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_003860305.1_ASM386030v1	CP034182	Bordetella pertussis strain BPD1 chromosome, complete genome	1	396362-396455	1	CRISPRCasFinder	no	DEDDh	csa3,DEDDh,cas3,DinG	Unclear	GTGCCTGTCCCGGCGGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA,NA	NA|391aa|up_9|CP034182.1_385168_386341_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|326aa|up_8|CP034182.1_386466_387444_+	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|324aa|up_7|CP034182.1_387454_388426_-	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold	NA|262aa|up_6|CP034182.1_388492_389278_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|411aa|up_5|CP034182.1_389270_390503_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|252aa|up_4|CP034182.1_390698_391454_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_3|CP034182.1_391564_392083_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|467aa|up_2|CP034182.1_393871_395272_+	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|115aa|up_1|CP034182.1_395371_395716_+	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|157aa|up_0|CP034182.1_395804_396275_+	pfam00582, Usp, Universal stress protein family	NA|133aa|down_0|CP034182.1_396685_397084_+	PRK00007, PRK00007, elongation factor G; Reviewed	NA|317aa|down_1|CP034182.1_397215_398166_-	pfam00665, rve, Integrase core domain	DEDDh|245aa|down_2|CP034182.1_400610_401345_+	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|60aa|down_3|CP034182.1_401754_401934_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|438aa|down_4|CP034182.1_402124_403438_+	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|504aa|down_5|CP034182.1_403453_404965_-	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|402aa|down_6|CP034182.1_404961_406167_-	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|326aa|down_7|CP034182.1_406362_407340_-	pfam00665, rve, Integrase core domain	NA|165aa|down_8|CP034182.1_407432_407927_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|353aa|down_9|CP034182.1_408056_409115_+	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1
GCA_003860305.1_ASM386030v1	CP034182	Bordetella pertussis strain BPD1 chromosome, complete genome	2	577814-577898	2	CRISPRCasFinder	no		csa3,DEDDh,cas3,DinG	Orphan	CTGTCCCCGCGGGGACAGGCACC	23	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA,NA	NA|585aa|up_9|CP034182.1_565771_567526_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|300aa|up_8|CP034182.1_567632_568532_+	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|328aa|up_7|CP034182.1_568596_569580_-	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|327aa|up_6|CP034182.1_569715_570696_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|CP034182.1_570712_572104_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|CP034182.1_572255_572792_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|415aa|up_3|CP034182.1_572863_574108_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|213aa|up_2|CP034182.1_574250_574889_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|CP034182.1_574975_576865_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|CP034182.1_576861_577803_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|CP034182.1_577908_578958_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|CP034182.1_579210_579912_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|CP034182.1_579908_580607_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|CP034182.1_580607_581963_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|CP034182.1_581959_582451_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|CP034182.1_582469_583426_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|701aa|down_6|CP034182.1_584836_586939_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|348aa|down_7|CP034182.1_587109_588153_+	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|248aa|down_8|CP034182.1_588196_588940_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|137aa|down_9|CP034182.1_589961_590372_-	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase
GCA_003860305.1_ASM386030v1	CP034182	Bordetella pertussis strain BPD1 chromosome, complete genome	3	922067-922161	3	CRISPRCasFinder	no		csa3,DEDDh,cas3,DinG	Orphan	TAAAAGGGCACCCGCAAGGGTGTCCTTTT	29	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA|127aa|up_2|CP034182.1_920053_920434_+,NA	NA|310aa|up_9|CP034182.1_907564_908494_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|CP034182.1_908737_910564_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|CP034182.1_910646_911288_+	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|CP034182.1_911477_912512_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|300aa|up_5|CP034182.1_914348_915248_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|CP034182.1_916229_917138_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|CP034182.1_918625_919900_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|CP034182.1_920053_920434_+	NA	NA|291aa|up_1|CP034182.1_920441_921314_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|CP034182.1_921619_922000_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|CP034182.1_922210_922936_+	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|CP034182.1_923031_923982_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|CP034182.1_924086_925136_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|CP034182.1_925273_926290_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|CP034182.1_927798_928371_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|CP034182.1_928430_929162_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|CP034182.1_929213_930131_-	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|CP034182.1_930938_934118_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|84aa|down_8|CP034182.1_935567_935819_-	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|217aa|down_9|CP034182.1_935964_936615_-	cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold
GCA_003860305.1_ASM386030v1	CP034182	Bordetella pertussis strain BPD1 chromosome, complete genome	4	3335430-3335539	4	CRISPRCasFinder	no		csa3,DEDDh,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA|138aa|up_8|CP034182.1_3321729_3322143_-,NA	NA|317aa|up_9|CP034182.1_3320792_3321743_-	pfam00665, rve, Integrase core domain	NA|138aa|up_8|CP034182.1_3321729_3322143_-	NA	NA|993aa|up_7|CP034182.1_3322096_3325075_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|CP034182.1_3326001_3326880_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|CP034182.1_3328828_3329779_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|CP034182.1_3329775_3330243_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|CP034182.1_3330285_3331056_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|CP034182.1_3331076_3331877_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|CP034182.1_3331887_3333297_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|CP034182.1_3333391_3334177_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|CP034182.1_3335540_3335933_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|CP034182.1_3336070_3336751_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|CP034182.1_3336755_3337754_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|CP034182.1_3337822_3338773_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|CP034182.1_3340277_3340979_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|CP034182.1_3340978_3342403_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|CP034182.1_3343472_3344813_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|CP034182.1_3344928_3346692_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|CP034182.1_3346803_3347682_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|CP034182.1_3347794_3348610_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
