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
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	27282	70036	4108480	tRNA,transposase	Synechococcus_phage(50.0%)	42	NA	NA
WP_010929577.1|27282_28233_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_023995007.1|28314_28650_-	CoA transferase	NA	NA	NA	NA	NA
WP_010929578.1|28674_29109_-	hypothetical protein	NA	NA	NA	NA	NA
WP_019247164.1|29141_30359_-	thiolase family protein	NA	NA	NA	NA	NA
WP_010929580.1|30364_30862_-	MaoC family dehydratase	NA	NA	NA	NA	NA
WP_019247165.1|31069_32005_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010929582.1|32214_33006_+	enoyl-CoA hydratase/isomerase family protein	NA	NA	NA	NA	NA
WP_010929583.1|33048_34470_+	MmgE/PrpD family protein	NA	NA	NA	NA	NA
WP_010929584.1|34625_35576_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_077108685.1|35572_36763_-	MFS transporter	NA	NA	NA	NA	NA
WP_010929585.1|37012_37924_+|tRNA	glycine--tRNA ligase subunit alpha	tRNA	NA	NA	NA	NA
WP_010929586.1|37925_40064_+|tRNA	glycine--tRNA ligase subunit beta	tRNA	NA	NA	NA	NA
WP_003814404.1|40060_40600_+	D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase	NA	NA	NA	NA	NA
WP_003814405.1|40603_41332_+	1-acyl-sn-glycerol-3-phosphate acyltransferase	NA	NA	NA	NA	NA
WP_010929587.1|41318_42212_+	M48 family metallopeptidase	NA	NA	NA	NA	NA
WP_019247766.1|42282_42678_+	lactoylglutathione lyase	NA	NA	NA	NA	NA
WP_003814412.1|42687_43218_+	peptide deformylase	NA	E3SLL2	Synechococcus_phage	35.4	3.7e-12
WP_023852754.1|43346_43646_-	DUF1974 domain-containing protein	NA	NA	NA	NA	NA
WP_010929588.1|43663_44614_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929589.1|45200_45749_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003815265.1|45720_45957_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_003815255.1|46084_46978_+	membrane protein	NA	NA	NA	NA	NA
WP_010929590.1|48147_49395_+	homoserine O-acetyltransferase	NA	NA	NA	NA	NA
WP_003817748.1|49391_50006_+	methionine biosynthesis protein MetW	NA	NA	NA	NA	NA
WP_010929591.1|50141_51092_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_029443813.1|51134_52391_+	muropeptide transporter	NA	NA	NA	NA	NA
WP_010929592.1|53622_54357_-	aspartate/glutamate racemase family protein	NA	NA	NA	NA	NA
WP_019247224.1|54362_54953_-	amino acid ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	33.6	3.2e-20
WP_003817737.1|54977_55667_-	ABC transporter permease subunit	NA	NA	NA	NA	NA
WP_023852650.1|55663_56425_-	amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_010929594.1|56504_57404_-	amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_005012808.1|57497_58448_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929595.1|59248_60475_-	type II toxin-antitoxin system HipA family toxin	NA	NA	NA	NA	NA
WP_010929596.1|60474_60894_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_010929597.1|61077_62019_-	hypothetical protein	NA	NA	NA	NA	NA
WP_019248755.1|62442_63417_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010929599.1|63473_64055_-	DJ-1/PfpI family protein	NA	NA	NA	NA	NA
WP_010929600.1|64067_64370_-	Rieske 2Fe-2S domain-containing protein	NA	NA	NA	NA	NA
WP_029443770.1|64488_65547_-	2Fe-2S iron-sulfur cluster binding domain-containing protein	NA	NA	NA	NA	NA
WP_019247832.1|65581_66853_-	TRAP transporter large permease	NA	NA	NA	NA	NA
WP_010929603.1|67482_68664_-	TRAP transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010929584.1|69085_70036_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 2
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	77634	136108	4108480	tRNA,transposase	Planktothrix_phage(22.22%)	53	NA	NA
WP_005012067.1|77634_78585_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_041166334.1|78659_79604_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929608.1|79600_81475_-	polysaccharide biosynthesis protein	NA	A0A2P1ELS8	Moumouvirus	26.9	2.0e-23
WP_003807102.1|82822_83527_-	DUF2837 family protein	NA	NA	NA	NA	NA
WP_003807104.1|83523_84630_-	glycosyltransferase family 4 protein	NA	NA	NA	NA	NA
WP_010929610.1|84891_85485_-	sugar transferase	NA	NA	NA	NA	NA
WP_023853419.1|85481_86669_-	DegT/DnrJ/EryC1/StrS family aminotransferase	NA	NA	NA	NA	NA
WP_010929612.1|86731_87991_-	glycosyltransferase family 4 protein	NA	NA	NA	NA	NA
WP_010929613.1|88014_89103_-	UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)	NA	A0A0N9R0B2	Chrysochromulina_ericina_virus	36.3	4.8e-46
WP_010929614.1|89110_90211_-	DegT/DnrJ/EryC1/StrS family aminotransferase	NA	A0A2K9L0G1	Tupanvirus	29.7	3.3e-31
WP_003807114.1|90214_90790_-	N-acetyltransferase	NA	NA	NA	NA	NA
WP_003807115.1|90793_91846_-	Gfo/Idh/MocA family oxidoreductase	NA	NA	NA	NA	NA
WP_010929615.1|91976_92984_+	lipopolysaccharide heptosyltransferase I	NA	NA	NA	NA	NA
WP_010929616.1|92985_94272_+	3-deoxy-D-manno-octulosonic acid transferase	NA	NA	NA	NA	NA
WP_010929617.1|94468_95272_-	type III pantothenate kinase	NA	NA	NA	NA	NA
WP_010929618.1|95268_96135_-	biotin--[acetyl-CoA-carboxylase] ligase	NA	NA	NA	NA	NA
WP_010929619.1|96209_97340_+	ABC transporter permease	NA	NA	NA	NA	NA
WP_003807131.1|97339_98179_+	ATP-binding cassette domain-containing protein	NA	G9BWD6	Planktothrix_phage	32.4	9.1e-21
WP_010929620.1|99111_99714_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010929621.1|99743_100397_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
WP_003807138.1|100529_101786_+	D-alanyl-D-alanine carboxypeptidase	NA	B6DZZ7	Stx2-converting_phage	40.5	6.2e-66
WP_023853421.1|101866_102733_+	D-amino acid aminotransferase	NA	NA	NA	NA	NA
WP_003818417.1|102808_103084_+	YbeD family protein	NA	NA	NA	NA	NA
WP_010929623.1|103091_103754_+	lipoyl(octanoyl) transferase LipB	NA	NA	NA	NA	NA
WP_003807146.1|103815_104817_+	lipoyl synthase	NA	NA	NA	NA	NA
WP_003807148.1|104831_105380_-	dTDP-4-dehydrorhamnose 3,5-epimerase	NA	A0A291LA62	Escherichia_phage	53.4	3.7e-47
WP_010929624.1|105437_106334_-	dTDP-4-dehydrorhamnose reductase	NA	NA	NA	NA	NA
WP_010929625.1|106330_107392_-	dTDP-glucose 4,6-dehydratase	NA	A0A1D7XFE8	Escherichia_phage	44.8	1.6e-78
WP_010929626.1|107427_108378_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929627.1|109277_110471_+	cystathionine beta-lyase	NA	NA	NA	NA	NA
WP_010929628.1|110552_111182_-	thiol:disulfide interchange protein DsbA/DsbL	NA	NA	NA	NA	NA
WP_010927242.1|111243_111927_-	SPOR domain-containing protein	NA	NA	NA	NA	NA
WP_023853376.1|111936_113619_-|tRNA	arginine--tRNA ligase	tRNA	NA	NA	NA	NA
WP_003815933.1|113906_114254_+	DUF1840 domain-containing protein	NA	NA	NA	NA	NA
WP_003815930.1|114344_114662_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010931363.1|114944_115961_+|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_003815929.1|116036_116837_-	carbohydrate ABC transporter permease	NA	NA	NA	NA	NA
WP_003815927.1|116833_117709_-	sugar ABC transporter permease	NA	NA	NA	NA	NA
WP_010929633.1|117719_119012_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010929634.1|119054_120095_-	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	33.7	6.0e-22
WP_010929635.1|120200_121022_-	phosphodiesterase	NA	NA	NA	NA	NA
WP_005012067.1|121122_122073_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_014905488.1|122171_123077_-	ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	31.7	9.8e-21
WP_003815918.1|123073_123907_-	ABC transporter permease subunit	NA	NA	NA	NA	NA
WP_010929637.1|124743_125754_-	extracellular solute-binding protein	NA	NA	NA	NA	NA
WP_019247800.1|125750_126140_-	substrate-binding domain-containing protein	NA	NA	NA	NA	NA
WP_010929638.1|127033_128287_+	amidase	NA	NA	NA	NA	NA
WP_010929639.1|128377_130078_-	2-isopropylmalate synthase	NA	NA	NA	NA	NA
WP_010929640.1|130504_131152_-	hypothetical protein	NA	NA	NA	NA	NA
WP_023853393.1|131150_132590_+	RNA polymerase factor sigma-54	NA	NA	NA	NA	NA
WP_023853394.1|132700_132985_+	(2Fe-2S)-binding protein	NA	NA	NA	NA	NA
WP_010929512.1|133012_133891_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_005012067.1|135157_136108_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 3
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	164893	225403	4108480	tRNA,protease,transposase	Diachasmimorpha_longicaudata_entomopoxvirus(11.11%)	51	NA	NA
WP_005015810.1|164893_165844_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929659.1|167287_168190_-	YgcG family protein	NA	NA	NA	NA	NA
WP_003815889.1|168167_168797_-	LemA family protein	NA	NA	NA	NA	NA
WP_010929660.1|169079_170510_+	DEAD/DEAH box helicase	NA	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	29.8	5.8e-44
WP_010929661.1|170543_171173_+	LysE family transporter	NA	NA	NA	NA	NA
WP_003815895.1|171221_172829_+	peptide chain release factor 3	NA	A0A2K9L6L3	Tupanvirus	37.8	9.3e-14
WP_010929663.1|172853_173537_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003815898.1|173618_174095_-	bacterioferritin	NA	NA	NA	NA	NA
WP_010929591.1|174301_175252_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929664.1|176367_176895_+	META domain-containing protein	NA	NA	NA	NA	NA
WP_010929665.1|176986_177802_+	META and DUF4377 domain-containing protein	NA	NA	NA	NA	NA
WP_003808370.1|177862_178597_+	sulfurtransferase	NA	NA	NA	NA	NA
WP_010929666.1|178634_180713_-|tRNA	methionine--tRNA ligase	tRNA	A0A1V0SHR2	Klosneuvirus	23.6	1.5e-27
WP_003808374.1|180962_181235_-	hypothetical protein	NA	NA	NA	NA	NA
WP_033446322.1|181336_182422_+	iron-sulfur cluster carrier protein ApbC	NA	NA	NA	NA	NA
WP_010929668.1|182425_184330_+	BamA/TamA family outer membrane protein	NA	NA	NA	NA	NA
WP_014486044.1|184326_188001_+	DUF490 domain-containing protein	NA	NA	NA	NA	NA
WP_010929670.1|188061_188625_+	dCTP deaminase	NA	S5VM63	Pseudomonas_phage	75.3	2.6e-72
WP_003808385.1|188632_189055_-	glyoxalase	NA	NA	NA	NA	NA
WP_010929671.1|189082_189502_-	glyoxalase/bleomycin resistance/dioxygenase family protein	NA	NA	NA	NA	NA
WP_077274090.1|189530_189977_-	GNAT family N-acetyltransferase	NA	Q9AZG4	Lactococcus_phage	29.4	1.2e-08
WP_003808391.1|190103_190601_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003808393.1|190755_193026_+	arginine/lysine/ornithine decarboxylase	NA	NA	NA	NA	NA
WP_019249381.1|193101_194307_+	NAD(P)/FAD-dependent oxidoreductase	NA	NA	NA	NA	NA
WP_010929591.1|194404_195355_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929673.1|195457_196093_+	superoxide dismutase	NA	Q56AR7	Bacillus_thuringiensis_phage	73.8	2.8e-83
WP_019248671.1|196089_196983_+	ZIP family metal transporter	NA	NA	NA	NA	NA
WP_010929675.1|197377_198478_+	glycine cleavage system aminomethyltransferase GcvT	NA	NA	NA	NA	NA
WP_010929676.1|198559_198934_+	glycine cleavage system protein GcvH	NA	NA	NA	NA	NA
WP_010929677.1|198993_201858_+	aminomethyl-transferring glycine dehydrogenase	NA	E3SN07	Prochlorococcus_phage	51.4	1.2e-261
WP_010929678.1|202002_202743_-	FadR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010929679.1|202812_204024_+	CoA transferase	NA	NA	NA	NA	NA
WP_010929680.1|204052_205021_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010931070.1|205634_206585_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929699.1|206741_207065_+	phosphate starvation-inducible protein	NA	NA	NA	NA	NA
WP_023853200.1|207169_208210_-	cyclase	NA	NA	NA	NA	NA
WP_010929697.1|208215_208995_-	3-oxoadipate enol-lactonase	NA	NA	NA	NA	NA
WP_003807672.1|209040_209337_-	YciI family protein	NA	NA	NA	NA	NA
WP_003807674.1|209362_209638_-	muconolactone Delta-isomerase	NA	NA	NA	NA	NA
WP_003819086.1|209694_210339_-	CoA transferase subunit B	NA	NA	NA	NA	NA
WP_010929696.1|210338_211025_-	3-oxoacid CoA-transferase subunit A	NA	NA	NA	NA	NA
WP_033446325.1|211223_212006_+	IclR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010929694.1|212056_212782_-	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_010929693.1|212813_214163_-	short-chain fatty acid transporter	NA	NA	NA	NA	NA
WP_010929692.1|214274_215207_-	3-hydroxyacyl-CoA dehydrogenase family protein	NA	NA	NA	NA	NA
WP_033455792.1|215664_218460_-|protease	serine protease autotransporter SphB1	protease	NA	NA	NA	NA
WP_023994893.1|219053_221897_-	phosphoenolpyruvate carboxylase	NA	NA	NA	NA	NA
WP_010929689.1|222067_222787_+	7-cyano-7-deazaguanine synthase QueC	NA	A0A0A0RPC6	Escherichia_phage	43.9	8.0e-50
WP_010929688.1|222825_223374_-	N-acetyltransferase	NA	A0A2H4J136	uncultured_Caudovirales_phage	41.7	1.2e-21
WP_010929687.1|223528_224428_+	virginiamycin B lyase	NA	NA	NA	NA	NA
WP_005012808.1|224452_225403_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 4
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	233335	286923	4108480	tRNA,protease,transposase	Bacillus_phage(25.0%)	47	NA	NA
WP_005012067.1|233335_234286_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010927663.1|234372_235323_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930742.1|235319_236270_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929700.1|236368_237166_-	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_003814363.1|238115_238526_+	4-carboxymuconolactone decarboxylase	NA	NA	NA	NA	NA
WP_003814358.1|239547_240291_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003814356.1|240334_241378_-	TRAP transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_003814355.1|241548_243651_+	TRAP transporter large permease subunit	NA	NA	NA	NA	NA
WP_003814351.1|245061_246018_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010929701.1|246036_246528_-	2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase	NA	NA	NA	NA	NA
WP_010929702.1|246524_247880_-	polynucleotide adenylyltransferase PcnB	NA	A0A1B1IVF3	uncultured_Mediterranean_phage	36.8	3.4e-25
WP_010929703.1|247880_248579_-	HAD-IB family hydrolase	NA	NA	NA	NA	NA
WP_010929704.1|248575_249277_-	DnaA regulatory inactivator Hda	NA	NA	NA	NA	NA
WP_003814339.1|249529_250579_+	phosphoribosylformylglycinamidine cyclo-ligase	NA	Q58MH8	Prochlorococcus_phage	43.6	5.6e-68
WP_003814337.1|250684_251626_-|tRNA	tRNA (adenosine(37)-N6)-dimethylallyltransferase MiaA	tRNA	NA	NA	NA	NA
WP_010929705.1|251622_253512_-	DNA mismatch repair endonuclease MutL	NA	A0A1B2LRQ5	Wolbachia_phage	32.8	3.3e-79
WP_003814332.1|253598_254237_+	membrane protein	NA	NA	NA	NA	NA
WP_019247543.1|254379_255765_-	N-acetylmuramoyl-L-alanine amidase	NA	A0A2H4JCM7	uncultured_Caudovirales_phage	30.3	4.5e-17
WP_010929706.1|255695_256232_-|tRNA	bifunctional alanine racemase/tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE	tRNA	NA	NA	NA	NA
WP_010929707.1|256383_257775_+	class II fumarate hydratase	NA	NA	NA	NA	NA
WP_010929708.1|257791_258772_-	AEC family transporter	NA	NA	NA	NA	NA
WP_003814324.1|258907_259891_+	tripartite tricarboxylate transporter substrate binding protein BugE	NA	NA	NA	NA	NA
WP_010929709.1|259955_260855_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003814321.1|260961_262716_+	gamma-glutamyltransferase	NA	NA	NA	NA	NA
WP_010929710.1|262723_263848_-	CoA transferase	NA	NA	NA	NA	NA
WP_010929711.1|263861_264842_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_005012067.1|265572_266523_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929712.1|267082_267628_+	GbsR/MarR family transcriptional regulator	NA	NA	NA	NA	NA
WP_023852659.1|267753_269331_+	cytochrome d ubiquinol oxidase subunit I	NA	NA	NA	NA	NA
WP_004567834.1|269346_270501_+	cytochrome d ubiquinol oxidase subunit II	NA	NA	NA	NA	NA
WP_003817696.1|270514_270640_+	cytochrome bd-I oxidase subunit CydX	NA	NA	NA	NA	NA
WP_010929714.1|270636_272388_+	thiol reductant ABC exporter subunit CydD	NA	W8CYL7	Bacillus_phage	23.8	3.4e-09
WP_010929715.1|272384_274064_+	thiol reductant ABC exporter subunit CydC	NA	W8CYL7	Bacillus_phage	27.6	3.6e-16
WP_010929716.1|274126_274675_+	adenine phosphoribosyltransferase	NA	A0A1V0SKE5	Klosneuvirus	43.1	1.3e-28
WP_010929717.1|275817_276096_+	DUF4148 domain-containing protein	NA	NA	NA	NA	NA
WP_005012067.1|277139_278090_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_077068974.1|278076_278292_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010929718.1|278367_278529_+	DUF4224 domain-containing protein	NA	NA	NA	NA	NA
WP_003815821.1|279195_279645_-|protease	ClpXP protease specificity-enhancing factor	protease	NA	NA	NA	NA
WP_003815819.1|279654_280266_-	stringent starvation protein A	NA	NA	NA	NA	NA
WP_010929720.1|280424_281273_-	cytochrome c1	NA	NA	NA	NA	NA
WP_003815816.1|281298_282681_-	cytochrome bc complex cytochrome b subunit	NA	NA	NA	NA	NA
WP_003815815.1|282745_283387_-	ubiquinol-cytochrome c reductase iron-sulfur subunit	NA	NA	NA	NA	NA
WP_010929721.1|283526_283985_+	large conductance mechanosensitive channel protein MscL	NA	NA	NA	NA	NA
WP_010927226.1|284009_284786_-	Nif3-like dinuclear metal center hexameric protein	NA	NA	NA	NA	NA
WP_014906092.1|284839_285976_+|protease	trypsin-like serine protease	protease	W5SAB9	Pithovirus	31.2	1.2e-07
WP_005015810.1|285972_286923_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 5
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	390856	448365	4108480	transposase	Orpheovirus(14.29%)	50	NA	NA
WP_005012067.1|390856_391807_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010927231.1|391943_392861_+	reductase	NA	NA	NA	NA	NA
WP_003815842.1|392857_393106_+	glutaredoxin family protein	NA	NA	NA	NA	NA
WP_003815840.1|393102_394308_+	CoA transferase	NA	NA	NA	NA	NA
WP_014486045.1|394380_395376_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_014486046.1|395398_396619_-	CoA transferase	NA	NA	NA	NA	NA
WP_014486047.1|396615_397260_-	hypothetical protein	NA	NA	NA	NA	NA
WP_019248476.1|398990_399800_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
WP_014486048.1|400104_401058_+	thioredoxin-disulfide reductase	NA	A0A2I2L5E1	Orpheovirus	42.5	5.6e-59
WP_014486049.1|401156_402140_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_014486050.1|402066_402768_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_014486051.1|402816_403587_-	enoyl-CoA hydratase/isomerase family protein	NA	NA	NA	NA	NA
WP_019247259.1|403583_404762_-	CoA transferase	NA	NA	NA	NA	NA
WP_014486052.1|404929_406636_-	thiamine pyrophosphate-requiring protein	NA	NA	NA	NA	NA
WP_014486053.1|406632_407529_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_014486054.1|407569_409159_-	sulfurtransferase	NA	NA	NA	NA	NA
WP_003807867.1|409208_410201_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_003807865.1|410269_410869_-	hypothetical protein	NA	NA	NA	NA	NA
WP_014486055.1|411329_412310_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010929577.1|412385_413336_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_047122777.1|413424_414339_+	DMT family transporter	NA	NA	NA	NA	NA
WP_010929782.1|414335_414995_+	LysE family translocator	NA	NA	NA	NA	NA
WP_003814709.1|415084_416008_+	alpha/beta fold hydrolase	NA	A0A1C9C5K3	Heterosigma_akashiwo_virus	27.2	4.8e-07
WP_010929783.1|416013_416469_-	multidrug/biocide efflux PACE transporter	NA	NA	NA	NA	NA
WP_010929784.1|416465_417569_-	ChbG/HpnK family deacetylase	NA	NA	NA	NA	NA
WP_157734656.1|417527_417797_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010927086.1|417756_419376_-	glycosyltransferase family 39 protein	NA	NA	NA	NA	NA
WP_003814720.1|419372_420431_-	glycosyltransferase family 2 protein	NA	I1TED8	Salmonella_phage	40.5	2.8e-59
WP_033446199.1|420560_421055_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
WP_022997984.1|421147_422125_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929785.1|422320_423526_+	sodium/glutamate symporter	NA	NA	NA	NA	NA
WP_010929786.1|423522_425034_+	TAXI family TRAP transporter solute-binding subunit	NA	NA	NA	NA	NA
WP_003814726.1|425049_426363_-	short-chain fatty acid transporter	NA	NA	NA	NA	NA
WP_003814728.1|426553_426733_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003814730.1|427142_427877_-	DNA polymerase III subunit epsilon	NA	A0A1X9SH08	Bradyrhizobium_phage	43.8	1.4e-41
WP_010929577.1|430321_431272_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_019247421.1|431403_431802_-	GTP-binding protein	NA	E4ZFJ7	Streptococcus_phage	44.3	9.0e-19
WP_003814701.1|432212_432683_-	universal stress protein	NA	NA	NA	NA	NA
WP_003820700.1|432771_433116_-	TIGR01244 family phosphatase	NA	NA	NA	NA	NA
WP_010929788.1|433215_434616_-	PLP-dependent aminotransferase family protein	NA	NA	NA	NA	NA
WP_010929789.1|436404_436923_-	MgtC/SapB family protein	NA	G3MA03	Bacillus_virus	38.9	2.1e-12
WP_003814694.1|437033_437789_+	TerC family protein	NA	A0A0R6PEZ3	Moraxella_phage	40.8	2.9e-42
WP_003814691.1|437984_439217_+	CoA transferase	NA	NA	NA	NA	NA
WP_010929791.1|439209_439995_+	crotonase/enoyl-CoA hydratase family protein	NA	NA	NA	NA	NA
WP_003814685.1|440061_441033_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_003814681.1|441043_442021_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_019247419.1|442146_443319_+	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
WP_010929793.1|443345_444374_+	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
WP_003814674.1|444439_445633_+	acetyl-CoA C-acyltransferase	NA	NA	NA	NA	NA
WP_005012067.1|447414_448365_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 6
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	590419	651611	4108480	protease,transposase	uncultured_Mediterranean_phage(40.0%)	56	NA	NA
WP_005013747.1|590419_591370_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_033446133.1|591845_592736_+	phosphonate ABC transporter, permease protein PhnE	NA	NA	NA	NA	NA
WP_010931496.1|592732_593554_+	phosphonate ABC transporter, permease protein PhnE	NA	NA	NA	NA	NA
WP_019247235.1|593754_594246_+	CYTH domain-containing protein	NA	NA	NA	NA	NA
WP_019247236.1|594264_595338_+	CHAD domain-containing protein	NA	NA	NA	NA	NA
WP_023853086.1|595384_596488_-	signal recognition particle-docking protein FtsY	NA	NA	NA	NA	NA
WP_003808577.1|596563_597184_+	16S rRNA (guanine(966)-N(2))-methyltransferase RsmD	NA	NA	NA	NA	NA
WP_003808574.1|597204_597714_+	pantetheine-phosphate adenylyltransferase	NA	A0A1B1IVQ3	uncultured_Mediterranean_phage	42.1	1.2e-28
WP_003808570.1|597768_598020_+	YfhL family 4Fe-4S dicluster ferredoxin	NA	A0A1B1IWY9	uncultured_Mediterranean_phage	53.4	1.6e-18
WP_010931494.1|598083_599217_+	benzoate/H(+) symporter BenE family transporter	NA	NA	NA	NA	NA
WP_003808567.1|599224_599611_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010931493.1|599607_602127_-	AsmA family protein	NA	NA	NA	NA	NA
WP_003808563.1|602555_602894_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_003808562.1|602890_603397_+	SRPBCC family protein	NA	NA	NA	NA	NA
WP_010931492.1|603458_604259_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010931491.1|604369_605311_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010931490.1|605404_606940_-	M81 family metallopeptidase	NA	NA	NA	NA	NA
WP_010931489.1|608619_610470_-	dipeptide ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	29.2	1.6e-17
WP_003808549.1|610473_611307_-	ABC transporter permease	NA	NA	NA	NA	NA
WP_010931488.1|611306_612248_-	ABC transporter permease	NA	NA	NA	NA	NA
WP_010931487.1|612499_613471_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010931486.1|613612_615901_+	NADP-dependent malic enzyme	NA	NA	NA	NA	NA
WP_003808542.1|616207_617116_+	TauD/TfdA family dioxygenase	NA	NA	NA	NA	NA
WP_010931485.1|617170_618136_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_062810229.1|618210_619872_+	thiamine pyrophosphate-binding protein	NA	NA	NA	NA	NA
WP_010931483.1|619943_620654_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
WP_154698388.1|620620_620785_-	hypothetical protein	NA	NA	NA	NA	NA
WP_005012067.1|620802_621753_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003814152.1|622451_622835_+	membrane protein	NA	NA	NA	NA	NA
WP_010927005.1|622892_623495_+	DUF2946 family protein	NA	NA	NA	NA	NA
WP_003820995.1|623512_623914_-	DoxX family protein	NA	NA	NA	NA	NA
WP_010931482.1|624029_624941_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010931481.1|624937_625519_+	NUDIX hydrolase	NA	NA	NA	NA	NA
WP_003814165.1|626313_627048_+	arginyltransferase	NA	NA	NA	NA	NA
WP_010931480.1|627088_628138_+	quinone-dependent dihydroorotate dehydrogenase	NA	NA	NA	NA	NA
WP_003814172.1|628285_628864_-	TIGR01841 family phasin	NA	NA	NA	NA	NA
WP_010931479.1|629250_630228_+	tripartite tricarboxylate transporter substrate binding protein BugD	NA	NA	NA	NA	NA
WP_010931478.1|630321_634716_-	dermonecrotic toxin	NA	NA	NA	NA	NA
WP_003814178.1|634916_635765_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010931477.1|635923_636736_-	competence/damage-inducible protein A	NA	NA	NA	NA	NA
WP_005015810.1|636791_637742_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931453.1|637840_638641_-	EI24 domain-containing protein	NA	NA	NA	NA	NA
WP_003814185.1|638702_639086_+	thioredoxin family protein	NA	NA	NA	NA	NA
WP_033446148.1|639097_640450_-	DEAD/DEAH box helicase	NA	Q5GF26	Diachasmimorpha_longicaudata_entomopoxvirus	34.4	2.1e-51
WP_003814188.1|640737_641067_-	AzlD domain-containing protein	NA	NA	NA	NA	NA
WP_010931455.1|641069_641819_-	AzlC family ABC transporter permease	NA	NA	NA	NA	NA
WP_010931456.1|642001_642922_+	branched-chain amino acid transaminase	NA	NA	NA	NA	NA
WP_003814195.1|642968_643181_+	zinc-finger domain-containing protein	NA	NA	NA	NA	NA
WP_010931457.1|643203_643626_+	SnoaL-like domain-containing protein	NA	NA	NA	NA	NA
WP_010931458.1|643642_644743_+	alpha/beta fold hydrolase	NA	NA	NA	NA	NA
WP_010931459.1|644839_646357_-|protease	M48 family metalloprotease	protease	NA	NA	NA	NA
WP_003814203.1|646432_647272_+	UTP--glucose-1-phosphate uridylyltransferase GalU	NA	A0A127AW70	Bacillus_phage	48.9	1.1e-66
WP_033446149.1|647293_648166_-	cytochrome c oxidase assembly protein	NA	NA	NA	NA	NA
WP_003814206.1|648256_649351_-	porin	NA	NA	NA	NA	NA
WP_076879617.1|649644_650595_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_041166340.1|650669_651611_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 7
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	656935	703126	4108480	tail,tRNA,terminase,transposase	uncultured_Caudovirales_phage(18.18%)	51	NA	NA
WP_023995141.1|656935_657961_+|tRNA	tRNA dihydrouridine synthase DusB	tRNA	NA	NA	NA	NA
WP_003814221.1|658001_658241_+	DNA-binding protein	NA	NA	NA	NA	NA
WP_010931464.1|658310_659900_+	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase	NA	Q58MG4	Prochlorococcus_phage	47.2	8.7e-65
WP_010931465.1|659899_660448_+	crossover junction endodeoxyribonuclease RuvC	NA	NA	NA	NA	NA
WP_003814226.1|660528_661101_+	Holliday junction branch migration protein RuvA	NA	NA	NA	NA	NA
WP_010927008.1|661119_662031_-	complex I NDUFA9 subunit family protein	NA	NA	NA	NA	NA
WP_003814230.1|662104_663073_-	threo-3-hydroxy-L-aspartate ammonia-lyase	NA	NA	NA	NA	NA
WP_010931466.1|663195_664269_+	Holliday junction branch migration DNA helicase RuvB	NA	A0A127AWE7	Bacillus_phage	25.7	2.3e-08
WP_010931467.1|664273_666094_-	DNA helicase RecQ	NA	L7RCS0	Acanthamoeba_polyphaga_moumouvirus	35.3	3.1e-74
WP_010930800.1|666170_667121_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_033446132.1|667209_667545_+	ASCH domain-containing protein	NA	NA	NA	NA	NA
WP_003819076.1|667678_668329_+	carbonic anhydrase	NA	NA	NA	NA	NA
WP_010931468.1|668350_669769_-	amidase	NA	NA	NA	NA	NA
WP_019248554.1|669838_670594_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_019247734.1|670562_671321_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_010931471.1|671331_672213_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_010931472.1|672229_672937_+	ABC transporter ATP-binding protein	NA	W8CYL7	Bacillus_phage	25.4	8.2e-07
WP_010931473.1|672939_673698_+	ABC transporter ATP-binding protein	NA	W6JKT0	Anomala_cuprea_entomopoxvirus	24.4	4.4e-14
WP_010931474.1|673907_675650_+	nitrite/sulfite reductase	NA	NA	NA	NA	NA
WP_010925795.1|675642_676167_+	DUF934 domain-containing protein	NA	NA	NA	NA	NA
WP_010931475.1|676206_677001_-	MetQ/NlpA family ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_019248926.1|677168_678242_+	hypothetical protein	NA	NA	NA	NA	NA
WP_005012067.1|678340_679291_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_019247378.1|679542_679749_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010931451.1|679820_680432_-	S24 family peptidase	NA	NA	NA	NA	NA
WP_023853179.1|680986_681238_+	transcriptional regulator	NA	NA	NA	NA	NA
WP_161633094.1|681230_681920_+	hypothetical protein	NA	NA	NA	NA	NA
WP_023853183.1|681937_682159_-	hypothetical protein	NA	NA	NA	NA	NA
WP_005012067.1|682176_683127_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_019247942.1|683766_684252_+|transposase	transposase	transposase	C7U0W1	Enterobacteria_phage	61.5	7.3e-39
WP_010931447.1|684238_685516_+|terminase	terminase	terminase	A0A1B1P9C9	Acinetobacter_phage	64.7	2.4e-150
WP_010931446.1|685518_686937_+	DUF4055 domain-containing protein	NA	R9TF43	Synechococcus_phage	42.1	2.2e-99
WP_010931445.1|686965_688021_+	hypothetical protein	NA	A0A0H5BBX3	Pseudomonas_phage	50.6	2.6e-97
WP_010931444.1|688026_688269_+	hypothetical protein	NA	A0A0H5AUE5	Pseudomonas_phage	53.2	5.6e-16
WP_010931443.1|688391_688994_+	hypothetical protein	NA	R9TF81	Synechococcus_phage	43.6	7.9e-27
WP_005012808.1|689422_690373_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931442.1|691047_691299_+	hypothetical protein	NA	NA	NA	NA	NA
WP_019247789.1|691361_691844_+	hypothetical protein	NA	A0A2H4JE38	uncultured_Caudovirales_phage	37.1	1.8e-13
WP_162096760.1|691857_692046_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010931439.1|692045_692441_+	hypothetical protein	NA	A0A2D2W284	Stenotrophomonas_phage	35.0	7.8e-07
WP_010931438.1|692437_692836_+	hypothetical protein	NA	I6PCW1	Cronobacter_phage	38.0	4.2e-16
WP_010931437.1|692832_693255_+	DUF4128 domain-containing protein	NA	NA	NA	NA	NA
WP_010931436.1|693262_693763_+	HNH endonuclease	NA	A0A1I9SEX5	Klebsiella_phage	45.1	4.4e-31
WP_010931435.1|694017_694536_+	hypothetical protein	NA	A0A1S5R1H0	Pseudomonas_phage	38.3	5.4e-24
WP_003813412.1|694545_694875_+	hypothetical protein	NA	A0A2H4J121	uncultured_Caudovirales_phage	44.0	2.9e-15
WP_010931434.1|694892_695183_+	DUF1799 domain-containing protein	NA	A0A2H4JBP7	uncultured_Caudovirales_phage	45.2	3.7e-14
WP_010931433.1|695208_697821_+|tail	phage tail tape measure protein	tail	A0A2H4J107	uncultured_Caudovirales_phage	38.6	4.9e-105
WP_010931432.1|697830_698190_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010931431.1|698257_698791_+	DUF1833 family protein	NA	A5A3Q9	Burkholderia_phage	46.9	1.1e-40
WP_010931430.1|698787_699177_+	C40 family peptidase	NA	A0A0G3EYJ9	Achromobacter_phage	50.0	3.0e-35
WP_010931429.1|699169_703126_+	DUF1983 domain-containing protein	NA	A0A0B5A1N2	Achromobacter_phage	40.8	3.9e-215
>prophage 8
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	709292	763222	4108480	tRNA,transposase	Planktothrix_phage(50.0%)	46	NA	NA
WP_003814636.1|709292_711023_+|tRNA	proline--tRNA ligase	tRNA	A0A2K9L3R9	Tupanvirus	29.4	4.6e-11
WP_010931419.1|711075_711504_+	tol-pal system-associated acyl-CoA thioesterase	NA	NA	NA	NA	NA
WP_003814641.1|711506_712187_+	protein TolQ	NA	NA	NA	NA	NA
WP_003814643.1|712186_712645_+	protein TolR	NA	NA	NA	NA	NA
WP_010931418.1|712681_713656_+	cell envelope integrity protein TolA	NA	NA	NA	NA	NA
WP_010931417.1|713672_714989_+	Tol-Pal system protein TolB	NA	NA	NA	NA	NA
WP_003814650.1|715020_715518_+	peptidoglycan-associated lipoprotein Pal	NA	NA	NA	NA	NA
WP_003814652.1|715604_716294_+	tol-pal system protein YbgF	NA	NA	NA	NA	NA
WP_010931416.1|716293_717343_+	iron ABC transporter permease	NA	NA	NA	NA	NA
WP_003814657.1|717339_718134_+	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	30.6	2.4e-15
WP_019247923.1|718302_718653_+	hypothetical protein	NA	NA	NA	NA	NA
WP_019247922.1|718628_719186_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_005012808.1|720315_721266_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929184.1|723403_724633_+	spore maturation protein	NA	NA	NA	NA	NA
WP_003814419.1|724635_726078_-	pyruvate kinase	NA	NA	NA	NA	NA
WP_010931414.1|726182_727328_+	glycerate kinase	NA	W6LM47	Streptococcus_phage	42.2	1.7e-41
WP_010931413.1|727359_728157_-	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))- dimethyltransferase RsmA	NA	NA	NA	NA	NA
WP_010931412.1|728181_729741_-	chaperone SurA	NA	NA	NA	NA	NA
WP_010931411.1|729737_732110_-	LPS-assembly protein LptD	NA	NA	NA	NA	NA
WP_010931410.1|732219_733323_+	phosphotransferase	NA	NA	NA	NA	NA
WP_010931409.1|733322_734015_+	nucleotidyltransferase family protein	NA	NA	NA	NA	NA
WP_003814436.1|734158_734860_+	membrane protein	NA	NA	NA	NA	NA
WP_003814437.1|734844_735222_-	4a-hydroxytetrahydrobiopterin dehydratase	NA	NA	NA	NA	NA
WP_005012067.1|735953_736904_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003814441.1|737063_737936_-	oxaloacetate decarboxylase	NA	NA	NA	NA	NA
WP_003814443.1|738276_738495_+	DUF1059 domain-containing protein	NA	NA	NA	NA	NA
WP_019247242.1|738534_739914_-	aminotransferase class III-fold pyridoxal phosphate-dependent enzyme	NA	NA	NA	NA	NA
WP_010929976.1|739955_741353_-	amidase family protein	NA	NA	NA	NA	NA
WP_010927038.1|741392_743045_-	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	30.8	6.0e-16
WP_010929977.1|743048_743933_-	ABC transporter permease	NA	NA	NA	NA	NA
WP_010929978.1|743932_744874_-	ABC transporter permease	NA	NA	NA	NA	NA
WP_010929979.1|744952_746572_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010929980.1|746738_747554_+	IclR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003814459.1|747621_748191_-	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA	NA
WP_005013747.1|748191_749142_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003814461.1|749796_750894_+	carboxynorspermidine decarboxylase	NA	NA	NA	NA	NA
WP_003814462.1|750927_752193_+	saccharopine dehydrogenase family protein	NA	NA	NA	NA	NA
WP_010929591.1|752350_753301_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929982.1|753544_754135_+	polyisoprenoid-binding protein	NA	NA	NA	NA	NA
WP_010929983.1|754150_756595_-	TonB-dependent siderophore receptor	NA	NA	NA	NA	NA
WP_003814467.1|756714_757686_-	FecR family protein	NA	NA	NA	NA	NA
WP_023852739.1|757817_758342_+	sigma-70 family RNA polymerase sigma factor	NA	NA	NA	NA	NA
WP_005012067.1|758301_759252_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929984.1|759473_761669_-	DUF1156 domain-containing protein	NA	NA	NA	NA	NA
WP_020699729.1|761741_762149_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_005012808.1|762271_763222_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 9
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	885811	953787	4108480	transposase	Bacillus_phage(33.33%)	56	NA	NA
WP_023994644.1|885811_886828_-|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_003813988.1|887024_888008_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010930019.1|889606_890995_-	MmgE/PrpD family protein	NA	NA	NA	NA	NA
WP_003813991.1|891025_892015_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_003813992.1|892125_893358_-	methylaspartate ammonia-lyase	NA	NA	NA	NA	NA
WP_003813993.1|893639_894440_+	IclR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930018.1|894462_896694_-	BCCT family transporter	NA	NA	NA	NA	NA
WP_010930017.1|897481_897928_-	preprotein translocase subunit SecG	NA	NA	NA	NA	NA
WP_003813996.1|897949_898696_-	triose-phosphate isomerase	NA	NA	NA	NA	NA
WP_003813997.1|898839_899817_-	NAD(P)H-quinone oxidoreductase	NA	NA	NA	NA	NA
WP_010930016.1|900450_901062_+	PIN domain-containing protein	NA	K4HZX4	Acidithiobacillus_phage	32.5	3.3e-12
WP_003813999.1|901055_902273_-	threonine ammonia-lyase	NA	NA	NA	NA	NA
WP_005013747.1|902413_903364_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003814000.1|903360_904080_-	lipoprotein	NA	NA	NA	NA	NA
WP_003821234.1|904200_906360_-	polyribonucleotide nucleotidyltransferase	NA	NA	NA	NA	NA
WP_003814002.1|906450_906720_-	30S ribosomal protein S15	NA	NA	NA	NA	NA
WP_005019401.1|906808_907015_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003814003.1|907013_907541_+	lipoprotein	NA	NA	NA	NA	NA
WP_003814004.1|907559_908339_-	CDP-diacylglycerol--serine O-phosphatidyltransferase	NA	NA	NA	NA	NA
WP_010930015.1|908506_909523_-	ketol-acid reductoisomerase	NA	NA	NA	NA	NA
WP_003814006.1|909595_910087_-	acetolactate synthase small subunit	NA	NA	NA	NA	NA
WP_003814007.1|910097_911813_-	acetolactate synthase 3 catalytic subunit	NA	A0A0P0CDR3	Ostreococcus_lucimarinus_virus	30.3	3.1e-60
WP_005012067.1|912976_913927_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930051.1|913923_915756_-	ABC transporter ATP-binding protein	NA	W8CYL7	Bacillus_phage	26.4	1.3e-27
WP_010930052.1|916154_916814_+	thiopurine S-methyltransferase	NA	NA	NA	NA	NA
WP_010930054.1|917341_918022_-	DUF3313 domain-containing protein	NA	NA	NA	NA	NA
WP_010930055.1|918303_919020_+	flagellar brake protein	NA	NA	NA	NA	NA
WP_010930056.1|919034_920336_-	phospholipase	NA	NA	NA	NA	NA
WP_029444137.1|922480_925369_+	HD domain-containing protein	NA	NA	NA	NA	NA
WP_010930057.1|925592_926945_+	MmgE/PrpD family protein	NA	NA	NA	NA	NA
WP_004568140.1|926973_927495_+	acetyl-CoA carboxylase biotin carboxyl carrier protein	NA	NA	NA	NA	NA
WP_003819989.1|927491_928946_+	carboxylase	NA	NA	NA	NA	NA
WP_023852826.1|928980_929229_+	hypothetical protein	NA	NA	NA	NA	NA
WP_019247557.1|929334_930210_+	amidohydrolase	NA	NA	NA	NA	NA
WP_010930060.1|930235_931291_+	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_010930061.1|931303_932095_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930062.1|932127_933498_+	acetyl-CoA carboxylase biotin carboxylase subunit	NA	NA	NA	NA	NA
WP_005012067.1|934674_935625_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930064.1|935677_935899_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003810832.1|936058_936271_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003810835.1|936390_937509_+	mannose-6-phosphate isomerase	NA	NA	NA	NA	NA
WP_003810837.1|937605_937821_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003810839.1|938014_938266_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930066.1|938378_939329_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003810840.1|939325_939709_-	Rieske 2Fe-2S domain-containing protein	NA	NA	NA	NA	NA
WP_023852913.1|939763_941578_-	ABC transporter ATP-binding protein/permease	NA	W8CYL7	Bacillus_phage	27.9	5.7e-44
WP_010930068.1|941727_942555_+	oxidoreductase	NA	A0A2H4PQR8	Staphylococcus_phage	47.4	1.7e-67
WP_010930069.1|942600_943581_+	aldo/keto reductase	NA	NA	NA	NA	NA
WP_003810850.1|943577_943790_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003810851.1|943786_944968_-	PepSY domain-containing protein	NA	NA	NA	NA	NA
WP_019248496.1|945131_945866_+	serine/threonine protein phosphatase	NA	A0A2H4J0P0	uncultured_Caudovirales_phage	49.2	1.9e-62
WP_010930071.1|945867_948480_-	PBP1A family penicillin-binding protein	NA	NA	NA	NA	NA
WP_003810859.1|948615_950529_-	S9 family peptidase	NA	NA	NA	NA	NA
WP_010930072.1|951144_951555_-	PaaI family thioesterase	NA	NA	NA	NA	NA
WP_003810865.1|951652_952738_+	DNA polymerase IV	NA	NA	NA	NA	NA
WP_005012067.1|952836_953787_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 10
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	997316	1069833	4108480	tRNA,transposase	Enterococcus_phage(14.29%)	60	NA	NA
WP_005012067.1|997316_998267_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930118.1|998371_999421_+	NADP(H)-dependent aldo-keto reductase	NA	NA	NA	NA	NA
WP_010929632.1|999558_1000575_-|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_010926548.1|1002083_1002656_-	chorismate lyase	NA	NA	NA	NA	NA
WP_010930119.1|1002715_1003447_+	rRNA pseudouridine synthase	NA	NA	NA	NA	NA
WP_029443805.1|1003498_1004416_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930121.1|1005223_1008403_+	efflux RND transporter permease subunit	NA	NA	NA	NA	NA
WP_014486063.1|1008399_1009782_+	efflux transporter outer membrane subunit	NA	NA	NA	NA	NA
WP_010930123.1|1009851_1010103_-	GlsB/YeaQ/YmgE family stress response membrane protein	NA	NA	NA	NA	NA
WP_010930124.1|1010248_1010863_-	SCO family protein	NA	NA	NA	NA	NA
WP_010930125.1|1011049_1013110_-	M3 family metallopeptidase	NA	NA	NA	NA	NA
WP_003811948.1|1013239_1014091_-	bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD	NA	A0A249XZQ2	Enterococcus_phage	39.8	2.1e-33
WP_010930126.1|1014087_1014714_-	response regulator transcription factor	NA	NA	NA	NA	NA
WP_003817147.1|1014710_1016465_-	PAS domain S-box protein	NA	NA	NA	NA	NA
WP_010930127.1|1016757_1019463_+	pyruvate dehydrogenase (acetyl-transferring), homodimeric type	NA	NA	NA	NA	NA
WP_010930128.1|1019475_1021137_+	dihydrolipoyllysine-residue acetyltransferase	NA	NA	NA	NA	NA
WP_010930129.1|1021149_1022940_+	dihydrolipoyl dehydrogenase	NA	A0A2K5B2C5	Erysipelothrix_phage	25.2	2.4e-39
WP_003817151.1|1023161_1024337_-	FliC/FljB family flagellin	NA	NA	NA	NA	NA
WP_010929584.1|1024379_1025330_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930130.1|1025428_1026169_-	16S rRNA (uracil(1498)-N(3))-methyltransferase	NA	NA	NA	NA	NA
WP_010930131.1|1026363_1028400_+	transketolase	NA	NA	NA	NA	NA
WP_010930132.1|1028417_1029428_+	type I glyceraldehyde-3-phosphate dehydrogenase	NA	NA	NA	NA	NA
WP_010930133.1|1029545_1030739_+	phosphoglycerate kinase	NA	NA	NA	NA	NA
WP_010930134.1|1030768_1031542_-	enoyl-ACP reductase FabI	NA	NA	NA	NA	NA
WP_010930135.1|1031538_1032729_-	acetate kinase	NA	NA	NA	NA	NA
WP_003809454.1|1032754_1033693_-	phosphate acetyltransferase	NA	NA	NA	NA	NA
WP_010930136.1|1033689_1036038_-	DUF3141 domain-containing protein	NA	NA	NA	NA	NA
WP_010930137.1|1036192_1036834_-	glutathione transferase	NA	NA	NA	NA	NA
WP_023994624.1|1038163_1038316_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010930138.1|1038347_1038896_-	diguanylate cyclase	NA	NA	NA	NA	NA
WP_003819814.1|1038914_1039400_-	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
WP_010930139.1|1039577_1040516_+	DnaJ domain-containing protein	NA	A0A0P0YMJ9	Yellowstone_lake_phycodnavirus	24.1	5.6e-11
WP_003809467.1|1040518_1040836_+	MerR family transcriptional regulator	NA	NA	NA	NA	NA
WP_019247197.1|1040881_1041826_+	AzlC family ABC transporter permease	NA	NA	NA	NA	NA
WP_010930141.1|1043506_1044157_+	molybdopterin adenylyltransferase	NA	NA	NA	NA	NA
WP_003809479.1|1044210_1044546_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930142.1|1044542_1045403_+	M23 family metallopeptidase	NA	A0A292GJG6	Xanthomonas_phage	36.1	2.6e-15
WP_003819817.1|1045419_1045701_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003809486.1|1045774_1046038_-	translation initiation factor IF-1	NA	NA	NA	NA	NA
WP_005012067.1|1046281_1047232_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003811933.1|1047530_1048268_-	RNA polymerase sigma factor FliA	NA	NA	NA	NA	NA
WP_010930143.1|1048703_1049027_+	flagellar transcriptional regulator FlhD	NA	NA	NA	NA	NA
WP_003811929.1|1049061_1049622_+	flagellar transcriptional regulator FlhC	NA	NA	NA	NA	NA
WP_003811927.1|1049742_1050618_+	flagellar motor stator protein MotA	NA	NA	NA	NA	NA
WP_003817154.1|1050630_1051578_+	flagellar motor protein MotB	NA	NA	NA	NA	NA
WP_019247393.1|1051679_1051973_+	response regulator	NA	NA	NA	NA	NA
WP_010930144.1|1051999_1054057_+	chemotaxis protein CheA	NA	NA	NA	NA	NA
WP_003811919.1|1054071_1054572_+	chemotaxis protein CheW	NA	NA	NA	NA	NA
WP_010930145.1|1054645_1056352_+	HAMP domain-containing protein	NA	A0A2H4J162	uncultured_Caudovirales_phage	41.7	1.4e-12
WP_010930146.1|1057215_1058268_+	chemotaxis response regulator protein-glutamate methylesterase	NA	NA	NA	NA	NA
WP_003811911.1|1058320_1058710_+	chemotaxis protein CheY	NA	Q56AR1	Bacillus_thuringiensis_phage	33.3	5.7e-10
WP_003817162.1|1058718_1059351_+	protein phosphatase CheZ	NA	NA	NA	NA	NA
WP_010931363.1|1059450_1060467_-|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_003819773.1|1061297_1062305_+	aldo/keto reductase	NA	NA	NA	NA	NA
WP_014486064.1|1062301_1063945_-	apolipoprotein N-acyltransferase	NA	NA	NA	NA	NA
WP_010930149.1|1063941_1064829_-	CBS domain-containing protein	NA	NA	NA	NA	NA
WP_003809396.1|1064969_1065443_-	rRNA maturation RNase YbeY	NA	NA	NA	NA	NA
WP_010930151.1|1065432_1066455_-	PhoH family protein	NA	A0A0S0MVD6	Pseudomonas_phage	45.4	8.7e-50
WP_015041211.1|1066451_1067879_-|tRNA	tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB	tRNA	NA	NA	NA	NA
WP_010931363.1|1068816_1069833_-|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
>prophage 11
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	1073586	1135662	4108480	tRNA,holin,transposase	Catovirus(20.0%)	53	NA	NA
WP_010930155.1|1073586_1074723_-|tRNA	tRNA guanosine(34) transglycosylase Tgt	tRNA	A0A1B1IVQ4	uncultured_Mediterranean_phage	44.4	1.9e-85
WP_023853534.1|1074719_1075793_-|tRNA	tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA	tRNA	NA	NA	NA	NA
WP_003809423.1|1075950_1077387_+	D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase	NA	NA	NA	NA	NA
WP_010930157.1|1077477_1078119_+	uracil phosphoribosyltransferase	NA	NA	NA	NA	NA
WP_023853536.1|1078454_1079471_+|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_005012808.1|1081513_1082464_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930160.1|1083666_1085088_-	uroporphyrinogen-III C-methyltransferase	NA	NA	NA	NA	NA
WP_003809431.1|1085351_1086068_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003809432.1|1086152_1086470_+	DUF883 domain-containing protein	NA	NA	NA	NA	NA
WP_003819794.1|1086510_1086924_+|holin	phage holin family protein	holin	NA	NA	NA	NA
WP_010930161.1|1086925_1087285_+	hypothetical protein	NA	NA	NA	NA	NA
WP_023853525.1|1087327_1088872_-	4-hydroxy-3-polyprenylbenzoate decarboxylase	NA	NA	NA	NA	NA
WP_010930163.1|1088955_1089786_+	lytic transglycosylase domain-containing protein	NA	NA	NA	NA	NA
WP_010930164.1|1089820_1090975_-	pyridoxal phosphate-dependent aminotransferase	NA	NA	NA	NA	NA
WP_010930165.1|1091017_1091890_+	hypothetical protein	NA	NA	NA	NA	NA
WP_014486065.1|1092006_1094295_+	NADP-dependent malic enzyme	NA	NA	NA	NA	NA
WP_003809441.1|1095501_1095966_+	barstar family protein	NA	NA	NA	NA	NA
WP_005013747.1|1095992_1096943_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_154698393.1|1096960_1097098_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930167.1|1097310_1098087_-	phosphate ABC transporter ATP-binding protein PstB	NA	G9BWD6	Planktothrix_phage	28.7	4.3e-17
WP_003809638.1|1098131_1098989_-	phosphate ABC transporter permease PstA	NA	NA	NA	NA	NA
WP_010930169.1|1099010_1100027_-	phosphate ABC transporter permease subunit PstC	NA	NA	NA	NA	NA
WP_014486066.1|1100161_1101202_-	phosphate ABC transporter substrate-binding protein PstS	NA	M4QHS4	Cyanophage	40.2	2.1e-51
WP_010930171.1|1101396_1103478_-	polyphosphate kinase 1	NA	NA	NA	NA	NA
WP_010930172.1|1103713_1105207_+	exopolyphosphatase	NA	NA	NA	NA	NA
WP_003809629.1|1105437_1106232_-	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
WP_003819875.1|1106452_1107811_-	phosphoglucosamine mutase	NA	NA	NA	NA	NA
WP_010930173.1|1107807_1108650_-	dihydropteroate synthase	NA	A0A0B5J4J5	Pandoravirus	32.5	3.2e-26
WP_010930174.1|1108668_1110555_-	ATP-dependent metallopeptidase FtsH/Yme1/Tma family protein	NA	M4QMW8	Micromonas_pusilla_virus	41.5	1.4e-109
WP_162096758.1|1110496_1110748_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930175.1|1110792_1111425_-	RlmE family RNA methyltransferase	NA	NA	NA	NA	NA
WP_003809618.1|1111443_1112046_+	YhbY family RNA-binding protein	NA	NA	NA	NA	NA
WP_010929591.1|1112197_1113148_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_161633091.1|1113728_1114436_+	DUF192 domain-containing protein	NA	NA	NA	NA	NA
WP_003812707.1|1114794_1115781_-	homoserine kinase	NA	NA	NA	NA	NA
WP_010930178.1|1115920_1116934_+|tRNA	tRNA dihydrouridine(20/20a) synthase DusA	tRNA	NA	NA	NA	NA
WP_005012067.1|1116930_1117881_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_155120815.1|1117898_1118039_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003812703.1|1117993_1118452_-	CBS domain-containing protein	NA	NA	NA	NA	NA
WP_003812701.1|1118488_1119802_-	YihY family inner membrane protein	NA	NA	NA	NA	NA
WP_010930180.1|1119819_1120191_+	DUF2069 domain-containing protein	NA	NA	NA	NA	NA
WP_019248549.1|1120187_1121651_+	YdiU family protein	NA	A0A075BSJ0	Microcystis_phage	32.5	1.7e-43
WP_010930182.1|1121791_1122520_+	response regulator transcription factor	NA	NA	NA	NA	NA
WP_010930183.1|1122501_1125351_-	EAL domain-containing protein	NA	NA	NA	NA	NA
WP_010929591.1|1125563_1126514_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930184.1|1126681_1127506_+	ABC transporter ATP-binding protein	NA	A0A2R8FG22	Brazilian_cedratvirus	22.7	1.0e-08
WP_010930185.1|1127505_1128384_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_010930186.1|1129288_1130404_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_020699602.1|1130432_1131227_+	ABC transporter ATP-binding protein	NA	W6JKT0	Anomala_cuprea_entomopoxvirus	23.3	1.2e-11
WP_010930188.1|1131223_1133089_+	long-chain fatty acid--CoA ligase	NA	A0A1V0SBX8	Catovirus	23.3	9.3e-50
WP_003812436.1|1133167_1133800_+	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930189.1|1133796_1134099_-	membrane protein	NA	NA	NA	NA	NA
WP_010930190.1|1134141_1135662_-|tRNA	lysine--tRNA ligase	tRNA	A0A1V0SAC0	Catovirus	36.0	1.2e-82
>prophage 12
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	1153232	1219751	4108480	tRNA,transposase	Erysipelothrix_phage(33.33%)	54	NA	NA
WP_023853221.1|1153232_1155029_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_019248398.1|1155028_1155997_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
WP_003816844.1|1156066_1156912_+	PHP domain-containing protein	NA	NA	NA	NA	NA
WP_003812405.1|1156979_1157534_+	transcription elongation factor GreB	NA	NA	NA	NA	NA
WP_010930198.1|1157580_1158531_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930199.1|1158629_1159262_-	fimbrial protein	NA	NA	NA	NA	NA
WP_010930200.1|1159426_1161709_-	NADP-dependent malic enzyme	NA	NA	NA	NA	NA
WP_010930201.1|1161863_1164560_-	alpha-ketoglutarate dehydrogenase	NA	NA	NA	NA	NA
WP_010930202.1|1164685_1165174_+	Lrp/AsnC family transcriptional regulator	NA	NA	NA	NA	NA
WP_003813631.1|1167584_1170455_+	2-oxoglutarate dehydrogenase E1 component	NA	NA	NA	NA	NA
WP_010930204.1|1170500_1171715_+	2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase	NA	NA	NA	NA	NA
WP_003813626.1|1171944_1173372_+	dihydrolipoyl dehydrogenase	NA	A0A2K5B2C5	Erysipelothrix_phage	28.1	2.1e-41
WP_023853245.1|1173469_1174561_+	cell division protein ZapE	NA	NA	NA	NA	NA
WP_010930206.1|1174573_1175332_-	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_003813621.1|1175419_1176322_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_005012067.1|1176318_1177269_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930207.1|1177398_1178382_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_003813618.1|1178436_1179159_-	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_010930211.1|1180637_1181993_+|tRNA	tryptophan--tRNA ligase	tRNA	NA	NA	NA	NA
WP_010930212.1|1182073_1184449_-	RNA-binding transcriptional accessory protein	NA	NA	NA	NA	NA
WP_010930213.1|1184613_1186689_+	ATP-dependent DNA helicase	NA	A0A127AW80	Bacillus_phage	30.0	2.4e-75
WP_033446255.1|1186750_1187545_-	outer membrane protein assembly factor BamD	NA	NA	NA	NA	NA
WP_010930214.1|1187652_1188615_+	RluA family pseudouridine synthase	NA	NA	NA	NA	NA
WP_019247742.1|1188602_1189358_+	peptidoglycan editing factor PgeF	NA	NA	NA	NA	NA
WP_010930216.1|1189465_1191103_+	class I poly(R)-hydroxyalkanoic acid synthase	NA	NA	NA	NA	NA
WP_003813586.1|1191170_1191908_+	acetoacetyl-CoA reductase	NA	NA	NA	NA	NA
WP_003813585.1|1192010_1192586_+	polyhydroxyalkanoate synthesis repressor PhaR	NA	NA	NA	NA	NA
WP_010930217.1|1192758_1193295_+	membrane protein	NA	NA	NA	NA	NA
WP_033451623.1|1193327_1193642_+	cupredoxin domain-containing protein	NA	NA	NA	NA	NA
WP_010930218.1|1193657_1194503_+	membrane protein	NA	NA	NA	NA	NA
WP_003821443.1|1194541_1195921_+	4Fe-4S binding protein	NA	NA	NA	NA	NA
WP_003813574.1|1195998_1196880_+	PhzF family phenazine biosynthesis protein	NA	NA	NA	NA	NA
WP_010929956.1|1196978_1197929_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_003811632.1|1197925_1198336_-	VOC family protein	NA	NA	NA	NA	NA
WP_010930219.1|1198443_1199298_-	amidohydrolase family protein	NA	NA	NA	NA	NA
WP_003811636.1|1199290_1200253_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010930220.1|1200298_1201423_-	mandelate racemase/muconate lactonizing enzyme family protein	NA	Q6A202	Oenococcus_phage	28.3	1.5e-31
WP_019247966.1|1201528_1202407_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930222.1|1202531_1203311_+	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_010930223.1|1203464_1204886_+	MFS transporter	NA	NA	NA	NA	NA
WP_010930224.1|1205320_1207018_+	sodium:solute symporter family protein	NA	NA	NA	NA	NA
WP_010930225.1|1207244_1208186_-	LD-carboxypeptidase	NA	NA	NA	NA	NA
WP_010930226.1|1208512_1209259_+	aldolase	NA	NA	NA	NA	NA
WP_033446252.1|1209266_1210193_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930228.1|1210314_1211232_+	NAD(P)-dependent oxidoreductase	NA	NA	NA	NA	NA
WP_003811660.1|1211271_1212225_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_003811662.1|1212249_1212828_+	amino acid synthesis family protein	NA	NA	NA	NA	NA
WP_010930229.1|1214501_1215110_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930230.1|1215187_1215541_-	NirD/YgiW/YdeI family stress tolerance protein	NA	NA	NA	NA	NA
WP_010930231.1|1215624_1216614_-	succinylglutamate desuccinylase	NA	NA	NA	NA	NA
WP_023852977.1|1216610_1216799_-	hypothetical protein	NA	NA	NA	NA	NA
WP_076879566.1|1216816_1217767_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010927663.1|1217853_1218804_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931070.1|1218800_1219751_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 13
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	1270679	1327890	4108480	transposase	Klosneuvirus(16.67%)	49	NA	NA
WP_010931070.1|1270679_1271630_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931041.1|1275376_1275988_-	DUF2239 family protein	NA	NA	NA	NA	NA
WP_003812368.1|1276210_1277671_+	IMP dehydrogenase	NA	A0A1V0SHK8	Klosneuvirus	41.3	1.6e-97
WP_010931040.1|1277767_1279360_+	glutamine-hydrolyzing GMP synthase	NA	A0A1V0SH76	Hokovirus	33.3	1.0e-17
WP_019247974.1|1279713_1279971_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_003816876.1|1279972_1281313_+	type II toxin-antitoxin system HipA family toxin	NA	NA	NA	NA	NA
WP_010931038.1|1281408_1282098_-	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA	NA
WP_019247976.1|1282110_1283541_+	MFS transporter	NA	NA	NA	NA	NA
WP_014905903.1|1285265_1286087_+	IclR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010931036.1|1286097_1287669_+	amidohydrolase	NA	NA	NA	NA	NA
WP_010931035.1|1287697_1288675_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010931034.1|1288701_1289505_+	ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	38.2	2.7e-30
WP_010931033.1|1289501_1290296_+	ABC transporter permease	NA	NA	NA	NA	NA
WP_003816890.1|1290303_1291539_+	DUF521 domain-containing protein	NA	NA	NA	NA	NA
WP_019247978.1|1291552_1291966_+	DUF126 domain-containing protein	NA	NA	NA	NA	NA
WP_005013747.1|1292715_1293666_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931031.1|1294287_1296015_-	sulfate permease	NA	NA	NA	NA	NA
WP_010931030.1|1296126_1297485_+	MBL fold metallo-hydrolase	NA	NA	NA	NA	NA
WP_023853289.1|1297541_1297760_-	hypothetical protein	NA	NA	NA	NA	NA
WP_005013747.1|1297777_1298728_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931029.1|1298768_1299839_+	FUSC family protein	NA	NA	NA	NA	NA
WP_010931028.1|1299861_1300740_-	MBL fold metallo-hydrolase	NA	NA	NA	NA	NA
WP_010931027.1|1300911_1301883_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_010931026.1|1302045_1302888_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010931025.1|1303049_1303730_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010931024.1|1303723_1304893_+	NAD(P)-binding protein	NA	NA	NA	NA	NA
WP_010931023.1|1304889_1305921_+	alcohol dehydrogenase catalytic domain-containing protein	NA	A0A2K9L339	Tupanvirus	27.8	1.8e-26
WP_023853282.1|1305988_1307206_+	MFS transporter	NA	NA	NA	NA	NA
WP_010931021.1|1307240_1308773_-	PLP-dependent aminotransferase family protein	NA	NA	NA	NA	NA
WP_010931020.1|1308853_1309477_+	FMN-binding negative transcriptional regulator	NA	NA	NA	NA	NA
WP_010931019.1|1309507_1310119_+	LysE family translocator	NA	NA	NA	NA	NA
WP_010931018.1|1310154_1310625_+	DUF1801 domain-containing protein	NA	NA	NA	NA	NA
WP_019248147.1|1311056_1312061_+	M20/M25/M40 family metallo-hydrolase	NA	NA	NA	NA	NA
WP_010931017.1|1312097_1313612_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010931016.1|1313615_1314575_+	ABC transporter permease	NA	NA	NA	NA	NA
WP_010931015.1|1314603_1315407_+	ABC transporter permease	NA	NA	NA	NA	NA
WP_010931014.1|1315408_1317043_+	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	31.1	2.9e-15
WP_010931013.1|1317126_1318188_+	LacI family transcriptional regulator	NA	NA	NA	NA	NA
WP_004567322.1|1318386_1318656_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010931012.1|1318659_1319184_+	DNA-binding protein	NA	J9Q7G7	Salmonella_phage	32.9	6.5e-09
WP_010929591.1|1319599_1320550_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931011.1|1320546_1321581_-	metal-dependent hydrolase	NA	NA	NA	NA	NA
WP_003816758.1|1321689_1322328_+	DedA family protein	NA	NA	NA	NA	NA
WP_019247724.1|1322622_1322850_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
WP_003820420.1|1322972_1323686_+	class I SAM-dependent methyltransferase	NA	NA	NA	NA	NA
WP_005013747.1|1323930_1324881_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_023853496.1|1325020_1325266_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010931008.1|1325380_1326829_-	PLP-dependent aminotransferase family protein	NA	NA	NA	NA	NA
WP_005012808.1|1326939_1327890_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 14
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	1418121	1470273	4108480	tRNA,transposase	Salmonella_phage(25.0%)	45	NA	NA
WP_005013747.1|1418121_1419072_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_023999730.1|1419089_1419242_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003814065.1|1419238_1419592_+	cytochrome c	NA	NA	NA	NA	NA
WP_003814063.1|1419604_1419967_+	cytochrome c	NA	NA	NA	NA	NA
WP_003814061.1|1420008_1420434_-	DUF1841 family protein	NA	NA	NA	NA	NA
WP_003814059.1|1420636_1421893_+	NADP-dependent isocitrate dehydrogenase	NA	Q77Z09	Phage_21	64.8	1.2e-11
WP_003814057.1|1422091_1423072_+	hypothetical protein	NA	NA	NA	NA	NA
WP_005015028.1|1423221_1424463_+	O-antigen ligase family protein	NA	NA	NA	NA	NA
WP_005013747.1|1424561_1425512_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003814052.1|1425520_1426216_-	two-component system response regulator KdpE	NA	NA	NA	NA	NA
WP_003814050.1|1429036_1429636_-	potassium-transporting ATPase subunit KdpC	NA	NA	NA	NA	NA
WP_010930950.1|1429646_1431812_-	potassium-transporting ATPase subunit KdpB	NA	M1HBF8	Paramecium_bursaria_Chlorella_virus	27.1	1.2e-24
WP_010930949.1|1431835_1433620_-	potassium-transporting ATPase subunit KdpA	NA	NA	NA	NA	NA
WP_017685545.1|1433619_1433709_-	K(+)-transporting ATPase subunit F	NA	NA	NA	NA	NA
WP_003814042.1|1434403_1434676_+	DUF4212 domain-containing protein	NA	NA	NA	NA	NA
WP_003814040.1|1434675_1436742_+	cation acetate symporter	NA	NA	NA	NA	NA
WP_010929577.1|1436738_1437689_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_005012067.1|1437787_1438738_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_005015014.1|1438853_1439186_-	multidrug transporter	NA	NA	NA	NA	NA
WP_010929073.1|1439182_1439869_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010930948.1|1439855_1440815_-	thioredoxin-disulfide reductase	NA	A0A2I2L5E1	Orpheovirus	40.2	3.1e-57
WP_010930947.1|1440847_1443217_+	DNA translocase FtsK	NA	S5VNE3	Mycobacterium_phage	48.0	7.6e-81
WP_010930946.1|1443216_1443849_+	outer membrane lipoprotein chaperone LolA	NA	NA	NA	NA	NA
WP_010930945.1|1443950_1445291_+	replication-associated recombination protein A	NA	G3MBE0	Bacillus_virus	38.9	1.6e-75
WP_010930944.1|1445337_1446693_+|tRNA	serine--tRNA ligase	tRNA	A0A1B1IVT2	uncultured_Mediterranean_phage	47.5	1.6e-83
WP_005014990.1|1446983_1447220_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003814024.1|1447407_1447725_-	virulence factor	NA	NA	NA	NA	NA
WP_003814023.1|1447997_1448513_-	hypothetical protein	NA	T1SAR8	Salmonella_phage	44.6	5.1e-06
WP_003814021.1|1448783_1449539_-	GGDEF domain-containing protein	NA	NA	NA	NA	NA
WP_019247690.1|1449877_1450084_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003814020.1|1450091_1450751_-	NAAT family transporter	NA	NA	NA	NA	NA
WP_010930941.1|1451045_1453250_-	TonB-dependent alcaligin siderophore receptor FauA	NA	NA	NA	NA	NA
WP_010930940.1|1453360_1454584_-	alcaligin siderophore export MFS transporter Bcr	NA	S4TR35	Salmonella_phage	29.4	9.8e-24
WP_003814017.1|1454706_1455681_-	alcaligin siderophore biosynthesis transcriptional regulator AlcR	NA	NA	NA	NA	NA
WP_005013753.1|1455748_1456942_-	alcaligin siderophore biosynthesis protein AlcE	NA	NA	NA	NA	NA
WP_003814016.1|1456956_1457757_-	alcaligin siderophore biosynthesis protein AlcD	NA	NA	NA	NA	NA
WP_010930939.1|1457753_1459610_-	alcaligin siderophore biosynthesis protein AlcC	NA	NA	NA	NA	NA
WP_003814014.1|1459606_1460212_-	alcaligin siderophore biosynthesis protein AlcB	NA	NA	NA	NA	NA
WP_003814013.1|1460230_1461616_-	alcaligin siderophore biosynthesis protein AlcA	NA	NA	NA	NA	NA
WP_003814012.1|1462341_1463568_+	transporter	NA	NA	NA	NA	NA
WP_003814011.1|1463656_1464439_+	3-hydroxybutyrate dehydrogenase	NA	NA	NA	NA	NA
WP_005012067.1|1464537_1465488_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003814010.1|1465514_1466288_+	peroxide stress protein YaaA	NA	NA	NA	NA	NA
WP_003814009.1|1466299_1467541_+	MFS transporter	NA	NA	NA	NA	NA
WP_076879548.1|1469322_1470273_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 15
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	1514198	1582283	4108480	tRNA,transposase	Streptococcus_virus(11.11%)	57	NA	NA
WP_010930416.1|1514198_1514687_+|tRNA	Cys-tRNA(Pro) deacylase	tRNA	NA	NA	NA	NA
WP_019248504.1|1514804_1515383_+	DJ-1/PfpI family protein	NA	NA	NA	NA	NA
WP_010930418.1|1515488_1515857_+	ribbon-helix-helix domain-containing protein	NA	NA	NA	NA	NA
WP_005012067.1|1515955_1516906_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_023994932.1|1516912_1518025_-	D-alanyl-D-alanine endopeptidase	NA	NA	NA	NA	NA
WP_010930419.1|1518711_1519914_+	MFS transporter	NA	NA	NA	NA	NA
WP_010930420.1|1520117_1522778_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930421.1|1522790_1526195_+	UvrD-helicase domain-containing protein	NA	NA	NA	NA	NA
WP_023995689.1|1526862_1529088_+	DNA polymerase III subunit gamma/tau	NA	A0A1U9WR94	Streptococcus_virus	38.5	1.2e-43
WP_010930423.1|1529134_1529461_+	YbaB/EbfC family nucleoid-associated protein	NA	NA	NA	NA	NA
WP_010930424.1|1529511_1530120_+	recombination protein RecR	NA	NA	NA	NA	NA
WP_005013747.1|1530218_1531169_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930425.1|1531238_1532003_-	hypothetical protein	NA	NA	NA	NA	NA
WP_033446226.1|1531999_1532536_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010930427.1|1532702_1533554_-	membrane protein	NA	A0A1I9SA48	Rhodococcus_phage	35.3	7.0e-37
WP_010928449.1|1533613_1534240_+	threonylcarbamoyl-AMP synthase	NA	NA	NA	NA	NA
WP_005012067.1|1534236_1535187_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_019249265.1|1535285_1536398_-	DUF1513 domain-containing protein	NA	NA	NA	NA	NA
WP_019248041.1|1536387_1537389_-	imelysin family protein	NA	NA	NA	NA	NA
WP_019247498.1|1537494_1539006_-	c-type cytochrome	NA	NA	NA	NA	NA
WP_023853587.1|1539002_1540307_-	imelysin	NA	NA	NA	NA	NA
WP_010930431.1|1540418_1540979_-	membrane protein	NA	NA	NA	NA	NA
WP_010930432.1|1541246_1541801_+	NAD(P)H-dependent oxidoreductase	NA	A0A2P0ZL82	Lactobacillus_phage	32.0	1.7e-15
WP_010930433.1|1542256_1542472_-	dodecin domain-containing protein	NA	NA	NA	NA	NA
WP_033446228.1|1542726_1545324_+	DNA mismatch repair protein MutS	NA	A0A1V0SDQ0	Indivirus	22.6	1.5e-21
WP_010930435.1|1545320_1546508_+	cupin	NA	NA	NA	NA	NA
WP_010930436.1|1547165_1547780_+	serotype 3 fimbrial subunit	NA	NA	NA	NA	NA
WP_023994740.1|1547868_1548990_-	outer membrane protein assembly factor BamC	NA	NA	NA	NA	NA
WP_033446216.1|1549007_1549913_-	4-hydroxy-tetrahydrodipicolinate synthase	NA	NA	NA	NA	NA
WP_005012067.1|1550805_1551756_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930439.1|1551937_1552690_+	glutamine ABC transporter substrate-binding protein GlnH	NA	NA	NA	NA	NA
WP_003811112.1|1552758_1553418_+	glutamine ABC transporter permease GlnP	NA	NA	NA	NA	NA
WP_003811113.1|1553414_1554143_+	glutamine ABC transporter ATP-binding protein GlnQ	NA	G9BWD6	Planktothrix_phage	39.3	3.3e-35
WP_010930440.1|1554155_1556435_-	bifunctional (p)ppGpp synthetase/guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase	NA	A0A1B1IUF0	uncultured_Mediterranean_phage	32.1	5.9e-06
WP_010930441.1|1556459_1556663_-	DNA-directed RNA polymerase subunit omega	NA	NA	NA	NA	NA
WP_010930442.1|1556704_1557337_-	guanylate kinase	NA	A0A218KC48	Bacillus_phage	33.9	2.4e-13
WP_010930443.1|1557472_1558390_-	c-type cytochrome	NA	NA	NA	NA	NA
WP_010930444.1|1558386_1559100_-	c-type cytochrome	NA	NA	NA	NA	NA
WP_003811135.1|1559337_1560108_+	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_003811137.1|1560112_1560712_-	C40 family peptidase	NA	A0A0A8WF62	Clostridium_phage	41.6	1.4e-20
WP_003811138.1|1560956_1562447_+	AMP nucleosidase	NA	NA	NA	NA	NA
WP_010926696.1|1562505_1562790_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_003811148.1|1563355_1564282_-	YicC family protein	NA	NA	NA	NA	NA
WP_003811149.1|1564418_1565159_+	ribonuclease PH	NA	NA	NA	NA	NA
WP_010930446.1|1565325_1566702_-	MmgE/PrpD family protein	NA	NA	NA	NA	NA
WP_003811152.1|1566883_1567789_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930448.1|1569440_1571243_-	EAL domain-containing protein	NA	NA	NA	NA	NA
WP_003811159.1|1571360_1572011_+	RdgB/HAM1 family non-canonical purine NTP pyrophosphatase	NA	NA	NA	NA	NA
WP_005012808.1|1572109_1573060_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930450.1|1573081_1574302_+	oxygen-independent coproporphyrinogen III oxidase-like protein	NA	NA	NA	NA	NA
WP_003811164.1|1574487_1575900_+	type I glutamate--ammonia ligase	NA	NA	NA	NA	NA
WP_003811167.1|1575963_1577031_+	PAS domain-containing protein	NA	Q8QKV7	Ectocarpus_siliculosus_virus	23.5	1.1e-05
WP_010930451.1|1577030_1578518_+	nitrogen regulation protein NR(I)	NA	NA	NA	NA	NA
WP_010930452.1|1578527_1579472_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003811176.1|1579631_1580330_+	pirin family protein	NA	NA	NA	NA	NA
WP_010930453.1|1580407_1581313_+	pirin family protein	NA	NA	NA	NA	NA
WP_005012067.1|1581332_1582283_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 16
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	1618232	1673823	4108480	transposase	Brazilian_cedratvirus(25.0%)	47	NA	NA
WP_005013747.1|1618232_1619183_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930486.1|1619241_1620015_+	SDR family NAD(P)-dependent oxidoreductase	NA	NA	NA	NA	NA
WP_014486074.1|1620007_1621564_+	LTA synthase family protein	NA	NA	NA	NA	NA
WP_005013747.1|1621560_1622511_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003810741.1|1623837_1624440_-	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003810743.1|1624679_1625381_-	ABC transporter ATP-binding protein	NA	NA	NA	NA	NA
WP_003816696.1|1625374_1626157_-	ABC transporter ATP-binding protein	NA	A0A2R8FG22	Brazilian_cedratvirus	25.8	2.0e-09
WP_005012808.1|1626341_1627292_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930483.1|1627390_1628128_-	TerC family protein	NA	A0A0S4KZH7	Pseudomonas_phage	46.6	4.1e-41
WP_010926609.1|1628317_1629076_-	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_010930482.1|1629122_1630112_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010930481.1|1630289_1631258_-	transporter	NA	NA	NA	NA	NA
WP_010930480.1|1632797_1633766_+	AAA family ATPase	NA	NA	NA	NA	NA
WP_010930479.1|1633774_1634716_+	DUF58 domain-containing protein	NA	NA	NA	NA	NA
WP_010930478.1|1635189_1636200_+	VWA domain-containing protein	NA	NA	NA	NA	NA
WP_010930477.1|1636190_1637705_+	VWA domain-containing protein	NA	NA	NA	NA	NA
WP_010930476.1|1637701_1639048_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930475.1|1639050_1640085_+	haloacid dehalogenase-like hydrolase	NA	NA	NA	NA	NA
WP_023852967.1|1640134_1641760_+	arylsulfatase	NA	A0A2P0VMN7	Tetraselmis_virus	52.2	2.0e-149
WP_005012067.1|1642312_1643263_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930487.1|1643367_1644315_+	hypothetical protein	NA	NA	NA	NA	NA
WP_019247865.1|1644368_1646183_-	sensor histidine kinase	NA	NA	NA	NA	NA
WP_010930489.1|1646175_1646850_-	response regulator transcription factor	NA	NA	NA	NA	NA
WP_023995112.1|1646979_1650054_+	autotransporter SphB2	NA	NA	NA	NA	NA
WP_019247905.1|1650067_1650367_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_010930492.1|1650681_1651305_-	glutathione S-transferase	NA	NA	NA	NA	NA
WP_010930493.1|1651548_1652418_+	TauD/TfdA family dioxygenase	NA	NA	NA	NA	NA
WP_010930494.1|1652395_1653340_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_019247909.1|1653425_1654352_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_019247910.1|1654464_1655244_-	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_010930497.1|1655234_1656431_-	alpha-hydroxy-acid oxidizing protein	NA	NA	NA	NA	NA
WP_010930498.1|1656461_1657412_-	fumarylacetoacetate hydrolase family protein	NA	NA	NA	NA	NA
WP_010930499.1|1657633_1658323_+	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_010930500.1|1658387_1659143_+	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_010930501.1|1659194_1660187_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010930502.1|1660196_1661150_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003811538.1|1661265_1662228_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_019249376.1|1663629_1664058_+	hypothetical protein	NA	NA	NA	NA	NA
WP_005013747.1|1664054_1665005_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930503.1|1665298_1666021_-	arsenical resistance protein ArsH	NA	A0A2H4J5V6	uncultured_Caudovirales_phage	68.2	1.3e-87
WP_010930504.1|1666459_1667647_-	MFS transporter	NA	NA	NA	NA	NA
WP_010930505.1|1667650_1668001_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_010930506.1|1669750_1670722_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010930507.1|1670735_1671449_+	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_010930508.1|1671453_1672371_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003811452.1|1672477_1672774_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010929588.1|1672872_1673823_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 17
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	1831589	1890859	4108480	tRNA,protease,transposase	Klosneuvirus(40.0%)	51	NA	NA
WP_005013747.1|1831589_1832540_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930573.1|1832664_1833474_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
WP_010929577.1|1833674_1834625_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930574.1|1835898_1837116_+	four-carbon acid sugar kinase family protein	NA	NA	NA	NA	NA
WP_003818670.1|1838172_1839075_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930576.1|1839151_1840024_+	MOSC domain-containing protein	NA	NA	NA	NA	NA
WP_003818672.1|1840154_1840523_+	aspartate 1-decarboxylase	NA	NA	NA	NA	NA
WP_010930577.1|1840580_1841627_+	CDP-6-deoxy-delta-3,4-glucoseen reductase	NA	NA	NA	NA	NA
WP_010930578.1|1841822_1843079_+	D-amino acid dehydrogenase	NA	NA	NA	NA	NA
WP_003810623.1|1843083_1844421_+	extracellular solute-binding protein	NA	NA	NA	NA	NA
WP_003818676.1|1844570_1845527_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_019247555.1|1845629_1846562_-	acyclic terpene utilization AtuA family protein	NA	NA	NA	NA	NA
WP_019247554.1|1846677_1846998_+	hypothetical protein	NA	NA	NA	NA	NA
WP_019247553.1|1846990_1847350_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930581.1|1847397_1848972_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_003810637.1|1849024_1849969_+	ABC transporter permease	NA	NA	NA	NA	NA
WP_010930582.1|1849986_1850817_+	ABC transporter permease	NA	NA	NA	NA	NA
WP_010930583.1|1850809_1852444_+	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	32.7	8.2e-18
WP_010930584.1|1852440_1853796_+	amidase	NA	NA	NA	NA	NA
WP_010930585.1|1854702_1856280_+	lipoprotein	NA	NA	NA	NA	NA
WP_010930586.1|1856283_1857558_+	type 4b pilus protein PilO2	NA	NA	NA	NA	NA
WP_010930587.1|1857655_1858030_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930588.1|1859745_1860879_+	general secretion pathway protein	NA	NA	NA	NA	NA
WP_003810661.1|1860916_1861522_+	prepilin-type N-terminal cleavage/methylation domain-containing protein	NA	NA	NA	NA	NA
WP_010930589.1|1861518_1862337_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930590.1|1862408_1865033_+|tRNA	alanine--tRNA ligase	tRNA	A0A1V0SK38	Klosneuvirus	39.4	1.7e-81
WP_004568544.1|1865019_1865274_+	sulfurtransferase TusA family protein	NA	NA	NA	NA	NA
WP_010930591.1|1865340_1865922_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010926757.1|1866225_1866486_+	30S ribosomal protein S16	NA	NA	NA	NA	NA
WP_014905757.1|1866651_1867275_+	ribosome maturation factor RimM	NA	NA	NA	NA	NA
WP_003816734.1|1867274_1868048_+|tRNA	tRNA (guanosine(37)-N1)-methyltransferase TrmD	tRNA	NA	NA	NA	NA
WP_010930593.1|1868044_1869253_-	aminotransferase class V-fold PLP-dependent enzyme	NA	NA	NA	NA	NA
WP_010930594.1|1869278_1869752_-	RidA family protein	NA	NA	NA	NA	NA
WP_010930048.1|1869825_1870776_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_076879566.1|1870874_1871825_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930796.1|1871923_1873273_-	two-component sensor histidine kinase	NA	NA	NA	NA	NA
WP_023852900.1|1874038_1874794_+	MipA/OmpV family protein	NA	NA	NA	NA	NA
WP_010930794.1|1874886_1877769_-|tRNA	valine--tRNA ligase	tRNA	A0A1V0SK04	Klosneuvirus	37.1	3.7e-138
WP_003810689.1|1878091_1878517_+	nucleoside-diphosphate kinase	NA	D2E8E1	Anguillid_herpesvirus	43.2	2.1e-21
WP_004568542.1|1878544_1879693_+	23S rRNA (adenine(2503)-C(2))-methyltransferase RlmN	NA	NA	NA	NA	NA
WP_003810693.1|1879689_1880196_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_033446257.1|1880211_1881498_+	flavodoxin-dependent (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase	NA	NA	NA	NA	NA
WP_033446258.1|1881547_1882843_+|tRNA	histidine--tRNA ligase	tRNA	NA	NA	NA	NA
WP_010930791.1|1882844_1883483_+	tetratricopeptide repeat protein	NA	NA	NA	NA	NA
WP_023852925.1|1883488_1884646_+	outer membrane protein assembly factor BamB	NA	NA	NA	NA	NA
WP_003810703.1|1884672_1886028_+	ribosome biogenesis GTPase Der	NA	NA	NA	NA	NA
WP_010930790.1|1886031_1887102_+	histidinol-phosphate transaminase	NA	A0A1X6WGT4	Pacmanvirus	25.7	2.5e-15
WP_003810707.1|1887240_1887477_+	RNA chaperone Hfq	NA	NA	NA	NA	NA
WP_010930789.1|1887564_1888671_+	GTPase HflX	NA	NA	NA	NA	NA
WP_010930788.1|1888636_1889941_+|protease	FtsH protease activity modulator HflK	protease	NA	NA	NA	NA
WP_010930787.1|1889959_1890859_+|protease	protease modulator HflC	protease	NA	NA	NA	NA
>prophage 18
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	1901099	1945422	4108480	transposase	Staphylococcus_phage(25.0%)	45	NA	NA
WP_005013747.1|1901099_1902050_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_005013747.1|1902148_1903099_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930782.1|1903298_1904384_+	AI-2E family transporter	NA	NA	NA	NA	NA
WP_003810400.1|1904399_1905161_-	ABC transporter permease	NA	NA	NA	NA	NA
WP_010930781.1|1905157_1906081_-	ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	33.6	1.6e-23
WP_019248115.1|1906179_1906704_-	N-acetyltransferase	NA	NA	NA	NA	NA
WP_010930779.1|1906712_1907456_-	sulfite exporter TauE/SafE family protein	NA	NA	NA	NA	NA
WP_010930778.1|1907551_1907791_-	membrane protein	NA	NA	NA	NA	NA
WP_010930777.1|1907804_1907957_-	lipoprotein	NA	NA	NA	NA	NA
WP_010930776.1|1908042_1909533_-	cytochrome c oxidase accessory protein CcoG	NA	NA	NA	NA	NA
WP_010930775.1|1909624_1910563_-	cytochrome-c oxidase, cbb3-type subunit III	NA	NA	NA	NA	NA
WP_003818560.1|1910559_1910736_-	cytochrome oxidase	NA	NA	NA	NA	NA
WP_003810383.1|1910738_1911401_-	cytochrome-c oxidase, cbb3-type subunit II	NA	NA	NA	NA	NA
WP_003810379.1|1913022_1913166_-	cbb3-type cytochrome oxidase assembly protein CcoS	NA	NA	NA	NA	NA
WP_010930774.1|1913162_1914137_-	membrane protein	NA	NA	NA	NA	NA
WP_162268682.1|1914031_1914286_-	hypothetical protein	NA	NA	NA	NA	NA
WP_005012067.1|1914303_1915254_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930773.1|1915250_1916525_-	adenosylmethionine--8-amino-7-oxononanoate transaminase	NA	A0A1V0SKB7	Klosneuvirus	28.9	9.6e-14
WP_010930772.1|1916628_1917822_+	8-amino-7-oxononanoate synthase	NA	NA	NA	NA	NA
WP_010930771.1|1917818_1918472_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
WP_010930770.1|1918468_1919905_+	dethiobiotin synthase	NA	NA	NA	NA	NA
WP_010930769.1|1919892_1920252_+	CidA/LrgA family protein	NA	NA	NA	NA	NA
WP_162268681.1|1921066_1921207_-	hypothetical protein	NA	NA	NA	NA	NA
WP_005012067.1|1921224_1922175_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930768.1|1923220_1925086_-	sigma-54-dependent Fis family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930767.1|1925343_1926864_+	aldehyde dehydrogenase	NA	NA	NA	NA	NA
WP_003816959.1|1926951_1927602_-	flavodoxin family protein	NA	NA	NA	NA	NA
WP_010930766.1|1928550_1929846_+	DUF445 domain-containing protein	NA	NA	NA	NA	NA
WP_010930765.1|1929867_1930752_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930764.1|1930850_1931726_+	PhzF family phenazine biosynthesis protein	NA	NA	NA	NA	NA
WP_003816964.1|1931715_1932072_-	DUF1428 domain-containing protein	NA	NA	NA	NA	NA
WP_010930763.1|1932202_1933177_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_003812228.1|1933306_1933486_-	DUF3008 family protein	NA	NA	NA	NA	NA
WP_029443822.1|1933583_1934108_+	DUF302 domain-containing protein	NA	NA	NA	NA	NA
WP_010930761.1|1934118_1934955_-	alpha/beta hydrolase	NA	NA	NA	NA	NA
WP_003816971.1|1935067_1935439_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_010930760.1|1935435_1935987_+	SRPBCC family protein	NA	NA	NA	NA	NA
WP_003816975.1|1936002_1937694_-	STAS domain-containing protein	NA	A0A2H4J153	uncultured_Caudovirales_phage	27.3	5.0e-42
WP_003816977.1|1937742_1938423_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
WP_014905663.1|1938670_1939135_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010930758.1|1939304_1940234_+	ZIP family metal transporter	NA	NA	NA	NA	NA
WP_019247659.1|1940246_1940894_-	hypothetical protein	NA	NA	NA	NA	NA
WP_023997035.1|1940967_1942785_-	ABC transporter ATP-binding protein	NA	W8CYL7	Bacillus_phage	27.4	2.3e-37
WP_005012067.1|1942868_1943819_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929577.1|1944471_1945422_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 19
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	1975195	2039571	4108480	transposase	Vibrio_phage(20.0%)	51	NA	NA
WP_005013747.1|1975195_1976146_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_005015810.1|1976367_1977318_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_023852887.1|1977416_1978382_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010930740.1|1978519_1979419_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930739.1|1982013_1983501_+	hydroxymethylglutaryl-CoA synthase family protein	NA	NA	NA	NA	NA
WP_014486081.1|1983511_1984708_+	acetyl-CoA acetyltransferase	NA	NA	NA	NA	NA
WP_003816680.1|1984780_1986100_+	AMP-binding protein	NA	NA	NA	NA	NA
WP_010930737.1|1986096_1986972_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
WP_010930736.1|1987002_1988151_-	CoA transferase	NA	NA	NA	NA	NA
WP_010930735.1|1988168_1988483_-	2Fe-2S iron-sulfur cluster binding domain-containing protein	NA	NA	NA	NA	NA
WP_062810228.1|1988504_1989227_-	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_003816690.1|1989226_1990045_-	enoyl-CoA hydratase/isomerase family protein	NA	NA	NA	NA	NA
WP_003816691.1|1990049_1990577_-	aromatic-ring-hydroxylating dioxygenase subunit beta	NA	NA	NA	NA	NA
WP_010930733.1|1990582_1991839_-	Rieske 2Fe-2S domain-containing protein	NA	NA	NA	NA	NA
WP_010930732.1|1992197_1993337_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010930731.1|1993414_1994287_+	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_010930730.1|1995157_1996108_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930729.1|1996067_1996703_-	membrane protein	NA	NA	NA	NA	NA
WP_010930728.1|1997062_1998385_-	isocitrate lyase	NA	NA	NA	NA	NA
WP_010930727.1|1998703_1999525_+	NADPH-dependent 7-cyano-7-deazaguanine reductase QueF	NA	A0A2I7SAX1	Vibrio_phage	37.6	4.1e-42
WP_003810356.1|2000956_2001529_-	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase	NA	NA	NA	NA	NA
WP_010930726.1|2001568_2003398_-	excinuclease ABC subunit UvrC	NA	NA	NA	NA	NA
WP_010930725.1|2003360_2004419_-	beta-N-acetylhexosaminidase	NA	NA	NA	NA	NA
WP_010930724.1|2004456_2004918_-	holo-ACP synthase	NA	NA	NA	NA	NA
WP_003810344.1|2005002_2005749_-	pyridoxine 5'-phosphate synthase	NA	NA	NA	NA	NA
WP_019247651.1|2007239_2010470_-	multidrug efflux RND transporter permease subunit	NA	NA	NA	NA	NA
WP_019248531.1|2010536_2011868_-	efflux RND transporter periplasmic adaptor subunit	NA	NA	NA	NA	NA
WP_010930721.1|2012120_2012495_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_010930720.1|2012597_2013776_-	patatin-like phospholipase family protein	NA	NA	NA	NA	NA
WP_003810329.1|2013786_2014377_-	DUF4136 domain-containing protein	NA	NA	NA	NA	NA
WP_003818535.1|2014487_2015294_+	TOBE domain-containing protein	NA	NA	NA	NA	NA
WP_010930719.1|2015319_2016114_-	ABC transporter ATP-binding protein	NA	A0A1V0SE00	Indivirus	25.7	5.1e-05
WP_010930718.1|2017114_2018089_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_003818533.1|2018247_2018760_-	superoxide dismutase family protein	NA	Q9MC02	Salmonella_phage	52.3	1.8e-43
WP_003818532.1|2018916_2019888_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010930717.1|2021632_2022439_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
WP_010930716.1|2022435_2023737_-	malonyl-CoA decarboxylase	NA	NA	NA	NA	NA
WP_010930715.1|2023687_2024452_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930714.1|2024565_2025336_-	spermidine synthase	NA	NA	NA	NA	NA
WP_010930713.1|2025420_2026608_-	acetyl-CoA C-acyltransferase family protein	NA	NA	NA	NA	NA
WP_003818524.1|2026680_2027055_-	4-oxalocrotonate tautomerase	NA	NA	NA	NA	NA
WP_003810308.1|2027155_2028418_-	glycine betaine/L-proline ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	36.6	6.8e-28
WP_003810306.1|2028414_2029272_-	proline/glycine betaine ABC transporter permease	NA	NA	NA	NA	NA
WP_003818523.1|2029444_2030446_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010929591.1|2030897_2031848_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_033446265.1|2033411_2034563_+	multidrug effflux MFS transporter	NA	NA	NA	NA	NA
WP_003810297.1|2034931_2035168_+	50S ribosomal protein L28	NA	NA	NA	NA	NA
WP_010930711.1|2035231_2035399_+	50S ribosomal protein L33	NA	NA	NA	NA	NA
WP_023853105.1|2035512_2037408_-	STAS domain-containing protein	NA	A0A2H4J153	uncultured_Caudovirales_phage	27.5	2.3e-19
WP_062826579.1|2037571_2038522_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931070.1|2038620_2039571_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 20
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	2171100	2220753	4108480	tRNA,transposase	Synechococcus_phage(15.38%)	43	NA	NA
WP_005012067.1|2171100_2172051_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_076879626.1|2172149_2174144_-	phosphoribosylglycinamide formyltransferase	NA	M4QRX9	Synechococcus_phage	33.3	4.4e-21
WP_010930543.1|2174203_2175169_+	bifunctional riboflavin kinase/FAD synthetase	NA	NA	NA	NA	NA
WP_010930542.1|2175158_2178020_+|tRNA	isoleucine--tRNA ligase	tRNA	A0A1V0SJ93	Klosneuvirus	25.5	1.0e-71
WP_010930541.1|2178022_2178529_+	lipoprotein signal peptidase	NA	NA	NA	NA	NA
WP_010930540.1|2178633_2179842_+	bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase CoaBC	NA	Q9HH70	Methanothermobacter_phage	30.0	3.8e-36
WP_033446178.1|2179843_2180782_-	membrane protein	NA	NA	NA	NA	NA
WP_010930538.1|2180943_2181417_+	Lrp/AsnC family transcriptional regulator	NA	NA	NA	NA	NA
WP_005012808.1|2181413_2182364_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_004566334.1|2182474_2182915_-	DUF937 domain-containing protein	NA	NA	NA	NA	NA
WP_010930537.1|2183043_2184273_-	lytic murein transglycosylase	NA	NA	NA	NA	NA
WP_004566336.1|2184311_2185133_-	ferritin-like domain-containing protein	NA	NA	NA	NA	NA
WP_029443743.1|2185186_2186338_+	N-acetyltransferase	NA	NA	NA	NA	NA
WP_010930535.1|2186429_2186918_-	DUF1854 domain-containing protein	NA	NA	NA	NA	NA
WP_019247811.1|2189468_2192018_+	cyanophycin synthetase	NA	NA	NA	NA	NA
WP_010930533.1|2192088_2194662_+	cyanophycin synthetase	NA	NA	NA	NA	NA
WP_003813568.1|2194927_2195128_+	CsbD family protein	NA	NA	NA	NA	NA
WP_003813570.1|2195159_2195321_+	DUF1328 domain-containing protein	NA	NA	NA	NA	NA
WP_003813572.1|2195378_2195717_+	BON domain-containing protein	NA	NA	NA	NA	NA
WP_005012067.1|2195865_2196816_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_019247882.1|2197590_2198259_+	arylesterase	NA	NA	NA	NA	NA
WP_010930531.1|2198240_2200196_-	peptidyl-prolyl cis-trans isomerase	NA	NA	NA	NA	NA
WP_004568486.1|2200438_2201188_+	glycerophosphodiester phosphodiesterase	NA	A0A2H4PGQ5	Escherichia_phage	27.8	1.5e-14
WP_003816518.1|2201200_2202064_+	23S rRNA (adenine(2030)-N(6))-methyltransferase RlmJ	NA	NA	NA	NA	NA
WP_003816520.1|2202067_2203483_-	dihydrolipoyl dehydrogenase	NA	NA	NA	NA	NA
WP_010930530.1|2203616_2204345_-	redoxin family protein	NA	A0A1D8KSL1	Synechococcus_phage	56.8	9.6e-43
WP_003811035.1|2204483_2204684_-	heavy-metal-associated domain-containing protein	NA	NA	NA	NA	NA
WP_003816523.1|2204859_2205258_+	Cu(I)-responsive transcriptional regulator	NA	NA	NA	NA	NA
WP_003816525.1|2205281_2206682_-	23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA	A0A2K5B251	Erysipelothrix_phage	26.5	7.3e-31
WP_010930529.1|2206800_2207553_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003816527.1|2207841_2208519_-	hypothetical protein	NA	NA	NA	NA	NA
WP_019248494.1|2208545_2209325_-	3'-5' exonuclease	NA	NA	NA	NA	NA
WP_003811022.1|2209321_2210206_-	peptidoglycan DD-metalloendopeptidase family protein	NA	A0A292GJG6	Xanthomonas_phage	49.5	4.6e-15
WP_019247478.1|2210223_2211003_-	protein-L-isoaspartate(D-aspartate) O-methyltransferase	NA	A0A1B1IU40	uncultured_Mediterranean_phage	46.9	4.8e-32
WP_010930526.1|2210987_2211746_-	5'/3'-nucleotidase SurE	NA	A0A1B1ITZ2	uncultured_Mediterranean_phage	51.2	1.4e-68
WP_023852762.1|2211883_2212519_+	glycerol-3-phosphate 1-O-acyltransferase PlsY	NA	NA	NA	NA	NA
WP_010929632.1|2212786_2213803_+|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_010930524.1|2213900_2214941_-|tRNA	tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD	tRNA	A0A0R6PI74	Moraxella_phage	51.3	6.1e-91
WP_003811011.1|2215075_2216368_+	NCS2 family permease	NA	A0A0R6PHV4	Moraxella_phage	36.0	1.7e-66
WP_003811007.1|2217727_2218111_+	thioredoxin family protein	NA	V9SJ74	Achromobacter_phage	25.8	8.1e-09
WP_010930523.1|2218128_2218716_-	YigZ family protein	NA	A0A1X9I5T8	Streptococcus_phage	35.8	4.7e-16
WP_005012067.1|2218753_2219704_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930048.1|2219802_2220753_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 21
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	2477060	2535304	4108480	tRNA,transposase	Planktothrix_phage(28.57%)	54	NA	NA
WP_005012067.1|2477060_2478011_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930388.1|2478490_2479147_-	phosphoribosylanthranilate isomerase	NA	NA	NA	NA	NA
WP_010930387.1|2479161_2480829_-	TRAP transporter large permease subunit	NA	NA	NA	NA	NA
WP_010930386.1|2480831_2481461_-	TRAP transporter small permease subunit	NA	NA	NA	NA	NA
WP_014486072.1|2481672_2482767_-	TRAP transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010930384.1|2482911_2483724_-|tRNA	tRNA pseudouridine(38-40) synthase TruA	tRNA	NA	NA	NA	NA
WP_010930383.1|2483727_2485311_-	membrane protein	NA	NA	NA	NA	NA
WP_010930382.1|2485481_2486612_-	aspartate-semialdehyde dehydrogenase	NA	NA	NA	NA	NA
WP_010930381.1|2486798_2487875_-	3-isopropylmalate dehydrogenase	NA	NA	NA	NA	NA
WP_010930380.1|2487956_2488607_-	3-isopropylmalate dehydratase small subunit	NA	NA	NA	NA	NA
WP_010930379.1|2488621_2490025_-	3-isopropylmalate dehydratase large subunit	NA	NA	NA	NA	NA
WP_004567445.1|2490308_2491127_-	solute-binding protein	NA	NA	NA	NA	NA
WP_010930378.1|2491123_2491828_-	phosphate ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	30.0	2.6e-13
WP_010930377.1|2492727_2493843_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_004567447.1|2493876_2494251_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010930376.1|2494273_2495431_-	formate dehydrogenase subunit gamma	NA	NA	NA	NA	NA
WP_003812666.1|2495443_2495677_-	lipoprotein	NA	NA	NA	NA	NA
WP_019247523.1|2496311_2499281_-	formate dehydrogenase subunit alpha	NA	NA	NA	NA	NA
WP_023853518.1|2499295_2499505_-	hypothetical protein	NA	NA	NA	NA	NA
WP_019248667.1|2499656_2500286_-	hypothetical protein	NA	NA	NA	NA	NA
WP_023994978.1|2500282_2502340_-	4Fe-4S binding protein	NA	NA	NA	NA	NA
WP_010930372.1|2502396_2503077_-	DUF3306 domain-containing protein	NA	NA	NA	NA	NA
WP_003820494.1|2503073_2503634_-	DUF3305 domain-containing protein	NA	NA	NA	NA	NA
WP_004567450.1|2503640_2504738_-	iron-sulfur cluster carrier protein ApbC	NA	NA	NA	NA	NA
WP_010930371.1|2504890_2505484_+	molybdenum cofactor guanylyltransferase MobA	NA	NA	NA	NA	NA
WP_010930370.1|2505480_2506773_+	molybdopterin molybdotransferase MoeA	NA	NA	NA	NA	NA
WP_003812685.1|2506786_2507329_+	molybdopterin-guanine dinucleotide biosynthesis protein B	NA	NA	NA	NA	NA
WP_010930369.1|2507338_2508175_-	M48 family metallopeptidase	NA	NA	NA	NA	NA
WP_003820487.1|2508208_2509270_-	chorismate synthase	NA	A0A291AU41	Pandoravirus	42.8	2.9e-80
WP_019247210.1|2509311_2510364_-	EAL domain-containing protein	NA	NA	NA	NA	NA
WP_019247209.1|2510379_2510682_-	hypothetical protein	NA	NA	NA	NA	NA
WP_005012808.1|2510823_2511774_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_162268680.1|2511791_2511956_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930368.1|2511952_2513647_+	iron ABC transporter permease	NA	NA	NA	NA	NA
WP_003809599.1|2513643_2514729_+	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	37.7	6.4e-27
WP_010930367.1|2514776_2515676_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003809593.1|2515686_2516331_+	histidine phosphatase family protein	NA	NA	NA	NA	NA
WP_010930366.1|2517352_2520595_-	carbamoyl-phosphate synthase large subunit	NA	NA	NA	NA	NA
WP_023852833.1|2520605_2521760_-	glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit	NA	R4TGJ8	Halovirus	35.4	3.3e-53
WP_010930364.1|2521986_2522949_+	transaldolase	NA	H6WFR1	Cyanophage	29.2	7.5e-11
WP_076879624.1|2523047_2523998_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930363.1|2524096_2525047_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930362.1|2525056_2525746_-	VIT family protein	NA	NA	NA	NA	NA
WP_003811741.1|2525805_2526243_-	PaaI family thioesterase	NA	NA	NA	NA	NA
WP_003811743.1|2526288_2527182_-	3-hydroxyisobutyrate dehydrogenase	NA	NA	NA	NA	NA
WP_003811746.1|2527229_2528402_-	enoyl-CoA hydratase/isomerase family protein	NA	NA	NA	NA	NA
WP_003811748.1|2528398_2529553_-	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
WP_003811750.1|2529749_2530100_-	RnfH family protein	NA	NA	NA	NA	NA
WP_003811752.1|2530089_2530524_-	type II toxin-antitoxin system RatA family toxin	NA	NA	NA	NA	NA
WP_010930800.1|2530540_2531491_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003811754.1|2531638_2532106_+	SsrA-binding protein SmpB	NA	W5RAM5	Staphylococcus_phage	45.1	6.2e-27
WP_010930360.1|2532086_2533244_-	GGDEF domain-containing protein	NA	A0A127AWB9	Bacillus_phage	36.2	2.3e-14
WP_003811759.1|2533309_2534236_-	paraslipin	NA	NA	NA	NA	NA
WP_005012067.1|2534353_2535304_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 22
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	2577582	2644082	4108480	transposase	uncultured_Caudovirales_phage(40.0%)	56	NA	NA
WP_005012067.1|2577582_2578533_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003811850.1|2578902_2579475_+	flagellar basal body-associated protein FliL	NA	NA	NA	NA	NA
WP_003811852.1|2579477_2580488_+	flagellar motor switch protein FliM	NA	NA	NA	NA	NA
WP_010930335.1|2580480_2580981_+	flagellar motor switch protein FliN	NA	NA	NA	NA	NA
WP_003811855.1|2580991_2581333_+	flagellar biosynthetic protein FliO	NA	NA	NA	NA	NA
WP_010930334.1|2581401_2582136_+	flagellar type III secretion system pore protein FliP	NA	NA	NA	NA	NA
WP_003811859.1|2582152_2582422_+	flagellar biosynthesis protein FliQ	NA	NA	NA	NA	NA
WP_010930333.1|2582444_2583233_+	flagellar biosynthetic protein FliR	NA	NA	NA	NA	NA
WP_010929632.1|2583279_2584296_-|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_014486070.1|2584512_2585955_-	PAS domain-containing protein	NA	A0A1B0V854	Salmonella_phage	41.8	1.0e-35
WP_010930332.1|2586133_2587753_-	HAMP domain-containing protein	NA	A0A2H4J162	uncultured_Caudovirales_phage	45.3	1.5e-08
WP_010930331.1|2587873_2589694_-	HAMP domain-containing protein	NA	A0A2H4J162	uncultured_Caudovirales_phage	52.6	6.4e-11
WP_010930330.1|2589772_2591305_-	flagellar hook-associated protein 3	NA	NA	NA	NA	NA
WP_010930329.1|2591338_2592985_-	flagellar hook-associated protein FlgK	NA	NA	NA	NA	NA
WP_010930328.1|2593054_2594077_-	flagellar assembly peptidoglycan hydrolase FlgJ	NA	A0A088F6W1	Sulfitobacter_phage	31.4	1.9e-12
WP_010930327.1|2594094_2595228_-	flagellar basal body P-ring protein FlgI	NA	NA	NA	NA	NA
WP_010930326.1|2595230_2595920_-	flagellar basal body L-ring protein FlgH	NA	NA	NA	NA	NA
WP_010930325.1|2595919_2596705_-	flagellar basal-body rod protein FlgG	NA	NA	NA	NA	NA
WP_003817181.1|2596748_2597513_-	flagellar basal body rod protein FlgF	NA	NA	NA	NA	NA
WP_003817180.1|2597551_2598973_-	flagellar hook-basal body complex protein	NA	NA	NA	NA	NA
WP_010930324.1|2599038_2599743_-	flagellar basal body rod modification protein FlgD	NA	NA	NA	NA	NA
WP_003817176.1|2599790_2600210_-	flagellar basal body rod protein FlgC	NA	NA	NA	NA	NA
WP_010930323.1|2600222_2600630_-	flagellar basal body rod protein FlgB	NA	NA	NA	NA	NA
WP_010930322.1|2600813_2601524_+	flagellar basal body P-ring formation protein FlgA	NA	NA	NA	NA	NA
WP_003817172.1|2601650_2601941_+	flagellar biosynthesis anti-sigma factor FlgM	NA	NA	NA	NA	NA
WP_003817170.1|2601958_2602441_+	flagellar protein FlgN	NA	NA	NA	NA	NA
WP_010930321.1|2606946_2608101_-	flagellar type III secretion system protein FlhB	NA	NA	NA	NA	NA
WP_010931363.1|2608406_2609423_+|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_010930319.1|2609669_2610458_+	amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_003812020.1|2610524_2611205_+	amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_003812022.1|2611201_2611972_+	amino acid ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	39.1	9.8e-30
WP_010930208.1|2612070_2613021_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003811401.1|2613076_2613994_-	2-dehydropantoate 2-reductase	NA	NA	NA	NA	NA
WP_003811400.1|2614004_2615183_-	mandelate racemase/muconate lactonizing enzyme family protein	NA	NA	NA	NA	NA
WP_010930318.1|2615202_2616198_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_003811396.1|2617786_2618395_+	3-isopropylmalate dehydratase small subunit	NA	NA	NA	NA	NA
WP_003811393.1|2618382_2619423_+	LacI family transcriptional regulator	NA	NA	NA	NA	NA
WP_003811391.1|2619440_2620403_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_003811389.1|2620399_2621593_-	CoA transferase	NA	NA	NA	NA	NA
WP_010930317.1|2621589_2622387_-	citryl-CoA lyase	NA	NA	NA	NA	NA
WP_014486069.1|2622412_2623399_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010930316.1|2623417_2625457_-	acetyl-CoA synthetase	NA	NA	NA	NA	NA
WP_010930315.1|2625658_2626339_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930314.1|2626352_2627264_-	CoA ester lyase	NA	NA	NA	NA	NA
WP_003811381.1|2627260_2627839_-	NAD(P)H-dependent oxidoreductase	NA	NA	NA	NA	NA
WP_010930313.1|2627977_2628883_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930312.1|2628890_2632310_+	TM0106 family RecB-like putative nuclease	NA	NA	NA	NA	NA
WP_010930311.1|2632297_2634898_-	BP1344/BB2830 family autotransporter	NA	NA	NA	NA	NA
WP_003811375.1|2635853_2636486_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_003811372.1|2636879_2637638_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003811370.1|2637634_2638837_+	cardiolipin synthase ClsB	NA	NA	NA	NA	NA
WP_010930208.1|2639024_2639975_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930310.1|2640882_2642028_+	DUF3182 family protein	NA	NA	NA	NA	NA
WP_019247449.1|2642014_2642770_+	alpha/beta fold hydrolase	NA	NA	NA	NA	NA
WP_003811361.1|2642886_2643066_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010930208.1|2643131_2644082_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 23
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	2672197	2709609	4108480	transposase	Planktothrix_phage(33.33%)	39	NA	NA
WP_005012067.1|2672197_2673148_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_005012067.1|2673246_2674197_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003811316.1|2674289_2674829_+	peroxiredoxin	NA	NA	NA	NA	NA
WP_023852799.1|2674935_2675280_-	arsenate reductase (glutaredoxin)	NA	A0A2H4J8T1	uncultured_Caudovirales_phage	58.4	3.0e-31
WP_010930298.1|2675337_2676786_-	CoA transferase	NA	NA	NA	NA	NA
WP_003811313.1|2676973_2677309_-	tetratricopeptide repeat protein	NA	NA	NA	NA	NA
WP_010930297.1|2678936_2680115_+	DUF1501 domain-containing protein	NA	NA	NA	NA	NA
WP_003811310.1|2680197_2680698_+	glutathione peroxidase	NA	Q6VZR0	Canarypox_virus	38.4	4.7e-25
WP_010930296.1|2680807_2681509_+	thiol:disulfide oxidoreductase	NA	NA	NA	NA	NA
WP_010930295.1|2681520_2681985_+	GNAT family N-acetyltransferase	NA	NA	NA	NA	NA
WP_023852802.1|2681999_2682275_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003811306.1|2682271_2683048_+	lipoate--protein ligase family protein	NA	NA	NA	NA	NA
WP_010930294.1|2683076_2683904_+	DUF3298 domain-containing protein	NA	NA	NA	NA	NA
WP_010930293.1|2684029_2684500_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003811301.1|2684626_2685520_+	phosphatidylserine decarboxylase	NA	NA	NA	NA	NA
WP_010930292.1|2685567_2686749_+	alpha-hydroxy-acid oxidizing protein	NA	NA	NA	NA	NA
WP_003811298.1|2686761_2687577_-	exported protein	NA	NA	NA	NA	NA
WP_010930291.1|2687710_2688238_-	RES family NAD+ phosphorylase	NA	NA	NA	NA	NA
WP_003811295.1|2688234_2688732_-	DUF2384 domain-containing protein	NA	NA	NA	NA	NA
WP_003811293.1|2688879_2689257_+	DUF423 domain-containing protein	NA	NA	NA	NA	NA
WP_010929584.1|2689478_2690429_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_003811244.1|2690527_2691139_-	alpha/beta hydrolase	NA	NA	NA	NA	NA
WP_010930290.1|2691373_2692501_+	branched-chain amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010930289.1|2692611_2693700_-	sn-glycerol-3-phosphate import ATP-binding protein UgpC	NA	G9BWD6	Planktothrix_phage	31.2	2.2e-19
WP_003811259.1|2693752_2694604_-	sn-glycerol-3-phosphate ABC transporter permease UgpE	NA	NA	NA	NA	NA
WP_003811262.1|2694623_2695505_-	sn-glycerol-3-phosphate ABC transporter permease UgpA	NA	NA	NA	NA	NA
WP_010930288.1|2695681_2696995_-	sn-glycerol-3-phosphate ABC transporter substrate-binding protein UgpB	NA	NA	NA	NA	NA
WP_003811267.1|2697205_2698039_+	pyrroline-5-carboxylate reductase	NA	NA	NA	NA	NA
WP_010930287.1|2698035_2698617_+	queuosine precursor transporter	NA	A0A2I7SAW6	Vibrio_phage	37.3	9.4e-17
WP_005015810.1|2698970_2699921_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010930286.1|2699936_2701052_+	branched-chain amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_003811272.1|2701154_2702081_+	high-affinity branched-chain amino acid ABC transporter permease LivH	NA	NA	NA	NA	NA
WP_010930285.1|2702080_2703319_+	high-affinity branched-chain amino acid ABC transporter permease LivM	NA	NA	NA	NA	NA
WP_003811277.1|2703315_2704083_+	ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	26.4	1.2e-14
WP_010930284.1|2704083_2704785_+	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	30.4	1.3e-17
WP_019247793.1|2704866_2705313_-	glutamate racemase	NA	NA	NA	NA	NA
WP_010930283.1|2706202_2706841_+	glutathione S-transferase	NA	NA	NA	NA	NA
WP_005012808.1|2707609_2708560_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_005012808.1|2708658_2709609_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 24
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	2808736	2863253	4108480	transposase	Diachasmimorpha_longicaudata_entomopoxvirus(20.0%)	48	NA	NA
WP_023853639.1|2808736_2809687_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931071.1|2810015_2810621_+	fimbrial protein	NA	NA	NA	NA	NA
WP_010931072.1|2810674_2811988_-	phenylacetate--CoA ligase	NA	NA	NA	NA	NA
WP_003813284.1|2812062_2812533_-	hydroxyphenylacetyl-CoA thioesterase PaaI	NA	NA	NA	NA	NA
WP_010931073.1|2812532_2813321_-	2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase	NA	NA	NA	NA	NA
WP_010931074.1|2813331_2814984_-	phenylacetic acid degradation protein PaaN	NA	NA	NA	NA	NA
WP_010929591.1|2815071_2816022_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931075.1|2817183_2817690_-	phenylacetate-CoA oxygenase subunit PaaJ	NA	NA	NA	NA	NA
WP_003813293.1|2817686_2818451_-	phenylacetate-CoA oxygenase subunit PaaC	NA	NA	NA	NA	NA
WP_010931076.1|2818466_2818751_-	1,2-phenylacetyl-CoA epoxidase subunit B	NA	NA	NA	NA	NA
WP_003813298.1|2818815_2819805_-	1,2-phenylacetyl-CoA epoxidase subunit A	NA	NA	NA	NA	NA
WP_010931077.1|2819976_2820906_+	phenylacetic acid degradation operon negative regulatory protein PaaX	NA	NA	NA	NA	NA
WP_003813302.1|2820877_2821564_-	NAD(P)H-hydrate epimerase	NA	NA	NA	NA	NA
WP_003813303.1|2821597_2822143_-	oligoribonuclease	NA	Q8B5Y0	Diachasmimorpha_longicaudata_entomopoxvirus	37.7	2.1e-26
WP_003813306.1|2822187_2823453_+	M48 family metallopeptidase	NA	NA	NA	NA	NA
WP_003813309.1|2823449_2824352_+	ribosome small subunit-dependent GTPase A	NA	NA	NA	NA	NA
WP_019247679.1|2825533_2826478_-	ABC transporter permease	NA	NA	NA	NA	NA
WP_010931079.1|2826572_2828090_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010931080.1|2828131_2829760_-	gamma-glutamyltransferase	NA	NA	NA	NA	NA
WP_003811986.1|2829867_2830749_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010931081.1|2833861_2834236_+	endonuclease	NA	F4YXR7	Roseobacter_phage	54.4	2.1e-25
WP_003812004.1|2834260_2834599_-	P-II family nitrogen regulator	NA	NA	NA	NA	NA
WP_010931082.1|2834642_2836277_-	NAD+ synthase	NA	A0A2L0UZF5	Agrobacterium_phage	36.6	8.3e-87
WP_010931083.1|2836315_2837662_-	mechanosensitive ion channel	NA	NA	NA	NA	NA
WP_003812010.1|2837769_2839191_+	argininosuccinate lyase	NA	NA	NA	NA	NA
WP_010931084.1|2839260_2839845_-	nitroreductase	NA	NA	NA	NA	NA
WP_005012067.1|2839947_2840898_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931085.1|2841032_2842139_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_010931086.1|2842149_2843247_+	GTP 3',8-cyclase MoaA	NA	NA	NA	NA	NA
WP_010931087.1|2843391_2844597_-	molybdopterin molybdotransferase MoeA	NA	NA	NA	NA	NA
WP_010931088.1|2844603_2845125_-	molybdenum cofactor biosynthesis protein B	NA	NA	NA	NA	NA
WP_023853551.1|2845121_2845604_-	molybdenum cofactor biosynthesis protein MoaE	NA	NA	NA	NA	NA
WP_003819740.1|2845609_2845861_-	MoaD/ThiS family protein	NA	NA	NA	NA	NA
WP_003819741.1|2845841_2846327_-	cyclic pyranopterin monophosphate synthase MoaC	NA	NA	NA	NA	NA
WP_010931090.1|2846462_2849924_+	DUF748 domain-containing protein	NA	NA	NA	NA	NA
WP_010931091.1|2849941_2850826_+	dienelactone hydrolase family protein	NA	NA	NA	NA	NA
WP_010931092.1|2850835_2851267_-	lipoprotein	NA	NA	NA	NA	NA
WP_003809348.1|2851513_2852017_+	peroxiredoxin	NA	M1I839	Pelagibacter_phage	44.1	1.8e-24
WP_010931094.1|2852094_2853495_+	MFS transporter	NA	NA	NA	NA	NA
WP_010931095.1|2853569_2854445_-	membrane protein	NA	NA	NA	NA	NA
WP_023853546.1|2854441_2855449_-	biotin synthase BioB	NA	NA	NA	NA	NA
WP_010931097.1|2855916_2856222_+	DUF4148 domain-containing protein	NA	NA	NA	NA	NA
WP_003819753.1|2856312_2856903_+	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930525.1|2857093_2858110_-|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_010931098.1|2858301_2860638_-	heavy metal translocating P-type ATPase	NA	E4ZFI9	Streptococcus_phage	42.8	3.2e-124
WP_003812014.1|2860720_2861155_+	Cd(II)/Pb(II)-responsive transcriptional regulator	NA	NA	NA	NA	NA
WP_023995489.1|2861253_2862204_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_005013747.1|2862302_2863253_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 25
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	2871278	2928062	4108480	protease,transposase	uncultured_Mediterranean_phage(28.57%)	40	NA	NA
WP_005012067.1|2871278_2872229_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931105.1|2873935_2874202_-	accessory factor UbiK family protein	NA	NA	NA	NA	NA
WP_003812839.1|2874909_2875248_+	P-II family nitrogen regulator	NA	NA	NA	NA	NA
WP_010931107.1|2879800_2880403_-	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010931108.1|2880499_2881789_+	MFS transporter	NA	NA	NA	NA	NA
WP_003812846.1|2881846_2882578_-	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	31.0	1.4e-12
WP_010931109.1|2882574_2883378_-	ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	23.5	7.9e-14
WP_003812851.1|2883374_2884463_-	ABC transporter ATP-binding protein	NA	NA	NA	NA	NA
WP_003820410.1|2884459_2885389_-	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_003812857.1|2885537_2886683_-	branched-chain amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_154698391.1|2887671_2887830_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010931110.1|2887984_2891806_-	trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase	NA	NA	NA	NA	NA
WP_010931111.1|2891962_2892631_-	membrane integrity-associated transporter subunit PqiC	NA	NA	NA	NA	NA
WP_014905522.1|2892635_2894309_-	MCE family protein	NA	NA	NA	NA	NA
WP_003820402.1|2894327_2895647_-	PqiA/YebS family transporter subunit	NA	NA	NA	NA	NA
WP_010931114.1|2895651_2897967_-|protease	ATP-dependent Clp protease ATP-binding subunit ClpA	protease	A0A223W0B1	Agrobacterium_phage	41.9	4.1e-164
WP_010931115.1|2898022_2900191_-	penicillin-binding protein 1C	NA	NA	NA	NA	NA
WP_023853340.1|2900187_2905368_-	alpha-2-macroglobulin family protein	NA	NA	NA	NA	NA
WP_003820400.1|2905466_2905781_-|protease	ATP-dependent Clp protease adapter ClpS	protease	A0A1B1IT64	uncultured_Mediterranean_phage	43.8	1.2e-10
WP_003812875.1|2906008_2906254_+	cold-shock protein	NA	A0A2H4N7Y6	Lake_Baikal_phage	76.6	1.3e-20
WP_003820399.1|2906348_2906867_+	hypothetical protein	NA	A0A1B1IUW8	uncultured_Mediterranean_phage	42.2	5.1e-14
WP_010931117.1|2906966_2908172_-	3-oxoadipyl-CoA thiolase	NA	NA	NA	NA	NA
WP_019247560.1|2908287_2909685_-	chloride channel protein	NA	NA	NA	NA	NA
WP_010931119.1|2909801_2910380_-	superoxide dismutase [Fe]	NA	NA	NA	NA	NA
WP_010931120.1|2910452_2911844_-	exodeoxyribonuclease VII large subunit	NA	A0A1V0SD82	Indivirus	32.0	1.4e-29
WP_005012067.1|2912011_2912962_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003812889.1|2913242_2913863_+	MotA/TolQ/ExbB proton channel family protein	NA	NA	NA	NA	NA
WP_010931122.1|2913859_2914273_+	biopolymer transporter ExbD	NA	NA	NA	NA	NA
WP_010931123.1|2914269_2915313_+	tetraacyldisaccharide 4'-kinase	NA	NA	NA	NA	NA
WP_003812895.1|2915368_2915557_+	Trm112 family protein	NA	NA	NA	NA	NA
WP_010931124.1|2915566_2916331_+	3-deoxy-manno-octulosonate cytidylyltransferase	NA	NA	NA	NA	NA
WP_010931125.1|2916421_2917078_+	adenylate kinase	NA	NA	NA	NA	NA
WP_010931126.1|2917169_2917928_+	3-hydroxyacyl-CoA dehydrogenase	NA	NA	NA	NA	NA
WP_010931127.1|2917953_2919555_+	murein biosynthesis integral membrane protein MurJ	NA	NA	NA	NA	NA
WP_010931128.1|2919755_2920760_+	DUF4880 domain-containing protein	NA	NA	NA	NA	NA
WP_003812908.1|2920860_2921124_+	30S ribosomal protein S20	NA	NA	NA	NA	NA
WP_010931129.1|2921241_2922018_-	2-dehydro-3-deoxyglucarate aldolase	NA	NA	NA	NA	NA
WP_005012067.1|2922608_2923559_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931130.1|2925942_2927055_-	Ldh family oxidoreductase	NA	NA	NA	NA	NA
WP_005012808.1|2927111_2928062_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 26
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	2958448	3002139	4108480	transposase	Planktothrix_phage(33.33%)	41	NA	NA
WP_005012067.1|2958448_2959399_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_162268686.1|2959416_2959566_+	hypothetical protein	NA	NA	NA	NA	NA
WP_023852715.1|2959519_2960416_-	inositol monophosphatase	NA	NA	NA	NA	NA
WP_003814547.1|2962693_2964919_+	glycoside hydrolase family 31 protein	NA	NA	NA	NA	NA
WP_003814544.1|2965083_2966172_+	ATP-binding cassette domain-containing protein	NA	G9BWD6	Planktothrix_phage	36.4	8.7e-32
WP_019247918.1|2966128_2966782_+	ABC transporter permease	NA	NA	NA	NA	NA
WP_010931144.1|2966829_2967627_+	MetQ/NlpA family ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010930176.1|2968158_2969109_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_023994659.1|2969189_2970338_+	iron-containing alcohol dehydrogenase	NA	NA	NA	NA	NA
WP_005012067.1|2970394_2971345_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003814535.1|2971443_2971749_-	antibiotic biosynthesis monooxygenase	NA	NA	NA	NA	NA
WP_003820797.1|2971777_2972212_-	DUF126 domain-containing protein	NA	NA	NA	NA	NA
WP_010931147.1|2972213_2973458_-	DUF521 domain-containing protein	NA	NA	NA	NA	NA
WP_003820799.1|2973454_2974165_-	FadR family transcriptional regulator	NA	NA	NA	NA	NA
WP_033446288.1|2974179_2975091_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010931149.1|2975453_2975858_+	hypothetical protein	NA	NA	NA	NA	NA
WP_019247890.1|2975854_2976313_+	hypothetical protein	NA	NA	NA	NA	NA
WP_019247891.1|2976319_2977228_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010931150.1|2977224_2978091_+	sugar ABC transporter permease	NA	NA	NA	NA	NA
WP_003814524.1|2978077_2978905_+	carbohydrate ABC transporter permease	NA	NA	NA	NA	NA
WP_003820806.1|2978915_2980043_+	ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	32.3	1.2e-23
WP_023852748.1|2981120_2982359_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931152.1|2982400_2983663_+	extracellular solute-binding protein	NA	NA	NA	NA	NA
WP_010931153.1|2983669_2984422_+	DNA-binding protein	NA	NA	NA	NA	NA
WP_019248355.1|2984473_2984659_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003820813.1|2984934_2985399_+	redox-sensitive transcriptional activator SoxR	NA	NA	NA	NA	NA
WP_003820814.1|2985430_2986090_+	DNA-3-methyladenine glycosylase I	NA	NA	NA	NA	NA
WP_010931154.1|2986234_2988343_+	AsmA family protein	NA	NA	NA	NA	NA
WP_023852714.1|2988339_2989290_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931155.1|2989393_2990014_-	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003820818.1|2990117_2990858_+	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_019248356.1|2991992_2993117_-	hypothetical protein	NA	NA	NA	NA	NA
WP_019247402.1|2993162_2993531_-	hypothetical protein	NA	NA	NA	NA	NA
WP_005012067.1|2993772_2994723_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_019247492.1|2995758_2996301_-	hypothetical protein	NA	NA	NA	NA	NA
WP_023998107.1|2996498_2996669_-	hypothetical protein	NA	NA	NA	NA	NA
WP_005012067.1|2996686_2997637_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931157.1|2997633_2998542_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003815281.1|2998668_2999505_+	3-methyl-2-oxobutanoate hydroxymethyltransferase	NA	A0A0P0BXC9	Ostreococcus_lucimarinus_virus	33.3	1.6e-33
WP_010931158.1|3000017_3001127_+	porin	NA	NA	NA	NA	NA
WP_005012067.1|3001188_3002139_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 27
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	3026050	3094747	4108480	tRNA,protease,transposase	Staphylococcus_phage(16.67%)	52	NA	NA
WP_023997744.1|3026050_3027337_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931177.1|3028223_3029126_+	transcriptional regulator GcvA	NA	NA	NA	NA	NA
WP_010931178.1|3029073_3030294_-	MFS transporter	NA	NA	NA	NA	NA
WP_010931179.1|3030290_3030800_-	nucleoside deaminase	NA	NA	NA	NA	NA
WP_010926062.1|3030789_3031485_-	ankyrin repeat domain-containing protein	NA	NA	NA	NA	NA
WP_010931181.1|3031555_3032425_+	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010930208.1|3032774_3033725_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_014486089.1|3034585_3035275_-	ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	28.8	4.8e-12
WP_003818691.1|3036051_3037014_-	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_014486091.1|3037017_3037878_-	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_003808978.1|3037871_3038264_-	hypothetical protein	NA	NA	NA	NA	NA
WP_014486094.1|3040918_3041716_+	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_014486095.1|3041749_3042529_-	SDR family NAD(P)-dependent oxidoreductase	NA	NA	NA	NA	NA
WP_014486096.1|3042557_3043430_-	polysaccharide deacetylase family protein	NA	NA	NA	NA	NA
WP_003818698.1|3043451_3044201_-	ABC transporter ATP-binding protein	NA	G3M9Y6	Bacillus_virus	33.5	6.2e-29
WP_014486097.1|3044208_3045066_-	ABC transporter permease	NA	NA	NA	NA	NA
WP_019247597.1|3045106_3045670_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_019247598.1|3045700_3045997_-	hypothetical protein	NA	NA	NA	NA	NA
WP_014486098.1|3046077_3046881_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
WP_003818702.1|3046901_3048098_-	CoA transferase	NA	NA	NA	NA	NA
WP_019247599.1|3048100_3049102_-	amidase	NA	NA	NA	NA	NA
WP_019249309.1|3049454_3049625_-	hypothetical protein	NA	NA	NA	NA	NA
WP_014486100.1|3049719_3050382_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010929577.1|3050484_3051435_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_005012067.1|3051533_3052484_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_003813006.1|3052480_3053557_-	AI-2E family transporter	NA	NA	NA	NA	NA
WP_010931182.1|3053601_3054354_-	DUF3053 domain-containing protein	NA	NA	NA	NA	NA
WP_003813010.1|3054916_3055198_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003813013.1|3055259_3055955_+	cytochrome b561	NA	NA	NA	NA	NA
WP_003813017.1|3056039_3056498_-	cytochrome c	NA	NA	NA	NA	NA
WP_010931184.1|3056560_3057937_-	adenylosuccinate lyase	NA	A0A2H4UUU6	Bodo_saltans_virus	47.5	2.2e-109
WP_010931185.1|3058096_3058708_+	glutathione S-transferase	NA	NA	NA	NA	NA
WP_003813022.1|3058805_3059624_-	sulfite exporter TauE/SafE family protein	NA	NA	NA	NA	NA
WP_003813026.1|3059724_3060840_-|tRNA	tRNA 2-thiouridine(34) synthase MnmA	tRNA	NA	NA	NA	NA
WP_010931186.1|3060852_3061773_-	LysR family transcriptional regulator	NA	Q6JIH3	Burkholderia_virus	30.5	2.7e-26
WP_010931187.1|3061943_3062930_+	tripartite tricarboxylate transporter substrate binding protein BugE	NA	NA	NA	NA	NA
WP_010931188.1|3062990_3063866_+	N-formylglutamate amidohydrolase	NA	NA	NA	NA	NA
WP_010931189.1|3064120_3065239_+	Re/Si-specific NAD(P)(+) transhydrogenase subunit alpha	NA	NA	NA	NA	NA
WP_003813039.1|3065555_3066992_+	NAD(P)(+) transhydrogenase (Re/Si-specific) subunit beta	NA	NA	NA	NA	NA
WP_033446272.1|3067035_3068046_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_010931191.1|3068221_3070435_+	TonB-dependent siderophore receptor	NA	NA	NA	NA	NA
WP_010931192.1|3070437_3071349_+	alpha/beta hydrolase	NA	NA	NA	NA	NA
WP_003813047.1|3071339_3072569_-	glycolate oxidase subunit GlcF	NA	NA	NA	NA	NA
WP_003813049.1|3072601_3073711_-	glycolate oxidase subunit GlcE	NA	NA	NA	NA	NA
WP_010931193.1|3073722_3075222_-	FAD-binding protein	NA	NA	NA	NA	NA
WP_010931194.1|3075356_3076766_-	FAD-binding protein	NA	NA	NA	NA	NA
WP_023853656.1|3076895_3089549_+	filamentous hemagglutinin N-terminal domain-containing protein	NA	A0A0R6PJK4	Moraxella_phage	30.5	1.2e-15
WP_003813056.1|3089570_3090644_-	3-deoxy-7-phosphoheptulonate synthase AroG	NA	A0A2I6UFP9	Klebsiella_phage	46.4	3.9e-77
WP_010931196.1|3090900_3092361_-|protease	metalloprotease TldD	protease	NA	NA	NA	NA
WP_010931197.1|3092371_3093202_-	carbon-nitrogen hydrolase family protein	NA	NA	NA	NA	NA
WP_010931198.1|3093326_3093698_+	H-NS histone family protein	NA	NA	NA	NA	NA
WP_005012067.1|3093796_3094747_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 29
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	3383132	3436873	4108480	transposase	Staphylococcus_phage(33.33%)	48	NA	NA
WP_023995489.1|3383132_3384083_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931336.1|3384487_3385132_-	urease accessory protein UreG	NA	NA	NA	NA	NA
WP_019247677.1|3385156_3385741_-	urease accessory protein UreF	NA	NA	NA	NA	NA
WP_014905506.1|3385841_3386459_-	urease accessory protein UreE	NA	NA	NA	NA	NA
WP_010931337.1|3386461_3388177_-	urease subunit alpha	NA	NA	NA	NA	NA
WP_010931338.1|3388173_3388482_-	urease subunit beta	NA	NA	NA	NA	NA
WP_003814828.1|3388498_3389116_-	HupE/UreJ family protein	NA	NA	NA	NA	NA
WP_010931340.1|3389160_3389463_-	urease subunit gamma	NA	NA	NA	NA	NA
WP_003814832.1|3389563_3390418_-	urease accessory protein UreD	NA	NA	NA	NA	NA
WP_124740609.1|3390605_3390830_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010929281.1|3390999_3391272_+	MerR family DNA-binding transcriptional regulator	NA	NA	NA	NA	NA
WP_010929282.1|3391689_3392097_-	GFA family protein	NA	NA	NA	NA	NA
WP_010931341.1|3392466_3393261_-	GntR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010927102.1|3393361_3394597_+	methylaspartate ammonia-lyase	NA	NA	NA	NA	NA
WP_003814852.1|3394665_3395682_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010931342.1|3395693_3397070_+	MmgE/PrpD family protein	NA	NA	NA	NA	NA
WP_003814856.1|3397066_3398263_+	MFS transporter	NA	NA	NA	NA	NA
WP_003814858.1|3398259_3399798_-	SpoVR family protein	NA	NA	NA	NA	NA
WP_010931343.1|3399794_3401054_-	YeaH/YhbH family protein	NA	NA	NA	NA	NA
WP_005012067.1|3402994_3403945_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931344.1|3404711_3405806_-	CoA transferase	NA	NA	NA	NA	NA
WP_019247312.1|3405798_3407133_-	AMP-binding protein	NA	NA	NA	NA	NA
WP_003808193.1|3407086_3407770_-	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA	NA
WP_024000003.1|3407795_3408959_-	acyl-CoA dehydrogenase C-terminal domain protein	NA	NA	NA	NA	NA
WP_004566224.1|3408955_3409957_-	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_010931346.1|3409956_3410829_-	branched-chain amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_010931347.1|3410825_3411575_-	ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	27.8	1.9e-09
WP_010931348.1|3411571_3412363_-	ATP-binding cassette domain-containing protein	NA	A0A1M7XV31	Cedratvirus	29.4	1.7e-08
WP_010931349.1|3412359_3413499_-	amino acid ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_047122778.1|3413774_3414560_+	SDR family NAD(P)-dependent oxidoreductase	NA	NA	NA	NA	NA
WP_014486103.1|3414593_3415376_+	crotonase/enoyl-CoA hydratase family protein	NA	NA	NA	NA	NA
WP_010931351.1|3415379_3415769_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010931352.1|3416908_3417772_+	3-alpha,7-alpha, 12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase	NA	NA	NA	NA	NA
WP_010931353.1|3417807_3418896_+	NAD(P)H-binding protein	NA	NA	NA	NA	NA
WP_010931070.1|3418892_3419843_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_019247959.1|3420196_3423175_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003818344.1|3424101_3424980_+	fatty acid desaturase	NA	NA	NA	NA	NA
WP_005013747.1|3426928_3427879_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931354.1|3427875_3428343_-	ribonuclease HI	NA	J9Q745	Salmonella_phage	50.7	5.6e-36
WP_010931355.1|3428385_3429156_-	methyltransferase domain-containing protein	NA	NA	NA	NA	NA
WP_010927090.1|3429176_3429977_+	hydroxyacylglutathione hydrolase	NA	NA	NA	NA	NA
WP_010931356.1|3429987_3431397_+	transglycosylase SLT domain-containing protein	NA	NA	NA	NA	NA
WP_003814739.1|3431491_3432277_+	enoyl-ACP reductase FabI	NA	NA	NA	NA	NA
WP_010931561.1|3432516_3433533_+|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_003814742.1|3433640_3434033_-	OsmC family protein	NA	NA	NA	NA	NA
WP_010931357.1|3434170_3434851_+	tellurite resistance TerB family protein	NA	NA	NA	NA	NA
WP_023994844.1|3434855_3435827_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010930179.1|3435922_3436873_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 30
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	3443028	3502326	4108480	tRNA,transposase	Acinetobacter_phage(27.27%)	47	NA	NA
WP_003820957.1|3443028_3444792_+|tRNA	glutamine--tRNA ligase/YqeY domain fusion protein	tRNA	A0A222YZ70	Escherichia_phage	50.0	5.0e-162
WP_010931362.1|3444903_3445782_+	septum site-determining protein MinC	NA	NA	NA	NA	NA
WP_003814250.1|3445894_3446710_+	septum site-determining protein MinD	NA	NA	NA	NA	NA
WP_003814252.1|3446713_3446965_+	cell division topological specificity factor MinE	NA	NA	NA	NA	NA
WP_010929632.1|3447049_3448066_-|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_003814254.1|3448396_3448618_-	glycine zipper 2TM domain-containing protein	NA	NA	NA	NA	NA
WP_019247693.1|3450978_3451896_-	DMT family transporter	NA	NA	NA	NA	NA
WP_019247692.1|3452393_3453602_-	ABC transporter permease	NA	NA	NA	NA	NA
WP_010931365.1|3453681_3455253_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_003814275.1|3455370_3456306_-	glycosyltransferase family 2 protein	NA	NA	NA	NA	NA
WP_003814277.1|3456494_3457439_+	LysR family transcriptional regulator	NA	A0A2P0ZL89	Lactobacillus_phage	23.2	8.4e-07
WP_003814283.1|3458006_3463724_+	excinuclease ABC subunit UvrA	NA	A0A1B1IVR3	uncultured_Mediterranean_phage	39.5	1.0e-195
WP_010931367.1|3463729_3464857_+	aminodeoxychorismate synthase component I	NA	S4VT78	Pandoravirus	37.8	3.8e-38
WP_003814287.1|3464912_3465539_+	hypothetical protein	NA	NA	NA	NA	NA
WP_010931363.1|3465810_3466827_+|transposase	IS110-like element IS1663 family transposase	transposase	NA	NA	NA	NA
WP_010927020.1|3466922_3467633_-	SDR family oxidoreductase	NA	NA	NA	NA	NA
WP_010931368.1|3467629_3468619_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_010931369.1|3468714_3470346_+	AMP-binding protein	NA	NA	NA	NA	NA
WP_010931370.1|3470348_3471086_+	GntR family transcriptional regulator	NA	NA	NA	NA	NA
WP_019247745.1|3471241_3472114_-|tRNA	tRNA threonylcarbamoyladenosine dehydratase	tRNA	NA	NA	NA	NA
WP_023852703.1|3472463_3473603_+	MFS transporter	NA	NA	NA	NA	NA
WP_003814300.1|3473599_3474259_+	gamma-glutamylcyclotransferase	NA	NA	NA	NA	NA
WP_003814302.1|3474330_3474963_+	pyridoxamine 5'-phosphate oxidase	NA	NA	NA	NA	NA
WP_010931372.1|3474992_3475511_+	flavin reductase family protein	NA	NA	NA	NA	NA
WP_010931373.1|3475521_3476631_+	NAD(P)/FAD-dependent oxidoreductase	NA	NA	NA	NA	NA
WP_003814312.1|3476677_3477532_+	formyltetrahydrofolate deformylase	NA	NA	NA	NA	NA
WP_010931374.1|3477533_3478436_-	LysR family transcriptional regulator	NA	NA	NA	NA	NA
WP_005012067.1|3479658_3480609_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_023997720.1|3482363_3483353_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931375.1|3483528_3484317_-	indole-3-glycerol phosphate synthase TrpC	NA	A0A0P0IR83	Acinetobacter_phage	53.0	5.1e-66
WP_003817833.1|3484313_3485345_-	anthranilate phosphoribosyltransferase	NA	A0A0N7IRD9	Acinetobacter_phage	42.7	7.4e-73
WP_003815390.1|3485363_3485927_-	aminodeoxychorismate/anthranilate synthase component II	NA	A0A0P0IKJ1	Acinetobacter_phage	62.1	1.1e-65
WP_010931376.1|3485982_3487503_-	anthranilate synthase component I	NA	S4VT78	Pandoravirus	32.1	9.0e-43
WP_010931377.1|3487766_3488471_-	phosphoglycolate phosphatase	NA	NA	NA	NA	NA
WP_023852620.1|3488478_3489207_-	ribulose-phosphate 3-epimerase	NA	NA	NA	NA	NA
WP_003815381.1|3489321_3489696_+	Co2+/Mg2+ efflux protein ApaG	NA	NA	NA	NA	NA
WP_003815379.1|3489738_3491028_+	murein transglycosylase A	NA	NA	NA	NA	NA
WP_010931378.1|3491024_3492194_+	UbiH/UbiF family hydroxylase	NA	NA	NA	NA	NA
WP_010931379.1|3492190_3493030_+	thiol:disulfide interchange protein DsbC	NA	NA	NA	NA	NA
WP_010931380.1|3493089_3494025_+	D-2-hydroxyacid dehydrogenase family protein	NA	A0A1J0F959	Only_Syngen_Nebraska_virus	27.7	6.4e-15
WP_005012067.1|3494037_3494988_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931381.1|3495086_3496049_-|tRNA	tRNA 2-thiocytidine(32) synthetase TtcA	tRNA	A0A0U2S5Z2	Escherichia_phage	64.5	4.6e-93
WP_003817821.1|3496080_3496440_-	dihydroneopterin aldolase	NA	NA	NA	NA	NA
WP_010931382.1|3496564_3497467_+	NAD(P)/FAD-dependent oxidoreductase	NA	G3MA85	Bacillus_virus	24.0	1.9e-08
WP_010931383.1|3497468_3499241_-	M61 family metallopeptidase	NA	NA	NA	NA	NA
WP_003815367.1|3499275_3500052_+	enoyl-CoA hydratase	NA	NA	NA	NA	NA
WP_023852617.1|3501375_3502326_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 31
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	3517264	3575337	4108480	tRNA,transposase	Planktothrix_phage(12.5%)	47	NA	NA
WP_005012808.1|3517264_3518215_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931392.1|3518343_3519477_-	M20 family metallopeptidase	NA	NA	NA	NA	NA
WP_010931393.1|3519520_3520426_-	hydrolase	NA	NA	NA	NA	NA
WP_023852622.1|3520428_3522129_-	ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	32.7	1.0e-15
WP_010931394.1|3522125_3523046_-	ABC transporter permease	NA	NA	NA	NA	NA
WP_003817805.1|3523053_3524031_-	ABC transporter permease	NA	NA	NA	NA	NA
WP_010931395.1|3524089_3525124_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003815317.1|3527098_3527335_-	hypothetical protein	NA	NA	NA	NA	NA
WP_023995266.1|3527461_3528325_-	NAD(P)H-hydrate dehydratase	NA	NA	NA	NA	NA
WP_003815315.1|3528413_3529235_+	enoyl-CoA hydratase/isomerase family protein	NA	NA	NA	NA	NA
WP_003815313.1|3529314_3530052_-	enoyl-CoA hydratase	NA	NA	NA	NA	NA
WP_010931397.1|3530048_3531041_-	nitronate monooxygenase	NA	NA	NA	NA	NA
WP_010931398.1|3531193_3531817_+	TetR/AcrR family transcriptional regulator	NA	NA	NA	NA	NA
WP_010931399.1|3531861_3533010_+	acyl-CoA dehydrogenase	NA	NA	NA	NA	NA
WP_010931400.1|3535333_3536284_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_014486105.1|3536624_3537575_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_005013747.1|3537673_3538624_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_029443756.1|3538920_3539418_+	cupredoxin family protein	NA	NA	NA	NA	NA
WP_010931403.1|3539460_3541236_+	copper resistance system multicopper oxidase	NA	NA	NA	NA	NA
WP_010931404.1|3541243_3542110_+	copper resistance protein B	NA	NA	NA	NA	NA
WP_019249391.1|3542116_3542851_-	enoyl-CoA hydratase/isomerase family protein	NA	NA	NA	NA	NA
WP_010931406.1|3544020_3544815_-	IclR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003815296.1|3545104_3545695_+	cysteine dioxygenase	NA	NA	NA	NA	NA
WP_010931407.1|3545728_3547057_-	amidase	NA	NA	NA	NA	NA
WP_010931408.1|3547131_3548277_-	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_014905478.1|3548388_3549387_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_033446233.1|3549349_3549784_+	carbon monoxide dehydrogenase	NA	NA	NA	NA	NA
WP_010929974.1|3551300_3552185_+	DMT family transporter	NA	NA	NA	NA	NA
WP_010929973.1|3552181_3553387_-	cardiolipin synthase ClsB	NA	NA	NA	NA	NA
WP_010929972.1|3553383_3554244_-	endonuclease	NA	NA	NA	NA	NA
WP_003807038.1|3554356_3556147_-|tRNA	aspartate--tRNA ligase	tRNA	A0A1V0SAC0	Catovirus	25.5	6.5e-08
WP_033446243.1|3556187_3556832_-	DUF502 domain-containing protein	NA	A0A2I7S9X1	Vibrio_phage	28.4	8.5e-11
WP_010929971.1|3556853_3557162_-	FmdB family transcriptional regulator	NA	NA	NA	NA	NA
WP_010929970.1|3557327_3558614_-	membrane protein	NA	NA	NA	NA	NA
WP_077108686.1|3560047_3560998_-|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929968.1|3562949_3564164_-	formate-dependent phosphoribosylglycinamide formyltransferase	NA	NA	NA	NA	NA
WP_003815171.1|3564269_3565259_+	KpsF/GutQ family sugar-phosphate isomerase	NA	A0A2P0VNK5	Tetraselmis_virus	37.7	4.3e-38
WP_003815172.1|3565255_3565864_+	HAD-IIIA family hydrolase	NA	E3T535	Cafeteria_roenbergensis_virus	26.1	5.2e-10
WP_010929967.1|3565876_3566506_+	LPS export ABC transporter periplasmic protein LptC	NA	NA	NA	NA	NA
WP_003815175.1|3566502_3567123_+	lipopolysaccharide transport periplasmic protein LptA	NA	NA	NA	NA	NA
WP_003815177.1|3567154_3567946_+	LPS export ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	27.4	9.5e-20
WP_010929966.1|3568797_3569253_+	PTS transporter subunit EIIA	NA	NA	NA	NA	NA
WP_010929965.1|3569271_3570198_+	HPr kinase/phosphorylase	NA	NA	NA	NA	NA
WP_010929964.1|3570251_3571538_-	cytochrome c	NA	NA	NA	NA	NA
WP_003815183.1|3572468_3573341_+	RNase adapter RapZ	NA	A0A1P8D5W0	Corynebacterium_phage	34.5	2.4e-08
WP_010929963.1|3573337_3574288_+	septal ring lytic transglycosylase RlpA family protein	NA	F5B3X9	Synechococcus_phage	47.2	6.9e-17
WP_005012067.1|3574386_3575337_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
>prophage 33
NZ_CP013888	Bordetella pertussis strain J104 chromosome, complete genome	4108480	4007548	4072459	4108480	transposase	Planktothrix_phage(40.0%)	59	NA	NA
WP_039249574.1|4007548_4008034_+|transposase	transposase	transposase	NA	NA	NA	NA
WP_153302797.1|4008122_4008260_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010931647.1|4008252_4009233_+	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_019248461.1|4009499_4010309_+	pertussis toxin ADP-ribosyltransferase subunit PtxA	NA	NA	NA	NA	NA
WP_014906114.1|4010348_4011029_+	pertussis toxin binding subunit PtxB	NA	NA	NA	NA	NA
WP_010929491.1|4011022_4011481_+	pertussis toxin subunit 4	NA	NA	NA	NA	NA
WP_023853616.1|4011492_4011855_+	pertussis toxin binding subunit PtxD	NA	NA	NA	NA	NA
WP_010931651.1|4011937_4012621_+	pertussis toxin binding subunit PtxE	NA	NA	NA	NA	NA
WP_010929493.1|4012676_4012985_+	type IV secretion system protein PtlA	NA	NA	NA	NA	NA
WP_010929494.1|4013003_4013318_+	type IV secretion system protein PtlB	NA	NA	NA	NA	NA
WP_010931652.1|4013314_4015789_+	type IV secretion system protein PtlC	NA	NA	NA	NA	NA
WP_010929497.1|4017183_4017369_+	type IV secretion system protein PtlI	NA	NA	NA	NA	NA
WP_010929498.1|4017347_4018049_+	type IV secretion system peptidoglycanase PtlE	NA	NA	NA	NA	NA
WP_010931654.1|4018045_4018867_+	type IV secretion system protein PtlF	NA	NA	NA	NA	NA
WP_010931655.1|4018847_4019972_+	type IV secretion system protein PtlG	NA	NA	NA	NA	NA
WP_010929500.1|4019964_4020984_+	type IV secretion system protein PtlH	NA	NA	NA	NA	NA
WP_010931656.1|4021189_4022080_-	DMT family transporter	NA	NA	NA	NA	NA
WP_010929501.1|4022324_4023116_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_003815873.1|4023198_4023573_+	DUF1232 domain-containing protein	NA	NA	NA	NA	NA
WP_010931658.1|4023550_4024960_+	DUF2868 domain-containing protein	NA	NA	NA	NA	NA
WP_003815876.1|4024952_4026335_+	GTPase/DUF3482 domain-containing protein	NA	A0A0R6PHS5	Moraxella_phage	38.9	9.9e-57
WP_003815878.1|4026669_4028274_+	ABC transporter substrate-binding protein	NA	NA	NA	NA	NA
WP_010931659.1|4028351_4029323_+	ABC transporter permease	NA	NA	NA	NA	NA
WP_010931660.1|4029333_4030260_+	ABC transporter permease	NA	NA	NA	NA	NA
WP_010931661.1|4030650_4031601_-|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010931662.1|4031770_4032997_+	bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ	NA	NA	NA	NA	NA
WP_010931663.1|4033196_4034063_+	ATP-binding protein	NA	NA	NA	NA	NA
WP_003815027.1|4034055_4035018_+	Nudix family hydrolase	NA	A0A221LFJ1	Barns_Ness_breadcrumb_sponge_sobemo-like_virus	53.4	1.9e-06
WP_010927663.1|4035118_4036069_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
WP_005012067.1|4036167_4037118_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_010929577.1|4037216_4038167_+|transposase	IS481-like element IS481 family transposase	transposase	NA	NA	NA	NA
WP_023994937.1|4038163_4039657_-	efflux transporter outer membrane subunit	NA	NA	NA	NA	NA
WP_003815032.1|4039653_4042761_-	multidrug efflux RND transporter permease subunit	NA	NA	NA	NA	NA
WP_010931665.1|4042757_4045826_-	MdtB/MuxB family multidrug efflux RND transporter permease subunit	NA	NA	NA	NA	NA
WP_010931666.1|4045822_4047073_-	MdtA/MuxA family multidrug efflux RND transporter periplasmic adaptor subunit	NA	NA	NA	NA	NA
WP_023853184.1|4047253_4048006_-	cell division protein ZapD	NA	NA	NA	NA	NA
WP_010931667.1|4048047_4048692_-	dephospho-CoA kinase	NA	NA	NA	NA	NA
WP_010931668.1|4048700_4049681_-	prepilin peptidase	NA	NA	NA	NA	NA
WP_003815047.1|4049780_4050524_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003815049.1|4050606_4050954_-	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_003815051.1|4051051_4051894_-	pantoate--beta-alanine ligase	NA	NA	NA	NA	NA
WP_003815053.1|4051938_4052826_-	segregation/condensation protein A	NA	NA	NA	NA	NA
WP_003815055.1|4052852_4053041_-	DUF3460 family protein	NA	NA	NA	NA	NA
WP_010931669.1|4053138_4054596_+	DHA2 family efflux MFS transporter permease subunit	NA	NA	NA	NA	NA
WP_010931670.1|4054582_4056109_+	glycerol kinase GlpK	NA	NA	NA	NA	NA
WP_003815061.1|4056127_4056595_-	membrane protein	NA	NA	NA	NA	NA
WP_010931671.1|4056594_4057617_-	tripartite tricarboxylate transporter substrate binding protein	NA	NA	NA	NA	NA
WP_003815064.1|4057737_4058478_-	amino acid ABC transporter ATP-binding protein	NA	G9BWD6	Planktothrix_phage	39.7	4.4e-35
WP_003815066.1|4058532_4059633_-	amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_003815068.1|4059634_4060825_-	amino acid ABC transporter permease	NA	NA	NA	NA	NA
WP_003815070.1|4060944_4061961_-	amino acid ABC transporter substrate-binding protein	NA	A0A1B1IT51	uncultured_Mediterranean_phage	42.1	1.0e-71
WP_003815073.1|4062279_4062951_+	ATP-binding cassette domain-containing protein	NA	G9BWD6	Planktothrix_phage	38.2	9.5e-29
WP_010927126.1|4062947_4063856_+	FtsX-like permease family protein	NA	NA	NA	NA	NA
WP_010931672.1|4064067_4064715_+	chemoreceptor glutamine deamidase CheD	NA	NA	NA	NA	NA
WP_033446142.1|4068575_4069643_+	A/G-specific adenine glycosylase	NA	NA	NA	NA	NA
WP_003815084.1|4069653_4070463_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_023999981.1|4070552_4071326_+	class I SAM-dependent methyltransferase	NA	NA	NA	NA	NA
WP_023853189.1|4071326_4071491_-	hypothetical protein	NA	NA	NA	NA	NA
WP_010930363.1|4071508_4072459_+|transposase	IS481 family transposase	transposase	NA	NA	NA	NA
