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_001686505.1_ASM168650v1	NZ_CP015765	Bordetella pertussis strain VA-09, complete genome	1	676659-676752	1	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA|132aa|up_8|NZ_CP015765.1_668687_669083_+,NA	NA|134aa|up_9|NZ_CP015765.1_668289_668691_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|132aa|up_8|NZ_CP015765.1_668687_669083_+	NA	NA|131aa|up_7|NZ_CP015765.1_669079_669472_+	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|387aa|up_6|NZ_CP015765.1_669482_670643_+	cd01160, LCAD, Long chain acyl-CoA dehydrogenase	NA|324aa|up_5|NZ_CP015765.1_670680_671652_+	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_CP015765.1_671659_672808_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|297aa|up_3|NZ_CP015765.1_672804_673695_-	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_CP015765.1_673901_674849_+	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|317aa|up_1|NZ_CP015765.1_674947_675898_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP015765.1_676029_676428_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP015765.1_676838_677309_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP015765.1_677397_677742_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP015765.1_677841_679242_-	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_CP015765.1_681030_681549_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP015765.1_681659_682415_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP015765.1_682610_683843_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP015765.1_683835_684621_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP015765.1_684687_685659_+	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_CP015765.1_685669_686647_-	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_CP015765.1_686772_687945_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_001686505.1_ASM168650v1	NZ_CP015765	Bordetella pertussis strain VA-09, complete genome	2	1240975-1241069	2	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	TAAAAGGGCACCCGCAAGGGTGTCCTTTT	29	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA|127aa|up_2|NZ_CP015765.1_1238961_1239342_+,NA	NA|310aa|up_9|NZ_CP015765.1_1226491_1227421_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP015765.1_1227664_1229491_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP015765.1_1229573_1230215_+	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_CP015765.1_1230404_1231439_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP015765.1_1233275_1234340_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP015765.1_1235137_1236046_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP015765.1_1237533_1238808_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP015765.1_1238961_1239342_+	NA	NA|291aa|up_1|NZ_CP015765.1_1239349_1240222_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP015765.1_1240527_1240908_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP015765.1_1241118_1241844_+	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_CP015765.1_1241939_1242890_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP015765.1_1242994_1244044_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP015765.1_1244181_1245198_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP015765.1_1246706_1247279_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|NZ_CP015765.1_1247338_1248070_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|NZ_CP015765.1_1248121_1249039_-	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_CP015765.1_1249846_1253026_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|NZ_CP015765.1_1253022_1254405_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|NZ_CP015765.1_1254474_1254726_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_001686505.1_ASM168650v1	NZ_CP015765	Bordetella pertussis strain VA-09, complete genome	3	2136359-2136486	3	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA,NA	NA|152aa|up_9|NZ_CP015765.1_2125267_2125723_+	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_CP015765.1_2125736_2126540_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP015765.1_2126536_2126968_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP015765.1_2126964_2128122_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP015765.1_2128143_2128920_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|NZ_CP015765.1_2131084_2131801_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP015765.1_2131793_2132435_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP015765.1_2132469_2133201_+	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_CP015765.1_2133218_2133431_+	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_CP015765.1_2134001_2134952_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|NZ_CP015765.1_2136509_2137238_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP015765.1_2137288_2138491_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP015765.1_2138568_2140605_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP015765.1_2140857_2141349_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP015765.1_2141564_2142077_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP015765.1_2142094_2143306_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP015765.1_2143343_2143754_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP015765.1_2143755_2144079_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP015765.1_2144081_2144594_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP015765.1_2144723_2146586_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_001686505.1_ASM168650v1	NZ_CP015765	Bordetella pertussis strain VA-09, complete genome	4	3673975-3674084	4	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA|138aa|up_8|NZ_CP015765.1_3660274_3660688_-,NA	NA|317aa|up_9|NZ_CP015765.1_3659337_3660288_-	pfam00665, rve, Integrase core domain	NA|138aa|up_8|NZ_CP015765.1_3660274_3660688_-	NA	NA|993aa|up_7|NZ_CP015765.1_3660641_3663620_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP015765.1_3664546_3665425_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP015765.1_3667373_3668324_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP015765.1_3668320_3668788_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP015765.1_3668830_3669601_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP015765.1_3669621_3670422_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP015765.1_3670432_3671842_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP015765.1_3671936_3672722_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP015765.1_3674085_3674478_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP015765.1_3674615_3675296_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|NZ_CP015765.1_3675300_3676299_-	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_CP015765.1_3676367_3677318_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP015765.1_3678822_3679524_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP015765.1_3679523_3680948_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|NZ_CP015765.1_3682017_3683358_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|NZ_CP015765.1_3683473_3685237_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|NZ_CP015765.1_3685348_3686227_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|NZ_CP015765.1_3686339_3687155_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
GCF_001686505.1_ASM168650v1	NZ_CP015765	Bordetella pertussis strain VA-09, complete genome	5	4057207-4057291	5	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	CTGTCCCCGCGGGGACAGGCACC	23	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA,NA	NA|585aa|up_9|NZ_CP015765.1_4045164_4046919_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|300aa|up_8|NZ_CP015765.1_4047025_4047925_+	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_CP015765.1_4047989_4048973_-	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_CP015765.1_4049108_4050089_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|NZ_CP015765.1_4050105_4051497_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|NZ_CP015765.1_4051648_4052185_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|462aa|up_3|NZ_CP015765.1_4052115_4053501_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|213aa|up_2|NZ_CP015765.1_4053643_4054282_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|NZ_CP015765.1_4054368_4056258_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|NZ_CP015765.1_4056254_4057196_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|NZ_CP015765.1_4057301_4058351_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|NZ_CP015765.1_4058603_4059305_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|NZ_CP015765.1_4059301_4060000_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|NZ_CP015765.1_4060000_4061356_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|NZ_CP015765.1_4061352_4061844_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|NZ_CP015765.1_4061862_4062819_-	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_CP015765.1_4064229_4066332_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|348aa|down_7|NZ_CP015765.1_4066502_4067546_+	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_CP015765.1_4067589_4068333_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|137aa|down_9|NZ_CP015765.1_4069354_4069765_-	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase
