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_002859205.1_ASM285920v1	CP018039	Bordetella pertussis strain J294 chromosome, complete genome	1	250584-250668	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|252aa|up_9|CP018039.1_238769_239525_+	PRK15461, PRK15461, sulfolactaldehyde 3-reductase	NA|248aa|up_8|CP018039.1_239541_240285_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|CP018039.1_240328_241372_-	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|420aa|up_6|CP018039.1_242385_243645_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|CP018039.1_245055_246012_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|CP018039.1_246030_246522_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|CP018039.1_246518_247874_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|CP018039.1_247874_248573_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|CP018039.1_248569_249271_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|CP018039.1_249523_250573_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|CP018039.1_250678_251620_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|CP018039.1_251616_253506_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|207aa|down_2|CP018039.1_253610_254231_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|CP018039.1_254373_255759_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|CP018039.1_255689_256226_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|CP018039.1_256377_257769_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|CP018039.1_257785_258766_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|CP018039.1_258901_259885_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|CP018039.1_259949_260849_-	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|CP018039.1_260955_262710_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_002859205.1_ASM285920v1	CP018039	Bordetella pertussis strain J294 chromosome, complete genome	2	432024-432117	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|CP018039.1_419363_420422_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|CP018039.1_420551_421046_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|CP018039.1_421138_422116_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|CP018039.1_422311_423517_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|CP018039.1_423513_425025_+	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|CP018039.1_425040_426354_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|CP018039.1_426544_426724_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|CP018039.1_427133_427868_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|301aa|up_1|CP018039.1_430360_431263_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|CP018039.1_431394_431793_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|CP018039.1_432203_432674_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|CP018039.1_432762_433107_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|CP018039.1_433206_434607_-	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|CP018039.1_436395_436914_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|CP018039.1_437024_437780_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|CP018039.1_437975_439208_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|CP018039.1_439200_439986_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|CP018039.1_440052_441024_+	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|CP018039.1_441034_442012_-	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|CP018039.1_442137_443310_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCA_002859205.1_ASM285920v1	CP018039	Bordetella pertussis strain J294 chromosome, complete genome	3	996336-996430	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|CP018039.1_994322_994703_+,NA	NA|345aa|up_9|CP018039.1_985765_986800_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|68aa|up_8|CP018039.1_986815_987019_+	TIGR02139, permease_CysT, sulfate ABC transporter, permease protein CysT	NA|225aa|up_7|CP018039.1_987040_987715_+	TIGR02139, permease_CysT, sulfate ABC transporter, permease protein CysT	NA|261aa|up_6|CP018039.1_987829_988612_+	COG4208, CysW, ABC-type sulfate transport system, permease component [Inorganic ion transport and metabolism]	NA|355aa|up_5|CP018039.1_988636_989701_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|CP018039.1_990498_991407_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|CP018039.1_992894_994169_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|CP018039.1_994322_994703_+	NA	NA|291aa|up_1|CP018039.1_994710_995583_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|CP018039.1_995888_996269_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|229aa|down_0|CP018039.1_996518_997205_+	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|CP018039.1_997300_998251_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|CP018039.1_998355_999405_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|CP018039.1_999542_1000559_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|CP018039.1_1002067_1002640_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|CP018039.1_1002699_1003431_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|CP018039.1_1003482_1004400_-	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|CP018039.1_1005207_1008387_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|CP018039.1_1008383_1009766_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|CP018039.1_1009835_1010087_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCA_002859205.1_ASM285920v1	CP018039	Bordetella pertussis strain J294 chromosome, complete genome	4	1819234-1819361	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_4|CP018039.1_1815442_1815679_+,NA|120aa|up_1|CP018039.1_1817823_1818183_-,NA	NA|371aa|up_9|CP018039.1_1808138_1809251_+	cd02933, OYE_like_FMN, Old yellow enzyme (OYE)-like FMN binding domain	NA|213aa|up_8|CP018039.1_1809255_1809894_-	pfam13994, PgaD, PgaD-like protein	NA|420aa|up_7|CP018039.1_1809874_1811134_-	PRK11204, PRK11204, N-glycosyltransferase; Provisional	NA|702aa|up_6|CP018039.1_1811137_1813243_-	TIGR03938, hypothetical_protein_Pcar_2791, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB	NA|662aa|up_5|CP018039.1_1813248_1815234_-	TIGR03939, PGA_TPR_OMP, poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA	NA|79aa|up_4|CP018039.1_1815442_1815679_+	NA	NA|162aa|up_3|CP018039.1_1816023_1816509_+	COG1846, MarR, Transcriptional regulators [Transcription]	NA|317aa|up_2|CP018039.1_1816876_1817827_+	pfam00665, rve, Integrase core domain	NA|120aa|up_1|CP018039.1_1817823_1818183_-	NA	NA|310aa|up_0|CP018039.1_1818228_1819158_+	TIGR01414, Contains:_AIDA-I_translocator, outer membrane autotransporter barrel domain	NA|217aa|down_0|CP018039.1_1819384_1820035_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|CP018039.1_1820163_1821366_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|CP018039.1_1821443_1823480_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|CP018039.1_1823732_1824224_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|CP018039.1_1824439_1824952_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|CP018039.1_1824969_1826181_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|CP018039.1_1826218_1826629_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|CP018039.1_1826630_1826954_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|CP018039.1_1826956_1827469_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|CP018039.1_1827598_1829461_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCA_002859205.1_ASM285920v1	CP018039	Bordetella pertussis strain J294 chromosome, complete genome	5	3433971-3434080	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|993aa|up_9|CP018039.1_3420637_3423616_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_8|CP018039.1_3424542_3425421_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|111aa|up_7|CP018039.1_3425456_3425789_+	PRK06816, PRK06816, StlD/DarB family beta-ketosynthase	NA|507aa|up_6|CP018039.1_3425767_3427288_+	PRK06816, PRK06816, StlD/DarB family beta-ketosynthase	NA|317aa|up_5|CP018039.1_3427369_3428320_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|CP018039.1_3428316_3428784_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|CP018039.1_3428826_3429597_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|CP018039.1_3429617_3430418_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|CP018039.1_3430428_3431838_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|CP018039.1_3431932_3432718_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|CP018039.1_3434081_3434474_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|CP018039.1_3434611_3435292_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|CP018039.1_3435296_3436268_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|301aa|down_3|CP018039.1_3436363_3437266_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|CP018039.1_3438818_3439520_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|CP018039.1_3439519_3440944_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|352aa|down_6|CP018039.1_3440960_3442016_-	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|447aa|down_7|CP018039.1_3442012_3443353_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_8|CP018039.1_3443468_3445232_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_9|CP018039.1_3445343_3446222_+	PRK00030, minC, septum site-determining protein MinC
