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_004008475.1_ASM400847v1	CP025353	Bordetella pertussis strain J024 chromosome, complete genome	1	252682-252766	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|CP025353.1_240207_240618_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|CP025353.1_241639_242383_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|CP025353.1_242426_243470_-	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|CP025353.1_243640_245743_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|CP025353.1_247153_248110_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|CP025353.1_248128_248620_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|CP025353.1_248616_249972_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|CP025353.1_249972_250671_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|CP025353.1_250667_251369_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|CP025353.1_251621_252671_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|CP025353.1_252776_253718_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|CP025353.1_253714_255604_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|CP025353.1_255690_256329_+	PRK10847, PRK10847, DedA family protein	NA|415aa|down_3|CP025353.1_256471_257716_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|CP025353.1_257787_258324_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|CP025353.1_258475_259867_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|CP025353.1_259883_260864_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|CP025353.1_260999_261983_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|CP025353.1_262047_262947_-	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|CP025353.1_263053_264808_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_004008475.1_ASM400847v1	CP025353	Bordetella pertussis strain J024 chromosome, complete genome	2	435174-435267	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|CP025353.1_422513_423572_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|CP025353.1_423701_424196_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|CP025353.1_424288_425266_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|CP025353.1_425461_426667_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|CP025353.1_426663_428175_+	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|CP025353.1_428190_429504_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|CP025353.1_429694_429874_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|CP025353.1_430283_431018_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|CP025353.1_433462_434413_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|CP025353.1_434544_434943_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|CP025353.1_435353_435824_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|CP025353.1_435912_436257_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|CP025353.1_436356_437757_-	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|CP025353.1_439545_440064_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|CP025353.1_440174_440930_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|CP025353.1_441125_442358_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|CP025353.1_442350_443136_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|CP025353.1_443202_444174_+	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|CP025353.1_444184_445162_-	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|CP025353.1_445287_446460_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCA_004008475.1_ASM400847v1	CP025353	Bordetella pertussis strain J024 chromosome, complete genome	3	1000540-1000634	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|CP025353.1_998526_998907_+,NA	NA|310aa|up_9|CP025353.1_986056_986986_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|CP025353.1_987229_989056_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|CP025353.1_989138_989780_+	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|CP025353.1_989969_991004_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|CP025353.1_992840_993905_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|CP025353.1_994702_995611_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|CP025353.1_997098_998373_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|CP025353.1_998526_998907_+	NA	NA|291aa|up_1|CP025353.1_998914_999787_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|CP025353.1_1000092_1000473_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|CP025353.1_1000683_1001409_+	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|CP025353.1_1001504_1002455_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|CP025353.1_1002559_1003609_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|CP025353.1_1003746_1004763_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|CP025353.1_1006271_1006844_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|CP025353.1_1006903_1007635_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|CP025353.1_1007686_1008604_-	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|CP025353.1_1009411_1012591_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|CP025353.1_1012587_1013970_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|CP025353.1_1014039_1014291_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCA_004008475.1_ASM400847v1	CP025353	Bordetella pertussis strain J024 chromosome, complete genome	4	1895924-1896051	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|152aa|up_9|CP025353.1_1884832_1885288_+	cd03450, NodN, NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit	NA|268aa|up_8|CP025353.1_1885301_1886105_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|CP025353.1_1886101_1886533_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|CP025353.1_1886529_1887687_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|CP025353.1_1887708_1888485_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|CP025353.1_1890649_1891366_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|CP025353.1_1891358_1892000_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|CP025353.1_1892034_1892766_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|CP025353.1_1892783_1892996_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|CP025353.1_1893566_1894517_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|CP025353.1_1896074_1896803_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|CP025353.1_1896853_1898056_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|CP025353.1_1898133_1900170_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|CP025353.1_1900422_1900914_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|CP025353.1_1901129_1901642_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|CP025353.1_1901659_1902871_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|CP025353.1_1902908_1903319_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|CP025353.1_1903320_1903644_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|CP025353.1_1903646_1904159_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|CP025353.1_1904288_1906151_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCA_004008475.1_ASM400847v1	CP025353	Bordetella pertussis strain J024 chromosome, complete genome	5	3433524-3433633	5	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|CP025353.1_3419823_3420192_-,NA	NA|317aa|up_9|CP025353.1_3418886_3419837_-	pfam00665, rve, Integrase core domain	NA|123aa|up_8|CP025353.1_3419823_3420192_-	NA	NA|993aa|up_7|CP025353.1_3420190_3423169_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|CP025353.1_3424095_3424974_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|CP025353.1_3426922_3427873_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|CP025353.1_3427869_3428337_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|CP025353.1_3428379_3429150_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|CP025353.1_3429170_3429971_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|CP025353.1_3429981_3431391_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|CP025353.1_3431485_3432271_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|CP025353.1_3433634_3434027_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|CP025353.1_3434164_3434845_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|CP025353.1_3434849_3435848_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|CP025353.1_3435916_3436867_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|CP025353.1_3438371_3439073_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|CP025353.1_3439072_3440497_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|CP025353.1_3441566_3442907_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|CP025353.1_3443022_3444786_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|CP025353.1_3444897_3445776_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|CP025353.1_3445888_3446704_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
