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_001686465.1_ASM168646v1	NZ_CP015763	Bordetella pertussis strain VA-52, complete genome	1	357127-357254	1	CRISPRCasFinder	no		csa3,DEDDh,cas3,DinG	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA,NA	NA|152aa|up_9|NZ_CP015763.1_346035_346491_+	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_CP015763.1_346504_347308_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP015763.1_347304_347736_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP015763.1_347732_348890_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP015763.1_348911_349688_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|NZ_CP015763.1_351852_352569_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP015763.1_352561_353203_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP015763.1_353237_353969_+	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_CP015763.1_353986_354199_+	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_CP015763.1_354769_355720_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|NZ_CP015763.1_357277_358006_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP015763.1_358056_359259_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP015763.1_359336_361373_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP015763.1_361625_362117_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP015763.1_362332_362845_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP015763.1_362862_364074_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP015763.1_364111_364522_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP015763.1_364523_364847_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP015763.1_364849_365362_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP015763.1_365491_367354_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_001686465.1_ASM168646v1	NZ_CP015763	Bordetella pertussis strain VA-52, complete genome	2	1894740-1894849	2	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|NZ_CP015763.1_1881039_1881453_-,NA	NA|317aa|up_9|NZ_CP015763.1_1880102_1881053_-	pfam00665, rve, Integrase core domain	NA|138aa|up_8|NZ_CP015763.1_1881039_1881453_-	NA	NA|993aa|up_7|NZ_CP015763.1_1881406_1884385_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP015763.1_1885311_1886190_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP015763.1_1888138_1889089_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP015763.1_1889085_1889553_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP015763.1_1889595_1890366_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP015763.1_1890386_1891187_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP015763.1_1891197_1892607_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP015763.1_1892701_1893487_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP015763.1_1894850_1895243_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP015763.1_1895380_1896061_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|NZ_CP015763.1_1896065_1897064_-	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_CP015763.1_1897132_1898083_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP015763.1_1899587_1900289_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP015763.1_1900288_1901713_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|NZ_CP015763.1_1902782_1904123_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|NZ_CP015763.1_1904238_1906002_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|NZ_CP015763.1_1906113_1906992_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|NZ_CP015763.1_1907104_1907920_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
GCF_001686465.1_ASM168646v1	NZ_CP015763	Bordetella pertussis strain VA-52, complete genome	3	2268173-2268257	3	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|NZ_CP015763.1_2256130_2257885_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|300aa|up_8|NZ_CP015763.1_2257991_2258891_+	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_CP015763.1_2258955_2259939_-	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_CP015763.1_2260074_2261055_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|NZ_CP015763.1_2261071_2262463_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|NZ_CP015763.1_2262614_2263151_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|462aa|up_3|NZ_CP015763.1_2263081_2264467_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|213aa|up_2|NZ_CP015763.1_2264609_2265248_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|NZ_CP015763.1_2265334_2267224_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|NZ_CP015763.1_2267220_2268162_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|NZ_CP015763.1_2268267_2269317_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|NZ_CP015763.1_2269569_2270271_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|NZ_CP015763.1_2270267_2270966_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|NZ_CP015763.1_2270966_2272322_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|NZ_CP015763.1_2272318_2272810_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|NZ_CP015763.1_2272828_2273785_-	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_CP015763.1_2275195_2277298_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|348aa|down_7|NZ_CP015763.1_2277468_2278512_+	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_CP015763.1_2278555_2279299_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|137aa|down_9|NZ_CP015763.1_2280320_2280731_-	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase
GCF_001686465.1_ASM168646v1	NZ_CP015763	Bordetella pertussis strain VA-52, complete genome	4	3001728-3001821	4	CRISPRCasFinder	no		csa3,DEDDh,cas3,DinG	Orphan	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA|132aa|up_8|NZ_CP015763.1_2993756_2994152_+,NA	NA|134aa|up_9|NZ_CP015763.1_2993358_2993760_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|132aa|up_8|NZ_CP015763.1_2993756_2994152_+	NA	NA|131aa|up_7|NZ_CP015763.1_2994148_2994541_+	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|387aa|up_6|NZ_CP015763.1_2994551_2995712_+	cd01160, LCAD, Long chain acyl-CoA dehydrogenase	NA|324aa|up_5|NZ_CP015763.1_2995749_2996721_+	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_CP015763.1_2996728_2997877_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|297aa|up_3|NZ_CP015763.1_2997873_2998764_-	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_CP015763.1_2998970_2999918_+	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|317aa|up_1|NZ_CP015763.1_3000016_3000967_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP015763.1_3001098_3001497_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP015763.1_3001907_3002378_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP015763.1_3002466_3002811_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP015763.1_3002910_3004311_-	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_CP015763.1_3006099_3006618_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP015763.1_3006728_3007484_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP015763.1_3007679_3008912_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP015763.1_3008904_3009690_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP015763.1_3009756_3010728_+	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_CP015763.1_3010738_3011716_-	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_CP015763.1_3011841_3013014_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_001686465.1_ASM168646v1	NZ_CP015763	Bordetella pertussis strain VA-52, complete genome	5	3566041-3566135	5	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|NZ_CP015763.1_3564027_3564408_+,NA	NA|310aa|up_9|NZ_CP015763.1_3551557_3552487_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP015763.1_3552730_3554557_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP015763.1_3554639_3555281_+	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_CP015763.1_3555470_3556505_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP015763.1_3558341_3559406_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP015763.1_3560203_3561112_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP015763.1_3562599_3563874_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP015763.1_3564027_3564408_+	NA	NA|291aa|up_1|NZ_CP015763.1_3564415_3565288_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP015763.1_3565593_3565974_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP015763.1_3566184_3566910_+	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_CP015763.1_3567005_3567956_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP015763.1_3568060_3569110_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP015763.1_3569247_3570264_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP015763.1_3571772_3572345_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|NZ_CP015763.1_3572404_3573136_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|NZ_CP015763.1_3573187_3574105_-	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_CP015763.1_3574912_3578092_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|NZ_CP015763.1_3578088_3579471_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|NZ_CP015763.1_3579540_3579792_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
