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_001989295.1_ASM198929v1	NZ_CP013905	Bordetella pertussis strain J210 chromosome, complete genome	1	251641-251725	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_CP013905.1_239166_239577_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|NZ_CP013905.1_240598_241342_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|NZ_CP013905.1_241385_242429_-	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_CP013905.1_242599_244702_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|NZ_CP013905.1_246112_247069_+	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_CP013905.1_247087_247579_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|NZ_CP013905.1_247575_248931_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|NZ_CP013905.1_248931_249630_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|NZ_CP013905.1_249626_250328_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|NZ_CP013905.1_250580_251630_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NZ_CP013905.1_251735_252677_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NZ_CP013905.1_252673_254563_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NZ_CP013905.1_254649_255288_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NZ_CP013905.1_255430_256816_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NZ_CP013905.1_256746_257283_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NZ_CP013905.1_257434_258826_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NZ_CP013905.1_258842_259823_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NZ_CP013905.1_259958_260942_+	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_CP013905.1_261006_261906_-	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_CP013905.1_262012_263767_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_001989295.1_ASM198929v1	NZ_CP013905	Bordetella pertussis strain J210 chromosome, complete genome	2	434133-434226	2	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|72aa|up_2|NZ_CP013905.1_432219_432435_+,NA	NA|153aa|up_9|NZ_CP013905.1_426526_426985_-	PRK13952, mscL, large conductance mechanosensitive channel protein MscL	NA|214aa|up_8|NZ_CP013905.1_427124_427766_+	TIGR01416, Rieske_proteo, ubiquinol-cytochrome c reductase, iron-sulfur subunit	NA|461aa|up_7|NZ_CP013905.1_427830_429213_+	COG1290, QcrB, Cytochrome b subunit of the bc complex [Energy production and conversion]	NA|283aa|up_6|NZ_CP013905.1_429238_430087_+	COG2857, CYT1, Cytochrome c1 [Energy production and conversion]	NA|204aa|up_5|NZ_CP013905.1_430245_430857_+	PRK09481, sspA, stringent starvation protein A; Provisional	NA|150aa|up_4|NZ_CP013905.1_430866_431316_+	PRK11798, PRK11798, ClpXP protease specificity-enhancing factor; Provisional	NA|54aa|up_3|NZ_CP013905.1_431982_432144_-	pfam13986, DUF4224, Domain of unknown function (DUF4224)	NA|72aa|up_2|NZ_CP013905.1_432219_432435_+	NA	NA|317aa|up_1|NZ_CP013905.1_432421_433372_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP013905.1_433503_433902_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP013905.1_434312_434783_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP013905.1_434871_435216_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP013905.1_435315_436716_-	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_CP013905.1_438504_439023_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP013905.1_439133_439889_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP013905.1_440084_441317_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP013905.1_441309_442095_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP013905.1_442161_443133_+	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_CP013905.1_443143_444121_-	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_CP013905.1_444246_445419_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_001989295.1_ASM198929v1	NZ_CP013905	Bordetella pertussis strain J210 chromosome, complete genome	3	998452-998546	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_CP013905.1_996438_996819_+,NA	NA|310aa|up_9|NZ_CP013905.1_983968_984898_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP013905.1_985141_986968_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP013905.1_987050_987692_+	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_CP013905.1_987881_988916_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP013905.1_990752_991817_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP013905.1_992614_993523_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP013905.1_995010_996285_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP013905.1_996438_996819_+	NA	NA|291aa|up_1|NZ_CP013905.1_996826_997699_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP013905.1_998004_998385_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP013905.1_998595_999321_+	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_CP013905.1_999416_1000367_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP013905.1_1000471_1001521_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP013905.1_1001658_1002675_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP013905.1_1004183_1004756_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|NZ_CP013905.1_1004815_1005547_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|NZ_CP013905.1_1005598_1006516_-	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_CP013905.1_1007323_1010503_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|84aa|down_8|NZ_CP013905.1_1011952_1012204_-	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|205aa|down_9|NZ_CP013905.1_1012349_1012964_-	cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold
GCF_001989295.1_ASM198929v1	NZ_CP013905	Bordetella pertussis strain J210 chromosome, complete genome	4	1895921-1896048	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|134aa|up_9|NZ_CP013905.1_1884883_1885285_+	cd03450, NodN, NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit	NA|266aa|up_8|NZ_CP013905.1_1885304_1886102_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP013905.1_1886098_1886530_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP013905.1_1886526_1887684_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP013905.1_1887705_1888482_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|223aa|up_4|NZ_CP013905.1_1890694_1891363_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP013905.1_1891355_1891997_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP013905.1_1892031_1892763_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|NZ_CP013905.1_1892780_1892993_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|NZ_CP013905.1_1893563_1894514_+	pfam00665, rve, Integrase core domain	NA|217aa|down_0|NZ_CP013905.1_1896071_1896722_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP013905.1_1896850_1898053_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP013905.1_1898130_1900167_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP013905.1_1900419_1900911_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP013905.1_1901126_1901639_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP013905.1_1901656_1902868_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP013905.1_1902905_1903316_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP013905.1_1903317_1903641_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP013905.1_1903643_1904156_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP013905.1_1904285_1906148_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_001989295.1_ASM198929v1	NZ_CP013905	Bordetella pertussis strain J210 chromosome, complete genome	5	3434594-3434703	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|317aa|up_9|NZ_CP013905.1_3418907_3419858_-	pfam00665, rve, Integrase core domain	NA|993aa|up_8|NZ_CP013905.1_3420211_3423190_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_7|NZ_CP013905.1_3424116_3424995_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_6|NZ_CP013905.1_3425959_3426910_-	pfam00665, rve, Integrase core domain	NA|317aa|up_5|NZ_CP013905.1_3427992_3428943_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP013905.1_3428939_3429407_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP013905.1_3429449_3430220_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP013905.1_3430240_3431041_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP013905.1_3431051_3432461_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP013905.1_3432555_3433341_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP013905.1_3434704_3435097_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP013905.1_3435234_3435915_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|NZ_CP013905.1_3435919_3436891_-	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_CP013905.1_3436986_3437937_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP013905.1_3439441_3440143_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP013905.1_3440142_3441567_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|352aa|down_6|NZ_CP013905.1_3441583_3442639_-	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|447aa|down_7|NZ_CP013905.1_3442635_3443976_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_8|NZ_CP013905.1_3444091_3445855_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_9|NZ_CP013905.1_3445966_3446845_+	PRK00030, minC, septum site-determining protein MinC
