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_002859785.1_ASM285978v1	CP018040	Bordetella pertussis strain J304 chromosome, complete genome	1	250574-250658	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|CP018040.1_238759_239515_+	PRK15461, PRK15461, sulfolactaldehyde 3-reductase	NA|248aa|up_8|CP018040.1_239531_240275_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|CP018040.1_240318_241362_-	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|CP018040.1_242375_243635_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|CP018040.1_245045_246002_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|CP018040.1_246020_246512_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|CP018040.1_246508_247864_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|CP018040.1_247864_248563_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|CP018040.1_248559_249261_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|CP018040.1_249513_250563_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|CP018040.1_250668_251610_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|CP018040.1_251606_253496_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|207aa|down_2|CP018040.1_253600_254221_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|CP018040.1_254363_255749_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|CP018040.1_255679_256216_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|CP018040.1_256367_257759_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|CP018040.1_257775_258756_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|CP018040.1_258891_259875_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|CP018040.1_259939_260839_-	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|CP018040.1_260945_262700_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_002859785.1_ASM285978v1	CP018040	Bordetella pertussis strain J304 chromosome, complete genome	2	432012-432105	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|CP018040.1_419351_420410_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|CP018040.1_420539_421034_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|CP018040.1_421126_422104_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|CP018040.1_422299_423505_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|CP018040.1_423501_425013_+	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|CP018040.1_425028_426342_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|CP018040.1_426532_426712_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|CP018040.1_427121_427856_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|301aa|up_1|CP018040.1_430348_431251_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|CP018040.1_431382_431781_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|CP018040.1_432191_432662_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|CP018040.1_432750_433095_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|CP018040.1_433194_434595_-	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|CP018040.1_436383_436902_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|CP018040.1_437012_437768_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|CP018040.1_437963_439196_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|CP018040.1_439188_439974_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|CP018040.1_440040_441012_+	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|CP018040.1_441022_442000_-	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|CP018040.1_442125_443298_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCA_002859785.1_ASM285978v1	CP018040	Bordetella pertussis strain J304 chromosome, complete genome	3	995255-995349	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|CP018040.1_993241_993622_+,NA	NA|345aa|up_9|CP018040.1_984684_985719_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|68aa|up_8|CP018040.1_985734_985938_+	TIGR02139, permease_CysT, sulfate ABC transporter, permease protein CysT	NA|225aa|up_7|CP018040.1_985959_986634_+	TIGR02139, permease_CysT, sulfate ABC transporter, permease protein CysT	NA|261aa|up_6|CP018040.1_986748_987531_+	COG4208, CysW, ABC-type sulfate transport system, permease component [Inorganic ion transport and metabolism]	NA|355aa|up_5|CP018040.1_987555_988620_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|CP018040.1_989417_990326_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|CP018040.1_991813_993088_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|CP018040.1_993241_993622_+	NA	NA|291aa|up_1|CP018040.1_993629_994502_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|CP018040.1_994807_995188_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|229aa|down_0|CP018040.1_995437_996124_+	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|CP018040.1_996219_997170_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|CP018040.1_997274_998324_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|CP018040.1_998461_999478_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|CP018040.1_1000985_1001558_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|CP018040.1_1001617_1002349_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|CP018040.1_1002400_1003318_-	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|CP018040.1_1004125_1007305_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|CP018040.1_1007301_1008684_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|CP018040.1_1008753_1009005_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCA_002859785.1_ASM285978v1	CP018040	Bordetella pertussis strain J304 chromosome, complete genome	4	1146759-1146892	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	CCCCCTTGGGGGCAGCAAGCCCGCACAGCGGGCGCAGCGTGGGGGCCTTTT	51	1	3	1146810-1146841|1146810-1146841|1146810-1146841	CP018040.1_1354656-1354625|CP018040.1_1820700-1820731|CP018040.1_1996844-1996813	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|101aa|up_8|CP018040.1_1133739_1134042_-,NA	NA|211aa|up_9|CP018040.1_1133110_1133743_+	pfam17932, TetR_C_24, Tetracyclin repressor-like, C-terminal domain	NA|101aa|up_8|CP018040.1_1133739_1134042_-	NA	NA|252aa|up_7|CP018040.1_1135610_1136366_-	PRK07023, PRK07023, SDR family oxidoreductase	NA|311aa|up_6|CP018040.1_1136395_1137328_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|567aa|up_5|CP018040.1_1137602_1139303_-	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|314aa|up_4|CP018040.1_1139284_1140226_-	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|411aa|up_3|CP018040.1_1140319_1141552_+	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|232aa|up_2|CP018040.1_1141544_1142240_+	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|CP018040.1_1142273_1143101_+	cd01310, TatD_DNAse, TatD like proteins;  E	NA|1077aa|up_0|CP018040.1_1143382_1146613_+	pfam03797, Autotransporter, Autotransporter beta-domain	NA|1298aa|down_0|CP018040.1_1147379_1151273_+	pfam11924, IAT_beta, Inverse autotransporter, beta-domain	NA|323aa|down_1|CP018040.1_1154968_1155937_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|282aa|down_2|CP018040.1_1156006_1156852_+	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]	NA|185aa|down_3|CP018040.1_1156919_1157474_+	PRK01885, greB, transcription elongation factor GreB; Reviewed	NA|301aa|down_4|CP018040.1_1157520_1158423_-	pfam00665, rve, Integrase core domain	NA|208aa|down_5|CP018040.1_1158569_1159193_-	pfam16970, FimA, Type-1 fimbrial protein, A	NA|761aa|down_6|CP018040.1_1159366_1161649_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|899aa|down_7|CP018040.1_1161803_1164500_-	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional	NA|163aa|down_8|CP018040.1_1164625_1165114_+	COG1522, Lrp, Transcriptional regulators [Transcription]	NA|621aa|down_9|CP018040.1_1165149_1167012_+	COG1297, COG1297, Predicted membrane protein [Function unknown]
GCA_002859785.1_ASM285978v1	CP018040	Bordetella pertussis strain J304 chromosome, complete genome	5	1820725-1820850	5	CRISPRCasFinder	no	csa3	DEDDh,csa3,cas3,DinG	Type I-A	AAAAAGCCCCCTCGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	45	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|79aa|up_4|CP018040.1_1816933_1817170_+,NA|120aa|up_1|CP018040.1_1819314_1819674_-,NA	NA|371aa|up_9|CP018040.1_1809629_1810742_+	cd02933, OYE_like_FMN, Old yellow enzyme (OYE)-like FMN binding domain	NA|213aa|up_8|CP018040.1_1810746_1811385_-	pfam13994, PgaD, PgaD-like protein	NA|420aa|up_7|CP018040.1_1811365_1812625_-	PRK11204, PRK11204, N-glycosyltransferase; Provisional	NA|702aa|up_6|CP018040.1_1812628_1814734_-	TIGR03938, hypothetical_protein_Pcar_2791, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB	NA|662aa|up_5|CP018040.1_1814739_1816725_-	TIGR03939, PGA_TPR_OMP, poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA	NA|79aa|up_4|CP018040.1_1816933_1817170_+	NA	NA|162aa|up_3|CP018040.1_1817514_1818000_+	COG1846, MarR, Transcriptional regulators [Transcription]	NA|301aa|up_2|CP018040.1_1818415_1819318_+	pfam00665, rve, Integrase core domain	NA|120aa|up_1|CP018040.1_1819314_1819674_-	NA	NA|310aa|up_0|CP018040.1_1819719_1820649_+	TIGR01414, Contains:_AIDA-I_translocator, outer membrane autotransporter barrel domain	NA|217aa|down_0|CP018040.1_1820873_1821524_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|CP018040.1_1821652_1822855_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|164aa|down_2|CP018040.1_1825220_1825712_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_3|CP018040.1_1825927_1826440_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_4|CP018040.1_1826457_1827669_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_5|CP018040.1_1827706_1828117_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_6|CP018040.1_1828118_1828442_+	TIGR02011, Protein_yfhF	NA|171aa|down_7|CP018040.1_1828444_1828957_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_8|CP018040.1_1829086_1830949_+	PRK05183, hscA, chaperone protein HscA; Provisional	NA|114aa|down_9|CP018040.1_1830958_1831300_+	TIGR02007, 2Fe-2S_ferredoxin, ferredoxin, 2Fe-2S type, ISC system
GCA_002859785.1_ASM285978v1	CP018040	Bordetella pertussis strain J304 chromosome, complete genome	6	3432000-3432109	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|363aa|up_9|CP018040.1_3416279_3417368_+	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs	NA|993aa|up_8|CP018040.1_3418667_3421646_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_7|CP018040.1_3422572_3423451_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|111aa|up_6|CP018040.1_3423486_3423819_+	PRK06816, PRK06816, StlD/DarB family beta-ketosynthase	NA|507aa|up_5|CP018040.1_3423797_3425318_+	PRK06816, PRK06816, StlD/DarB family beta-ketosynthase	NA|317aa|up_4|CP018040.1_3425399_3426350_+	pfam00665, rve, Integrase core domain	NA|156aa|up_3|CP018040.1_3426346_3426814_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_2|CP018040.1_3426856_3427627_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_1|CP018040.1_3427647_3428448_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|262aa|up_0|CP018040.1_3429961_3430747_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|CP018040.1_3432110_3432503_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|CP018040.1_3432640_3433321_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|CP018040.1_3433325_3434297_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|301aa|down_3|CP018040.1_3434392_3435295_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|CP018040.1_3436847_3437549_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|CP018040.1_3437548_3438973_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|CP018040.1_3440042_3441383_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|CP018040.1_3441498_3443262_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|CP018040.1_3443373_3444252_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|CP018040.1_3444364_3445180_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
