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_001987955.1_ASM198795v1	NZ_CP011765	Bordetella pertussis strain J098 chromosome, complete genome	1	251639-251723	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_CP011765.1_239164_239575_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|NZ_CP011765.1_240596_241340_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|NZ_CP011765.1_241383_242427_-	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_CP011765.1_242597_244700_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|NZ_CP011765.1_246110_247067_+	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_CP011765.1_247085_247577_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|NZ_CP011765.1_247573_248929_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|NZ_CP011765.1_248929_249628_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|NZ_CP011765.1_249624_250326_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|NZ_CP011765.1_250578_251628_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|NZ_CP011765.1_251733_252675_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|NZ_CP011765.1_252671_254561_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|NZ_CP011765.1_254647_255286_+	PRK10847, PRK10847, DedA family protein	NA|462aa|down_3|NZ_CP011765.1_255428_256814_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|NZ_CP011765.1_256744_257281_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|NZ_CP011765.1_257432_258824_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|NZ_CP011765.1_258840_259821_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|NZ_CP011765.1_259956_260940_+	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_CP011765.1_261004_261904_-	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_CP011765.1_262010_263765_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCF_001987955.1_ASM198795v1	NZ_CP011765	Bordetella pertussis strain J098 chromosome, complete genome	2	433082-433175	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_CP011765.1_420421_421480_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|NZ_CP011765.1_421609_422104_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|NZ_CP011765.1_422196_423174_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|NZ_CP011765.1_423369_424575_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|NZ_CP011765.1_424571_426083_+	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_CP011765.1_426098_427412_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|NZ_CP011765.1_427602_427782_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|NZ_CP011765.1_428191_428926_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|NZ_CP011765.1_431370_432321_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|NZ_CP011765.1_432452_432851_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|NZ_CP011765.1_433261_433732_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|NZ_CP011765.1_433820_434165_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|NZ_CP011765.1_434264_435665_-	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_CP011765.1_437453_437972_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|NZ_CP011765.1_438082_438838_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|NZ_CP011765.1_439033_440266_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|NZ_CP011765.1_440258_441044_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|NZ_CP011765.1_441110_442082_+	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_CP011765.1_442092_443070_-	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_CP011765.1_443195_444368_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCF_001987955.1_ASM198795v1	NZ_CP011765	Bordetella pertussis strain J098 chromosome, complete genome	3	998449-998543	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_CP011765.1_996435_996816_+,NA	NA|310aa|up_9|NZ_CP011765.1_983965_984895_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|NZ_CP011765.1_985138_986965_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|NZ_CP011765.1_987047_987689_+	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_CP011765.1_987878_988913_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|NZ_CP011765.1_990749_991814_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|NZ_CP011765.1_992611_993520_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|NZ_CP011765.1_995007_996282_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|NZ_CP011765.1_996435_996816_+	NA	NA|291aa|up_1|NZ_CP011765.1_996823_997696_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|NZ_CP011765.1_998001_998382_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|NZ_CP011765.1_998592_999318_+	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_CP011765.1_999413_1000364_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|NZ_CP011765.1_1000468_1001518_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|NZ_CP011765.1_1001655_1002672_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|NZ_CP011765.1_1004180_1004753_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|NZ_CP011765.1_1004812_1005544_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|NZ_CP011765.1_1005595_1006513_-	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_CP011765.1_1007320_1010500_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|NZ_CP011765.1_1010496_1011879_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|NZ_CP011765.1_1011948_1012200_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_001987955.1_ASM198795v1	NZ_CP011765	Bordetella pertussis strain J098 chromosome, complete genome	4	1896983-1897110	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_CP011765.1_1885945_1886347_+	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_CP011765.1_1886366_1887164_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP011765.1_1887160_1887592_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP011765.1_1887588_1888746_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP011765.1_1888767_1889544_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|223aa|up_4|NZ_CP011765.1_1891756_1892425_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP011765.1_1892417_1893059_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP011765.1_1893093_1893825_+	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_CP011765.1_1893842_1894055_+	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_CP011765.1_1894625_1895576_+	pfam00665, rve, Integrase core domain	NA|217aa|down_0|NZ_CP011765.1_1897133_1897784_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP011765.1_1897912_1899115_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP011765.1_1899192_1901229_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP011765.1_1901481_1901973_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP011765.1_1902188_1902701_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP011765.1_1902718_1903930_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP011765.1_1903967_1904378_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP011765.1_1904379_1904703_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP011765.1_1904705_1905218_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP011765.1_1905347_1907210_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_001987955.1_ASM198795v1	NZ_CP011765	Bordetella pertussis strain J098 chromosome, complete genome	5	3433570-3433679	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|363aa|up_9|NZ_CP011765.1_3417847_3418936_+	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs	NA|317aa|up_8|NZ_CP011765.1_3418932_3419883_-	pfam00665, rve, Integrase core domain	NA|993aa|up_7|NZ_CP011765.1_3420236_3423215_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|NZ_CP011765.1_3424141_3425020_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|NZ_CP011765.1_3426968_3427919_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|NZ_CP011765.1_3427915_3428383_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|NZ_CP011765.1_3428425_3429196_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|NZ_CP011765.1_3429216_3430017_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|NZ_CP011765.1_3430027_3431437_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|NZ_CP011765.1_3431531_3432317_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|NZ_CP011765.1_3433680_3434073_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|NZ_CP011765.1_3434210_3434891_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|324aa|down_2|NZ_CP011765.1_3434895_3435867_-	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_CP011765.1_3435962_3436913_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|NZ_CP011765.1_3438417_3439119_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|NZ_CP011765.1_3439118_3440543_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|NZ_CP011765.1_3441612_3442953_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|NZ_CP011765.1_3443068_3444832_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|NZ_CP011765.1_3444943_3445822_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|NZ_CP011765.1_3445934_3446750_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
