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_002442735.1_ASM244273v1	NZ_CP017164	Bordetella pertussis strain J224 chromosome, complete genome	1	250581-250665	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|NZ_CP017164.1_238106_238517_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|NZ_CP017164.1_239538_240282_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|NZ_CP017164.1_240325_241369_-	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|NZ_CP017164.1_241539_243642_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|NZ_CP017164.1_245052_246009_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|NZ_CP017164.1_246027_246519_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|NZ_CP017164.1_246515_247871_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|NZ_CP017164.1_247871_248570_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|NZ_CP017164.1_248566_249268_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|NZ_CP017164.1_249520_250570_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NZ_CP017164.1_250675_251617_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NZ_CP017164.1_251613_253503_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NZ_CP017164.1_253589_254228_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NZ_CP017164.1_254370_255756_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NZ_CP017164.1_255686_256223_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NZ_CP017164.1_256374_257766_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NZ_CP017164.1_257782_258763_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NZ_CP017164.1_258898_259882_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|NZ_CP017164.1_259946_260846_-	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|NZ_CP017164.1_260952_262707_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_002442735.1_ASM244273v1	NZ_CP017164	Bordetella pertussis strain J224 chromosome, complete genome	2	432020-432113	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|NZ_CP017164.1_419359_420418_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|NZ_CP017164.1_420547_421042_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|NZ_CP017164.1_421134_422112_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|NZ_CP017164.1_422307_423513_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|NZ_CP017164.1_423509_425021_+	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|NZ_CP017164.1_425036_426350_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|NZ_CP017164.1_426540_426720_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|NZ_CP017164.1_427129_427864_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|NZ_CP017164.1_430308_431259_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP017164.1_431390_431789_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP017164.1_432199_432670_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP017164.1_432758_433103_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP017164.1_433202_434603_-	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_CP017164.1_436391_436910_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP017164.1_437020_437776_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP017164.1_437971_439204_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP017164.1_439196_439982_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP017164.1_440048_441020_+	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_CP017164.1_441030_442008_-	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_CP017164.1_442133_443306_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_002442735.1_ASM244273v1	NZ_CP017164	Bordetella pertussis strain J224 chromosome, complete genome	3	996328-996422	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|NZ_CP017164.1_994314_994695_+,NA	NA|310aa|up_9|NZ_CP017164.1_981845_982775_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP017164.1_983018_984845_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP017164.1_984927_985569_+	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_CP017164.1_985758_986793_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP017164.1_988628_989693_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP017164.1_990490_991399_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP017164.1_992886_994161_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP017164.1_994314_994695_+	NA	NA|291aa|up_1|NZ_CP017164.1_994702_995575_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP017164.1_995880_996261_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP017164.1_996471_997197_+	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_CP017164.1_997292_998243_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP017164.1_998347_999397_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP017164.1_999534_1000551_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP017164.1_1002059_1002632_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|NZ_CP017164.1_1002691_1003423_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|NZ_CP017164.1_1003474_1004392_-	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_CP017164.1_1005199_1008379_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|NZ_CP017164.1_1008375_1009758_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|NZ_CP017164.1_1009827_1010079_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_002442735.1_ASM244273v1	NZ_CP017164	Bordetella pertussis strain J224 chromosome, complete genome	4	1146789-1146922	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	CCCCTTGGGGGGCAGCAAGCCCGCACAGCGGGCGCAGCGTGGGGGCCTTTT	51	1	3	1146840-1146871|1146840-1146871|1146840-1146871	NZ_CP017164.1_1354689-1354658|NZ_CP017164.1_1819737-1819768|NZ_CP017164.1_1996929-1996898	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|101aa|up_9|NZ_CP017164.1_1133768_1134071_-,NA	NA|101aa|up_9|NZ_CP017164.1_1133768_1134071_-	NA	NA|507aa|up_8|NZ_CP017164.1_1134113_1135634_-	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed	NA|252aa|up_7|NZ_CP017164.1_1135640_1136396_-	PRK07023, PRK07023, SDR family oxidoreductase	NA|368aa|up_6|NZ_CP017164.1_1136425_1137530_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|567aa|up_5|NZ_CP017164.1_1137632_1139333_-	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|326aa|up_4|NZ_CP017164.1_1139314_1140292_-	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|427aa|up_3|NZ_CP017164.1_1140301_1141582_+	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|232aa|up_2|NZ_CP017164.1_1141574_1142270_+	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein	NA|276aa|up_1|NZ_CP017164.1_1142303_1143131_+	cd01310, TatD_DNAse, TatD like proteins;  E	NA|1077aa|up_0|NZ_CP017164.1_1143412_1146643_+	pfam03797, Autotransporter, Autotransporter beta-domain	NA|1309aa|down_0|NZ_CP017164.1_1147376_1151303_+	pfam11924, IAT_beta, Inverse autotransporter, beta-domain	NA|599aa|down_1|NZ_CP017164.1_1153202_1154999_+	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|323aa|down_2|NZ_CP017164.1_1154998_1155967_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|282aa|down_3|NZ_CP017164.1_1156036_1156882_+	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]	NA|185aa|down_4|NZ_CP017164.1_1156949_1157504_+	PRK01885, greB, transcription elongation factor GreB; Reviewed	NA|317aa|down_5|NZ_CP017164.1_1157550_1158501_-	pfam00665, rve, Integrase core domain	NA|211aa|down_6|NZ_CP017164.1_1158599_1159232_-	pfam16970, FimA, Type-1 fimbrial protein, A	NA|761aa|down_7|NZ_CP017164.1_1159396_1161679_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|899aa|down_8|NZ_CP017164.1_1161833_1164530_-	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional	NA|163aa|down_9|NZ_CP017164.1_1164655_1165144_+	COG1522, Lrp, Transcriptional regulators [Transcription]
GCF_002442735.1_ASM244273v1	NZ_CP017164	Bordetella pertussis strain J224 chromosome, complete genome	5	1819762-1819889	5	CRISPRCasFinder	no	csa3	DEDDh,csa3,cas3,DinG	Type I-A	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|79aa|up_2|NZ_CP017164.1_1815970_1816207_+,NA	NA|150aa|up_9|NZ_CP017164.1_1807657_1808107_-	cd03443, PaaI_thioesterase, PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria	csa3|100aa|up_8|NZ_CP017164.1_1808314_1808614_+	COG0640, ArsR, Predicted transcriptional regulators [Transcription]	NA|371aa|up_7|NZ_CP017164.1_1808666_1809779_+	cd02933, OYE_like_FMN, Old yellow enzyme (OYE)-like FMN binding domain	NA|213aa|up_6|NZ_CP017164.1_1809783_1810422_-	pfam13994, PgaD, PgaD-like protein	NA|420aa|up_5|NZ_CP017164.1_1810402_1811662_-	PRK11204, PRK11204, N-glycosyltransferase; Provisional	NA|702aa|up_4|NZ_CP017164.1_1811665_1813771_-	TIGR03938, hypothetical_protein_Pcar_2791, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB	NA|662aa|up_3|NZ_CP017164.1_1813776_1815762_-	TIGR03939, PGA_TPR_OMP, poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA	NA|79aa|up_2|NZ_CP017164.1_1815970_1816207_+	NA	NA|162aa|up_1|NZ_CP017164.1_1816551_1817037_+	COG1846, MarR, Transcriptional regulators [Transcription]	NA|317aa|up_0|NZ_CP017164.1_1817404_1818355_+	pfam00665, rve, Integrase core domain	NA|217aa|down_0|NZ_CP017164.1_1819912_1820563_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP017164.1_1820691_1821894_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP017164.1_1821971_1824008_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP017164.1_1824260_1824752_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP017164.1_1824967_1825480_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP017164.1_1825497_1826709_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP017164.1_1826746_1827157_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP017164.1_1827158_1827482_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP017164.1_1827484_1827997_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP017164.1_1828126_1829989_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_002442735.1_ASM244273v1	NZ_CP017164	Bordetella pertussis strain J224 chromosome, complete genome	6	3432390-3432499	6	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|288aa|up_9|NZ_CP017164.1_3415769_3416633_+	PLN02864, PLN02864, enoyl-CoA hydratase	NA|363aa|up_8|NZ_CP017164.1_3416668_3417757_+	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs	NA|993aa|up_7|NZ_CP017164.1_3419056_3422035_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP017164.1_3422961_3423840_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP017164.1_3425788_3426739_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP017164.1_3426735_3427203_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP017164.1_3427245_3428016_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP017164.1_3428036_3428837_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP017164.1_3428847_3430257_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP017164.1_3430351_3431137_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP017164.1_3432500_3432893_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP017164.1_3433030_3433711_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|NZ_CP017164.1_3433715_3434687_-	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_CP017164.1_3434782_3435733_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP017164.1_3437237_3437939_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP017164.1_3437938_3439363_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|NZ_CP017164.1_3440432_3441773_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|NZ_CP017164.1_3441888_3443652_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|NZ_CP017164.1_3443763_3444642_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|NZ_CP017164.1_3444754_3445570_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
