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_004009575.1_ASM400957v1	CP025477	Bordetella pertussis strain I859 chromosome, complete genome	1	250590-250674	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|CP025477.1_238115_238526_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|CP025477.1_239547_240291_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|CP025477.1_240334_241378_-	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|CP025477.1_241548_243651_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|CP025477.1_245061_246018_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|CP025477.1_246036_246528_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|CP025477.1_246524_247880_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|CP025477.1_247880_248579_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|CP025477.1_248575_249277_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|CP025477.1_249529_250579_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|CP025477.1_250684_251626_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|CP025477.1_251622_253512_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|CP025477.1_253598_254237_+	PRK10847, PRK10847, DedA family protein	NA|415aa|down_3|CP025477.1_254379_255624_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|CP025477.1_255695_256232_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|CP025477.1_256383_257775_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|CP025477.1_257791_258772_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|CP025477.1_258907_259891_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|CP025477.1_259955_260855_-	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|CP025477.1_260961_262716_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_004009575.1_ASM400957v1	CP025477	Bordetella pertussis strain I859 chromosome, complete genome	2	432033-432126	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|CP025477.1_419372_420431_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|CP025477.1_420560_421055_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|CP025477.1_421147_422125_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|CP025477.1_422320_423526_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|CP025477.1_423522_425034_+	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|CP025477.1_425049_426363_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|CP025477.1_426553_426733_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|CP025477.1_427142_427877_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|CP025477.1_430321_431272_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|CP025477.1_431403_431802_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|CP025477.1_432212_432683_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|CP025477.1_432771_433116_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|CP025477.1_433215_434616_-	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|CP025477.1_436404_436923_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|CP025477.1_437033_437789_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|CP025477.1_437984_439217_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|CP025477.1_439209_439995_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|CP025477.1_440061_441033_+	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|CP025477.1_441043_442021_-	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|CP025477.1_442146_443319_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCA_004009575.1_ASM400957v1	CP025477	Bordetella pertussis strain I859 chromosome, complete genome	3	995302-995396	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|CP025477.1_993288_993669_+,NA	NA|310aa|up_9|CP025477.1_980818_981748_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|CP025477.1_981991_983818_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|CP025477.1_983900_984542_+	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|CP025477.1_984731_985766_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|CP025477.1_987602_988667_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|CP025477.1_989464_990373_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|CP025477.1_991860_993135_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|CP025477.1_993288_993669_+	NA	NA|291aa|up_1|CP025477.1_993676_994549_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|CP025477.1_994854_995235_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|CP025477.1_995445_996171_+	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|CP025477.1_996266_997217_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|CP025477.1_997321_998371_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|CP025477.1_998508_999525_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|CP025477.1_1001033_1001606_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|CP025477.1_1001665_1002397_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|CP025477.1_1002448_1003366_-	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|CP025477.1_1004173_1007353_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|CP025477.1_1007349_1008732_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|CP025477.1_1008801_1009053_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCA_004009575.1_ASM400957v1	CP025477	Bordetella pertussis strain I859 chromosome, complete genome	4	1820855-1820982	4	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|CP025477.1_1817063_1817300_+,NA	NA|150aa|up_9|CP025477.1_1808750_1809200_-	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|CP025477.1_1809407_1809707_+	COG0640, ArsR, Predicted transcriptional regulators [Transcription]	NA|371aa|up_7|CP025477.1_1809759_1810872_+	cd02933, OYE_like_FMN, Old yellow enzyme (OYE)-like FMN binding domain	NA|213aa|up_6|CP025477.1_1810876_1811515_-	pfam13994, PgaD, PgaD-like protein	NA|420aa|up_5|CP025477.1_1811495_1812755_-	PRK11204, PRK11204, N-glycosyltransferase; Provisional	NA|702aa|up_4|CP025477.1_1812758_1814864_-	TIGR03938, hypothetical_protein_Pcar_2791, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB	NA|662aa|up_3|CP025477.1_1814869_1816855_-	TIGR03939, PGA_TPR_OMP, poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA	NA|79aa|up_2|CP025477.1_1817063_1817300_+	NA	NA|162aa|up_1|CP025477.1_1817644_1818130_+	COG1846, MarR, Transcriptional regulators [Transcription]	NA|317aa|up_0|CP025477.1_1818497_1819448_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|CP025477.1_1821005_1821734_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|CP025477.1_1821784_1822987_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|CP025477.1_1823064_1825101_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|CP025477.1_1825353_1825845_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|CP025477.1_1826060_1826573_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|CP025477.1_1826590_1827802_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|CP025477.1_1827839_1828250_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|CP025477.1_1828251_1828575_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|CP025477.1_1828577_1829090_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|CP025477.1_1829219_1831082_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCA_004009575.1_ASM400957v1	CP025477	Bordetella pertussis strain I859 chromosome, complete genome	5	3432482-3432591	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|123aa|up_8|CP025477.1_3418781_3419150_-,NA	NA|317aa|up_9|CP025477.1_3417844_3418795_-	pfam00665, rve, Integrase core domain	NA|123aa|up_8|CP025477.1_3418781_3419150_-	NA	NA|993aa|up_7|CP025477.1_3419148_3422127_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|CP025477.1_3423053_3423932_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|CP025477.1_3425880_3426831_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|CP025477.1_3426827_3427295_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|CP025477.1_3427337_3428108_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|CP025477.1_3428128_3428929_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|CP025477.1_3428939_3430349_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|CP025477.1_3430443_3431229_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|CP025477.1_3432592_3432985_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|CP025477.1_3433122_3433803_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|CP025477.1_3433807_3434806_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|CP025477.1_3434874_3435825_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|CP025477.1_3437329_3438031_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|CP025477.1_3438030_3439455_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|CP025477.1_3440524_3441865_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|CP025477.1_3441980_3443744_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|CP025477.1_3443855_3444734_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|CP025477.1_3444846_3445662_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
