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_002859825.1_ASM285982v1	NZ_CP018042	Bordetella pertussis strain J313 chromosome, complete genome	1	250582-250666	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|266aa|up_9|NZ_CP018042.1_236361_237159_-	cd08940, HBDH_SDR_c, d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs	NA|137aa|up_8|NZ_CP018042.1_238108_238519_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_7|NZ_CP018042.1_239540_240284_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_6|NZ_CP018042.1_240327_241371_-	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_5|NZ_CP018042.1_241541_243644_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_4|NZ_CP018042.1_245054_246011_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_3|NZ_CP018042.1_246029_246521_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_2|NZ_CP018042.1_246517_247873_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_1|NZ_CP018042.1_247873_248572_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|350aa|up_0|NZ_CP018042.1_249521_250571_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NZ_CP018042.1_250676_251618_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NZ_CP018042.1_251614_253504_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NZ_CP018042.1_253590_254229_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NZ_CP018042.1_254371_255757_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NZ_CP018042.1_255687_256224_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NZ_CP018042.1_256375_257767_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NZ_CP018042.1_257783_258764_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NZ_CP018042.1_258899_259883_+	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_CP018042.1_259947_260847_-	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_CP018042.1_260953_262708_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_002859825.1_ASM285982v1	NZ_CP018042	Bordetella pertussis strain J313 chromosome, complete genome	2	432021-432114	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_CP018042.1_419360_420419_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|NZ_CP018042.1_420548_421043_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|NZ_CP018042.1_421135_422113_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|NZ_CP018042.1_422308_423514_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|NZ_CP018042.1_423510_425022_+	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_CP018042.1_425037_426351_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|NZ_CP018042.1_426541_426721_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|NZ_CP018042.1_427130_427865_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|NZ_CP018042.1_430309_431260_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP018042.1_431391_431790_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP018042.1_432200_432671_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP018042.1_432759_433104_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP018042.1_433203_434604_-	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_CP018042.1_436392_436911_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP018042.1_437021_437777_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP018042.1_437972_439205_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP018042.1_439197_439983_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP018042.1_440049_441021_+	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_CP018042.1_441031_442009_-	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_CP018042.1_442134_443307_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_002859825.1_ASM285982v1	NZ_CP018042	Bordetella pertussis strain J313 chromosome, complete genome	3	997377-997471	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_CP018042.1_995363_995744_+,NA	NA|310aa|up_9|NZ_CP018042.1_982893_983823_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP018042.1_984066_985893_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP018042.1_985975_986617_+	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_CP018042.1_986806_987841_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP018042.1_989677_990742_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP018042.1_991539_992448_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP018042.1_993935_995210_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP018042.1_995363_995744_+	NA	NA|291aa|up_1|NZ_CP018042.1_995751_996624_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP018042.1_996929_997310_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP018042.1_997520_998246_+	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_CP018042.1_998341_999292_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP018042.1_999396_1000446_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP018042.1_1000583_1001600_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP018042.1_1003108_1003681_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|NZ_CP018042.1_1003740_1004472_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|NZ_CP018042.1_1004523_1005441_-	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_CP018042.1_1006248_1009428_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|NZ_CP018042.1_1009424_1010807_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|NZ_CP018042.1_1010876_1011128_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_002859825.1_ASM285982v1	NZ_CP018042	Bordetella pertussis strain J313 chromosome, complete genome	4	1820755-1820882	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_3|NZ_CP018042.1_1816963_1817200_+,NA|57aa|up_1|NZ_CP018042.1_1818240_1818411_+,NA	csa3|100aa|up_9|NZ_CP018042.1_1809307_1809607_+	COG0640, ArsR, Predicted transcriptional regulators [Transcription]	NA|371aa|up_8|NZ_CP018042.1_1809659_1810772_+	cd02933, OYE_like_FMN, Old yellow enzyme (OYE)-like FMN binding domain	NA|213aa|up_7|NZ_CP018042.1_1810776_1811415_-	pfam13994, PgaD, PgaD-like protein	NA|420aa|up_6|NZ_CP018042.1_1811395_1812655_-	PRK11204, PRK11204, N-glycosyltransferase; Provisional	NA|702aa|up_5|NZ_CP018042.1_1812658_1814764_-	TIGR03938, hypothetical_protein_Pcar_2791, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB	NA|662aa|up_4|NZ_CP018042.1_1814769_1816755_-	TIGR03939, PGA_TPR_OMP, poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA	NA|79aa|up_3|NZ_CP018042.1_1816963_1817200_+	NA	NA|162aa|up_2|NZ_CP018042.1_1817544_1818030_+	COG1846, MarR, Transcriptional regulators [Transcription]	NA|57aa|up_1|NZ_CP018042.1_1818240_1818411_+	NA	NA|317aa|up_0|NZ_CP018042.1_1818397_1819348_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|NZ_CP018042.1_1820905_1821634_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP018042.1_1821684_1822887_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP018042.1_1822964_1825001_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP018042.1_1825253_1825745_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP018042.1_1825960_1826473_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP018042.1_1826490_1827702_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP018042.1_1827739_1828150_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP018042.1_1828151_1828475_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP018042.1_1828477_1828990_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP018042.1_1829119_1830982_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_002859825.1_ASM285982v1	NZ_CP018042	Bordetella pertussis strain J313 chromosome, complete genome	5	3435492-3435601	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|138aa|up_8|NZ_CP018042.1_3421792_3422206_-,NA	NA|317aa|up_9|NZ_CP018042.1_3420855_3421806_-	pfam00665, rve, Integrase core domain	NA|138aa|up_8|NZ_CP018042.1_3421792_3422206_-	NA	NA|993aa|up_7|NZ_CP018042.1_3422159_3425138_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP018042.1_3426064_3426943_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP018042.1_3428890_3429841_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP018042.1_3429837_3430305_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP018042.1_3430347_3431118_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP018042.1_3431138_3431939_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP018042.1_3431949_3433359_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP018042.1_3433453_3434239_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP018042.1_3435602_3435995_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP018042.1_3436132_3436813_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|NZ_CP018042.1_3436817_3437816_-	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_CP018042.1_3437884_3438835_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP018042.1_3440339_3441041_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP018042.1_3441040_3442465_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|NZ_CP018042.1_3443534_3444875_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|NZ_CP018042.1_3444990_3446754_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|NZ_CP018042.1_3446865_3447744_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|NZ_CP018042.1_3447856_3448672_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
