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
GCF_001686485.1_ASM168648v1	NZ_CP015764	Bordetella pertussis strain VA-198, complete genome	1	31195-31289	1	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh	Orphan	TAAAAGGGCACCCGCAAGGGTGTCCTTTT	29	0	0	NA	NA	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh	NA|127aa|up_2|NZ_CP015764.1_29181_29562_+,NA	NA|310aa|up_9|NZ_CP015764.1_16711_17641_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP015764.1_17884_19711_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP015764.1_19793_20435_+	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|NZ_CP015764.1_20624_21659_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP015764.1_23495_24560_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP015764.1_25357_26266_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP015764.1_27753_29028_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP015764.1_29181_29562_+	NA	NA|291aa|up_1|NZ_CP015764.1_29569_30442_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP015764.1_30747_31128_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP015764.1_31338_32064_+	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|NZ_CP015764.1_32159_33110_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP015764.1_33214_34264_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP015764.1_34401_35418_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP015764.1_36926_37499_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|NZ_CP015764.1_37558_38290_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|NZ_CP015764.1_38341_39259_-	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|NZ_CP015764.1_40066_43246_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|NZ_CP015764.1_43242_44625_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|NZ_CP015764.1_44694_44946_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_001686485.1_ASM168648v1	NZ_CP015764	Bordetella pertussis strain VA-198, complete genome	2	1210581-1210708	2	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh	NA,NA	NA|152aa|up_9|NZ_CP015764.1_1199489_1199945_+	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|NZ_CP015764.1_1199958_1200762_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP015764.1_1200758_1201190_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP015764.1_1201186_1202344_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP015764.1_1202365_1203142_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|NZ_CP015764.1_1205306_1206023_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP015764.1_1206015_1206657_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP015764.1_1206691_1207423_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|NZ_CP015764.1_1207440_1207653_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|NZ_CP015764.1_1208223_1209174_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|NZ_CP015764.1_1210731_1211460_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP015764.1_1211510_1212713_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP015764.1_1212790_1214827_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP015764.1_1215079_1215571_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP015764.1_1215786_1216299_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP015764.1_1216316_1217528_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP015764.1_1217565_1217976_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP015764.1_1217977_1218301_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP015764.1_1218303_1218816_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP015764.1_1218945_1220808_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_001686485.1_ASM168648v1	NZ_CP015764	Bordetella pertussis strain VA-198, complete genome	3	2467330-2467439	3	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh	NA|138aa|up_8|NZ_CP015764.1_2453629_2454043_-,NA	NA|317aa|up_9|NZ_CP015764.1_2452692_2453643_-	pfam00665, rve, Integrase core domain	NA|138aa|up_8|NZ_CP015764.1_2453629_2454043_-	NA	NA|993aa|up_7|NZ_CP015764.1_2453996_2456975_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP015764.1_2457901_2458780_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP015764.1_2460728_2461679_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP015764.1_2461675_2462143_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP015764.1_2462185_2462956_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP015764.1_2462976_2463777_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP015764.1_2463787_2465197_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP015764.1_2465291_2466077_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP015764.1_2467440_2467833_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP015764.1_2467970_2468651_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|NZ_CP015764.1_2468655_2469654_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|NZ_CP015764.1_2469722_2470673_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP015764.1_2472177_2472879_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP015764.1_2472878_2474303_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|NZ_CP015764.1_2475372_2476713_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|NZ_CP015764.1_2476828_2478592_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|NZ_CP015764.1_2478703_2479582_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|NZ_CP015764.1_2479694_2480510_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
GCF_001686485.1_ASM168648v1	NZ_CP015764	Bordetella pertussis strain VA-198, complete genome	4	2841812-2841896	4	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh	Orphan	CTGTCCCCGCGGGGACAGGCACC	23	0	0	NA	NA	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh	NA,NA	NA|585aa|up_9|NZ_CP015764.1_2829769_2831524_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|300aa|up_8|NZ_CP015764.1_2831630_2832530_+	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|NZ_CP015764.1_2832594_2833578_-	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|327aa|up_6|NZ_CP015764.1_2833713_2834694_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|NZ_CP015764.1_2834710_2836102_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|NZ_CP015764.1_2836253_2836790_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|462aa|up_3|NZ_CP015764.1_2836720_2838106_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|213aa|up_2|NZ_CP015764.1_2838248_2838887_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|NZ_CP015764.1_2838973_2840863_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|NZ_CP015764.1_2840859_2841801_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|NZ_CP015764.1_2841906_2842956_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|NZ_CP015764.1_2843208_2843910_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|NZ_CP015764.1_2843906_2844605_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|NZ_CP015764.1_2844605_2845961_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|NZ_CP015764.1_2845957_2846449_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|NZ_CP015764.1_2846467_2847424_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|701aa|down_6|NZ_CP015764.1_2848834_2850937_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|348aa|down_7|NZ_CP015764.1_2851107_2852151_+	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|NZ_CP015764.1_2852194_2852938_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|137aa|down_9|NZ_CP015764.1_2853959_2854370_-	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase
GCF_001686485.1_ASM168648v1	NZ_CP015764	Bordetella pertussis strain VA-198, complete genome	5	3577465-3577558	5	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh	Orphan	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh	NA|132aa|up_8|NZ_CP015764.1_3569493_3569889_+,NA	NA|134aa|up_9|NZ_CP015764.1_3569095_3569497_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|132aa|up_8|NZ_CP015764.1_3569493_3569889_+	NA	NA|131aa|up_7|NZ_CP015764.1_3569885_3570278_+	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|387aa|up_6|NZ_CP015764.1_3570288_3571449_+	cd01160, LCAD, Long chain acyl-CoA dehydrogenase	NA|324aa|up_5|NZ_CP015764.1_3571486_3572458_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|383aa|up_4|NZ_CP015764.1_3572465_3573614_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|297aa|up_3|NZ_CP015764.1_3573610_3574501_-	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|316aa|up_2|NZ_CP015764.1_3574707_3575655_+	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|317aa|up_1|NZ_CP015764.1_3575753_3576704_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP015764.1_3576835_3577234_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP015764.1_3577644_3578115_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP015764.1_3578203_3578548_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP015764.1_3578647_3580048_-	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|NZ_CP015764.1_3581836_3582355_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP015764.1_3582465_3583221_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP015764.1_3583416_3584649_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP015764.1_3584641_3585427_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP015764.1_3585493_3586465_+	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|NZ_CP015764.1_3586475_3587453_-	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|NZ_CP015764.1_3587578_3588751_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
