assembly_id	genome_id	genome_def	crispr_array_locus_merge	crispr_array_location_merge	crispr_locus_id	crispr_pred_method	array_in_prot	prot_within_array_20000	prot_in_genome	crispr_type_by_cas_prot	consensus_repeat	repeat_length	self-targeting_spacer_number	self-targeting_target_number	spacer_location	protospacer_location	repeat_type	spacer_locus_num	spacer_num	correct_crispr_type	genome_cas_prots	unknown_protein_around_crispr	L10	L10_domain	L9	L9_domain	L8	L8_domain	L7	L7_domain	L6	L6_domain	L5	L5_domain	L4	L4_domain	L3	L3_domain	L2	L2_domain	L1	L1_domain	R1	R1_domain	R2	R2_domain	R3	R3_domain	R4	R4_domain	R5	R5_domain	R6	R6_domain	R7	R7_domain	R8	R8_domain	R9	R9_domain	R10	R10_domain
GCA_004007155.1_ASM400715v1	CP025344	Bordetella pertussis strain J077 chromosome, complete genome	1	250584-250668	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	GGTGCCTGTCCCCGCGGGGACAG	23	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|137aa|up_9|CP025344.1_238109_238520_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|CP025344.1_239541_240285_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|CP025344.1_240328_241372_-	cd13602, PBP2_TRAP_BpDctp6_7, Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold	NA|701aa|up_6|CP025344.1_241542_243645_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|CP025344.1_245055_246012_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|CP025344.1_246030_246522_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|CP025344.1_246518_247874_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|CP025344.1_247874_248573_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|CP025344.1_248569_249271_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|CP025344.1_249523_250573_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|CP025344.1_250678_251620_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|CP025344.1_251616_253506_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|CP025344.1_253592_254231_+	PRK10847, PRK10847, DedA family protein	NA|415aa|down_3|CP025344.1_254373_255618_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|CP025344.1_255689_256226_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|CP025344.1_256377_257769_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|CP025344.1_257785_258766_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|CP025344.1_258901_259885_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|CP025344.1_259949_260849_-	cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold	NA|585aa|down_9|CP025344.1_260955_262710_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_004007155.1_ASM400715v1	CP025344	Bordetella pertussis strain J077 chromosome, complete genome	2	432026-432119	2	CRISPRCasFinder	no	DEDDh	DEDDh,csa3,cas3,DinG	Unclear	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|353aa|up_9|CP025344.1_419365_420424_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|CP025344.1_420553_421048_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|CP025344.1_421140_422118_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|CP025344.1_422313_423519_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|CP025344.1_423515_425027_+	cd13520, PBP2_TAXI_TRAP, Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold	NA|438aa|up_4|CP025344.1_425042_426356_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|CP025344.1_426546_426726_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|CP025344.1_427135_427870_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|CP025344.1_430314_431265_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|CP025344.1_431396_431795_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|CP025344.1_432205_432676_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|CP025344.1_432764_433109_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|CP025344.1_433208_434609_-	COG1167, ARO8, Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]	NA|173aa|down_3|CP025344.1_436397_436916_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|CP025344.1_437026_437782_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|CP025344.1_437977_439210_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|CP025344.1_439202_439988_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|CP025344.1_440054_441026_+	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold	NA|326aa|down_8|CP025344.1_441036_442014_-	cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold	NA|391aa|down_9|CP025344.1_442139_443312_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCA_004007155.1_ASM400715v1	CP025344	Bordetella pertussis strain J077 chromosome, complete genome	3	996341-996435	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TAAAAGGGCACCCGCAAGGGTGTCCTTTT	29	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|127aa|up_2|CP025344.1_994327_994708_+,NA	NA|310aa|up_9|CP025344.1_981857_982787_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|CP025344.1_983030_984857_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|CP025344.1_984939_985581_+	cd03016, PRX_1cys, Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine	NA|345aa|up_6|CP025344.1_985770_986805_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|CP025344.1_988641_989706_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|CP025344.1_990503_991412_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|CP025344.1_992899_994174_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|CP025344.1_994327_994708_+	NA	NA|291aa|up_1|CP025344.1_994715_995588_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|CP025344.1_995893_996274_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|CP025344.1_996484_997210_+	cd03426, CoAse, Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes	NA|317aa|down_1|CP025344.1_997305_998256_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|CP025344.1_998360_999410_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|CP025344.1_999547_1000564_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|CP025344.1_1002072_1002645_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|CP025344.1_1002704_1003436_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|CP025344.1_1003487_1004405_-	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain	NA|1060aa|down_7|CP025344.1_1005212_1008392_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|CP025344.1_1008388_1009771_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|CP025344.1_1009840_1010092_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCA_004007155.1_ASM400715v1	CP025344	Bordetella pertussis strain J077 chromosome, complete genome	4	3433499-3433608	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|123aa|up_8|CP025344.1_3419798_3420167_-,NA	NA|363aa|up_9|CP025344.1_3417777_3418866_+	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs	NA|123aa|up_8|CP025344.1_3419798_3420167_-	NA	NA|993aa|up_7|CP025344.1_3420165_3423144_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|CP025344.1_3424070_3424949_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|CP025344.1_3426897_3427848_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|CP025344.1_3427844_3428312_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|CP025344.1_3428354_3429125_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|CP025344.1_3429145_3429946_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|CP025344.1_3429956_3431366_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|CP025344.1_3431460_3432246_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|CP025344.1_3433609_3434002_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|CP025344.1_3434139_3434820_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|CP025344.1_3434824_3435823_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|CP025344.1_3435891_3436842_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|CP025344.1_3438346_3439048_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|CP025344.1_3439047_3440472_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|352aa|down_6|CP025344.1_3440488_3441544_-	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|447aa|down_7|CP025344.1_3441540_3442881_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_8|CP025344.1_3442996_3444760_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_9|CP025344.1_3444871_3445750_+	PRK00030, minC, septum site-determining protein MinC
