048_34470_+	2-methylcitrate dehydratase	NA	NA	NA	NA	NA
AUL09807.1|35571_36762_-	MFS transporter	NA	NA	NA	NA	NA
AUL09808.1|37011_37923_+|tRNA	glycine--tRNA ligase subunit alpha	tRNA	NA	NA	NA	NA
AUL09809.1|37924_40063_+|tRNA	glycine--tRNA ligase subunit beta	tRNA	NA	NA	NA	NA
AUL09810.1|40059_40599_+	D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase	NA	NA	NA	NA	NA
AUL09811.1|40602_41331_+	1-acyl-sn-glycerol-3-phosphate acyltransferase	NA	NA	NA	NA	NA
AUL09812.1|41317_42211_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09813.1|42281_42677_+	lactoylglutathione lyase	NA	NA	NA	NA	NA
AUL09814.1|42686_43217_+	peptide deformylase	NA	E3SLL2	Synechococcus_phage	35.4	3.7e-12
AUL09815.1|43345_43525_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09816.1|43662_44613_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL13100.1|45223_45748_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09817.1|45719_45956_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
AUL09818.1|46083_46977_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09819.1|48146_49394_+	homoserine O-acetyltransferase	NA	NA	NA	NA	NA
AUL09820.1|49390_50005_+	methionine biosynthesis protein MetW	NA	NA	NA	NA	NA
AUL09821.1|51132_52389_+	muropeptide transporter AmpG	NA	NA	NA	NA	NA
AUL09822.1|53620_54355_-	glutamate racemase	NA	NA	NA	NA	NA
AUL09823.1|54360_54951_-	arginine transporter ATP-binding subunit	NA	G9BWD6	Planktothrix_phage	33.6	3.2e-20
AUL09824.1|54975_55665_-	amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL09825.1|55661_56423_-	glutamate ABC transporter permease	NA	NA	NA	NA	NA
AUL09826.1|56502_57402_-	amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL09827.1|57495_58446_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09828.1|59246_60473_-	serine kinase HipA	NA	NA	NA	NA	NA
AUL09829.1|60472_60892_-	transcriptional regulator	NA	NA	NA	NA	NA
AUL13101.1|61075_62017_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09830.1|62440_63415_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09831.1|63471_64053_-|protease	protease	protease	NA	NA	NA	NA
AUL09832.1|64065_64368_-	ferredoxin	NA	NA	NA	NA	NA
AUL09833.1|64486_65545_-	oxidoreductase	NA	NA	NA	NA	NA
AUL09834.1|65579_66851_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09835.1|66881_67136_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09836.1|67480_68662_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09837.1|69131_70034_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09838.1|70127_70442_+|transposase	transposase	transposase	NA	NA	NA	NA
>prophage 2
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	77632	136105	4109385	tRNA,transposase	Planktothrix_phage(22.22%)	57	NA	NA
AUL09845.1|77632_78583_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL13102.1|78657_79602_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09846.1|79598_81473_-	polysaccharide biosynthesis protein	NA	A0A2P1ELS8	Moumouvirus	26.9	2.0e-23
AUL09847.1|82820_83525_-	lipopolysaccharide biosynthesis protein	NA	NA	NA	NA	NA
AUL09848.1|83521_84628_-	glycosyl transferase	NA	NA	NA	NA	NA
AUL09849.1|84889_85483_-	sugar transferase	NA	NA	NA	NA	NA
AUL09850.1|85479_86667_-	UDP-4-amino-4, 6-dideoxy-N-acetyl-beta-L-altrosamine transaminase	NA	NA	NA	NA	NA
AUL09851.1|86729_87989_-	glycosyltransferase WbuB	NA	NA	NA	NA	NA
AUL09852.1|88012_89101_-	UDP-N-acetylglucosamine 2-epimerase	NA	A0A0N9R0B2	Chrysochromulina_ericina_virus	36.3	4.8e-46
AUL09853.1|89108_90209_-	aminotransferase DegT	NA	A0A2K9L0G1	Tupanvirus	29.7	3.3e-31
AUL09854.1|90212_90788_-	N-acetyltransferase	NA	NA	NA	NA	NA
AUL09855.1|90791_91844_-	oxidoreductase	NA	NA	NA	NA	NA
AUL13103.1|91974_92982_+	lipopolysaccharide heptosyltransferase I	NA	NA	NA	NA	NA
AUL09856.1|92983_94270_+	3-deoxy-D-manno-octulosonic acid transferase	NA	NA	NA	NA	NA
AUL09857.1|94286_94442_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09858.1|94466_95270_-	pantothenate kinase	NA	NA	NA	NA	NA
AUL09859.1|95266_96133_-	biotin--[acetyl-CoA-carboxylase] ligase	NA	NA	NA	NA	NA
AUL09860.1|96207_97338_+	ABC transporter permease	NA	NA	NA	NA	NA
AUL09861.1|97337_98177_+	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	32.4	9.1e-21
AUL09862.1|98330_98798_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09863.1|98887_99109_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09864.1|99109_99712_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09865.1|99741_100395_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL13104.1|100605_101784_+	peptidase	NA	B6DZZ7	Stx2-converting_phage	40.5	5.8e-66
AUL09866.1|101864_102731_+	D-amino acid aminotransferase	NA	NA	NA	NA	NA
AUL09867.1|102806_103082_+	DUF493 domain-containing protein	NA	NA	NA	NA	NA
AUL09868.1|103089_103752_+	octanoyltransferase	NA	NA	NA	NA	NA
AUL09869.1|103813_104815_+	lipoyl synthase	NA	NA	NA	NA	NA
AUL09870.1|104829_105378_-	dTDP-4-dehydrorhamnose 3,5-epimerase	NA	A0A291LA62	Escherichia_phage	53.4	3.7e-47
AUL09871.1|105435_106332_-	dTDP-4-dehydrorhamnose reductase	NA	NA	NA	NA	NA
AUL09872.1|106328_107390_-	dTDP-glucose 4,6-dehydratase	NA	A0A1D7XFE8	Escherichia_phage	44.8	1.6e-78
AUL09873.1|107425_108328_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09874.1|109275_110469_+	cystathionine beta-lyase	NA	NA	NA	NA	NA
AUL09875.1|110550_111180_-	thiol:disulfide interchange protein	NA	NA	NA	NA	NA
AUL09876.1|111241_111925_-	cell division protein	NA	NA	NA	NA	NA
AUL09877.1|111934_113617_-|tRNA	arginine--tRNA ligase	tRNA	NA	NA	NA	NA
AUL13105.1|113904_114252_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09878.1|114342_114660_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13106.1|114942_115959_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL09879.1|116034_116835_-	ABC transporter permease	NA	NA	NA	NA	NA
AUL09880.1|116831_117707_-	ABC transporter permease	NA	NA	NA	NA	NA
AUL09881.1|117717_119010_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL09882.1|119052_120093_-	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	33.7	6.0e-22
AUL09883.1|120198_121020_-	phosphodiesterase	NA	NA	NA	NA	NA
AUL09884.1|121120_122071_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09885.1|122168_123074_-	ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	31.7	9.8e-21
AUL09886.1|123070_123904_-	ABC transporter permease	NA	NA	NA	NA	NA
AUL09887.1|124740_125751_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL09888.1|125747_126137_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09889.1|126120_126732_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09890.1|127018_128284_+	amidase	NA	NA	NA	NA	NA
AUL09891.1|128374_130075_-	2-isopropylmalate synthase	NA	NA	NA	NA	NA
AUL09892.1|130501_131149_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09893.1|131147_132587_+	RNA polymerase sigma-54 factor	NA	NA	NA	NA	NA
AUL09894.1|132697_132982_+	bacterioferritin	NA	NA	NA	NA	NA
AUL09895.1|133009_133888_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL09896.1|135154_136105_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 3
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	164889	236263	4109385	tRNA,transposase	Diachasmimorpha_longicaudata_entomopoxvirus(12.5%)	58	NA	NA
AUL09920.1|164889_165840_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09921.1|167283_168186_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09922.1|168163_168793_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09923.1|169075_170506_+	RNA helicase	NA	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	29.8	5.8e-44
AUL09924.1|170539_171169_+	threonine transporter RhtB	NA	NA	NA	NA	NA
AUL09925.1|171217_172825_+	peptide chain release factor 3	NA	A0A2K9L6L3	Tupanvirus	37.8	9.3e-14
AUL09926.1|172861_173533_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13109.1|173614_174091_-	bacterioferritin	NA	NA	NA	NA	NA
AUL09927.1|174345_175248_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09928.1|176363_176891_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09929.1|176982_177798_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09930.1|177858_178593_+	sulfurtransferase	NA	NA	NA	NA	NA
AUL09931.1|178630_180709_-|tRNA	methionine--tRNA ligase	tRNA	A0A1V0SHR2	Klosneuvirus	23.6	1.5e-27
AUL09932.1|180958_181231_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09933.1|181332_182418_+	ATP-binding protein	NA	NA	NA	NA	NA
AUL09934.1|182421_184326_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09935.1|184322_187997_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09936.1|188057_188621_+	dCTP deaminase	NA	S5VM63	Pseudomonas_phage	75.3	2.6e-72
AUL09937.1|188628_189051_-	glyoxalase	NA	NA	NA	NA	NA
AUL09938.1|189078_189498_-	glyoxalase	NA	NA	NA	NA	NA
AUL09939.1|189526_189874_-	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL13110.1|190147_190597_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09940.1|190751_193022_+	lysine decarboxylase	NA	NA	NA	NA	NA
AUL09941.1|193097_194303_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09942.1|194448_195351_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09943.1|195453_196089_+	superoxide dismutase	NA	Q56AR7	Bacillus_thuringiensis_phage	73.8	2.8e-83
AUL09944.1|196085_196979_+	ZIP family metal transporter	NA	NA	NA	NA	NA
AUL09945.1|197373_198474_+	glycine cleavage system protein T	NA	NA	NA	NA	NA
AUL09946.1|198555_198930_+	glycine cleavage system protein H	NA	NA	NA	NA	NA
AUL09947.1|198989_201854_+	glycine dehydrogenase (aminomethyl-transferring)	NA	E3SN07	Prochlorococcus_phage	51.4	1.2e-261
AUL09948.1|201998_202739_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL09949.1|202808_204020_+	formyl-CoA transferase	NA	NA	NA	NA	NA
AUL09950.1|204048_205017_+	hypothetical protein	NA	NA	NA	NA	NA
AUL09951.1|206736_207060_+	PsiF repeat family protein	NA	NA	NA	NA	NA
AUL13111.1|207164_208205_-	cyclase	NA	NA	NA	NA	NA
AUL09952.1|208210_208990_-	3-oxoadipate enol-lactonase	NA	NA	NA	NA	NA
AUL09953.1|209035_209332_-	hypothetical protein	NA	NA	NA	NA	NA
AUL09954.1|209357_209633_-	muconolactone delta-isomerase	NA	NA	NA	NA	NA
AUL09955.1|209689_210334_-	3-oxoadipate CoA-transferase	NA	NA	NA	NA	NA
AUL09956.1|210333_211020_-	3-oxoadipate CoA-transferase	NA	NA	NA	NA	NA
AUL13112.1|211218_212001_+	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL09957.1|212051_212777_-	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL09958.1|212808_214158_-	short-chain fatty acid transporter	NA	NA	NA	NA	NA
AUL09959.1|214269_215202_-	3-hydroxybutyryl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL09960.1|215659_218455_-	peptidase S8	NA	NA	NA	NA	NA
AUL09961.1|219048_221892_-	phosphoenolpyruvate carboxylase	NA	NA	NA	NA	NA
AUL09962.1|222062_222782_+	7-cyano-7-deazaguanine synthase QueC	NA	A0A0A0RPC6	Escherichia_phage	43.9	8.0e-50
AUL09963.1|222820_223369_-	GNAT family N-acetyltransferase	NA	A0A2H4J136	uncultured_Caudovirales_phage	41.7	1.2e-21
AUL09964.1|223523_224423_+	virginiamycin B lyase	NA	NA	NA	NA	NA
AUL09965.1|224447_225398_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09966.1|225615_226311_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL09967.1|226327_227740_+	hydroxyacid dehydrogenase	NA	NA	NA	NA	NA
AUL09968.1|227852_229283_+	aldehyde dehydrogenase family protein	NA	NA	NA	NA	NA
AUL09969.1|229324_231238_-	phosphomethylpyrimidine synthase ThiC	NA	NA	NA	NA	NA
AUL09970.1|231556_232123_+	preprotein translocase subunit SecD	NA	NA	NA	NA	NA
AUL09971.1|232213_233215_+	restriction endonuclease	NA	NA	NA	NA	NA
AUL09972.1|234365_235316_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL09973.1|235312_236263_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 4
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	390845	448353	4109385	transposase	Orpheovirus(14.29%)	49	NA	NA
AUL10111.1|390845_391796_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10112.1|391938_392850_+	reductase	NA	NA	NA	NA	NA
AUL10113.1|392846_393095_+	NrdH-redoxin	NA	NA	NA	NA	NA
AUL10114.1|393091_394297_+	CoA transferase	NA	NA	NA	NA	NA
AUL10115.1|394369_395365_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10116.1|395387_396608_-	acyl-CoA transferase	NA	NA	NA	NA	NA
AUL10117.1|396604_397249_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10118.1|397245_397638_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10119.1|397526_398879_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10120.1|398979_399789_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL13121.1|400093_401047_+	thioredoxin-disulfide reductase	NA	A0A2I2L5E1	Orpheovirus	42.5	5.6e-59
AUL10121.1|401145_402129_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10122.1|402805_403576_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL10123.1|403572_404751_-	carnitine dehydratase	NA	NA	NA	NA	NA
AUL10124.1|406620_407517_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10125.1|407557_409147_-	sulfurtransferase	NA	NA	NA	NA	NA
AUL10126.1|409196_410189_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10127.1|410257_410857_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10128.1|411317_412298_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10129.1|412373_413276_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10130.1|413412_414327_+	EamA family transporter	NA	NA	NA	NA	NA
AUL10131.1|414323_414983_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10132.1|415072_415996_+	alpha/beta hydrolase	NA	A0A1C9C5K3	Heterosigma_akashiwo_virus	27.2	4.8e-07
AUL10133.1|416001_416457_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10134.1|416453_417557_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10135.1|417744_419364_-	dolichyl-phosphate-mannose--protein mannosyltransferase	NA	NA	NA	NA	NA
AUL10136.1|419360_420419_-	glycosyltransferase	NA	I1TED8	Salmonella_phage	40.5	2.8e-59
AUL10137.1|420548_421043_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL10138.1|421135_422113_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10139.1|422308_423514_+	sodium/glutamate symporter	NA	NA	NA	NA	NA
AUL10140.1|423510_425022_+	TRAP ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL13122.1|425037_426351_-	short-chain fatty acid transporter	NA	NA	NA	NA	NA
AUL10141.1|426541_426721_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10142.1|427130_427865_-	DNA polymerase III subunit epsilon	NA	A0A1X9SH08	Bradyrhizobium_phage	43.8	1.4e-41
AUL10143.1|430357_431260_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10144.1|431391_431790_-	elongation factor G	NA	E4ZFJ7	Streptococcus_phage	44.3	9.0e-19
AUL10145.1|432200_432671_-	universal stress protein	NA	NA	NA	NA	NA
AUL10146.1|432759_433104_-	TIGR01244 family protein	NA	NA	NA	NA	NA
AUL10147.1|433203_434604_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10148.1|436392_436911_-	methyltransferase	NA	G3MA03	Bacillus_virus	38.9	2.1e-12
AUL10149.1|437021_437777_+	hypothetical protein	NA	A0A0R6PEZ3	Moraxella_phage	40.8	2.9e-42
AUL10150.1|437972_439205_+	CoA transferase	NA	NA	NA	NA	NA
AUL10151.1|439197_439983_+	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL10152.1|440049_441021_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL10153.1|441031_442009_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10154.1|442134_443307_+	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL10155.1|443333_444362_+	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL10156.1|444427_445621_+	acetyl-CoA acetyltransferase	NA	NA	NA	NA	NA
AUL10157.1|447402_448353_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 5
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	620783	722294	4109385	terminase,tRNA,transposase,tail	uncultured_Caudovirales_phage(14.29%)	109	NA	NA
AUL10309.1|620783_621734_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10310.1|622432_622816_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10311.1|622873_623476_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13129.1|623493_623895_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10312.1|624010_624922_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10313.1|624918_625500_+	NUDIX hydrolase	NA	NA	NA	NA	NA
AUL13130.1|626303_627029_+	arginyltransferase	NA	NA	NA	NA	NA
AUL10314.1|627069_628119_+	dihydroorotate dehydrogenase (quinone)	NA	NA	NA	NA	NA
AUL10315.1|628266_628845_-	Phasin (PHA-granule associated protein)	NA	NA	NA	NA	NA
AUL10316.1|629231_630209_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL10317.1|630302_634697_-	dermonecrotic toxin	NA	NA	NA	NA	NA
AUL10318.1|634897_635746_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10319.1|635904_636717_-	competence/damage-inducible protein A	NA	NA	NA	NA	NA
AUL10320.1|636772_637723_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10321.1|637821_638622_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10322.1|638683_639067_+	thiol reductase thioredoxin	NA	NA	NA	NA	NA
AUL10323.1|639078_640512_-	ATP-dependent RNA helicase	NA	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	34.4	1.5e-52
AUL10324.1|640718_641048_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10325.1|641050_641800_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10326.1|641982_642903_+	branched chain amino acid aminotransferase	NA	NA	NA	NA	NA
AUL10327.1|642949_643162_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10328.1|643184_643607_+	DUF4440 domain-containing protein	NA	NA	NA	NA	NA
AUL10329.1|643623_644724_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL10330.1|644820_646338_-	peptidase	NA	NA	NA	NA	NA
AUL10331.1|646413_647253_+	UTP--glucose-1-phosphate uridylyltransferase	NA	A0A127AW70	Bacillus_phage	48.9	1.1e-66
AUL13131.1|647274_648147_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10332.1|648237_649332_-	porin	NA	NA	NA	NA	NA
AUL10333.1|649625_650528_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL13132.1|650650_651592_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10334.1|651675_652035_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10335.1|652416_653454_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10336.1|653770_655111_+	Xaa-Pro aminopeptidase	NA	NA	NA	NA	NA
AUL10337.1|655120_655573_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10338.1|655678_656851_+	monooxygenase	NA	NA	NA	NA	NA
AUL10339.1|656916_657942_+|tRNA	tRNA dihydrouridine synthase DusB	tRNA	NA	NA	NA	NA
AUL10340.1|657982_658222_+	Fis family transcriptional regulator	NA	NA	NA	NA	NA
AUL10341.1|658291_659881_+	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase	NA	Q58MG4	Prochlorococcus_phage	47.2	8.7e-65
AUL10342.1|659880_660429_+	crossover junction endodeoxyribonuclease RuvC	NA	NA	NA	NA	NA
AUL10343.1|660509_661082_+	Holliday junction DNA helicase RuvA	NA	NA	NA	NA	NA
AUL10344.1|661100_662012_-	NAD-dependent dehydratase	NA	NA	NA	NA	NA
AUL10345.1|662085_663054_-	serine dehydratase	NA	NA	NA	NA	NA
AUL10346.1|663176_664250_+	Holliday junction DNA helicase RuvB	NA	A0A127AWE7	Bacillus_phage	25.7	2.3e-08
AUL10347.1|664254_666075_-	ATP-dependent DNA helicase RecQ	NA	L7RCS0	Acanthamoeba_polyphaga_moumouvirus	35.3	3.1e-74
AUL10348.1|667189_667525_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10349.1|667658_668309_+	carbonate dehydratase	NA	NA	NA	NA	NA
AUL10350.1|668330_669749_-	amidase	NA	NA	NA	NA	NA
AUL10351.1|669818_670574_-	hypothetical protein	NA	NA	NA	NA	NA
AUL13133.1|670542_671301_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL10352.1|671311_672193_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL10353.1|672209_672917_+	ABC transporter ATP-binding protein	NA	W8CYL7	Bacillus_phage	25.4	8.2e-07
AUL10354.1|672919_673678_+	ABC transporter ATP-binding protein	NA	W6JKT0	Anomala_cuprea_entomopoxvirus	24.4	4.4e-14
AUL10355.1|673887_675630_+	sulfite reductase	NA	NA	NA	NA	NA
AUL10356.1|675622_676147_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10357.1|676186_676981_-	metal ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL10358.1|677148_678222_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10359.1|678320_679271_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10360.1|679369_680320_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10361.1|680571_680778_-	hypothetical protein	NA	NA	NA	NA	NA
AUL13134.1|680849_681461_-	LexA family transcriptional repressor	NA	NA	NA	NA	NA
AUL10362.1|681940_682261_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10363.1|682253_682952_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10364.1|682966_683188_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10365.1|683253_684156_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10366.1|684795_685281_+|terminase	terminase	terminase	C7U0W1	Enterobacteria_phage	61.5	7.3e-39
AUL10367.1|685267_686545_+|terminase	terminase	terminase	A0A1B1P9C9	Acinetobacter_phage	64.7	2.4e-150
AUL10368.1|686547_687966_+	hypothetical protein	NA	R9TF43	Synechococcus_phage	42.1	2.2e-99
AUL10369.1|687937_689050_+	hypothetical protein	NA	A0A0H5BBX3	Pseudomonas_phage	49.7	2.1e-102
AUL10370.1|689055_689298_+	hypothetical protein	NA	A0A0H5AUE5	Pseudomonas_phage	53.2	5.6e-16
AUL10371.1|689420_690023_+	hypothetical protein	NA	R9TF81	Synechococcus_phage	43.6	7.9e-27
AUL10372.1|690451_691402_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10373.1|692076_692328_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10374.1|692390_692873_+	hypothetical protein	NA	A0A2H4JE38	uncultured_Caudovirales_phage	37.1	1.8e-13
AUL10375.1|692874_693075_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10376.1|693074_693470_+	hypothetical protein	NA	A0A2D2W284	Stenotrophomonas_phage	35.0	7.8e-07
AUL10377.1|693466_693865_+	hypothetical protein	NA	I6PCW1	Cronobacter_phage	38.0	4.2e-16
AUL10378.1|693861_694284_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10379.1|694291_694792_+	HNH endonuclease	NA	A0A1I9SEX5	Klebsiella_phage	45.1	4.4e-31
AUL10380.1|695046_695565_+|tail	phage tail protein	tail	A0A1S5R1H0	Pseudomonas_phage	38.3	5.4e-24
AUL10381.1|695574_695904_+	hypothetical protein	NA	A0A2H4J121	uncultured_Caudovirales_phage	44.0	2.9e-15
AUL10382.1|695921_696212_+	hypothetical protein	NA	A0A2H4JBP7	uncultured_Caudovirales_phage	45.2	3.7e-14
AUL10383.1|696237_698850_+|tail	phage tail tape measure protein	tail	A0A2H4J107	uncultured_Caudovirales_phage	38.6	4.9e-105
AUL10384.1|698859_699219_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10385.1|699286_699820_+	hypothetical protein	NA	A5A3Q9	Burkholderia_phage	46.9	1.1e-40
AUL10386.1|699816_700206_+	hypothetical protein	NA	A0A0G3EYJ9	Achromobacter_phage	50.0	3.0e-35
AUL10387.1|700198_704155_+	hypothetical protein	NA	A0A0B5A1N2	Achromobacter_phage	40.8	3.9e-215
AUL10388.1|704159_704576_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10389.1|704794_705058_+	hypothetical protein	NA	A0A1B0V3F2	Roseobacter_phage	41.8	7.2e-09
AUL10390.1|705057_705870_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10391.1|705874_706117_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10392.1|706095_706647_+	lysozyme	NA	NA	NA	NA	NA
AUL10393.1|706646_707162_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10394.1|707158_707440_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10395.1|707439_707661_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10396.1|707989_708661_-	hypothetical protein	NA	Q5QF62	Pseudomonas_virus	39.9	4.7e-36
AUL10397.1|708588_708957_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10398.1|709016_709703_-	DNA-binding response regulator	NA	NA	NA	NA	NA
AUL10399.1|709683_710256_-	RNA pyrophosphohydrolase	NA	NA	NA	NA	NA
AUL10400.1|710321_712052_+|tRNA	proline--tRNA ligase	tRNA	A0A2K9L3R9	Tupanvirus	29.4	4.6e-11
AUL10401.1|712104_712533_+	tol-pal system-associated acyl-CoA thioesterase	NA	NA	NA	NA	NA
AUL10402.1|712535_713216_+	protein TolQ	NA	NA	NA	NA	NA
AUL10403.1|713215_713674_+	protein TolR	NA	NA	NA	NA	NA
AUL10404.1|714700_716017_+	Tol-Pal system beta propeller repeat protein TolB	NA	NA	NA	NA	NA
AUL10405.1|716048_716546_+	peptidoglycan-associated lipoprotein	NA	NA	NA	NA	NA
AUL10406.1|716632_717322_+	tol-pal system protein YbgF	NA	NA	NA	NA	NA
AUL10407.1|717321_718371_+	iron-siderophore ABC transporter permease	NA	NA	NA	NA	NA
AUL10408.1|718367_719162_+	iron ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	30.6	2.4e-15
AUL10409.1|719330_719681_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10410.1|719656_720214_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10411.1|721343_722294_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 6
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	860822	914952	4109385	holin,transposase	Vibrio_phage(25.0%)	44	NA	NA
AUL10517.1|860822_862781_-|holin	choline transporter	holin	A0A2I7QNT1	Vibrio_phage	30.3	8.0e-28
AUL10518.1|862863_863814_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10519.1|864034_864703_+	transcriptional regulator	NA	NA	NA	NA	NA
AUL10520.1|864826_865933_+	efflux transporter periplasmic adaptor subunit	NA	NA	NA	NA	NA
AUL10521.1|865945_869059_+	multidrug efflux protein	NA	S5VTK5	Leptospira_phage	21.5	4.5e-57
AUL10522.1|869055_870549_+	RND transporter	NA	NA	NA	NA	NA
AUL10523.1|870563_871235_+	MarR family transcriptional regulator	NA	NA	NA	NA	NA
AUL13144.1|871278_871731_-	azurin	NA	NA	NA	NA	NA
AUL10524.1|871913_872561_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL13145.1|872664_874713_+	hydantoinase	NA	NA	NA	NA	NA
AUL10525.1|874709_876722_+	hydantoin utilization protein B	NA	NA	NA	NA	NA
AUL10526.1|876747_878082_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10527.1|878190_879183_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10528.1|879249_881334_-	rhodanese-like domain-containing protein	NA	NA	NA	NA	NA
AUL10529.1|881358_882330_-	hypothetical protein	NA	NA	NA	NA	NA
AUL13146.1|882458_883460_-	peptidase M14	NA	NA	NA	NA	NA
AUL10530.1|883493_884645_-	cystathionine beta-lyase	NA	NA	NA	NA	NA
AUL10531.1|884848_885739_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10532.1|885816_886641_+	3-oxoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL13147.1|886837_887854_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL10533.1|888050_889034_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL10534.1|889092_890220_-	argininosuccinate lyase	NA	NA	NA	NA	NA
AUL10535.1|890210_890585_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10536.1|890632_892021_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10537.1|892051_893041_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10538.1|893151_894384_-	methylaspartate ammonia-lyase	NA	NA	NA	NA	NA
AUL10539.1|894665_895466_+	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10540.1|895488_897642_-|holin	high-affinity choline transporter BetT	holin	NA	NA	NA	NA
AUL10541.1|898506_898953_-	preprotein translocase subunit SecG	NA	NA	NA	NA	NA
AUL10542.1|898974_899721_-	triose-phosphate isomerase	NA	NA	NA	NA	NA
AUL10543.1|899864_900842_-	NAD(P)H-quinone oxidoreductase	NA	NA	NA	NA	NA
AUL10544.1|901475_902087_+	PIN domain-containing protein	NA	K4HZX4	Acidithiobacillus_phage	32.5	3.3e-12
AUL10545.1|902080_903298_-	threonine ammonia-lyase	NA	NA	NA	NA	NA
AUL10546.1|903438_904389_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10547.1|904385_905105_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10548.1|905225_907385_-	polyribonucleotide nucleotidyltransferase	NA	NA	NA	NA	NA
AUL10549.1|907475_907745_-	30S ribosomal protein S15	NA	NA	NA	NA	NA
AUL13148.1|908038_908566_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10550.1|908584_909364_-	CDP-diacylglycerol--serine O-phosphatidyltransferase	NA	NA	NA	NA	NA
AUL10551.1|909531_910548_-	ketol-acid reductoisomerase	NA	NA	NA	NA	NA
AUL10552.1|910620_911112_-	acetolactate synthase small subunit	NA	NA	NA	NA	NA
AUL10553.1|911122_912838_-	acetolactate synthase, large subunit, biosynthetic type	NA	A0A0P0CDR3	Ostreococcus_lucimarinus_virus	30.3	3.1e-60
AUL10554.1|913308_913920_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10555.1|914001_914952_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 7
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	939451	1001600	4109385	transposase	Bacillus_virus(15.38%)	57	NA	NA
AUL10577.1|939451_940354_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10578.1|940350_940734_-	Rieske (2Fe-2S) protein	NA	NA	NA	NA	NA
AUL10579.1|940788_942603_-	metal ABC transporter permease	NA	W8CYL7	Bacillus_phage	27.9	5.7e-44
AUL13149.1|942752_943580_+	oxidoreductase	NA	A0A2H4PQR8	Staphylococcus_phage	47.4	1.7e-67
AUL10580.1|943625_944606_+	alcohol dehydrogenase	NA	NA	NA	NA	NA
AUL10581.1|944602_944815_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10582.1|944811_945993_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10583.1|946156_946891_+	serine/threonine protein phosphatase	NA	A0A2H4J0P0	uncultured_Caudovirales_phage	49.2	1.9e-62
AUL10584.1|946892_949505_-	penicillin-binding protein	NA	NA	NA	NA	NA
AUL10585.1|949640_951554_-	S9 family peptidase	NA	NA	NA	NA	NA
AUL10586.1|952169_952580_-	phenylacetic acid degradation protein	NA	NA	NA	NA	NA
AUL10587.1|952677_953763_+	DNA polymerase IV	NA	NA	NA	NA	NA
AUL10588.1|953861_954812_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10589.1|954808_955783_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10590.1|955928_956819_+	LysR family transcriptional regulator	NA	Q6JIH3	Burkholderia_virus	27.6	4.3e-05
AUL10591.1|957095_957488_-	hypothetical protein	NA	A0A0R6PJ17	Moraxella_phage	45.0	4.8e-25
AUL10592.1|957617_958568_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10593.1|958597_958780_-	addiction module toxin, HicA family	NA	A0A1L2JY37	Aeribacillus_phage	56.1	3.7e-12
AUL10594.1|959552_960734_-	MFS transporter	NA	NA	NA	NA	NA
AUL10595.1|960949_961627_-	phosphoglycolate phosphatase	NA	NA	NA	NA	NA
AUL10596.1|961623_962349_-	bifunctional 3-demethylubiquinol 3-O-methyltransferase/2-polyprenyl-6-hydroxyphenol methylase	NA	NA	NA	NA	NA
AUL10597.1|962474_963056_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10598.1|963426_966108_+	DNA gyrase subunit A	NA	G3M9Z5	Bacillus_virus	33.5	3.2e-104
AUL13150.1|966110_967241_+	phosphoserine transaminase	NA	M1Q1P2	Streptococcus_phage	44.0	4.9e-78
AUL10599.1|967233_968319_+	chorismate mutase	NA	NA	NA	NA	NA
AUL10600.1|968405_969305_+	prephenate dehydrogenase	NA	NA	NA	NA	NA
AUL10601.1|969301_970630_+	3-phosphoshikimate 1-carboxyvinyltransferase	NA	NA	NA	NA	NA
AUL10602.1|970644_971316_+	cytidylate kinase	NA	NA	NA	NA	NA
AUL10603.1|971503_973219_+	30S ribosomal protein S1	NA	NA	NA	NA	NA
AUL10604.1|973220_973580_+	integration host factor subunit beta	NA	NA	NA	NA	NA
AUL10605.1|973771_974086_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10606.1|974128_975349_+	lipopolysaccharide assembly protein LapB	NA	NA	NA	NA	NA
AUL10607.1|975345_976287_+	hypothetical protein	NA	A0A2H4N7X4	Lake_Baikal_phage	28.1	1.5e-16
AUL10608.1|976283_977273_+	ADP-glyceromanno-heptose 6-epimerase	NA	E3SJ87	Synechococcus_phage	34.4	2.2e-26
AUL13151.1|977562_977892_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10609.1|977990_978941_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10610.1|979021_979933_+	cysteine synthase B	NA	A0A1X9I5K7	Streptococcus_phage	38.8	8.0e-47
AUL10611.1|979993_981139_-	lytic murein transglycosylase B	NA	NA	NA	NA	NA
AUL10612.1|981158_982073_+	deacetylase	NA	A0A2K9KZC4	Tupanvirus	34.7	9.8e-45
AUL10613.1|982144_982894_+	electron transporter RnfB	NA	NA	NA	NA	NA
AUL10614.1|982893_983823_+	electron transfer flavoprotein subunit alpha	NA	NA	NA	NA	NA
AUL10615.1|984066_985893_+	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL10616.1|985975_986617_+	peroxidase	NA	NA	NA	NA	NA
AUL10617.1|986806_987841_+	sulfate transporter subunit	NA	NA	NA	NA	NA
AUL10618.1|987856_988060_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10619.1|988081_988756_+	sulfate ABC transporter permease subunit CysT	NA	NA	NA	NA	NA
AUL10620.1|988870_989653_+	sulfate ABC transporter permease subunit CysW	NA	NA	NA	NA	NA
AUL10621.1|989677_990742_+	sulfate ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	30.3	3.8e-24
AUL13152.1|991539_992448_+	sulfate adenylyltransferase small subunit	NA	NA	NA	NA	NA
AUL10622.1|993935_995210_+	radical SAM protein	NA	NA	NA	NA	NA
AUL10623.1|995363_995744_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10624.1|995751_996624_-	multidrug DMT transporter permease	NA	NA	NA	NA	NA
AUL10625.1|996929_997310_+	50S ribosomal protein L19	NA	NA	NA	NA	NA
AUL10626.1|997559_998246_+	coenzyme A pyrophosphatase	NA	NA	NA	NA	NA
AUL10627.1|998341_999292_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10628.1|999396_1000446_+	aldo/keto reductase	NA	NA	NA	NA	NA
AUL13153.1|1000583_1001600_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
>prophage 8
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	1060415	1118845	4109385	tRNA,transposase	uncultured_Mediterranean_phage(37.5%)	45	NA	NA
AUL13157.1|1060415_1061432_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL13158.1|1062262_1063270_+	aldo/keto reductase	NA	NA	NA	NA	NA
AUL10667.1|1063266_1064910_-	apolipoprotein N-acyltransferase	NA	NA	NA	NA	NA
AUL10668.1|1064906_1065794_-	magnesium/cobalt efflux protein	NA	NA	NA	NA	NA
AUL10669.1|1065934_1066408_-	rRNA maturation RNase YbeY	NA	NA	NA	NA	NA
AUL10670.1|1066397_1067420_-	phosphate starvation-inducible protein PhoH	NA	A0A0S0MVD6	Pseudomonas_phage	45.4	8.7e-50
AUL10671.1|1067416_1068844_-|tRNA	tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB	tRNA	NA	NA	NA	NA
AUL13159.1|1069781_1070798_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL10672.1|1071130_1072066_-	protein-export membrane protein SecF	NA	A0A1B1IVP7	uncultured_Mediterranean_phage	35.5	3.0e-41
AUL10673.1|1072115_1073996_-	protein-export membrane protein SecD	NA	NA	NA	NA	NA
AUL10674.1|1074062_1074407_-	preprotein translocase subunit YajC	NA	A0A1B1IVR5	uncultured_Mediterranean_phage	40.4	1.0e-10
AUL10675.1|1074551_1075688_-|tRNA	tRNA guanosine(34) transglycosylase Tgt	tRNA	A0A1B1IVQ4	uncultured_Mediterranean_phage	44.4	1.9e-85
AUL10676.1|1075684_1076758_-|tRNA	tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA	tRNA	NA	NA	NA	NA
AUL10677.1|1076915_1078352_+	D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase	NA	NA	NA	NA	NA
AUL13160.1|1078442_1079084_+	uracil phosphoribosyltransferase	NA	NA	NA	NA	NA
AUL13161.1|1079419_1080436_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL13162.1|1082478_1083429_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL13163.1|1084631_1086053_-	uroporphyrinogen-III C-methyltransferase	NA	NA	NA	NA	NA
AUL13164.1|1086319_1087033_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10678.1|1087117_1087435_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10679.1|1087475_1087889_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10680.1|1087890_1088250_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10681.1|1088292_1089837_-	3-octaprenyl-4-hydroxybenzoate decarboxylase	NA	NA	NA	NA	NA
AUL10682.1|1089920_1090751_+	lytic transglycosylase	NA	NA	NA	NA	NA
AUL10683.1|1090785_1091940_-	aminotransferase	NA	NA	NA	NA	NA
AUL10684.1|1091982_1092855_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10685.1|1092971_1095260_+	NADP-dependent malic enzyme	NA	NA	NA	NA	NA
AUL10686.1|1096466_1096931_+	barstar family protein 2	NA	NA	NA	NA	NA
AUL10687.1|1096957_1097908_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL13165.1|1098275_1099052_-	phosphate ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	28.7	4.3e-17
AUL10688.1|1099096_1099933_-	phosphate ABC transporter, permease protein PstA	NA	NA	NA	NA	NA
AUL10689.1|1099975_1100992_-	phosphate ABC transporter permease subunit PstC	NA	NA	NA	NA	NA
AUL10690.1|1101126_1102167_-	phosphate ABC transporter substrate-binding protein PstS	NA	M4QHS4	Cyanophage	40.2	2.1e-51
AUL10691.1|1102361_1104443_-	RNA degradosome polyphosphate kinase	NA	NA	NA	NA	NA
AUL10692.1|1104678_1106172_+	exopolyphosphatase	NA	NA	NA	NA	NA
AUL10693.1|1106402_1107197_-	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL10694.1|1107417_1108776_-	phosphoglucosamine mutase	NA	NA	NA	NA	NA
AUL10695.1|1108772_1109615_-	dihydropteroate synthase	NA	A0A0B5J4J5	Pandoravirus	32.5	3.2e-26
AUL10696.1|1109633_1111520_-	cell division protein FtsH	NA	M4QMW8	Micromonas_pusilla_virus	41.5	1.4e-109
AUL10697.1|1111757_1112390_-	rRNA methyltransferase	NA	NA	NA	NA	NA
AUL10698.1|1112408_1113011_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10699.1|1114914_1115715_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10700.1|1115758_1116745_-	homoserine kinase	NA	NA	NA	NA	NA
AUL10701.1|1116920_1117898_+|tRNA	tRNA dihydrouridine(20/20a) synthase DusA	tRNA	NA	NA	NA	NA
AUL10702.1|1117894_1118845_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 9
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	1158544	1237165	4109385	tRNA,transposase	Erysipelothrix_phage(25.0%)	56	NA	NA
AUL10730.1|1158544_1159447_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10731.1|1159593_1160217_-	fimbrial protein	NA	NA	NA	NA	NA
AUL10732.1|1160390_1162673_-	NADP-dependent malic enzyme	NA	NA	NA	NA	NA
AUL10733.1|1162827_1165524_-	pyruvate dehydrogenase (acetyl-transferring), homodimeric type	NA	NA	NA	NA	NA
AUL10734.1|1165649_1166138_+	ArsR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10735.1|1166173_1168036_+	oligopeptide transporter, OPT family	NA	NA	NA	NA	NA
AUL10736.1|1168014_1168224_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10737.1|1168548_1171419_+	2-oxoglutarate dehydrogenase E1 component	NA	NA	NA	NA	NA
AUL10738.1|1171464_1172679_+	dihydrolipoamide succinyltransferase	NA	NA	NA	NA	NA
AUL10739.1|1172908_1174336_+	dihydrolipoyl dehydrogenase	NA	A0A2K5B2C5	Erysipelothrix_phage	28.1	2.1e-41
AUL10740.1|1174433_1175525_+	cell division protein ZapE	NA	NA	NA	NA	NA
AUL10741.1|1175537_1176296_-	3-oxoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL10742.1|1176383_1177286_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10743.1|1177282_1178233_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10744.1|1178362_1179346_-	LacI family transcriptional regulator	NA	NA	NA	NA	NA
AUL10745.1|1179400_1180123_-	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL10746.1|1181601_1182957_+|tRNA	tryptophan--tRNA ligase	tRNA	NA	NA	NA	NA
AUL10747.1|1183037_1185413_-	RNA-binding transcriptional accessory protein	NA	NA	NA	NA	NA
AUL10748.1|1185577_1187653_+	helicase	NA	A0A127AW80	Bacillus_phage	30.0	2.4e-75
AUL13168.1|1187714_1188509_-	outer membrane protein assembly factor BamD	NA	NA	NA	NA	NA
AUL10749.1|1188616_1189579_+	RNA pseudouridine synthase	NA	NA	NA	NA	NA
AUL10750.1|1189566_1190322_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10751.1|1190429_1192067_+	class I poly(R)-hydroxyalkanoic acid synthase	NA	NA	NA	NA	NA
AUL10752.1|1192134_1192872_+	beta-ketoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL10753.1|1192974_1193550_+	polyhydroxyalkanoate synthesis repressor PhaR	NA	NA	NA	NA	NA
AUL10754.1|1193722_1194259_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13169.1|1194291_1194606_+	periplasmic lipoprotein involved in iron transport	NA	NA	NA	NA	NA
AUL10755.1|1194621_1195467_+	FTR1 family iron permease	NA	NA	NA	NA	NA
AUL10756.1|1195505_1196885_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10757.1|1196962_1197844_+	phenazine biosynthesis protein PhzC/PhzF	NA	NA	NA	NA	NA
AUL10758.1|1197989_1198892_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10759.1|1198888_1199299_-	lactoylglutathione lyase	NA	NA	NA	NA	NA
AUL10760.1|1199406_1200261_-	2-pyrone-4,6-dicarboxylate hydrolase	NA	NA	NA	NA	NA
AUL10761.1|1200253_1201216_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10762.1|1201261_1202386_-	racemase	NA	Q6A202	Oenococcus_phage	28.3	1.5e-31
AUL10763.1|1202491_1203370_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10764.1|1203494_1204274_+	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL10765.1|1204427_1205849_+	MFS transporter	NA	NA	NA	NA	NA
AUL10766.1|1206283_1207981_+	sodium:proline symporter	NA	NA	NA	NA	NA
AUL10767.1|1208009_1208132_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13170.1|1208207_1209149_-	LD-carboxypeptidase	NA	NA	NA	NA	NA
AUL10768.1|1209475_1210222_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10769.1|1210229_1211156_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL10770.1|1211277_1212195_+	oxidoreductase	NA	NA	NA	NA	NA
AUL10771.1|1212234_1213188_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL10772.1|1213212_1213791_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10773.1|1215464_1216073_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10774.1|1216150_1216504_-	hypothetical protein	NA	NA	NA	NA	NA
AUL13171.1|1216587_1217520_-	succinylglutamate desuccinylase	NA	NA	NA	NA	NA
AUL10775.1|1217827_1218730_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10776.1|1218816_1219767_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10777.1|1220973_1222002_-	C4-dicarboxylate ABC transporter	NA	NA	NA	NA	NA
AUL10778.1|1222081_1223380_-	C4-dicarboxylate ABC transporter	NA	NA	NA	NA	NA
AUL10779.1|1223376_1223913_-	TRAP transporter small permease protein	NA	NA	NA	NA	NA
AUL10780.1|1224270_1228317_+	phosphoribosylformylglycinamidine synthase	NA	A9YX36	Burkholderia_phage	67.4	6.3e-160
AUL10781.1|1236214_1237165_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 10
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	1419077	1471229	4109385	tRNA,transposase	Salmonella_phage(25.0%)	45	NA	NA
AUL10937.1|1419077_1420028_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10938.1|1420194_1420548_+	cytochrome C	NA	NA	NA	NA	NA
AUL10939.1|1420560_1420923_+	cytochrome	NA	NA	NA	NA	NA
AUL10940.1|1420964_1421390_-	hypothetical protein	NA	NA	NA	NA	NA
AUL10941.1|1421592_1422849_+	NADP-dependent isocitrate dehydrogenase	NA	Q77Z09	Phage_21	64.8	1.2e-11
AUL10942.1|1423047_1424028_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10943.1|1424177_1425419_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10944.1|1425517_1426468_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10945.1|1426476_1427172_-	two-component system response regulator KdpE	NA	NA	NA	NA	NA
AUL10946.1|1429992_1430592_-	potassium-transporting ATPase subunit C	NA	NA	NA	NA	NA
AUL10947.1|1430602_1432768_-	potassium-transporting ATPase subunit B	NA	M1HBF8	Paramecium_bursaria_Chlorella_virus	27.1	1.2e-24
AUL10948.1|1432791_1434576_-	potassium-transporting ATPase subunit KdpA	NA	NA	NA	NA	NA
AUL10949.1|1434575_1434665_-	potassium-transporting ATPase subunit F	NA	NA	NA	NA	NA
AUL10950.1|1435359_1435632_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10951.1|1435631_1437698_+	cation acetate symporter	NA	NA	NA	NA	NA
AUL10952.1|1437694_1438597_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10953.1|1438743_1439694_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10954.1|1439809_1440142_-	QacE family quaternary ammonium compound efflux SMR transporter	NA	NA	NA	NA	NA
AUL10955.1|1440138_1440825_-	DNA mismatch repair protein MutS	NA	NA	NA	NA	NA
AUL10956.1|1440811_1441771_-	thioredoxin-disulfide reductase	NA	A0A2I2L5E1	Orpheovirus	40.2	3.1e-57
AUL10957.1|1441803_1444173_+	cell division protein FtsK	NA	S5VNE3	Mycobacterium_phage	48.0	7.6e-81
AUL10958.1|1444172_1444805_+	outer membrane lipoprotein carrier protein LolA	NA	NA	NA	NA	NA
AUL10959.1|1444906_1446247_+	recombination factor protein RarA	NA	G3MBE0	Bacillus_virus	38.9	1.6e-75
AUL10960.1|1446293_1447649_+|tRNA	serine--tRNA ligase	tRNA	A0A1B1IVT2	uncultured_Mediterranean_phage	47.5	1.6e-83
AUL10961.1|1447939_1448176_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10962.1|1448363_1448681_-	virulence factor	NA	NA	NA	NA	NA
AUL10963.1|1448953_1449469_-	hypothetical protein	NA	T1SAR8	Salmonella_phage	44.6	5.1e-06
AUL10964.1|1449562_1449724_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10965.1|1449739_1450495_-	GGDEF domain-containing protein	NA	NA	NA	NA	NA
AUL10966.1|1450833_1451040_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10967.1|1451047_1451707_-	antibiotic resistance protein	NA	NA	NA	NA	NA
AUL10968.1|1452001_1454206_-	porin	NA	NA	NA	NA	NA
AUL10969.1|1454316_1455540_-	multidrug transporter	NA	S4TR35	Salmonella_phage	29.4	9.8e-24
AUL10970.1|1455662_1456637_-	AraC family transcriptional regulator	NA	NA	NA	NA	NA
AUL10971.1|1456704_1457898_-	Rieske (2Fe-2S) protein	NA	NA	NA	NA	NA
AUL10972.1|1457912_1458713_-	siderophore ferric iron reductase	NA	NA	NA	NA	NA
AUL10973.1|1458709_1460566_-	IucA/IucC family protein	NA	NA	NA	NA	NA
AUL10974.1|1460562_1461168_-	siderophore biosynthesis protein	NA	NA	NA	NA	NA
AUL10975.1|1461186_1462572_-	alcaligin biosynthesis protein	NA	NA	NA	NA	NA
AUL10976.1|1463297_1464524_+	transporter	NA	NA	NA	NA	NA
AUL10977.1|1464612_1465395_+	3-hydroxybutyrate dehydrogenase	NA	NA	NA	NA	NA
AUL10978.1|1465541_1466444_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL10979.1|1466470_1467244_+	peroxide stress protein YaaA	NA	NA	NA	NA	NA
AUL10980.1|1467255_1468497_+	hypothetical protein	NA	NA	NA	NA	NA
AUL10981.1|1470326_1471229_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 12
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	1573064	1644169	4109385	transposase	Ectocarpus_siliculosus_virus(11.11%)	54	NA	NA
AUL11074.1|1573064_1574015_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11075.1|1574036_1575257_+	YggW family oxidoreductase	NA	NA	NA	NA	NA
AUL11076.1|1575442_1576855_+	type I glutamate--ammonia ligase	NA	NA	NA	NA	NA
AUL11077.1|1576918_1577986_+	PAS domain-containing sensor histidine kinase	NA	Q8QKV7	Ectocarpus_siliculosus_virus	23.5	1.1e-05
AUL11078.1|1577985_1579473_+	nitrogen regulation protein NR(I)	NA	NA	NA	NA	NA
AUL13191.1|1579482_1580427_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11079.1|1580586_1581285_+	quercetin 2,3-dioxygenase	NA	NA	NA	NA	NA
AUL11080.1|1581362_1582268_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11081.1|1582287_1583190_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11082.1|1583336_1584131_-	ABC transporter	NA	G9BWD6	Planktothrix_phage	29.4	8.3e-16
AUL11083.1|1584135_1585806_-	iron ABC transporter permease	NA	NA	NA	NA	NA
AUL11084.1|1585929_1586979_-	iron ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11085.1|1587300_1588077_+	ferredoxin--NADP(+) reductase	NA	NA	NA	NA	NA
AUL11086.1|1588141_1589044_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11087.1|1590337_1591141_+	2,5-didehydrogluconate reductase B	NA	A0A2H4PQR8	Staphylococcus_phage	32.4	2.0e-33
AUL11088.1|1593834_1594221_+	reactive intermediate/imine deaminase	NA	NA	NA	NA	NA
AUL11089.1|1594236_1596327_+	ATP-dependent DNA helicase RecG	NA	NA	NA	NA	NA
AUL11090.1|1596378_1597332_+	LysR family transcriptional regulator	NA	A0A2P0ZL89	Lactobacillus_phage	26.5	7.2e-14
AUL13192.1|1597346_1598234_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11091.1|1598371_1599898_+	methylmalonate-semialdehyde dehydrogenase (acylating)	NA	NA	NA	NA	NA
AUL13193.1|1599996_1600497_+	DNA starvation/stationary phase protection protein	NA	W5S6G8	Pithovirus	35.5	6.4e-14
AUL11092.1|1600820_1602776_-	capsular biosynthesis protein	NA	NA	NA	NA	NA
AUL13194.1|1605053_1605479_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11093.1|1606694_1607465_+	polyhydroxyalkanoate biosynthesis repressor PhaR	NA	NA	NA	NA	NA
AUL11094.1|1607464_1608205_+	sugar ABC transporter ATP-binding protein	NA	NA	NA	NA	NA
AUL11095.1|1608246_1609416_+	capsule biosynthesis protein	NA	NA	NA	NA	NA
AUL11096.1|1609447_1611532_+	Vi polysaccharide biosynthesis protein TviE	NA	NA	NA	NA	NA
AUL11097.1|1611528_1612419_+	capsular biosynthesis protein	NA	NA	NA	NA	NA
AUL11098.1|1612415_1613513_+	capsule biosynthesis protein CapA	NA	NA	NA	NA	NA
AUL11099.1|1613535_1614825_+	Vi polysaccharide biosynthesis protein VipA/TviB	NA	NA	NA	NA	NA
AUL11100.1|1614836_1615862_+	LPS biosynthesis protein WbpP	NA	A0A2K9L4U8	Tupanvirus	44.2	4.7e-72
AUL11101.1|1615858_1617916_+	beta-3-deoxy-D-manno-oct-2-ulosonic acid transferase	NA	NA	NA	NA	NA
AUL11102.1|1617929_1619105_+	capsule biosynthesis protein CapA	NA	NA	NA	NA	NA
AUL11103.1|1619186_1620137_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11104.1|1620195_1620969_+	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL11105.1|1620961_1622518_+	capsular biosynthesis protein	NA	NA	NA	NA	NA
AUL11106.1|1622514_1623465_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11107.1|1624791_1625394_-	TetR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11108.1|1625633_1626335_-	ABC transporter ATP-binding protein	NA	NA	NA	NA	NA
AUL11109.1|1626328_1627111_-	high-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG	NA	A0A2R8FG22	Brazilian_cedratvirus	25.8	2.0e-09
AUL11110.1|1627295_1628246_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11111.1|1628344_1629082_-	hypothetical protein	NA	A0A0S4KZH7	Pseudomonas_phage	46.6	4.1e-41
AUL11112.1|1629271_1630030_-	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL11113.1|1630076_1631078_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11114.1|1631243_1632212_-	phenol degradation protein meta	NA	NA	NA	NA	NA
AUL11115.1|1633751_1634720_+	AAA family ATPase	NA	NA	NA	NA	NA
AUL11116.1|1634728_1635670_+	MoxR protein	NA	NA	NA	NA	NA
AUL13195.1|1636143_1637154_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13197.1|1637144_1638659_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11117.1|1638655_1640002_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13196.1|1640004_1641039_+	haloacid dehalogenase	NA	NA	NA	NA	NA
AUL11118.1|1641088_1642714_+	arylsulfatase	NA	A0A2P0VMN7	Tetraselmis_virus	52.2	2.0e-149
AUL11119.1|1642807_1643287_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11120.1|1643266_1644169_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 13
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	1665008	1726355	4109385	tRNA,transposase	uncultured_Caudovirales_phage(12.5%)	53	NA	NA
AUL11137.1|1665008_1665959_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11138.1|1666067_1666256_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13200.1|1666252_1666975_-	arsenical resistance protein ArsH	NA	A0A2H4J5V6	uncultured_Caudovirales_phage	68.2	1.3e-87
AUL11139.1|1667413_1668601_-	hypothetical protein	NA	NA	NA	NA	NA
AUL13201.1|1668604_1668955_-	transcriptional regulator	NA	NA	NA	NA	NA
AUL13202.1|1670703_1671675_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11140.1|1671688_1672402_+	3-oxoacyl-[acyl-carrier-protein] reductase	NA	NA	NA	NA	NA
AUL11141.1|1672406_1673324_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11142.1|1673430_1673727_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11143.1|1673873_1674776_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11144.1|1675934_1678868_+	monovalent cation/H+ antiporter subunit A	NA	NA	NA	NA	NA
AUL11145.1|1678867_1679212_+	Na+/H+ antiporter subunit C	NA	NA	NA	NA	NA
AUL11146.1|1679208_1680837_+	monovalent cation/H+ antiporter subunit D	NA	NA	NA	NA	NA
AUL11147.1|1680836_1681313_+	Na+/H+ antiporter subunit E	NA	NA	NA	NA	NA
AUL11148.1|1681312_1681594_+	K+/H+ antiporter subunit F	NA	NA	NA	NA	NA
AUL11149.1|1681590_1681917_+	cation:proton antiporter	NA	NA	NA	NA	NA
AUL11150.1|1682072_1683023_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11151.1|1683066_1683609_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11152.1|1683706_1684555_+	hydrolase	NA	NA	NA	NA	NA
AUL13203.1|1684604_1685054_+|tRNA	tRNA-specific adenosine deaminase	tRNA	S4VYT2	Pandoravirus	38.2	2.0e-06
AUL11153.1|1685050_1686052_+	LD-carboxypeptidase	NA	NA	NA	NA	NA
AUL11154.1|1686064_1686859_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL11155.1|1686907_1688809_-	C4-dicarboxylate ABC transporter	NA	NA	NA	NA	NA
AUL11156.1|1688805_1689429_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11157.1|1689555_1690680_-	C4-dicarboxylate ABC transporter	NA	NA	NA	NA	NA
AUL11158.1|1691060_1692665_+	ABC-F family ATPase	NA	A0A1V0SKJ1	Klosneuvirus	28.9	1.2e-53
AUL11159.1|1692820_1693597_+	ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	34.2	1.2e-30
AUL11160.1|1693681_1694680_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11161.1|1694676_1695450_+	ABC transporter permease	NA	NA	NA	NA	NA
AUL11162.1|1696434_1697385_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11163.1|1697408_1697873_-|tRNA	glutamyl-tRNA amidotransferase	tRNA	A0A0K2FLI9	Brevibacillus_phage	32.4	3.9e-05
AUL11164.1|1698019_1699228_+	nitric oxide dioxygenase	NA	NA	NA	NA	NA
AUL11165.1|1699271_1699709_+	BadM/Rrf2 family transcriptional regulator	NA	NA	NA	NA	NA
AUL11166.1|1699827_1701117_+	D-amino acid dehydrogenase small subunit	NA	NA	NA	NA	NA
AUL11167.1|1703857_1704760_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11168.1|1704906_1705923_-	folate-binding protein YgfZ	NA	NA	NA	NA	NA
AUL11169.1|1706101_1707136_+	aminodeoxychorismate lyase	NA	NA	NA	NA	NA
AUL11170.1|1707132_1707759_+	dTMP kinase	NA	A0A1L2BX49	Bacteriophage	35.1	1.6e-22
AUL11171.1|1707755_1708808_+	DNA polymerase III subunit delta'	NA	NA	NA	NA	NA
AUL11172.1|1708857_1709628_+	DNAase	NA	NA	NA	NA	NA
AUL11173.1|1709678_1710515_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11174.1|1710710_1711451_+	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11175.1|1711525_1712269_+	glutamine ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11176.1|1712930_1713704_+	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	37.7	3.1e-31
AUL13204.1|1714841_1716131_+	glutamate dehydrogenase	NA	NA	NA	NA	NA
AUL11177.1|1717741_1718989_-	Zn-dependent hydrolase	NA	NA	NA	NA	NA
AUL11178.1|1718998_1720708_-	thiamine pyrophosphate-binding protein	NA	A0A0P0YLY7	Yellowstone_lake_phycodnavirus	27.3	5.9e-35
AUL11179.1|1720704_1721643_-	CoA ester lyase	NA	NA	NA	NA	NA
AUL11180.1|1721639_1722923_-	C4-dicarboxylate ABC transporter permease	NA	NA	NA	NA	NA
AUL11181.1|1722926_1723409_-	TRAP transporter small permease protein	NA	NA	NA	NA	NA
AUL11182.1|1723409_1724396_-	C4-dicarboxylate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11183.1|1724568_1725288_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11184.1|1725404_1726355_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 14
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	1834672	1905096	4109385	tRNA,transposase	Klosneuvirus(22.22%)	59	NA	NA
AUL11262.1|1834672_1835575_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11263.1|1835720_1836623_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11264.1|1837896_1839114_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11265.1|1839110_1840166_+	4-hydroxythreonine-4-phosphate dehydrogenase PdxA	NA	NA	NA	NA	NA
AUL11266.1|1840170_1841073_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11267.1|1841149_1842022_+	MOSC domain-containing protein	NA	NA	NA	NA	NA
AUL11268.1|1842152_1842521_+	aspartate 1-decarboxylase	NA	NA	NA	NA	NA
AUL11269.1|1842578_1843625_+	CDP-6-deoxy-delta-3,4-glucoseen reductase	NA	NA	NA	NA	NA
AUL11270.1|1843820_1845077_+	amino acid dehydrogenase	NA	NA	NA	NA	NA
AUL11271.1|1845081_1846419_+	glycerol-3-phosphate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11272.1|1846568_1847525_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11273.1|1848982_1849348_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11274.1|1849395_1850970_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11275.1|1851022_1851967_+	peptide ABC transporter	NA	NA	NA	NA	NA
AUL13212.1|1851894_1852815_+	peptide ABC transporter permease	NA	NA	NA	NA	NA
AUL11276.1|1852807_1854442_+	microcin ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	32.7	8.2e-18
AUL11277.1|1854438_1855794_+	amidase	NA	NA	NA	NA	NA
AUL11278.1|1856700_1858278_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11279.1|1858281_1859556_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13213.1|1859653_1860028_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11280.1|1861743_1862877_+	general secretion pathway protein	NA	NA	NA	NA	NA
AUL11281.1|1862914_1863520_+	prepilin-type N-terminal cleavage/methylation domain-containing protein	NA	NA	NA	NA	NA
AUL11282.1|1863516_1864335_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11283.1|1864406_1867031_+|tRNA	alanine--tRNA ligase	tRNA	A0A1V0SK38	Klosneuvirus	39.4	1.7e-81
AUL11284.1|1867017_1867272_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11285.1|1867338_1867920_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11286.1|1868223_1868484_+	30S ribosomal protein S16	NA	NA	NA	NA	NA
AUL11287.1|1868649_1869273_+	ribosome maturation factor RimM	NA	NA	NA	NA	NA
AUL11288.1|1869272_1870046_+|tRNA	tRNA (guanosine(37)-N1)-methyltransferase TrmD	tRNA	NA	NA	NA	NA
AUL11289.1|1870042_1871251_-	class V aminotransferase	NA	NA	NA	NA	NA
AUL11290.1|1871276_1871750_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11291.1|1871823_1872774_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11292.1|1872872_1873775_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11293.1|1873920_1875270_-	two-component sensor histidine kinase	NA	NA	NA	NA	NA
AUL11294.1|1876035_1876791_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11295.1|1876883_1879766_-|tRNA	valine--tRNA ligase	tRNA	A0A1V0SK04	Klosneuvirus	37.1	3.7e-138
AUL11296.1|1880088_1880514_+	nucleoside-diphosphate kinase	NA	D2E8E1	Anguillid_herpesvirus	43.2	2.1e-21
AUL11297.1|1880541_1881690_+	23S rRNA (adenine(2503)-C(2))-methyltransferase	NA	NA	NA	NA	NA
AUL11298.1|1881686_1882193_+	transcriptional regulator	NA	NA	NA	NA	NA
AUL11299.1|1882208_1883495_+	4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase	NA	NA	NA	NA	NA
AUL13214.1|1883544_1884840_+|tRNA	histidine--tRNA ligase	tRNA	NA	NA	NA	NA
AUL11300.1|1884841_1885480_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13215.1|1885485_1886643_+	outer membrane protein assembly factor BamB	NA	NA	NA	NA	NA
AUL11301.1|1886669_1888025_+	ribosome biogenesis GTPase Der	NA	NA	NA	NA	NA
AUL11302.1|1888028_1889099_+	histidinol-phosphate transaminase	NA	A0A1X6WGT4	Pacmanvirus	25.7	2.5e-15
AUL11303.1|1889237_1889474_+	RNA chaperone Hfq	NA	NA	NA	NA	NA
AUL11304.1|1889561_1890668_+	GTPase HflX	NA	NA	NA	NA	NA
AUL11305.1|1890633_1891938_+	HflK protein	NA	NA	NA	NA	NA
AUL11306.1|1891956_1892856_+	HflC protein	NA	NA	NA	NA	NA
AUL11307.1|1893039_1894197_+	ATP phosphoribosyltransferase regulatory subunit	NA	NA	NA	NA	NA
AUL11308.1|1894273_1895569_+	adenylosuccinate synthase	NA	A0A160ER07	Powai_lake_megavirus	33.5	3.0e-63
AUL11309.1|1895682_1896222_+	nicotinate phosphoribosyltransferase	NA	NA	NA	NA	NA
AUL11310.1|1896499_1896712_+	30S ribosomal protein S21	NA	NA	NA	NA	NA
AUL11311.1|1896731_1898762_+	DNA primase	NA	A0A0K1LMQ9	Caulobacter_phage	41.9	1.0e-65
AUL11312.1|1899447_1901730_+	RNA polymerase sigma factor RpoD	NA	A0A2I7SAT0	Vibrio_phage	30.1	3.2e-36
AUL11313.1|1902139_1902439_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11314.1|1902723_1903137_+	transcriptional regulator	NA	A0A222YXG1	Escherichia_phage	59.0	3.8e-36
AUL11315.1|1903096_1904047_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11316.1|1904145_1905096_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 15
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	1916347	1964758	4109385	transposase	Klosneuvirus(16.67%)	47	NA	NA
AUL11327.1|1916347_1917250_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11328.1|1917246_1918521_-	adenosylmethionine--8-amino-7-oxononanoate transaminase	NA	A0A1V0SKB7	Klosneuvirus	28.9	9.6e-14
AUL11329.1|1918624_1919818_+	8-amino-7-oxononanoate synthase	NA	NA	NA	NA	NA
AUL11330.1|1919814_1920468_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL11331.1|1920464_1921901_+	dethiobiotin synthase	NA	NA	NA	NA	NA
AUL11332.1|1921888_1922248_+	CidA/LrgA family protein	NA	NA	NA	NA	NA
AUL11333.1|1922333_1922984_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11334.1|1923268_1924171_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11335.1|1924269_1925133_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11336.1|1925216_1927082_-	sigma-54-dependent Fis family transcriptional regulator	NA	NA	NA	NA	NA
AUL13219.1|1927339_1928860_+	aldehyde dehydrogenase	NA	NA	NA	NA	NA
AUL11337.1|1928947_1929598_-	NAD(P)H dehydrogenase	NA	NA	NA	NA	NA
AUL11338.1|1930546_1931842_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11339.1|1931863_1932748_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL13220.1|1932846_1933722_+	PhzF family phenazine biosynthesis protein	NA	NA	NA	NA	NA
AUL11340.1|1933711_1934068_-	RNA signal recognition particle	NA	NA	NA	NA	NA
AUL11341.1|1934198_1935173_+	AraC family transcriptional regulator	NA	NA	NA	NA	NA
AUL11342.1|1935302_1935482_-	DUF3008 domain-containing protein	NA	NA	NA	NA	NA
AUL11343.1|1935624_1936104_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11344.1|1936114_1936951_-	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL11345.1|1937063_1937435_+	transcriptional regulator	NA	NA	NA	NA	NA
AUL11346.1|1937431_1937983_+	ATPase	NA	NA	NA	NA	NA
AUL11347.1|1937998_1939690_-	sodium-independent anion transporter	NA	A0A2H4J153	uncultured_Caudovirales_phage	27.3	5.0e-42
AUL11348.1|1939738_1940419_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11349.1|1940666_1941131_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11350.1|1941300_1942230_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13221.1|1942242_1942836_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11351.1|1942963_1944781_-	ABC transporter ATP-binding protein	NA	W8CYL7	Bacillus_phage	27.4	2.3e-37
AUL11352.1|1944864_1945815_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL13222.1|1945913_1946393_-	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL11353.1|1946515_1947418_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11354.1|1947436_1947784_-	aldehyde-activating protein	NA	NA	NA	NA	NA
AUL11355.1|1947812_1949252_-	MFS transporter	NA	A0A0M3UL24	Mycobacterium_phage	37.4	7.4e-55
AUL11356.1|1949270_1949666_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11357.1|1949840_1950449_+	peptidase S16	NA	NA	NA	NA	NA
AUL11358.1|1950461_1951280_+	hypothetical protein	NA	A0A1B1INV8	uncultured_Mediterranean_phage	28.8	2.3e-16
AUL11359.1|1951231_1952206_-	AraC family transcriptional regulator	NA	NA	NA	NA	NA
AUL11360.1|1952234_1953296_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11361.1|1953292_1955509_-	aldehyde oxidase	NA	NA	NA	NA	NA
AUL11362.1|1955522_1955981_-	(2Fe-2S)-binding protein	NA	NA	NA	NA	NA
AUL11363.1|1956138_1956483_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11364.1|1956639_1957545_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL13223.1|1957631_1958645_+	pyridoxamine 5'-phosphate oxidase	NA	NA	NA	NA	NA
AUL13224.1|1960624_1961641_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL11365.1|1961783_1963136_-	glutathione-disulfide reductase	NA	A0A2K5B2C5	Erysipelothrix_phage	27.6	2.9e-45
AUL11366.1|1963310_1963607_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11367.1|1963753_1964758_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 16
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	1977191	2041511	4109385	transposase	Vibrio_phage(20.0%)	54	NA	NA
AUL11381.1|1977191_1978142_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11382.1|1978363_1979314_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11383.1|1979412_1980378_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11384.1|1980515_1981415_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11385.1|1981942_1983769_+	DUF3604 domain-containing protein	NA	NA	NA	NA	NA
AUL11386.1|1984126_1985497_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11387.1|1985507_1986704_+	acetyl-CoA acetyltransferase	NA	NA	NA	NA	NA
AUL11388.1|1986776_1988096_+	acyl--CoA ligase	NA	NA	NA	NA	NA
AUL11389.1|1988092_1988968_+	esterase	NA	NA	NA	NA	NA
AUL11390.1|1988998_1990147_-	carnitine dehydratase	NA	NA	NA	NA	NA
AUL11391.1|1990164_1990479_-	2Fe-2S ferredoxin	NA	NA	NA	NA	NA
AUL11392.1|1990500_1991223_-	3-oxoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL11393.1|1991222_1992041_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL11394.1|1992045_1992573_-	ring-hydroxylating dioxygenase subunit beta	NA	NA	NA	NA	NA
AUL11395.1|1992578_1993835_-	ring-hydroxylating oxygenase subunit alpha	NA	NA	NA	NA	NA
AUL11396.1|1994193_1995333_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11397.1|1995410_1996283_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL11398.1|1997201_1998104_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11399.1|1998063_1998699_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11400.1|1999058_2000381_-	isocitrate lyase	NA	NA	NA	NA	NA
AUL11401.1|2000699_2001521_+	NADPH-dependent 7-cyano-7-deazaguanine reductase QueF	NA	A0A2I7SAX1	Vibrio_phage	37.6	4.1e-42
AUL11402.1|2001456_2001798_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11403.1|2001807_2002776_-	MFS transporter	NA	NA	NA	NA	NA
AUL11404.1|2002945_2003518_-	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase	NA	NA	NA	NA	NA
AUL11405.1|2003557_2005387_-	excinuclease ABC subunit C	NA	NA	NA	NA	NA
AUL11406.1|2005349_2006408_-	beta-N-acetylhexosaminidase	NA	NA	NA	NA	NA
AUL11407.1|2006445_2006907_-	holo-ACP synthase	NA	NA	NA	NA	NA
AUL11408.1|2006991_2007738_-	pyridoxine 5'-phosphate synthase	NA	NA	NA	NA	NA
AUL11409.1|2009228_2012459_-	multidrug efflux RND transporter permease subunit	NA	NA	NA	NA	NA
AUL11410.1|2012525_2013857_-	efflux transporter periplasmic adaptor subunit	NA	NA	NA	NA	NA
AUL11411.1|2014109_2014484_-	DNA-binding protein	NA	NA	NA	NA	NA
AUL11412.1|2014586_2015765_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11413.1|2015775_2016366_-	hypothetical protein	NA	NA	NA	NA	NA
AUL13226.1|2016476_2017283_+	molybdenum-dependent transcriptional regulator	NA	NA	NA	NA	NA
AUL11414.1|2017308_2018103_-	ABC transporter ATP-binding protein	NA	A0A1V0SE00	Indivirus	25.7	5.1e-05
AUL11415.1|2019103_2020078_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11416.1|2020236_2020749_-	superoxide dismutase	NA	Q9MC02	Salmonella_phage	52.3	1.8e-43
AUL11417.1|2020905_2021877_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11418.1|2023621_2024428_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL11419.1|2024424_2025726_-	malonyl-CoA decarboxylase	NA	NA	NA	NA	NA
AUL11420.1|2025676_2026441_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL13227.1|2026554_2027283_-	spermidine synthase	NA	NA	NA	NA	NA
AUL11421.1|2027408_2028596_-	acetyl-CoA acetyltransferase	NA	NA	NA	NA	NA
AUL11422.1|2028668_2029043_-	4-oxalocrotonate tautomerase	NA	NA	NA	NA	NA
AUL11423.1|2029143_2030406_-	glycine/betaine ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	36.6	6.8e-28
AUL11424.1|2030402_2031260_-	ABC transporter permease	NA	NA	NA	NA	NA
AUL11425.1|2031432_2032434_-	glycine/betaine ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11426.1|2032885_2033788_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL13228.1|2035399_2036551_+	Bcr/CflA family drug resistance efflux transporter	NA	NA	NA	NA	NA
AUL11427.1|2036919_2037156_+	50S ribosomal protein L28	NA	NA	NA	NA	NA
AUL11428.1|2037219_2037387_+	50S ribosomal protein L33	NA	NA	NA	NA	NA
AUL11429.1|2037500_2039306_-	sulfate transporter	NA	A0A2H4J153	uncultured_Caudovirales_phage	27.5	2.2e-19
AUL11430.1|2039559_2040462_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11431.1|2040608_2041511_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 17
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	2173085	2222738	4109385	tRNA,transposase	uncultured_Mediterranean_phage(16.67%)	43	NA	NA
AUL11529.1|2173085_2173988_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL13236.1|2174134_2175532_-	rRNA methyltransferase	NA	NA	NA	NA	NA
AUL11530.1|2176188_2177154_+	riboflavin biosynthesis protein RibF	NA	NA	NA	NA	NA
AUL11531.1|2177143_2180005_+|tRNA	isoleucine--tRNA ligase	tRNA	A0A1V0SJ93	Klosneuvirus	25.5	1.0e-71
AUL11532.1|2180007_2180514_+	signal peptidase II	NA	NA	NA	NA	NA
AUL11533.1|2180618_2181827_+	phosphopantothenate synthase	NA	Q9HH70	Methanothermobacter_phage	30.0	3.8e-36
AUL11534.1|2181828_2182767_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11535.1|2182928_2183402_+	AsnC family transcriptional regulator	NA	NA	NA	NA	NA
AUL11536.1|2183398_2184349_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11537.1|2184459_2184900_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11538.1|2185028_2186258_-	lytic transglycosylase	NA	NA	NA	NA	NA
AUL11539.1|2186296_2187118_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11540.1|2187171_2188323_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL11541.1|2188414_2188885_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11542.1|2191453_2194003_+	cyanophycin synthetase	NA	NA	NA	NA	NA
AUL11543.1|2194073_2196647_+	cyanophycin synthetase	NA	NA	NA	NA	NA
AUL11544.1|2196912_2197113_+	general stress protein CsbD	NA	NA	NA	NA	NA
AUL11545.1|2197144_2197306_+	DUF1328 domain-containing protein	NA	NA	NA	NA	NA
AUL11546.1|2197363_2197702_+	phospholipid-binding protein	NA	NA	NA	NA	NA
AUL11547.1|2197850_2198753_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11548.1|2199575_2200244_+	arylesterase	NA	NA	NA	NA	NA
AUL13237.1|2200225_2202181_-	peptidylprolyl isomerase	NA	NA	NA	NA	NA
AUL11549.1|2202423_2203173_+	glycerophosphodiester phosphodiesterase	NA	A0A2H4PGQ5	Escherichia_phage	27.8	1.5e-14
AUL11550.1|2203185_2204049_+	23S rRNA (adenine(2030)-N(6))-methyltransferase RlmJ	NA	NA	NA	NA	NA
AUL11551.1|2204052_2205468_-	dihydrolipoyl dehydrogenase	NA	NA	NA	NA	NA
AUL11552.1|2205601_2206330_-	glutathione peroxidase	NA	A0A1D8KSL1	Synechococcus_phage	56.8	9.6e-43
AUL11553.1|2206468_2206669_-	heavy metal transporter	NA	NA	NA	NA	NA
AUL11554.1|2206844_2207243_+	Cu(I)-responsive transcriptional regulator	NA	NA	NA	NA	NA
AUL11555.1|2207266_2208667_-	23S rRNA (uracil(1939)-C(5))-methyltransferase	NA	A0A2K5B251	Erysipelothrix_phage	26.5	7.3e-31
AUL11556.1|2208785_2209538_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11557.1|2209826_2210426_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11558.1|2210530_2211310_-	3'-5' exonuclease	NA	NA	NA	NA	NA
AUL11559.1|2211306_2212191_-	peptidase	NA	A0A292GJG6	Xanthomonas_phage	49.5	4.6e-15
AUL11560.1|2212208_2212988_-	protein-L-isoaspartate O-methyltransferase	NA	A0A1B1IU40	uncultured_Mediterranean_phage	46.9	4.8e-32
AUL11561.1|2212972_2213731_-	5'/3'-nucleotidase SurE	NA	A0A1B1ITZ2	uncultured_Mediterranean_phage	51.2	1.4e-68
AUL13238.1|2213868_2214504_+	glycerol-3-phosphate acyltransferase	NA	NA	NA	NA	NA
AUL13239.1|2214771_2215788_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL11562.1|2215885_2216926_-|tRNA	tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD	tRNA	A0A0R6PI74	Moraxella_phage	51.3	6.1e-91
AUL11563.1|2217060_2218353_+	guanine permease	NA	A0A0R6PHV4	Moraxella_phage	36.0	1.7e-66
AUL11564.1|2219712_2220096_+	thiol reductase thioredoxin	NA	V9SJ74	Achromobacter_phage	25.8	8.1e-09
AUL11565.1|2220113_2220701_-	thymidylate synthase	NA	A0A1X9I5T8	Streptococcus_phage	35.8	4.7e-16
AUL11566.1|2220738_2221641_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11567.1|2221787_2222738_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 18
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	2579608	2646059	4109385	transposase	uncultured_Caudovirales_phage(40.0%)	58	NA	NA
AUL11856.1|2579608_2580511_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11857.1|2580526_2580739_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11858.1|2580880_2581453_+	flagellar basal body protein FliL	NA	NA	NA	NA	NA
AUL11859.1|2581455_2582466_+	flagellar motor switch protein FliM	NA	NA	NA	NA	NA
AUL11860.1|2582458_2582959_+	flagellar motor switch protein FliN	NA	NA	NA	NA	NA
AUL11861.1|2582969_2583311_+	flagellar biosynthetic protein FliO	NA	NA	NA	NA	NA
AUL13267.1|2583379_2584114_+	flagellar biosynthetic protein FliP	NA	NA	NA	NA	NA
AUL11862.1|2584130_2584400_+	EscS/YscS/HrcS family type III secretion system export apparatus protein	NA	NA	NA	NA	NA
AUL11863.1|2584422_2585211_+	flagellar biosynthetic protein FliR	NA	NA	NA	NA	NA
AUL13268.1|2585257_2586274_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL11864.1|2586490_2587933_-	chemotaxis protein	NA	A0A1B0V854	Salmonella_phage	41.8	1.0e-35
AUL11865.1|2588111_2589731_-	methyl-accepting chemotaxis protein	NA	A0A2H4J162	uncultured_Caudovirales_phage	45.3	1.5e-08
AUL11866.1|2589851_2591672_-	methyl-accepting chemotaxis protein	NA	A0A2H4J162	uncultured_Caudovirales_phage	52.6	6.4e-11
AUL11867.1|2591750_2593283_-	flagellar hook-associated protein 3	NA	NA	NA	NA	NA
AUL11868.1|2593316_2594963_-	flagellar hook-associated protein FlgK	NA	NA	NA	NA	NA
AUL11869.1|2595032_2596055_-	flagellar rod assembly protein/muramidase FlgJ	NA	A0A088F6W1	Sulfitobacter_phage	31.4	1.9e-12
AUL11870.1|2596072_2597206_-	flagellar biosynthesis protein FlgI	NA	NA	NA	NA	NA
AUL11871.1|2597208_2597898_-	flagellar basal body L-ring protein	NA	NA	NA	NA	NA
AUL11872.1|2597897_2598683_-	flagellar basal-body rod protein FlgG	NA	NA	NA	NA	NA
AUL11873.1|2598726_2599491_-	flagellar biosynthesis protein FlgF	NA	NA	NA	NA	NA
AUL11874.1|2599529_2600951_-	flagellar hook protein FlgE	NA	NA	NA	NA	NA
AUL11875.1|2601016_2601721_-	flagellar basal body rod modification protein	NA	NA	NA	NA	NA
AUL11876.1|2601768_2602188_-	flagellar basal body rod protein FlgC	NA	NA	NA	NA	NA
AUL11877.1|2602200_2602608_-	flagellar basal body rod protein FlgB	NA	NA	NA	NA	NA
AUL13269.1|2602791_2603502_+	flagella basal body P-ring formation protein FlgA	NA	NA	NA	NA	NA
AUL11878.1|2603628_2603919_+	flagellar biosynthesis anti-sigma factor FlgM	NA	NA	NA	NA	NA
AUL11879.1|2603936_2604419_+	flagellar protein FlgN	NA	NA	NA	NA	NA
AUL11880.1|2608924_2610079_-	flagellar biosynthesis protein FlhB	NA	NA	NA	NA	NA
AUL13270.1|2610384_2611401_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL11881.1|2611647_2612436_+	amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11882.1|2612502_2613183_+	cysteine ABC transporter permease	NA	NA	NA	NA	NA
AUL11883.1|2613179_2613950_+	ATP-binding protein	NA	G9BWD6	Planktothrix_phage	39.1	9.8e-30
AUL11884.1|2614047_2614998_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11885.1|2615053_2615971_-	2-dehydropantoate 2-reductase	NA	NA	NA	NA	NA
AUL11886.1|2615981_2617160_-	mandelate racemase	NA	NA	NA	NA	NA
AUL11887.1|2617179_2618175_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11888.1|2619763_2620372_+	3-isopropylmalate dehydratase small subunit	NA	NA	NA	NA	NA
AUL11889.1|2620359_2621400_+	LacI family transcriptional regulator	NA	NA	NA	NA	NA
AUL11890.1|2621417_2622380_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11891.1|2622376_2623570_-	CoA transferase	NA	NA	NA	NA	NA
AUL11892.1|2623566_2624364_-	citryl-CoA lyase	NA	NA	NA	NA	NA
AUL11893.1|2624389_2625376_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11894.1|2625394_2627434_-	acetyl-CoA synthetase	NA	NA	NA	NA	NA
AUL13271.1|2627635_2628316_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11895.1|2628329_2629241_-	CoA ester lyase	NA	NA	NA	NA	NA
AUL11896.1|2629237_2629816_-	NADPH-dependent FMN reductase	NA	NA	NA	NA	NA
AUL11897.1|2629954_2630860_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11898.1|2630867_2634287_+	nuclease	NA	NA	NA	NA	NA
AUL11899.1|2634274_2636875_-	autotransporter outer membrane beta-barrel domain-containing protein	NA	NA	NA	NA	NA
AUL11900.1|2637830_2638463_-	PadR family transcriptional regulator	NA	NA	NA	NA	NA
AUL11901.1|2638856_2639615_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11902.1|2639611_2640814_+	cardiolipin synthase B	NA	NA	NA	NA	NA
AUL11903.1|2640810_2641011_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11904.1|2641001_2641952_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11905.1|2642859_2644005_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11906.1|2643991_2644747_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL11907.1|2644863_2645043_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11908.1|2645108_2646059_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 19
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	2674219	2711582	4109385	transposase	Planktothrix_phage(33.33%)	40	NA	NA
AUL11927.1|2674219_2675122_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11928.1|2675268_2676171_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11929.1|2676263_2676803_+	peroxiredoxin	NA	NA	NA	NA	NA
AUL11930.1|2676909_2677254_-	arsenate reductase (glutaredoxin)	NA	A0A2H4J8T1	uncultured_Caudovirales_phage	58.4	3.0e-31
AUL11931.1|2677311_2678760_-	carnitine dehydratase	NA	NA	NA	NA	NA
AUL13274.1|2678947_2679274_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11932.1|2680910_2682089_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11933.1|2682171_2682672_+	glutathione peroxidase	NA	Q6VZR0	Canarypox_virus	38.4	4.7e-25
AUL11934.1|2682781_2683483_+	thiol:disulfide oxidoreductase	NA	NA	NA	NA	NA
AUL11935.1|2683494_2683959_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
AUL11936.1|2683973_2684249_+	biotin--protein ligase	NA	NA	NA	NA	NA
AUL11937.1|2684245_2685022_+	lipoate--protein ligase	NA	NA	NA	NA	NA
AUL11938.1|2685050_2685878_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11939.1|2686003_2686474_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11940.1|2686600_2687494_+	phosphatidylserine decarboxylase	NA	NA	NA	NA	NA
AUL11941.1|2687541_2688723_+	alpha-hydroxy-acid oxidizing enzyme	NA	NA	NA	NA	NA
AUL11942.1|2688735_2689551_-	iron ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11943.1|2689684_2690212_-	hypothetical protein	NA	NA	NA	NA	NA
AUL13275.1|2690208_2690706_-	hypothetical protein	NA	NA	NA	NA	NA
AUL11944.1|2690853_2691231_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11945.1|2691188_2691473_+	hypothetical protein	NA	NA	NA	NA	NA
AUL11946.1|2691452_2692355_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL13276.1|2692501_2693113_-	alpha/beta hydrolase	NA	NA	NA	NA	NA
AUL11947.1|2693347_2694475_+	leucine ABC transporter subunit substrate-binding protein LivK	NA	NA	NA	NA	NA
AUL11948.1|2694585_2695674_-	sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC	NA	G9BWD6	Planktothrix_phage	31.2	2.2e-19
AUL11949.1|2695726_2696578_-	glycerol-3-phosphate transporter	NA	NA	NA	NA	NA
AUL11950.1|2696597_2697479_-	glycerol-3-phosphate transporter permease	NA	NA	NA	NA	NA
AUL13277.1|2697655_2698969_-	sn-glycerol-3-phosphate ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL11951.1|2699179_2700013_+	pyrroline-5-carboxylate reductase	NA	NA	NA	NA	NA
AUL11952.1|2700009_2700591_+	hypothetical protein	NA	A0A2I7SAW6	Vibrio_phage	37.3	9.4e-17
AUL11953.1|2700944_2701895_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11954.1|2701910_2703026_+	leucine ABC transporter subunit substrate-binding protein LivK	NA	NA	NA	NA	NA
AUL11955.1|2703128_2704055_+	branched-chain amino acid ABC transporter permease LivH	NA	NA	NA	NA	NA
AUL11956.1|2704054_2705293_+	high-affinity branched-chain amino acid ABC transporter permease LivM	NA	NA	NA	NA	NA
AUL11957.1|2705289_2706057_+	high-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG	NA	A0A2H4PQG7	Staphylococcus_phage	26.4	1.2e-14
AUL11958.1|2706057_2706759_+	branched-chain amino acid ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	30.4	1.3e-17
AUL13278.1|2706840_2707287_-	glutamate racemase	NA	NA	NA	NA	NA
AUL11959.1|2708176_2708815_+	glutathione S-transferase	NA	NA	NA	NA	NA
AUL11960.1|2709582_2710533_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL11961.1|2710631_2711582_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 20
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	2841919	2907752	4109385	protease,transposase	Pelagibacter_phage(16.67%)	48	NA	NA
AUL12067.1|2841919_2842870_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12068.1|2843004_2844111_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12069.1|2844121_2845219_+	cyclic pyranopterin phosphate synthase	NA	NA	NA	NA	NA
AUL12070.1|2845363_2846569_-	molybdopterin molybdenumtransferase MoeA	NA	NA	NA	NA	NA
AUL12071.1|2846575_2847097_-	molybdenum cofactor biosynthesis protein B	NA	NA	NA	NA	NA
AUL13288.1|2847093_2847576_-	molybdenum cofactor biosynthesis protein MoaE	NA	NA	NA	NA	NA
AUL12072.1|2847581_2847833_-	molybdopterin synthase sulfur carrier subunit	NA	NA	NA	NA	NA
AUL12073.1|2847813_2848299_-	molybdenum cofactor biosynthesis protein C	NA	NA	NA	NA	NA
AUL12074.1|2848434_2851896_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12075.1|2851913_2852798_+	carboxymethylenebutenolidase	NA	NA	NA	NA	NA
AUL12076.1|2852807_2853239_-	hypothetical protein	NA	NA	NA	NA	NA
AUL13289.1|2853485_2853989_+	peroxiredoxin	NA	M1I839	Pelagibacter_phage	44.1	1.8e-24
AUL12077.1|2854066_2855467_+	MFS transporter	NA	NA	NA	NA	NA
AUL12078.1|2855541_2856417_-	hypothetical protein	NA	NA	NA	NA	NA
AUL13290.1|2856413_2857421_-	biotin synthase BioB	NA	NA	NA	NA	NA
AUL12079.1|2857888_2858194_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12080.1|2858284_2858875_+	TetR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12081.1|2860272_2862609_-	copper-translocating P-type ATPase	NA	E4ZFI9	Streptococcus_phage	42.8	3.2e-124
AUL12082.1|2862691_2863126_+	Cd(II)/Pb(II)-responsive transcriptional regulator	NA	NA	NA	NA	NA
AUL12083.1|2864272_2865223_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12084.1|2865219_2866014_-	N-formylglutamate deformylase	NA	NA	NA	NA	NA
AUL12085.1|2866045_2866750_-	3-oxoacyl-ACP reductase	NA	NA	NA	NA	NA
AUL12086.1|2866824_2867625_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12087.1|2867621_2868029_-	cytochrome o ubiquinol oxidase subunit IV	NA	NA	NA	NA	NA
AUL12088.1|2868025_2868667_-	cytochrome o ubiquinol oxidase subunit III	NA	NA	NA	NA	NA
AUL13291.1|2868659_2870660_-	cytochrome o ubiquinol oxidase subunit I	NA	NA	NA	NA	NA
AUL12089.1|2871920_2873252_+	arabinose ABC transporter permease	NA	NA	NA	NA	NA
AUL12090.1|2873248_2874151_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12091.1|2875905_2876172_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12092.1|2876879_2877218_+	transcriptional regulator	NA	NA	NA	NA	NA
AUL12093.1|2878546_2880826_-	autotransporter outer membrane beta-barrel domain-containing protein	NA	NA	NA	NA	NA
AUL12094.1|2880803_2881508_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12095.1|2881770_2882373_-	TetR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12096.1|2882469_2883759_+	MFS transporter	NA	NA	NA	NA	NA
AUL12097.1|2883816_2884548_-	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	31.0	1.4e-12
AUL12098.1|2884544_2885348_-	ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	23.5	7.9e-14
AUL12099.1|2885344_2886433_-	ABC transporter ATP-binding protein	NA	NA	NA	NA	NA
AUL12100.1|2886429_2887359_-	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL12101.1|2887507_2888653_-	branched chain amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL12102.1|2888674_2889577_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12103.1|2889955_2893777_-	trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase	NA	NA	NA	NA	NA
AUL12104.1|2893933_2894602_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12105.1|2894606_2896280_-	paraquat-inducible protein B	NA	NA	NA	NA	NA
AUL12106.1|2896298_2897618_-	paraquat-inducible membrane protein A	NA	NA	NA	NA	NA
AUL12107.1|2897622_2899938_-|protease	ATP-dependent Clp protease ATP-binding subunit ClpA	protease	A0A223W0B1	Agrobacterium_phage	41.9	4.1e-164
AUL13292.1|2899993_2902162_-	penicillin-binding protein 1C	NA	NA	NA	NA	NA
AUL13293.1|2902158_2906724_-	alpha-2-macroglobulin	NA	NA	NA	NA	NA
AUL12108.1|2907437_2907752_-|protease	ATP-dependent Clp protease adapter ClpS	protease	A0A1B1IT64	uncultured_Mediterranean_phage	43.8	1.2e-10
>prophage 21
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	2913982	2973315	4109385	transposase	Burkholderia_phage(25.0%)	53	NA	NA
AUL12115.1|2913982_2914933_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12116.1|2915213_2915834_+	flagellar motor protein MotA	NA	NA	NA	NA	NA
AUL12117.1|2915830_2916244_+	biopolymer transporter ExbD	NA	NA	NA	NA	NA
AUL12118.1|2916240_2917284_+	tetraacyldisaccharide 4'-kinase	NA	NA	NA	NA	NA
AUL12119.1|2917339_2917528_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12120.1|2917537_2918302_+	3-deoxy-manno-octulosonate cytidylyltransferase	NA	NA	NA	NA	NA
AUL12121.1|2918392_2919049_+	adenylate kinase	NA	NA	NA	NA	NA
AUL12122.1|2919140_2919899_+	3-hydroxyacyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL12123.1|2919924_2921526_+	murein biosynthesis integral membrane protein MurJ	NA	NA	NA	NA	NA
AUL12124.1|2921726_2922731_+	iron dicitrate transport regulator FecR	NA	NA	NA	NA	NA
AUL12125.1|2922831_2923095_+	30S ribosomal protein S20	NA	NA	NA	NA	NA
AUL12126.1|2923212_2923989_-	2-dehydro-3-deoxyglucarate aldolase	NA	NA	NA	NA	NA
AUL12127.1|2924579_2925530_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12128.1|2927913_2929026_-	malate dehydrogenase	NA	NA	NA	NA	NA
AUL12129.1|2929082_2930033_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12130.1|2930241_2930463_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12131.1|2930676_2932083_-	threonine synthase	NA	NA	NA	NA	NA
AUL12132.1|2932079_2933384_-	homoserine dehydrogenase	NA	NA	NA	NA	NA
AUL12133.1|2933380_2934568_-	alanine transaminase	NA	NA	NA	NA	NA
AUL12134.1|2934784_2935237_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12135.1|2935239_2935704_+	peroxiredoxin	NA	NA	NA	NA	NA
AUL12136.1|2937566_2938544_+	4-hydroxythreonine-4-phosphate dehydrogenase PdxA	NA	NA	NA	NA	NA
AUL12137.1|2938623_2939592_+	bile acid:sodium symporter	NA	NA	NA	NA	NA
AUL12138.1|2939612_2940986_-	replicative DNA helicase	NA	C7BGG1	Burkholderia_phage	58.2	4.0e-135
AUL12139.1|2940982_2941819_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12140.1|2941935_2942391_-	50S ribosomal protein L9	NA	NA	NA	NA	NA
AUL12141.1|2942406_2942679_-	30S ribosomal protein S18	NA	NA	NA	NA	NA
AUL12142.1|2942771_2943095_-	primosomal replication protein N	NA	NA	NA	NA	NA
AUL12143.1|2943142_2943523_-	30S ribosomal protein S6	NA	NA	NA	NA	NA
AUL12144.1|2943742_2944540_-	GTP cyclohydrolase	NA	NA	NA	NA	NA
AUL12145.1|2944696_2946559_-	1-deoxy-D-xylulose-5-phosphate synthase	NA	NA	NA	NA	NA
AUL12146.1|2946608_2947520_-	geranyl transferase	NA	NA	NA	NA	NA
AUL12147.1|2947524_2947791_-	exodeoxyribonuclease VII small subunit	NA	NA	NA	NA	NA
AUL13294.1|2947877_2948708_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12148.1|2948882_2949848_+	MFS transporter	NA	NA	NA	NA	NA
AUL12149.1|2950018_2951029_+	hypothetical protein	NA	A0A0F6TJ51	Escherichia_coli_O157_typing_phage	24.6	3.6e-16
AUL12150.1|2951176_2952328_+	Rieske (2Fe-2S) protein	NA	NA	NA	NA	NA
AUL12151.1|2952411_2953275_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12152.1|2953470_2954943_-	magnesium transporter	NA	NA	NA	NA	NA
AUL12153.1|2954953_2955364_-	acyl-CoA thioesterase	NA	NA	NA	NA	NA
AUL12154.1|2955427_2956474_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12155.1|2956580_2957459_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12156.1|2957472_2958669_-	amidohydrolase	NA	NA	NA	NA	NA
AUL12157.1|2958730_2960422_+	long-chain fatty acid--CoA ligase	NA	A0A2H4PQU7	Staphylococcus_phage	28.1	9.4e-33
AUL12158.1|2960418_2961321_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12159.1|2961489_2962386_-	inositol monophosphatase	NA	NA	NA	NA	NA
AUL12160.1|2964663_2966889_+	glycosyl hydrolase	NA	NA	NA	NA	NA
AUL12161.1|2967053_2968142_+	phosphate ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	36.4	8.7e-32
AUL12162.1|2968098_2968752_+	DL-methionine transporter permease subunit	NA	NA	NA	NA	NA
AUL12163.1|2968799_2969597_+	metal ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL12164.1|2970176_2971079_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12165.1|2971159_2972308_+	alcohol dehydrogenase	NA	NA	NA	NA	NA
AUL12166.1|2972364_2973315_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 22
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	3238665	3286282	4109385	tRNA,transposase	Erwinia_phage(10.0%)	46	NA	NA
AUL12376.1|3238665_3239616_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12377.1|3240060_3240372_-	cell division protein ZapA	NA	NA	NA	NA	NA
AUL12378.1|3240371_3240902_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12379.1|3241064_3242015_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12380.1|3242304_3242769_+	tricarboxylate transporter	NA	NA	NA	NA	NA
AUL12381.1|3242783_3244289_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12382.1|3244545_3246150_+	gamma-glutamyltransferase	NA	NA	NA	NA	NA
AUL12383.1|3246205_3247111_+	oxidoreductase	NA	NA	NA	NA	NA
AUL12384.1|3247551_3248454_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12385.1|3248600_3249503_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12386.1|3249631_3250213_-	ATP:cob(I)alamin adenosyltransferase	NA	NA	NA	NA	NA
AUL13311.1|3250637_3250943_+	RND transporter	NA	NA	NA	NA	NA
AUL12387.1|3250956_3252291_-	HslU--HslV peptidase ATPase subunit	NA	A0A191ZC11	Erwinia_phage	29.6	3.5e-43
AUL12388.1|3252312_3252852_-	HslU--HslV peptidase proteolytic subunit	NA	NA	NA	NA	NA
AUL12389.1|3252999_3253464_-	RNA polymerase-binding protein DksA	NA	NA	NA	NA	NA
AUL12390.1|3253606_3254722_-	cobalamin biosynthesis protein CobW	NA	NA	NA	NA	NA
AUL12391.1|3254998_3255502_-	transcriptional repressor	NA	NA	NA	NA	NA
AUL12392.1|3255639_3255840_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12393.1|3255830_3256553_+	ABC transporter	NA	A0A2R8FG22	Brazilian_cedratvirus	30.0	1.1e-11
AUL12394.1|3256549_3257446_+	zinc ABC transporter permease	NA	NA	NA	NA	NA
AUL12395.1|3257442_3258378_+	metal ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL12396.1|3258338_3259007_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12397.1|3258997_3259966_+	nickel transporter	NA	NA	NA	NA	NA
AUL12398.1|3260014_3262156_+	TonB-dependent receptor	NA	NA	NA	NA	NA
AUL12399.1|3262168_3263149_-	tyrosine recombinase XerC	NA	A0A166YH27	Gordonia_phage	30.5	3.3e-14
AUL12400.1|3263163_3263856_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12401.1|3263882_3264794_-	diaminopimelate epimerase	NA	NA	NA	NA	NA
AUL12402.1|3264836_3265727_-	acyltransferase	NA	NA	NA	NA	NA
AUL12403.1|3265723_3266578_-	lipid A biosynthesis lauroyl acyltransferase	NA	NA	NA	NA	NA
AUL12404.1|3266861_3268025_+	methionine adenosyltransferase	NA	A0A2H4PQS6	Staphylococcus_phage	60.8	5.0e-126
AUL12405.1|3268135_3268387_+	DUF1289 domain-containing protein	NA	NA	NA	NA	NA
AUL12406.1|3268466_3269507_+	alpha-mannosyltransferase	NA	NA	NA	NA	NA
AUL12407.1|3269786_3271205_+	adenosylhomocysteinase	NA	S4VPF6	Pandoravirus	29.4	8.7e-40
AUL12408.1|3271275_3271611_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12409.1|3271610_3272453_+	methylenetetrahydrofolate reductase [NAD(P)H]	NA	NA	NA	NA	NA
AUL12410.1|3272599_3273502_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12411.1|3273566_3274538_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12412.1|3274601_3275621_-	acetylpolyamine amidohydrolase	NA	A0A2K9L473	Tupanvirus	31.7	3.4e-22
AUL12413.1|3275622_3276963_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL13312.1|3277273_3277954_-	5-formyltetrahydrofolate cyclo-ligase	NA	NA	NA	NA	NA
AUL13313.1|3278029_3280093_+	lytic transglycosylase	NA	A0A0S2SXL7	Bacillus_phage	36.6	5.3e-14
AUL12414.1|3280089_3281184_+|tRNA	CCA tRNA nucleotidyltransferase	tRNA	A0A0F6YPT7	Sinorhizobium_phage	50.5	2.4e-50
AUL12415.1|3281198_3282389_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12416.1|3282477_3284166_-	RNA helicase	NA	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	32.9	1.6e-48
AUL12417.1|3284440_3285193_-	uracil-DNA glycosylase	NA	A0A1Y0B680	Bovine_alphaherpesvirus	47.5	2.5e-46
AUL12418.1|3285331_3286282_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 23
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	3404957	3450028	4109385	tRNA,transposase	Staphylococcus_phage(16.67%)	39	NA	NA
AUL12505.1|3404957_3405860_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12506.1|3406674_3407769_-	CoA transferase	NA	NA	NA	NA	NA
AUL12507.1|3407761_3409096_-	CoA ligase	NA	NA	NA	NA	NA
AUL12508.1|3409049_3409733_-	TetR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12509.1|3409758_3410922_-	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL12510.1|3410918_3411920_-	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL12511.1|3411919_3412792_-	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
AUL12512.1|3412788_3413538_-	ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	27.8	1.9e-09
AUL12513.1|3413534_3414326_-	ABC transporter ATP-binding protein	NA	A0A1M7XV31	Cedratvirus	29.4	1.7e-08
AUL12514.1|3414322_3415462_-	ABC transporter	NA	NA	NA	NA	NA
AUL12515.1|3415737_3416523_+	3-hydroxyacyl-CoA dehydrogenase	NA	NA	NA	NA	NA
AUL12516.1|3416556_3417339_+	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL12517.1|3417342_3417732_+	DNA-binding protein	NA	NA	NA	NA	NA
AUL12518.1|3418871_3419735_+	3-alpha,7-alpha, 12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL12519.1|3419770_3420859_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12520.1|3420855_3421758_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12521.1|3422159_3425138_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12522.1|3426064_3426943_+	fatty acid desaturase	NA	NA	NA	NA	NA
AUL12523.1|3426978_3427311_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12524.1|3427289_3428792_+	hypothetical protein	NA	A0A1V0S9J5	Catovirus	45.3	8.7e-14
AUL12525.1|3428890_3429841_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12526.1|3429837_3430305_-	ribonuclease HI	NA	J9Q745	Salmonella_phage	50.7	5.6e-36
AUL12527.1|3430347_3431118_-	SAM-dependent methyltransferase	NA	NA	NA	NA	NA
AUL12528.1|3431138_3431939_+	hydroxyacylglutathione hydrolase	NA	NA	NA	NA	NA
AUL12529.1|3431949_3433359_+	lytic transglycosylase	NA	NA	NA	NA	NA
AUL12530.1|3433453_3434239_+	enoyl-[acyl-carrier-protein] reductase	NA	NA	NA	NA	NA
AUL13320.1|3434478_3435495_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL12531.1|3435602_3435995_-	osmotically inducible protein OsmC	NA	NA	NA	NA	NA
AUL12532.1|3436132_3436813_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12533.1|3436817_3437789_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL12534.1|3437884_3438787_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12535.1|3440339_3441041_+	two-component system response regulator OmpR	NA	W8CYM9	Bacillus_phage	36.6	5.6e-32
AUL12536.1|3441040_3442465_+	ATPase	NA	NA	NA	NA	NA
AUL12537.1|3443534_3444875_-	cytochrome ubiquinol oxidase subunit I	NA	NA	NA	NA	NA
AUL12538.1|3444990_3446754_+|tRNA	glutamine--tRNA ligase	tRNA	A0A222YZ70	Escherichia_phage	50.0	5.0e-162
AUL12539.1|3446865_3447744_+	septum site-determining protein MinC	NA	NA	NA	NA	NA
AUL12540.1|3447856_3448672_+	septum site-determining protein MinD	NA	NA	NA	NA	NA
AUL12541.1|3448675_3448927_+	cell division topological specificity factor MinE	NA	NA	NA	NA	NA
AUL13321.1|3449011_3450028_-|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
>prophage 24
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	3467772	3520177	4109385	tRNA,transposase	Acinetobacter_phage(37.5%)	50	NA	NA
AUL13323.1|3467772_3468789_+|transposase	IS110 family transposase	transposase	NA	NA	NA	NA
AUL12551.1|3468884_3469595_-	short-chain dehydrogenase	NA	NA	NA	NA	NA
AUL13324.1|3469591_3470581_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL12552.1|3470676_3472308_+	acyl-CoA synthetase	NA	NA	NA	NA	NA
AUL12553.1|3472310_3473048_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12554.1|3473203_3474076_-|tRNA	tRNA threonylcarbamoyladenosine dehydratase	tRNA	NA	NA	NA	NA
AUL12555.1|3474425_3475565_+	MFS transporter	NA	NA	NA	NA	NA
AUL12556.1|3475561_3476221_+	gamma-glutamylcyclotransferase	NA	NA	NA	NA	NA
AUL12557.1|3476292_3476925_+	pyridoxamine 5'-phosphate oxidase	NA	NA	NA	NA	NA
AUL12558.1|3476954_3477473_+	flavin reductase	NA	NA	NA	NA	NA
AUL12559.1|3477483_3478593_+	FAD-dependent oxidoreductase	NA	NA	NA	NA	NA
AUL12560.1|3478639_3479494_+	formyltetrahydrofolate deformylase	NA	NA	NA	NA	NA
AUL12561.1|3479495_3480398_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12562.1|3481620_3482571_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12563.1|3482667_3483801_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12564.1|3483837_3484086_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12565.1|3484325_3485315_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12566.1|3485490_3486279_-	indole-3-glycerol-phosphate synthase	NA	A0A0P0IR83	Acinetobacter_phage	53.0	5.1e-66
AUL12567.1|3486275_3487307_-	anthranilate phosphoribosyltransferase	NA	A0A0N7IRD9	Acinetobacter_phage	42.7	7.4e-73
AUL12568.1|3487325_3487889_-	anthranilate/aminodeoxychorismate synthase component II	NA	A0A0P0IKJ1	Acinetobacter_phage	62.1	1.1e-65
AUL12569.1|3487944_3489465_-	anthranilate synthase component I	NA	S4VT78	Pandoravirus	32.1	9.0e-43
AUL12570.1|3489728_3490433_-	phosphoglycolate phosphatase	NA	NA	NA	NA	NA
AUL12571.1|3490440_3491169_-	ribulose-phosphate 3-epimerase	NA	NA	NA	NA	NA
AUL12572.1|3491283_3491658_+	Co2+/Mg2+ efflux protein ApaG	NA	NA	NA	NA	NA
AUL12573.1|3491700_3492990_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12574.1|3492986_3494156_+	ubiquinone biosynthesis protein UbiH	NA	NA	NA	NA	NA
AUL12575.1|3494182_3494992_+	disulfide bond formation protein DsbC	NA	NA	NA	NA	NA
AUL12576.1|3495051_3495987_+	hydroxyacid dehydrogenase	NA	A0A1J0F959	Only_Syngen_Nebraska_virus	27.7	6.4e-15
AUL12577.1|3495999_3496950_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12578.1|3497048_3498011_-|tRNA	tRNA 2-thiocytidine(32) synthetase TtcA	tRNA	A0A0U2S5Z2	Escherichia_phage	64.5	4.6e-93
AUL12579.1|3498042_3498402_-	dihydroneopterin aldolase	NA	NA	NA	NA	NA
AUL12580.1|3498526_3499429_+	oxidoreductase	NA	G3MA85	Bacillus_virus	24.0	1.9e-08
AUL13325.1|3499430_3501197_-	peptidase M61	NA	NA	NA	NA	NA
AUL12581.1|3501237_3502014_+	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL12582.1|3503337_3504240_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12583.1|3504454_3504868_+	hypothetical protein	NA	NA	NA	NA	NA
AUL13326.1|3505139_3505460_+	ABC transporter permease	NA	NA	NA	NA	NA
AUL12584.1|3505532_3506414_+	F0F1 ATP synthase subunit A	NA	NA	NA	NA	NA
AUL12585.1|3506530_3506773_+	F0F1 ATP synthase subunit C	NA	NA	NA	NA	NA
AUL12586.1|3506910_3507381_+	F0F1 ATP synthase subunit B	NA	NA	NA	NA	NA
AUL12587.1|3507393_3507933_+	F0F1 ATP synthase subunit delta	NA	NA	NA	NA	NA
AUL12588.1|3507967_3509509_+	F0F1 ATP synthase subunit alpha	NA	NA	NA	NA	NA
AUL12589.1|3509607_3510513_+	F0F1 ATP synthase subunit gamma	NA	NA	NA	NA	NA
AUL12590.1|3510555_3511956_+	F0F1 ATP synthase subunit beta	NA	NA	NA	NA	NA
AUL12591.1|3511965_3512388_+	F0F1 ATP synthase subunit epsilon	NA	NA	NA	NA	NA
AUL13327.1|3512570_3513455_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12592.1|3513530_3514607_+	uroporphyrinogen decarboxylase	NA	NA	NA	NA	NA
AUL12593.1|3514913_3517016_+	primosomal protein N'	NA	NA	NA	NA	NA
AUL12594.1|3517058_3519128_+	ATP-dependent DNA helicase Rep	NA	A7KV33	Bacillus_phage	37.3	2.6e-101
AUL12595.1|3519226_3520177_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 25
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	3537342	3590046	4109385	tRNA,holin,transposase	Catovirus(10.0%)	49	NA	NA
AUL12606.1|3537342_3538245_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12607.1|3538585_3539536_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12608.1|3539682_3540585_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12609.1|3540881_3541379_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12610.1|3541421_3543197_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12611.1|3543204_3544071_+	copper resistance protein	NA	NA	NA	NA	NA
AUL12612.1|3544077_3544803_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL12613.1|3544972_3545203_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12614.1|3545240_3545462_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12615.1|3545981_3546752_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12616.1|3547065_3547656_+	cysteine dioxygenase	NA	NA	NA	NA	NA
AUL12617.1|3547689_3549018_-	amidase	NA	NA	NA	NA	NA
AUL12618.1|3549092_3550238_-	transporter	NA	NA	NA	NA	NA
AUL12619.1|3550349_3551348_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12620.1|3551310_3551745_+	carbon monoxide dehydrogenase	NA	NA	NA	NA	NA
AUL12621.1|3553261_3554146_+	EamA family transporter	NA	NA	NA	NA	NA
AUL12622.1|3554142_3555348_-	cardiolipin synthase B	NA	NA	NA	NA	NA
AUL12623.1|3555344_3556205_-	endonuclease	NA	NA	NA	NA	NA
AUL12624.1|3556317_3558108_-|tRNA	aspartate--tRNA ligase	tRNA	A0A1V0SAC0	Catovirus	25.5	6.5e-08
AUL13329.1|3558148_3558793_-	hypothetical protein	NA	A0A2I7S9X1	Vibrio_phage	28.4	8.5e-11
AUL12625.1|3558814_3559123_-	FmdB family transcriptional regulator	NA	NA	NA	NA	NA
AUL13330.1|3559288_3560575_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12626.1|3560701_3561961_-|holin	choline dehydrogenase	holin	A0A2I2L3D3	Orpheovirus	27.6	6.1e-13
AUL12627.1|3562008_3562959_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12628.1|3564910_3566125_-	phosphoribosylglycinamide formyltransferase 2	NA	NA	NA	NA	NA
AUL12629.1|3566230_3567220_+	D-arabinose 5-phosphate isomerase	NA	A0A2P0VNK5	Tetraselmis_virus	37.7	4.3e-38
AUL12630.1|3567216_3567825_+	phenylphosphate carboxylase subunit delta	NA	E3T535	Cafeteria_roenbergensis_virus	26.1	5.2e-10
AUL12631.1|3567837_3568467_+	LPS export ABC transporter periplasmic protein LptC	NA	NA	NA	NA	NA
AUL12632.1|3568463_3569084_+	lipopolysaccharide transport periplasmic protein LptA	NA	NA	NA	NA	NA
AUL12633.1|3569115_3569907_+	LPS export ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	27.4	9.5e-20
AUL12634.1|3570260_3570482_+	ribosomal subunit interface protein	NA	NA	NA	NA	NA
AUL12635.1|3570758_3571214_+	PTS sugar transporter subunit IIA	NA	NA	NA	NA	NA
AUL12636.1|3571232_3572159_+	HPr kinase/phosphorylase	NA	NA	NA	NA	NA
AUL12637.1|3572212_3573499_-	alcohol dehydrogenase	NA	NA	NA	NA	NA
AUL12638.1|3574429_3575302_+	RNase adaptor protein RapZ	NA	A0A1P8D5W0	Corynebacterium_phage	34.5	2.4e-08
AUL12639.1|3575298_3576249_+	hypothetical protein	NA	F5B3X9	Synechococcus_phage	47.2	6.9e-17
AUL12640.1|3576395_3577298_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL13331.1|3577402_3577633_-	hypothetical protein	NA	NA	NA	NA	NA
AUL13332.1|3577759_3578149_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12641.1|3578165_3580547_-	dehydrogenase	NA	NA	NA	NA	NA
AUL12642.1|3580539_3581049_-	4-hydroxybenzoyl-CoA reductase subunit gamma	NA	A0A0P0IVM8	Acinetobacter_phage	37.3	8.8e-19
AUL12643.1|3581931_3582927_-	4,5-dihydroxyphthalate decarboxylase	NA	NA	NA	NA	NA
AUL12644.1|3582945_3583938_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL12645.1|3584178_3584739_-	3-octaprenyl-4-hydroxybenzoate carboxy-lyase	NA	NA	NA	NA	NA
AUL12646.1|3584743_3585070_-	monothiol glutaredoxin, Grx4 family	NA	NA	NA	NA	NA
AUL12647.1|3585106_3585919_-	protein-(glutamine-N5) methyltransferase, release factor-specific	NA	NA	NA	NA	NA
AUL12648.1|3585929_3587012_-	peptide chain release factor 1	NA	A0A0S4KWG0	Pseudomonas_phage	40.7	3.3e-07
AUL12649.1|3587098_3588373_-|tRNA	glutamyl-tRNA reductase	tRNA	NA	NA	NA	NA
AUL12650.1|3589095_3590046_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 26
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	3708417	3751588	4109385	tRNA,transposase,integrase	Streptococcus_phage(11.11%)	41	3746427:3746445	3752211:3752229
AUL12744.1|3708417_3709320_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12745.1|3709467_3710370_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12746.1|3710366_3711002_-	lysine transporter LysE	NA	NA	NA	NA	NA
AUL12747.1|3711131_3712031_+	transcriptional regulator ArgP	NA	NA	NA	NA	NA
AUL12748.1|3712126_3712618_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12749.1|3712664_3713630_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL12750.1|3714763_3716005_+	2-aminoadipate aminotransferase	NA	A0A1X9I5H2	Streptococcus_phage	24.9	1.9e-14
AUL12751.1|3716118_3717135_+	amino acid ABC transporter substrate-binding protein	NA	A0A1B1IT51	uncultured_Mediterranean_phage	43.8	3.5e-75
AUL12752.1|3717169_3717646_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12753.1|3717788_3718697_-	hydroxymethylglutaryl-CoA lyase	NA	NA	NA	NA	NA
AUL12754.1|3718810_3719923_-	DNA protecting protein DprA	NA	S6BFL3	Thermus_phage	35.0	1.9e-21
AUL13341.1|3720023_3720509_-	AsnC family transcriptional regulator	NA	NA	NA	NA	NA
AUL12755.1|3720645_3721896_+	kynureninase	NA	NA	NA	NA	NA
AUL12756.1|3721997_3722510_+	peptide deformylase	NA	E3SLL2	Synechococcus_phage	43.3	8.5e-22
AUL12757.1|3722656_3723559_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12758.1|3723624_3724563_+|tRNA	methionyl-tRNA formyltransferase	tRNA	E3SNR5	Prochlorococcus_phage	35.7	1.4e-09
AUL12759.1|3724585_3725212_-	flavin-nucleotide-binding protein	NA	NA	NA	NA	NA
AUL12760.1|3725208_3725865_-	HAD family hydrolase	NA	NA	NA	NA	NA
AUL12761.1|3725861_3726464_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12762.1|3726470_3727058_-	Rossman fold protein, TIGR00730 family	NA	A0A2I2L3F0	Orpheovirus	23.3	1.1e-07
AUL12763.1|3727238_3727808_+	bacterioferritin	NA	NA	NA	NA	NA
AUL12764.1|3727878_3729198_-	ribosomal protein S12 methylthiotransferase	NA	NA	NA	NA	NA
AUL12765.1|3729304_3729496_-	4-oxalocrotonate tautomerase	NA	NA	NA	NA	NA
AUL12766.1|3729747_3731037_+	glycine/D-amino acid oxidase	NA	NA	NA	NA	NA
AUL12767.1|3731191_3732187_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12768.1|3732271_3732946_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12769.1|3732942_3733845_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12770.1|3734054_3735296_+	ornithine--oxo-acid transaminase	NA	A0A1V0SKB7	Klosneuvirus	25.2	4.0e-25
AUL12771.1|3735292_3736237_+	arginase	NA	A0A0N9R043	Chrysochromulina_ericina_virus	33.3	9.5e-27
AUL12772.1|3736403_3737306_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12773.1|3737265_3738195_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12774.1|3738248_3738584_-	alkylhydroperoxidase	NA	NA	NA	NA	NA
AUL12775.1|3738628_3739393_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
AUL12776.1|3739416_3740157_-	transcriptional regulator	NA	NA	NA	NA	NA
AUL12777.1|3740164_3741718_-	long-chain fatty acid--CoA ligase	NA	A0A2K9L3I8	Tupanvirus	22.6	1.5e-13
AUL12778.1|3741752_3742730_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12779.1|3743002_3743584_-	ureidoglycolate hydrolase	NA	NA	NA	NA	NA
AUL12780.1|3743635_3750769_-	autotransporter outer membrane beta-barrel domain-containing protein	NA	NA	NA	NA	NA
3746427:3746445	attL	GCGACCCGCAGCGTGCCGG	NA	NA	NA	NA
AUL12781.1|3750984_3751116_-	entericidin	NA	NA	NA	NA	NA
AUL13342.1|3751147_3751273_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12782.1|3751381_3751588_-|integrase	integrase	integrase	NA	NA	NA	NA
3752211:3752229	attR	GCGACCCGCAGCGTGCCGG	NA	NA	NA	NA
>prophage 27
CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4109385	3757522	3793197	4109385	transposase,integrase	Burkholderia_phage(11.11%)	37	3754061:3754078	3798701:3798718
3754061:3754078	attL	CAGCGTGCTGGCCACCGT	NA	NA	NA	NA
AUL12789.1|3757522_3758425_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12790.1|3758435_3759077_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12791.1|3759243_3759486_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12792.1|3759632_3760535_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12793.1|3760570_3761038_+	hypothetical protein	NA	Q3HQX1	Burkholderia_phage	71.3	2.1e-43
AUL12794.1|3761271_3761649_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12795.1|3761645_3761828_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12796.1|3761831_3762818_+	DNA recombinase	NA	H9C0R8	Aeromonas_phage	57.3	2.0e-67
AUL12797.1|3762814_3763462_+	exonuclease	NA	A0A0U2BXF3	Paracoccus_phage	41.4	2.0e-31
AUL12798.1|3763519_3764047_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12799.1|3764083_3765268_+	hypothetical protein	NA	A0A291L9X3	Bordetella_phage	37.8	1.5e-24
AUL12800.1|3765278_3765620_+	hypothetical protein	NA	A0A0H5ARN8	Pseudomonas_phage	45.3	1.0e-10
AUL12801.1|3765612_3765732_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12802.1|3765732_3765933_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12803.1|3765929_3766919_-|integrase	integrase	integrase	A0A1B1P9F9	Acinetobacter_phage	44.4	4.4e-75
AUL12804.1|3768405_3770376_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12805.1|3770617_3771016_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12806.1|3771024_3771948_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12807.1|3772453_3773356_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12808.1|3773586_3775278_-	membrane protein insertase YidC	NA	NA	NA	NA	NA
AUL12809.1|3775326_3775599_-	membrane protein insertion efficiency factor YidD	NA	A0A2H4PQM5	Staphylococcus_phage	52.2	7.0e-15
AUL12810.1|3775595_3775967_-	ribonuclease P protein component	NA	NA	NA	NA	NA
AUL12811.1|3776062_3776197_-	50S ribosomal protein L34	NA	NA	NA	NA	NA
AUL12812.1|3776602_3778012_+	chromosomal replication initiation protein DnaA	NA	NA	NA	NA	NA
AUL12813.1|3778014_3779124_+	DNA polymerase III subunit beta	NA	B4UTW9	Rhizobium_phage	32.6	1.2e-41
AUL12814.1|3779218_3781672_+	DNA gyrase subunit B	NA	G3M9Z3	Bacillus_virus	34.8	2.3e-112
AUL12815.1|3781790_3782582_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12816.1|3782701_3784129_+	amidase	NA	NA	NA	NA	NA
AUL13343.1|3784167_3785139_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
AUL12817.1|3785223_3785427_+	hypothetical protein	NA	NA	NA	NA	NA
AUL12818.1|3785557_3786721_+	alpha-hydroxy-acid oxidizing enzyme	NA	NA	NA	NA	NA
AUL12819.1|3786808_3787654_+	AraC family transcriptional regulator	NA	NA	NA	NA	NA
AUL12820.1|3789258_3790161_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
AUL12821.1|3790157_3790502_-	hypothetical protein	NA	NA	NA	NA	NA
AUL12822.1|3790715_3791090_-	MerR family transcriptional regulator	NA	NA	NA	NA	NA
AUL12823.1|3791164_3792223_+	Zn-dependent hydrolase	NA	NA	NA	NA	NA
AUL12824.1|3792246_3793197_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
3798701:3798718	attR	CAGCGTGCTGGCCACCGT	NA	NA	NA	NA
